IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.}, }
@article {pmid41973723, year = {2026}, author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB}, title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {229}, pages = {}, doi = {10.3791/70187}, pmid = {41973723}, issn = {1940-087X}, mesh = {Humans ; *Feces/virology ; *Metagenomics/methods ; *DNA, Viral/genetics/isolation & purification/chemistry ; *DNA Viruses/genetics/isolation & purification ; }, abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.}, }
@article {pmid41974680, year = {2026}, author = {Valverde, G and Sarhan, MS and Cook, R and Rota-Stabelli, O and Adriaenssens, EM and Zink, A and Maixner, F}, title = {An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71603-9}, pmid = {41974680}, issn = {2041-1723}, abstract = {Streptococcus pyogenes, or Group A Streptococcus (GAS), is a human pathogen responsible for a range of diseases, from mild infections to severe illnesses. Despite its significance in modern clinical settings, little is known about the pathogen's evolutionary history or its presence in ancient human populations. Here, we present genomic evidence of S. pyogenes in the pre-Columbian Americas. We analysed a tooth from a naturally mummified individual dating to the Late Intermediate Period (1283-1383 cal AD), housed in the National Museum of Archeology (MUNARQ) in La Paz, Bolivia. Mitochondrial DNA analysis confirmed the host's Native American ancestry. Shotgun metagenomic sequencing and de-novo assembly enabled the near-complete reconstruction of an ancient S. pyogenes genome displaying close similarity to contemporary strains linked to pharyngitis. The genome contains core virulence genes, but prophages lack streptococcal pyrogenic exotoxins. Phylogenetic analyses place the strain at the base of modern S. pyogenes diversity, and Bayesian analyses indicate that most extant lineages diversified globally within the past ~5,500 years. Our results push back the confirmed presence of S. pyogenes in the Americas by several centuries and suggest that the pathogen circulated among Indigenous populations prior to the European contact.}, }
@article {pmid41974697, year = {2026}, author = {Espinosa, CA and Njunge, JM and Tickell, KD and Diallo, AH and Sayeem Bin Shahid, ASM and Gazi, MA and Kazi, Z and Yoshioka, E and Tigoi, C and Mburu, M and Ngari, M and Ngao, N and Omer, E and Gumbi, W and Gichuki, BM and Mitchel, A and Williams, J and Gogain, J and Janjic, N and Mandal, R and Jenkins, B and Browne, HP and Shao, Y and Rozday, T and Stares, MD and Dawson, NJR and Berson, E and Chang, A and Kim, Y and Mataraso, SJ and Shu, CH and Phongpreecha, T and Xue, L and Saleem, A and Singa, B and Ahmed, T and Voskuijl, WP and Wishart, DS and Houpt, ER and Liu, J and Ali, A and Mupere, E and Chisti, MJ and Bandsma, RHJ and Lawley, TD and Koulman, A and Lancioni, CL and Aghaeepour, N and Berkley, JA and Walson, JL and , }, title = {Multiomics characterization of acute child illness and mortality in Africa and South Asia.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69754-w}, pmid = {41974697}, issn = {2041-1723}, abstract = {Childhood illnesses from infectious diseases in low- and middle-income countries contribute substantially to the global under-five mortality. Many hospitalized children experience incomplete recovery, readmission, and post-discharge mortality despite guideline-directed care. However, targeted interventions remain elusive due to limited understanding of underlying mechanisms. In this work, we employ multiomic profiling and multivariate modeling to investigate biological drivers of inpatient and post-discharge mortality in 3,101 acutely ill children across nine sites in sub-Saharan Africa and South Asia. In a nested case-cohort (N = 1008), we generate plasma proteomics, serum metabolomics and lipidomics, stool metagenomics, and fecal pathogen data at admission and discharge. Additionally, we profile 270 geographically matched community children for biological baselines. We identify a generalizable mortality signature marked by immune, inflammatory, and metabolic dysregulation with gut dysbiosis. We show that mortality-associated signals persist from admission through discharge, indicating unresolved disease and that malnourished children show greater baseline perturbations, explaining elevated risk. We also find some children with low clinical severity display high predicted mortality risk from targeted biomarkers. Finally, we distill predictive models to a clinically feasible biomarker panel and validate our findings in an independent cohort (N = 100). By linking inpatient and post-discharge mortality to specific biological mechanisms, our findings highlight why current care can fail and demonstrate how biomarker-guided risk stratification can identify vulnerable children currently missed by clinical assessments, enabling targeted interventions to reduce mortality in low- and middle-income countries.}, }
@article {pmid41974712, year = {2026}, author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y}, title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71718-z}, pmid = {41974712}, issn = {2041-1723}, support = {R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.}, }
@article {pmid41975031, year = {2026}, author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE}, title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10048-8}, pmid = {41975031}, issn = {2399-3642}, support = {DairyBio//Dairy Australia/ ; }, abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.}, }
@article {pmid41975041, year = {2026}, author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , }, title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {41975041}, issn = {1532-1827}, support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; }, abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).
METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.
RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa -notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.
CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.
PROSPERO: CRD42023433704.}, }
@article {pmid41975095, year = {2026}, author = {Guan, K and Ocampo, RF and Matheus Carnevali, PB and Castelle, CJ and Gonzalez-Osorio, L and Castanzo, DT and Thomas, NC and Brothers, M and Dangerfield, TL and Hooper, MM and West, MS and Appleby, NM and Krudop, I and Lamothe, RC and Aliaga Goltsman, DS and Alexander, LM and Butterfield, CN and Johnson, KA and Brown, CT and Taylor, DW}, title = {Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency.}, journal = {Nature structural & molecular biology}, volume = {}, number = {}, pages = {}, pmid = {41975095}, issn = {1545-9985}, abstract = {Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing because of their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here we identify and characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Alistipes sp. Cas12f (Al3Cas12f), which supports robust genome editing in human cells. Through structural, biochemical and kinetic analyses, we compare Al3Cas12f to two recently described orthologs, Oscillibacter sp. Cas12f and Ruminiclostridium herbifermentans Cas12f. These orthologs present divergent architectures and regulatory features governing protospacer-adjacent motif recognition, guide RNA (gRNA) binding, dimerization and DNA cleavage. Notably, Al3Cas12f achieves efficient R-loop formation through a stable dimer interface and a naturally optimized gRNA. Leveraging these structural insights, we generate an engineered Al3Cas12f variant (RKK) that increases editing and improves activity across several tested genomic loci. By overcoming locus-dependent variability and an apparent potency threshold, this engineered compact editor seems to expand the feasibility of low-dose, AAV-compatible therapeutic genome editing. Our results elucidate mechanistic determinants of Cas12f activity and offer a framework for engineering compact genome editors that may bear therapeutic potential.}, }
@article {pmid41975182, year = {2026}, author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A}, title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47528-0}, pmid = {41975182}, issn = {2045-2322}, support = {818431//Horizon 2020 Framework Programme/ ; }, abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.}, }
@article {pmid41975253, year = {2026}, author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V}, title = {Decoding the microbial landscape of endometrial cancer: a case-control study.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05017-4}, pmid = {41975253}, issn = {1471-2180}, support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; }, }
@article {pmid41975274, year = {2026}, author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN}, title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655793}, doi = {10.1080/19490976.2026.2655793}, pmid = {41975274}, issn = {1949-0984}, abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.}, }
@article {pmid41964456, year = {2026}, author = {Lefebvre, CS and Salmona, M and Hamane, S and Dellière, S and Charlier, V and Huguenin, A and Bonnal, C and Legoff, J and Feghoul, L and Dutkiewicz, M and Caméléna, F and Berçot, B and Charvet, E and Battistella, M and Alanio, A and Ghelfenstein-Ferreira, T}, title = {Shotgun metagenomic sequencing improves cross-kingdom diagnosis of mycetoma.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70450}, pmid = {41964456}, issn = {1468-3083}, }
@article {pmid41964564, year = {2026}, author = {Zhao, S and Lin, S and Chen, M and Yan, J and Yang, D and Guo, F and Qu, H and Chen, Y}, title = {Iron-Cycling-Constructed Wetland-Microbial Fuel Cell-Enhanced Removal of Sartans: The Overlooked Singlet Oxygen and Functional Microorganisms.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00492}, pmid = {41964564}, issn = {1520-5851}, abstract = {The global challenge of population aging has led to an increase in the utilization of cardiovascular drugs such as sartans, which are frequently detected in aquatic environments and necessitate advanced treatment. Current sartan removal technologies are limited by their requirement for strict reaction conditions and the potential formation of toxic byproducts. This study presents a novel iron-cycling-constructed wetland-microbial fuel cell (Fe-CWMFC) that combines biotic and abiotic processes to effectively degrade sartans (94.4 ± 3.5%-95.9% ± 3.3%). Mass balance analysis revealed that direct microbial degradation pathways made the highest contribution (40.7-44.5%), followed by ROS-driven degradation (20.3-21.8%), substrate adsorption (26.1-29.7%), and plant uptake (2.3-2.5%). Iron cycling enhanced ROS-driven degradation, with 11.3-13.3% derived from biotic [1]O2 and 7.0-9.3% derived from abiotic [1]O2. Metagenomic binning analysis identified 60 MAGs (e.g., Thiobacillus, Nitrosomonas) with sartan degradation potential, which harbor genes encoding functional enzymes (e.g., decarboxylase, dehydroxylase, and demethylase). By combining biodegradation and ROS-driven degradation to target functional groups (e.g., -COOH, -OH, and -CH3) in sartans, the toxicity was significantly reduced. This research enhances our understanding of the combined role of ROS and microorganisms in micropollutant removal and highlights Fe-CWMFC as a high-efficiency, sustainable, and low-toxicity treatment technology for complex environmental applications.}, }
@article {pmid41964658, year = {2026}, author = {Liu, H and Wang, C and Huang, Z and Wang, J and Cai, F and Tian, C and Feng, J and Shen, J and Wang, X}, title = {Progressive Decomposition of Algal Organic Matter Decouples Nitrogen Transformations in Lake Sediments: Evidence from Short-Term Incubation.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c08386}, pmid = {41964658}, issn = {1520-5851}, abstract = {Against the backdrop of global lake eutrophication, algal bloom decay is increasingly affecting ecosystems. Algal organic matter (AOM), a natural complex mixture, undergoes multiple release and transformation stages, yet its composition and pathways remain unclear. This study used spectroscopic, mass spectrometric, and metagenomic analyses to monitor a time-compressed algal decay experiment. Results showed that AOM release and transformation can be divided into three stages. Within 1 day, labile AOM consisting mainly of proteins (8.36%), lipids (8.22%), and unsaturated carbohydrates (7.72%) was rapidly released, reshaping nitrogen (N) cycling. Its high bioavailability promoted sediment mineralization and a positive priming effect, while anaerobic conditions reduced nitrification and denitrification rates by 88.7% and 34.5%. Within 3-7 days, semilabile AOM rich in tannins (19.2%) and carbohydrates (9.41%) was gradually decomposed, maintaining anaerobic conditions. The imbalance of excessive NH4[+] and depleted NO3[-] led to the decoupling of nitrification-denitrification. After 7 days, humic-like AOM dominated by lignins (56.8%) prevailed, reducing oxygen consumption and enabling rapid recovery of nitrification and slow rebound of denitrification. These findings clarify the phased transformations of AOM and their microbial interactions, providing mechanistic insights into the short-term fluctuations of lake water quality and microbial processes during bloom decay.}, }
@article {pmid41965517, year = {2026}, author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H}, title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05023-6}, pmid = {41965517}, issn = {1471-2180}, support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.
RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.
CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.}, }
@article {pmid41965741, year = {2026}, author = {Khangarot, R and Kumari, V and Mishra, R and Singh, A}, title = {Artificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance.}, journal = {Biomedical engineering online}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12938-026-01568-9}, pmid = {41965741}, issn = {1475-925X}, abstract = {Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in deep learning, transformer-based sequence models, graph neural networks, and multimodal architectures have greatly improved microbial classification accuracy, antibiotic resistance gene (ARG) detection, and resistance prediction. Taking metagenomic sequencing into consideration, these advancements have contributed to the development of sensitive, scalable, and non-invasive methods to profile microbiomes, determine novel resistance, and monitor AMR trends at the population level. This review summarizes recent advances in AI-aided microbiology, with a particular emphasis on AMR surveillance. Specific topics include deep learning frameworks for ARG annotation, emerging approaches to identifying new resistance genes, and multimodal applications (genomic and clinical metadata) aimed at improving phenotype prediction. The role of metagenome-assembled genomes (MAGs) to enhance AMR surveillance efforts is noted, along with their noted limitations relative to isolate genomes. The discussion includes the examination of explainable AI (XAI) techniques including SHAP, attention mechanism approaches, and gradient-based attribution approaches, with the aim of increasing transparency and clinical explainability. We also cover potential applications including AI-enabled non-invasive fecal microbiome diagnostics, laboratory automation, and environmental surveillance. While there has been significant progress, unresolved issues exist relating to dataset variations, liability of models to datasets, interpretability, and regulatory approval. Overcoming these barriers, however, will require standardized frameworks for these workflows, privacy-preserving federated learning methods, and interpretable AI frameworks for clinical and public health tools. AI could fundamentally change AMR surveillance by allowing for earlier resistance detection, advanced risk assessment recommendation, and improved monitoring strategies globally.}, }
@article {pmid41965996, year = {2026}, author = {Wang, C and Shen, J and Liu, H and Huang, Z and Wang, J and Tian, C and Cai, F and Feng, J and Sha, F and Wang, X}, title = {DNRA dominates over denitrification during algal blooms in a mesotrophic lake: Implications for nitrogen retention and eutrophication risk.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129621}, doi = {10.1016/j.jenvman.2026.129621}, pmid = {41965996}, issn = {1095-8630}, abstract = {Nitrogen (N) overloading threatens global lake ecosystems. However, how algal blooms affect the N balance in mesotrophic lakes by shaping N-cycling biogeographic patterns remains a critical knowledge gap. This study systematically elucidated N cycling patterns and microbial mechanisms driving N retention during algal blooms in Erhai Lake by integrating field monitoring,[15]N isotope pairing technique ([15]N-IPT), and absolute quantitative metagenomics. Results revealed that algal blooms shaped a N-cycling functional pattern in Erhai Lake characterized by organic degradation and synthesis (ODAS) dominance and dissimilatory nitrate reduction (DNR) as a key process. Notably, algal blooms disrupted traditional nitrification-denitrification coupling, shifting N cycling towards a retention mode dominated by dissimilatory nitrate reduction to ammonium (DNRA). Sedimentary DNRA contributed 69% (14.69 ± 5.57 μmol N L[-1] h[-1]) of total dissimilatory nitrate reduction (DNR) process, supported by significantly elevated NrfA (602.49 ± 121.04 μmol d[-1] g[-1]) and NirBD (361.29 ± 138.39 μmol d[-1] g[-1]) enzyme activities. Partial Least Squares Path Modeling (PLS-PM) identified the nitrogen retention index (NRI) as co-regulated by water depth and algal-mediated microbial activity/rates. High-NRI sediments were dominated by Bacteroidota (mainly orders Marinilabiliales and families Prolixibacteraceae) and Myxococcota (primarily families Anaeromyxobacteraceae), while low-NRI sediments were characterized by enrichment of Pseudomonadota (Thioalkalivibrio nitratireducens and Gallionellaceae) and Campylobacterota (Campylobacter sp. BCW_8712). DNRA outcompeted denitrification, diverting nitrate to ammonium rather than N2 gas and resulting in an internal N loading that was an order of magnitude higher than external inputs. This work challenges the denitrification-centric paradigm, revealing the microbial mechanisms of endogenous N accumulation under algal bloom conditions and providing a theoretical basis for the management of plateau lakes.}, }
@article {pmid41966291, year = {2026}, author = {Ashango, ZA and Seyum, EG and Nwogha, JS}, title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105941}, doi = {10.1016/j.meegid.2026.105941}, pmid = {41966291}, issn = {1567-7257}, abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.}, }
@article {pmid41966300, year = {2026}, author = {Bojko, J and Abd-Alla, A}, title = {'Invertebrate-virome sequence detection: implications for invertebrate products trading and regulations' - An editorial for the special issue.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108623}, doi = {10.1016/j.jip.2026.108623}, pmid = {41966300}, issn = {1096-0805}, abstract = {Invertebrates can be infected by many viruses that may either cause disease (invertebrate‑pathogenic viruses) or be transmitted to vertebrates or plants. Viral infections may occur in natural invertebrate populations as well as in mass‑reared colonies. The significant recent advances in genome‑sequencing technologies have provided fast and relatively inexpensive tools for detecting invertebrate viruses in both wild and mass‑rearing settings, even at very low levels. The presence of such viruses raises important questions regarding the impact of covert infections on invertebrate health, sanitation, and overall colony performance. The articles in this special issue address viral sequence detection, viral sequence diversity, the impact of viruses on invertebrates, and the relationship between food and feed, and policy.}, }
@article {pmid41966314, year = {2026}, author = {Liu, S and Qin, Y and Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H}, title = {Genomic Characterization, Antimicrobial Resistance and Virulence Profiles of Klebsiella pneumoniae Isolated from Mink in Northern China.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108485}, doi = {10.1016/j.micpath.2026.108485}, pmid = {41966314}, issn = {1096-1208}, abstract = {Klebsiella pneumoniae is an important opportunistic pathogen of One Health concern, and its multidrug-resistant (MDR) and hypervirulent strains pose serious threats to public health. However, the epidemiological characteristics, antimicrobial resistance profiles, and virulence potential of K. pneumoniae circulating in farmed minks remain poorly understood. In this study, we integrated phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis to investigate the epidemiology, resistance determinants, and virulence characteristics of K. pneumoniae isolated from farmed minks in northern China. A total of 41 K. pneumoniae strains from 325 fecal samples (isolation rate: 12.62%), including three hypervirulent strains. All isolates exhibited multidrug resistance, with complete resistance to florfenicol, azithromycin, and sulfisoxazole, but remained highly susceptible to carbapenems and polymyxin B. Whole-genome sequencing revealed that the isolates harbored 241 antibiotic resistance genes (ARGs), including ESBL-associated genes and the plasmid-mediated mcr-1.1, along with 7,111 virulence factor genes (VFGs) and 135 mobile genetic elements (MGEs). Metagenomic analysis further revealed a complex resistome and virulome, with 7,259 ARGs and 6,701 virulence-related genes identified across samples. Antibiotic target alteration and efflux were the dominant resistance mechanisms, while effector delivery systems, metabolic functions, and adherence were the major virulence categories. MGEs were abundant, especially transposases, indicating active genetic mobility within the microbial community. Overall, this study provides a comprehensive characterization of antimicrobial resistance and virulence features of mink-derived K. pneumoniae and highlights the potential role of farmed minks as reservoirs of multidrug-resistant bacteria within the One Health framework, offering important insights for antimicrobial resistance surveillance and public health risk assessment.}, }
@article {pmid41966472, year = {2026}, author = {Merkhan, K and Chaudhry, AS}, title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.}, journal = {Anaerobe}, volume = {98}, number = {}, pages = {103046}, doi = {10.1016/j.anaerobe.2026.103046}, pmid = {41966472}, issn = {1095-8274}, abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.
METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72 h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20 g kg[-1] DM) for each PFA.
RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20 g kg[-1] DM, followed by GBL with a 28.5% reduction at 10 g kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.
CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.}, }
@article {pmid41966559, year = {2026}, author = {Jordán, M and Bustos-Caparros, E and Gago, JF and Zhang, Z and Tian, Z and Singleton, DR and Rossello-Mora, R and Grifoll, M and Vila, J}, title = {Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142004}, doi = {10.1016/j.jhazmat.2026.142004}, pmid = {41966559}, issn = {1873-3336}, abstract = {Polycyclic aromatic nitrogen heterocycles (PANHs), also known as azaarenes, are common co-contaminants at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Recent non-target analysis of PAH-contaminated soil samples has revealed an unexpected abundance and diversity of PANHs, with acridine standing out as a predominant compound within this group. Despite its known toxicity and prevalence in contaminated soils, the microbial communities and biochemical mechanisms responsible for acridine degradation remain poorly understood. We conducted DNA-stable isotope probing (DNA-SIP) using newly synthesized uniformly labeled [13]C-acridine to comprehensively assess the bacterial taxa and functional genes involved in acridine biodegradation in a creosote-contaminated soil. Metagenomic analysis of [13]C-enriched DNA from soil incubations identified a member of the genus Sphingobium as the primary acridine degrader. Transcriptomic analysis based on its 16S rRNA gene expression demonstrated a strong correlation with acridine removal from the soil. Shotgun metagenomic sequencing enabled the reconstruction of one metagenome-assembled genome (MAG). Functional annotation of this MAG revealed five gene clusters potentially involved in acridine biodegradation, and their actual contribution was assessed by gene expression analysis in soil incubations. Based on these findings, we reconstructed the metabolic pathway for putative acridine degradation in PAH-contaminated soil.}, }
@article {pmid41966829, year = {2026}, author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, SÁ and Ferenczi, S and Szőke, Z}, title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104498}, doi = {10.1016/j.xpro.2026.104498}, pmid = {41966829}, issn = {2666-1667}, abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].}, }
@article {pmid41967167, year = {2026}, author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB}, title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {59}, number = {}, pages = {101830}, doi = {10.1016/j.cbd.2026.101830}, pmid = {41967167}, issn = {1878-0407}, abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.}, }
@article {pmid41967206, year = {2026}, author = {Moletta-Denat, M and Azam, O and Pourcher, AM and Manno, M and Zennaro, B and Bonin, E and Bonnafous, A and Chenon, P and Leboucher, A and Alvarez-Fraga, L and Godon, JJ and Wéry, N}, title = {Fate of pathogenic bacteria in five full-scale biogas plants monitored using cultivation, dPCR, and shotgun metagenomics: Insights from each approach.}, journal = {Waste management (New York, N.Y.)}, volume = {218}, number = {}, pages = {115505}, doi = {10.1016/j.wasman.2026.115505}, pmid = {41967206}, issn = {1879-2456}, abstract = {Current global standards for quantification of pathogenic or indicator bacteria in biogas plants primarily rely on culture-based methods using specific media. However, molecular techniques such as quantitative PCR, digital PCR (dPCR), and shotgun metagenomics are increasingly employed in research and may offer more effective pathogen monitoring for industrial applications. This study analyzed samples from five full-scale biogas plants using traditional culture-based methods, dPCR and shotgun metagenomics to monitor indicator bacteria (Escherichia coli, Enterococcus spp. and Clostridium perfringens) and pathogenic species (Salmonella enterica, Listeria monocytogenes, Staphylococcus aureus and Clostridium botulinum). The DNA extraction protocol was optimized to achieve quantification limits of 1.1 copies of gene g[-1] wet weight, compatible with regulatory thresholds. Comparing the three methods revealed that shotgun metagenomics detected a greater diversity of pathogenic species in biowaste, including S. aureus and C. botulinum. Acidophilic conditions in hydrolysis tank effectively hygienized the biowaste. In contrast, the four agricultural biogas plants showed limited effect on the three indicator bacteria, as indicated by dPCR. This study demonstrates, for the first time, the added value of combining dPCR and shotgun metagenomics to assess pathogen dynamics in biogas plants. Together, these methods provide a more comprehensive and specific view of microbial contaminants, as illustrated by the detection of Enterococcus cecorum in digestates.}, }
@article {pmid41967340, year = {2026}, author = {Li, M and Yao, K and Harindintwali, JD and Qian, M and Wu, N and Kan, Y and Song, Z and Xiao, X and Liu, P and Zhao, Y}, title = {Alkali-organic synergy rewires microbial acid tolerance to restore nitrogen cycling in acidic soils.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129619}, doi = {10.1016/j.jenvman.2026.129619}, pmid = {41967340}, issn = {1095-8630}, abstract = {Soil acidification in global croplands is intensifying, yet the microbial mechanisms by which amendments restore soil nitrogen (N) cycling remain poorly understood. Here, we used a decade-long field experiment in strongly acidic soils to elucidate how alkali slag and organic manure, alone and in combination, regulate acid-tolerant microbial functions and N transformation processes. By integrating soil physicochemical analyses, 16 S rRNA gene sequencing, and shotgun metagenomics, we show that the combined application of organic manure and alkali slag (OM + AS) most effectively increased soil pH (from 4.18 to 5.42) and reduced inorganic N accumulation relative to single amendments (Ammonium nitrogen, nitrate nitrogen, and total organic nitrogen decreased by 15.66 mg/kg, 12.56 mg/kg, and 46.09 mg/kg respectively). Metagenomic profiling revealed that OM + AS consistently up-regulated acid-tolerance pathways (proton pump increased by 6.12%, alkali production increased by 9.75%, acid consumption increased by 5.12%) together with key N cycling genes, with the strongest enhancement observed for nitrification (increased by 84.54%). Network analysis demonstrated significant positive co-occurrence between acid-tolerance and nitrification genes across the microbial community. Correspondingly, bacterial taxa harboring these functions, including Sphingomonas and Nitrospira, were most abundant under OM + AS. We propose that alkali slag and organic manure act synergistically to elevate soil pH, relieve acid stress on microbes, and promote a community with dual capacities for acid tolerance and active N transformation. These findings mechanistically link soil acidity amelioration with enhanced microbial-mediated N cycling and offer a functional basis for designing targeted soil remediation strategies.}, }
@article {pmid41967439, year = {2026}, author = {Tang, C and Wan, C and Gan, J and He, Z and Wei, C and Tan, H and Wu, R and Yu, F and Li, Y}, title = {Rhizosphere phosphorus and iron cycling accelerates manganese phytoextraction by Polygonum lapathifolium.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142033}, doi = {10.1016/j.jhazmat.2026.142033}, pmid = {41967439}, issn = {1873-3336}, abstract = {Manganese (Mn) contamination in mining soils poses persistent ecological risks due to its high mobility and potential accumulation in plants. Although exogenous microbial inoculation is increasingly used to improve phytoremediation, the mechanisms by which it regulates rhizosphere phosphorus (P) and iron (Fe) cycling, and thereby influences Mn bioavailability, remain poorly understood. We hypothesized that Enterobacter sp. inoculation would enhance Mn phytoextraction by stimulating rhizosphere P activation and Fe speciation transformation, thereby promoting nutrient acquisition and Mn mobilization. To test this hypothesis, we investigated the effects of Enterobacter sp. inoculation on rhizosphere P/Fe fractions, functional genes, and Mn phytoextraction. Enterobacter sp. significantly decreased rhizosphere soil pH and enhanced P-releasing enzyme activities, increasing available P by 26.7% under the C1.0 (3.8 ×10[7] CFU·g[-1] (soil)) treatment compared with the control (p < 0.05). Concurrently, Fe(II) and amorphous Fe increased by 11.9% and 15.1%, respectively (p < 0.05), indicating enhanced Fe transformation in the rhizosphere. These shifts facilitated plant P and Fe acquisition, promoted biomass production, enhanced Mn phytoextraction in Polygonum lapathifolium L. by strengthening rhizosphere redox conditions and mineral interfacial processes. Metagenomic analysis revealed that Enterobacter sp. inoculation increased the functional potential of genes related to P activation (e.g., gcd, phnP) and Fe biosynthesis/uptake (e.g., hemH, pchB), mainly associated with Pseudomonadota and Actinomycetota. Partial least squares path modeling further confirmed positive associations among P/Fe cycling genes, rhizosphere P/Fe fractions, enzymatic activities, and plant growth. Overall, microbial inoculation enhanced Mn phytoremediation by coordinating rhizosphere nutrient cycling processes, providing a promising strategy for the remediation of HMs-contaminated mining soils.}, }
@article {pmid41967476, year = {2026}, author = {Wang, H and Di, D and Du, S and Tateno, R and Peñuelas, J and Migliavacca, M and Chen, Q and Guan, J and Song, Y and Shi, W}, title = {Plant functional trait differentiation and microbial life-history strategy shifts drive soil respiration under long-term forest restoration.}, journal = {Tree physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/treephys/tpag042}, pmid = {41967476}, issn = {1758-4469}, abstract = {Soil respiration (Rs) represents a major carbon (C) flux linking plant productivity with microbial decomposition; however, the mechanisms by which contrasting forest restoration pathways regulate Rs and its components remain insufficiently understood. We conducted a six-year field observation (2017-2022) across abandoned farmland (AF), Quercus liaotungensis forest (QF), and Robinia pseudoacacia plantation (RP) on the Loess Plateau, China, integrating measurements of Rs, autotrophic (Ra), heterotrophic (Rh), plant functional traits, soil physicochemical properties, and microbial C metabolic potential. Afforestation significantly increased Rs, with a stronger enhancement observed in QF than in RP. Although Ra did not differ significantly between the two forest types, Rh accounted for approximately 70% of Rs and primarily explained the significant differences in Rs between restoration pathways. Elevated Rh in QF was strongly associated with greater abundances of microbial functional genes involved in the degradation of C substrates. Integrated analyses further revealed that differentiation in plant functional traits between QF (conservative strategy) and RP (acquisitive strategy) indirectly amplified Rh contributions to Rs by reshaping soil substrate availability and coordinating shifts in microbial life-history strategies. Collectively, our findings identify plant functional trait differentiation as a key driver of long-term Rs dynamics, mediated by shifts in microbial life-history strategies.}, }
@article {pmid41967488, year = {2026}, author = {Du, M and Xue, P and Minasny, B and Jang, HJ and McBratney, A}, title = {Macroecological processes impact Australian soil resistomes and climatically stable regions with anthropogenic activities serve as ARG hotspots.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag079}, pmid = {41967488}, issn = {1751-7370}, abstract = {Soil antibiotic resistance genes (ARGs) pose a global health threat, but a critical knowledge gap remains regarding how macro-scale pedoclimatic constraints interact with land-use intensification to determine the spatial distribution of the soil resistome. To address this, we conducted a continental-scale survey of Australian topsoils and used metagenomic analysis to reveal the hierarchy of drivers shaping the soil resistome. Machine learning was applied to predict the spatial ARG distribution across Australia. We found that, at the continental scale, climatic variability acts as the dominant filter on ARG distribution, overriding local soil properties and human disturbance. Unexpectedly, climatically stable regions, characterised by sandy and low-carbon soils in Southwestern Australia, emerged as ARG hotspots. We also demonstrated that anthropogenic land use amplifies ARG abundance within these climatically stable regions. Furthermore, spatial modelling revealed distinct geographical patterns: although total ARG abundance was enriched in coastal regions, specific resistance mechanisms showed unique distributions. As a continental-scale investigation of soil ARGs in Australia, this study provides a framework to identify high-risk regions where lower climatic variability and intensive farming interact to enhance antimicrobial resistance.}, }
@article {pmid41968394, year = {2026}, author = {Zhao, B and Yang, X and Feng, K and Wang, J and Liu, M and Wang, Y and Wang, D and Peng, X and He, Q and Lu, Y and Waseem, H and Wang, S and Deng, Y}, title = {Phylogenetic assembly of methanogenesis regulates methane yield in food-waste anaerobic digestion.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag083}, pmid = {41968394}, issn = {1751-7370}, abstract = {Anaerobic digestion (AD) of food waste (FW) is a key wate-to-energy strategy, yet daily biogas yield is often challenging to sustain, partly due to a limited understanding of the internal methanogens and their functional divergence. Here, we investigated seven full-scale mesophilic FW-AD systems distributed across China along a broad latitudinal gradient (>2,800 km), linking methane production variations (0.38-2.11 m3/m3•d-1) with the phylogenetic distributions of methanogens and their methanogenic genes. We found that hydrogenotrophic and aceticlastic pathways were ubiquitous, whereas methylotrophic methanogenesis showed regional enrichment in warmer regions, reflecting persistent influences of climate-associated upstream conditions on downstream methanogenic communities. Gene-level phylogeny of methanogenesis-related alleles, rather than species-level phylogeny, closely tracked biogas yield variation (Mantel's P < 0.05) and showed consistently stronger associations than gene-level compositions (mean standardized total effect: 0.491 vs. 0.298, P < 0.01). Higher methane yields (1.61 vs. 0.61 m3/m3•d-1 in high- vs. low-performing systems, P < 0.01) were significantly associated with reduced Faith's phylogenetic diversity (1.82 vs. 2.30, P < 0.01) and tighter clustering (mean pairwise phylogenetic distance, MPD: 0.25 vs. 0.30, P < 0.01) of methanogenic gene variants, suggesting that phylogenetic coherence may reflect ecological filtering favoring efficient methanogenesis, albeit at the expense of functional redundancy. These findings highlight gene-level trait phylogeny as a potential proxy for functional robustness, offering a framework for ecological design of AD microbiomes.}, }
@article {pmid41864063, year = {2026}, author = {Jian, X and Yu, P and Zhang, Y and Pan, H and Wu, K and Zhang, H and Zhang, H and Huang, Y and Zhao, Y and Wang, Y and Wang, Y and Zhou, Q and Zhang, X and Zhao, G and Li, B and Guo, J and Xia, K and Tang, B and Li, J}, title = {Large-scale profiling of blood microbial signatures in patients with Parkinson's disease and its association with disease progression: a cross-sectional study.}, journal = {EBioMedicine}, volume = {126}, number = {}, pages = {106224}, pmid = {41864063}, issn = {2352-3964}, mesh = {Humans ; *Parkinson Disease/microbiology/blood/diagnosis ; Disease Progression ; Male ; Female ; Aged ; Biomarkers/blood ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; Whole Genome Sequencing ; *Bacteria/genetics/classification ; Metagenomics/methods ; }, abstract = {BACKGROUND: Emerging evidence supports the presence of microbial signatures in the blood, yet their clinical relevance remains poorly understood. In this study, we profiled blood microbial signatures in patients with Parkinson's disease (PD) and investigated their associations with disease progression.
METHODS: We analysed 4018 whole-genome sequencing (WGS) data of blood samples from two independent cohorts. The high-quality non-human reads were extracted for microbial annotation using Kraken 2 and Bracken software with the PlusPF database. To identify PD-associated signatures, we implemented a population-based, cross-cohort filtration process with resequencing validation to minimise noise and putative contaminants.
FINDINGS: Microbial DNA signals, predominantly bacterial, were extensively detected in the sequencing data and were more abundant in individuals with PD than in controls. Across the two cohorts, 126 bacterial species were identified as key signatures, nearly two-thirds of which are known to colonise human body sites. Among these, 19 species exhibited increased abundance and higher prevalence in PD, and could serve as features to discriminate effectively patients from controls. Furthermore, several microbial signatures were correlated with more severe clinical manifestations, such as motor dysfunction and cognitive impairment.
INTERPRETATION: Our findings supported blood microbial signatures as promising biomarkers in PD, although their origin and functional relevance remain to be validated. The analytical framework may facilitate future investigations into the potential clinical implications of blood microbial signatures in disease contexts.
FUNDING: This work was supported by Hunan Innovative Province Construction Project, National Natural Science Foundation of China, and Natural Science Foundation of Hunan Province.}, }
@article {pmid41957864, year = {2026}, author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F}, title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00886-8}, pmid = {41957864}, issn = {2524-6372}, support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.
RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.
CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.}, }
@article {pmid41957950, year = {2026}, author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A}, title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.}, journal = {Oncoimmunology}, volume = {15}, number = {1}, pages = {2656514}, doi = {10.1080/2162402X.2026.2656514}, pmid = {41957950}, issn = {2162-402X}, mesh = {*Oncolytic Virotherapy/methods ; Humans ; Animals ; Mice ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Oncolytic Viruses ; Feces/microbiology ; Female ; *Neoplasms/therapy/microbiology ; Male ; }, abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.}, }
@article {pmid41958036, year = {2026}, author = {Shin, H and Jeon, MK and Hur, HG}, title = {A Cautionary Case for Host Assignment Based on Broad Environmental blaOXA Carriers.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70327}, doi = {10.1111/1758-2229.70327}, pmid = {41958036}, issn = {1758-2229}, support = {RS-2023-NR076613//National Research Foundation of Korea/ ; }, mesh = {*beta-Lactamases/genetics ; Metagenomics/methods ; *Bacteria/genetics/drug effects/enzymology/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; Wastewater/microbiology ; Metagenome ; *Bacterial Proteins/genetics ; Microbiota ; Drug Resistance, Bacterial/genetics ; }, abstract = {Metagenomic analyses rely heavily on contig assembly and reference databases, which can introduce substantial bias when predicting the hosts of antibiotic resistance genes (ARGs) in complex environmental microbiomes. Reference-based metagenomic pipelines assign ARGs mostly to clinically important pathogens because publicly available genomic repositories are dominated by clinically relevant isolates. Motivated by this limitation, we investigated whether metagenomic inferences accurately reflect the true bacterial hosts of ARGs in a wastewater treatment plant, also integrating culture-based validation. Metagenomic screening suggested that ARGs (blaOXA) were primarily associated with clinical taxa. In contrast, culture-based screening identified a wider host distribution of blaOXA genes. Our results imply that environmental bacteria, rather than clinically important taxa, are also hosts of blaOXA genes. Phenotypic testing showed elevated cephalosporin minimal but no carbapenem resistance, consistent with the nature of carbapenem-hydrolysing class D β-lactamases. Our findings reveal that reliance on reference-based metagenomic host prediction can underestimate the diversity of environmental ARG reservoirs. This integrated approach highlights the need for cautious interpretation of metagenomic host assignments and the importance of coupling metagenomic pipelines with culture-dependent validation when assessing ARG ecology in the natural environments.}, }
@article {pmid41958322, year = {2026}, author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B}, title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.}, journal = {American journal of primatology}, volume = {88}, number = {4}, pages = {e70148}, doi = {10.1002/ajp.70148}, pmid = {41958322}, issn = {1098-2345}, support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Macaca/virology/microbiology ; *Virome ; Tibet ; Male ; Animals, Zoo/virology ; Female ; }, abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.}, }
@article {pmid41958469, year = {2026}, author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A}, title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.}, journal = {Alzheimer's & dementia (New York, N. Y.)}, volume = {12}, number = {2}, pages = {e70239}, pmid = {41958469}, issn = {2352-8737}, abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.
METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.
RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).
DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.}, }
@article {pmid41958710, year = {2026}, author = {Nakamichi, K and Manandhar, A and Shrestha, S and Sundararajan, M and Poudel, MP and Karmacharya, BM and Bade, A and Banjara, P and Shrestha, A and Sandt, A and Turski, G and Buhr, ED and Chowdhary, A and Van Gelder, RN}, title = {Association of Seasonal Hyperacute Panuveitis Syndrome with S. pneumoniae Endophthalmitis.}, journal = {Ophthalmology science}, volume = {6}, number = {5}, pages = {101128}, pmid = {41958710}, issn = {2666-9145}, abstract = {PURPOSE: To identify potential infectious agents in cases of seasonal hyperacute panuveitis syndrome (SHAPU) from vitreous biopsies of patients with this disorder.
DESIGN: A retrospective cohort analysis.
SUBJECTS: Vitreous biopsies were obtained during the course of care from 53 subjects with SHAPU.
METHODS: DNA extraction and whole genome shotgun sequencing was performed using Oxford Nanopore long read sequencing. Sequences were matched against microbial and human databases. Visual outcomes at presentation and at 6 months were recorded.
MAIN OUTCOME MEASURES: Identification and characterization of metagenomic sequences in vitreous isolates from subjects with SHAPU.
RESULTS: Adequate DNA for sequencing was obtained from 32 SHAPU subjects. Fifteen samples yielded bacteria on culture, with 14 S. pneumoniae and 1 S. aureus isolate recovered. Bacterial DNA was detected by whole genome sequencing in 29 of 32 cases. S. pneumoniae was the predominant organism recovered. Bacterial genomic loads ranged up to 10 000 bacteria/human cell, indicating active infection. No pathogens were detected in control samples. Reconstruction of bacterial genome was possible in 7 SHAPU cases and indicated diverse S. pneumoniae subtypes associated with individual cases. Sufficient DNA remained for analysis of torque teno virus by qualitative polymerase chain reaction in 17 cases, of which 13 were positive. Visual outcomes were mixed, with 7 patients having hypotonous eyes at 6 months, but 8 patients having better than 20/200 vision. No relationship could be discerned between presenting bacterial load and visual outcome.
CONCLUSIONS: The majority of SHAPU cases show molecular evidence for concurrent S. pneumoniae infection. Good visual results are possible in treating SHAPU as endophthalmitis.
FINANCIAL DISCLOSURES: The authors have no proprietary or commercial interest in any materials discussed in this article.}, }
@article {pmid41959051, year = {2026}, author = {Weng, Y and Moyne, O and Walker, C and Haddad, E and Lieng, C and Chin, L and Rahman, G and McDonald, D and Knight, R and Zengler, K}, title = {A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.11.710980}, pmid = {41959051}, issn = {2692-8205}, abstract = {Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data by leveraging matched metagenomic coverage breadth to identify genomes likely to be truly present in a sample before aligning metatranslatomic and optional metatranscriptomic reads. MOPP generates taxon-by-gene count tables across genomic, transcriptional and translational layers, enabling integrated downstream analyses of microbial function. We evaluated MOPP using a defined 79-member synthetic human gut community profiled by metagenomics and metaRibo-Seq. Coverage breadth filtering markedly improved detection accuracy relative to a standard baseline workflow, with performance remaining robust across a broad intermediate threshold range and peaking at 92-95% coverage breadth. At a 92% threshold, MOPP reduced the number of distinct detected operational genomic units by 99.4% while retaining 87.8% of aligned metaRibo-Seq reads on average, and increased the F1 score from 0.02 to 0.61. Residual false positives were predominantly attributable to genomes with extremely high nucleotide similarity to true community members, whereas false negatives were enriched among low-abundance taxa, indicating that remaining errors are driven primarily by biological similarity and detection limits rather than widespread nonspecific mapping. Together, these results establish MOPP as a high-throughput workflow for robust processing of metaRibo-Seq in the context of matched metagenomics and position it as a scalable framework for integrated taxonomic and functional analysis of microbial communities across genomic, transcriptional and translational layers.}, }
@article {pmid41959121, year = {2026}, author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A}, title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.03.715941}, pmid = {41959121}, issn = {2692-8205}, abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.
OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.
METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.
MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.
CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.}, }
@article {pmid41959210, year = {2026}, author = {Muller, E and Baum, S and Borenstein, E}, title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714614}, pmid = {41959210}, issn = {2692-8205}, abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.
RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.
AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL .}, }
@article {pmid41959308, year = {2026}, author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ}, title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.11.711154}, pmid = {41959308}, issn = {2692-8205}, abstract = {UNLABELLED: Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.
IMPORTANCE: Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.}, }
@article {pmid41959338, year = {2026}, author = {Kramer, AM and Zhang, A and Ayala, N and de Sanctis, B and Karim, L and Hinrichs, AS and Walia, S and Turakhia, Y and Corbett-Detig, R}, title = {Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.29.711974}, pmid = {41959338}, issn = {2692-8205}, abstract = {Pangenomes capture population-level variation but remain computationally challenging at scale. We present Panmap, a tool that leverages evolutionary structure to place, align, and genotype sequencing reads against mutation-annotated pangenomes containing up to millions of genomes. Panmap introduces a phylogenetically compressed k -mer index that stores only sequence differences along branches, enabling efficient comparison of reads to both sampled genomes and inferred ancestors. This approach reduces index size by up to 600-fold and construction time by over three orders of magnitude relative to existing tools. Panmap places a 100× coverage SARS-CoV-2 sample onto 20,000 genomes in 0.4 seconds and onto 8 million genomes in under two minutes. Furthermore, it enables accurate haplotype identification and abundance estimation in metagenomic samples and sensitive placement of ancient environmental DNA without prior alignment. Our approach makes large-scale pangenomes directly amenable to read mapping, genome assembly, alignment-free phylogenetic placement, and metagenomic analysis.}, }
@article {pmid41959403, year = {2026}, author = {Maier, J and Gin, C and Rabasco, J and Spencer, W and Bass, A and Duerkop, BA and Callahan, B and Kleiner, M}, title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.31.715651}, pmid = {41959403}, issn = {2692-8205}, abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.
RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.
CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.}, }
@article {pmid41959459, year = {2026}, author = {Kim, M and Ardell, SM and Kryazhimskiy, S}, title = {Module-Selection Balance in the Evolution of Modular Organisms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.01.715873}, pmid = {41959459}, issn = {2692-8205}, abstract = {The architecture of the genotype-phenotype-fitness map (GPFM) is a key determinant of evolutionary dynamics. One salient feature of biological GPFMs is variational modularity, where each mutation affects only a small subset of functional traits. Variational modularity may constrain the dynamics of trait evolution, but these constraints are not well understood. Here, we use several extensions of the Fisher's geometric model with two functional traits to investigate these constrains. We find that on GPFMs with universal pleiotropy, populations evolve along the fitness gradient, which implies that the trait under stronger selection is optimized exponentially faster than the trait under weaker selection. In contrast, on modular GPFMs, populations approach a quasi-steady state that we term a "module-selection balance" where both traits improve at the same rate and their ratio remains constant. We demonstrate that the existence of a module-selection balance is robust with respect to the details of evolutionary dynamics and GPFMs themselves, as long as they are variationally modular. Our theory predicts that variationally modular organisms should exhibit stereotypical bi-phasic dynamics of genome evolution, especially in the strong clonal interference regime, and we find support for this prediction in metagenomic data from Lenski's long-term evolution experiment in bacterium Escherichia coli . We propose that module-selection balance is an inherent feature of variationally modular GPFMs, which imposes an important constraint on long-term trait evolution.}, }
@article {pmid41959466, year = {2026}, author = {Sapoval, N and Treangen, TJ and Nakhleh, L}, title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.10.710879}, pmid = {41959466}, issn = {2692-8205}, abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.
RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.
https://github.com/nsapoval/bd-gsl.}, }
@article {pmid41959535, year = {2026}, author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG}, title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.31.715631}, pmid = {41959535}, issn = {2692-8205}, abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.}, }
@article {pmid41959658, year = {2026}, author = {Funauchi, A and Hashimoto, K and Fukushima, K and Matsumoto, Y and Hamada, N and Hara, R and Niitsu, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H}, title = {Gastric Aspirate Isolate Demonstrates Strain-Level Concordance With Sputum Isolate in Nontuberculous Mycobacterial Pulmonary Disease.}, journal = {Open forum infectious diseases}, volume = {13}, number = {4}, pages = {ofag175}, pmid = {41959658}, issn = {2328-8957}, abstract = {The nontuberculous mycobacteria (NTM) isolated from gastric aspirate have demonstrated >85% strain concordance with those from the sputum, suggesting that they originate from the lungs rather than the environment. Gastric aspirate, although not yet internationally recognized, may be a useful supplementary specimen for diagnosing NTM pulmonary disease.}, }
@article {pmid41960427, year = {2026}, author = {Nuanmuang, N and Leekitcharoenphon, P and Njage, PMK and Jirakkakul, J and Dulsawat, S and Tachaleat, A and Svendsen, CA and Møller, FD and Otani, S and Cheevadhanarak, S and Aarestrup, FM}, title = {Comparative resistome from toilet waste in three different income areas, Bangkok, Thailand.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1790551}, pmid = {41960427}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a significant public health threat and is associated with millions of deaths worldwide each year. Besides antimicrobial usage, different socioeconomic factors have recently gained attention as being associated with increased AMR. Bangkok, a city with diverse income levels, provided a unique setting for this study, which aimed to explore the possible within-city association between income-level areas and the diversity and abundance of AMR. Twenty-seven toilet waste samples were collected from nine different sites (low-, middle-, and high-income) during March-April 2023, and metagenomic sequencing was performed. The sequencing data were quality checked, and sequences that passed quality control were mapped to antimicrobial, metal, and disinfectant resistance gene databases as well as bacterial taxonomy databases. We observed higher antibiotic resistance genes (ARGs), metal resistance, and disinfectant resistance abundance (fragments per kilobase per million mapped reads, FPKM) in low-income groups compared to middle- and high-income groups. This included both acquired ARGs and presumed intrinsic ARGs, including genes associated with completely novel antibiotics that have so far only been identified through functional cloning. Significant differences in individual ARGs were also observed between sites. Our study highlights the relative abundance of ARGs across different income groups, emphasizing how the development of resistance mechanisms revealed through metagenomic analysis can serve as a valuable tool for city-level surveillance of AMR from toilet waste, particularly in low-income settings.}, }
@article {pmid41960429, year = {2026}, author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL}, title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691133}, pmid = {41960429}, issn = {1664-302X}, abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.
METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.
RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.
DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.}, }
@article {pmid41960438, year = {2026}, author = {Zhao, Z and Xiang, L and Liu, Y and Xu, S and Chen, Y and Yu, M}, title = {Rare fungal keratitis caused by plant pathogens: report of two cases and review of the literature.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1785252}, pmid = {41960438}, issn = {2673-6128}, abstract = {Macrophomina phaseolina and Colletotrichum fructicola are notable plant pathogens, yet cases of keratitis from these fungi are rarely reported. Limited awareness of this keratitis etiology among ophthalmic professionals reduces the likelihood of accurate diagnosis and timely treatment. This report aims to improve the understanding of these rare infections in eye care. We present two cases of keratitis: one caused by M. phaseolina and another by C. fructicola, both of whom experienced a complicated treatment course. Traditional fungal exams yielded negative results, which limited disease identification and focused therapy. To determine the cause, we used metagenomic next-generation sequencing (mNGS) on clinical samples obtained from corneal scrapings. The mNGS report was received during therapy and quickly identified the pathogen. Based on this, we looked for treatment regimens for this kind of infection in previous literature, altered and implemented appropriate antifungal drug therapy, and the patient's condition improved. We review the literature from 1970 to 2025 on M. phaseolina and Colletotrichum spp. keratitis. We identified 10 cases of M. phaseolina keratitis from four studies and 72 cases of Colletotrichum spp. keratitis, including five of C. fructicola, in 43 articles. Misdiagnosis was common due to limited clinical and microbiologic suspicion. The rise of infections by rare pathogens highlights diagnostic challenges. Traditional methods often delay accurate diagnosis, while mNGS enables rapid identification of pathogen, crucial for effective treatment and vision preservation.}, }
@article {pmid41960830, year = {2026}, author = {Sun, S and Zhou, Y and Deng, F and Meng, Y and Zhu, X and Wang, H and Wei, D}, title = {Engineering an l-Threonine Aldolase from Staphylococcus epidermidis for Enhanced Diastereoselectivity in the Synthesis of a Chloramphenicol Intermediate.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c01578}, pmid = {41960830}, issn = {1520-5118}, abstract = {l-Threonine aldolase (LTA) is an attractive biocatalyst for the synthesis of l-syn-p-nitrophenylserine (l-syn-1b), a key intermediate in chloramphenicol synthesis. However, low diastereoselectivity has limited its broader application in stereospecific C-C bond formation. To overcome this limitation, a metagenomic library constructed from non-natural amino acid-enriched environments was screened, leading to the identification of an LTA from Staphylococcus epidermidis (SeLTA) that exhibits the highest diastereoselectivity toward l-syn-1b among naturally occurring LTAs reported to date. To further enhance its diastereoselectivity, structural comparison, alanine scanning, and tunnel analysis were employed to identify hotspots that modulate the diastereoselectivity of SeLTA. Subsequent saturation mutagenesis and iterative saturation mutagenesis at these positions yielded the quadruple variant A176G/Y202S/N7C/F129E (Mut4), which increased the diastereoselectivity from 32.5%syn to 92.7%syn. Furthermore, Mut4 exhibits markedly improved diastereoselectivity toward para- and meta-substituted benzaldehyde derivatives. Molecular dynamics (MD) simulations further elucidated the molecular basis underlying the enhanced diastereoselectivity of Mut4. This study provides a potential biocatalyst for the sustainable and efficient synthesis of a chloramphenicol intermediate.}, }
@article {pmid41961352, year = {2026}, author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H}, title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.}, journal = {Neurochemical research}, volume = {51}, number = {2}, pages = {}, pmid = {41961352}, issn = {1573-6903}, }
@article {pmid41961522, year = {2026}, author = {Song, W and Li, M and Yue, X and Meng, Y and Xie, Y and Zhang, Y and Hu, Y and Zheng, Y and Yue, X}, title = {Microbial succession and metabolic mechanisms driving flavor evolution in Northeast Chinese dajiang: a comprehensive review integrating insights from East Asian fermented soybean pastes.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/10408398.2026.2644602}, pmid = {41961522}, issn = {1549-7852}, abstract = {This review systematically explores the spatiotemporal microbial succession and flavor evolution during the fermentation of northeast Chinese soybean paste (dajiang), with a focus on the jiangpei (solid-state starter) and jianglao (brine fermentation) stages. By integrating metagenomic, metabolomic, and sensory data, this review synthesizes evidence linking microbial community dynamics-featuring Lactobacillus spp., Zygosaccharomyces rouxii, and Aspergillus oryzae-to the biosynthesis of key flavor compounds. These include umami amino acids (e.g., glutamic acid, 1.5-2.0 g/kg), fruity esters (e.g., ethyl acetate, 124.67 μg/kg), and phenolic antioxidants. Cross-feeding interactions (e.g., yeast utilization of lactic acid for ester synthesis) and environmental stressors (12%-18% NaCl, 25 °C-30 °C) are shown to enhance flavor complexity by modulating metabolic pathways like amino acid degradation and lipid β-oxidation. Unlike prior studies focusing on fragmented fermentation stages, this review systematically addresses the full fermentation continuum, highlighting how aerobic-to-anaerobic transitions drive functional metabolite accumulation. The review concludes by outlining a roadmap to modernize dajiang production through standardized quality control, precision flavor modulation, and traditional process optimization, enabled by culturomics/MAGs, multi-omics integration, and AI-assisted fermentation monitoring and control.}, }
@article {pmid41961886, year = {2026}, author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T}, title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0345919}, doi = {10.1371/journal.pone.0345919}, pmid = {41961886}, issn = {1932-6203}, mesh = {Humans ; *Metagenomics/methods ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; Neural Networks, Computer ; Multiomics ; }, abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.}, }
@article {pmid41962241, year = {2026}, author = {Lin, Z and Pang, S and Xu, T and Zhou, YL and Zhang, C and Qian, PY and Zhang, S}, title = {Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.}, journal = {Water research}, volume = {299}, number = {}, pages = {125879}, doi = {10.1016/j.watres.2026.125879}, pmid = {41962241}, issn = {1879-2448}, abstract = {The marine plastisphere affects nitrogen cycling processes, but its role in nrfA-dependent nitrite ammonification, a critical phase of dissimilatory nitrate reduction to ammonium (DNRA) with important implications for nitrogen retention and greenhouse gas dynamics, remains unexplored. In this study, we analyzed 269 plastisphere metagenomes and eight metatranscriptomes from global public datasets. The plastisphere contained elevated nrfA levels compared to seawater, and nrfA transcripts were consistently detected. A total of 285 putative nrfA-dependent nitrite ammonifying bacteria were identified, including 156 novel genera. Most plastisphere MAGs overlapped with other examined marine biofilms, whereas 109 MAGs were uniquely detected in plastisphere samples within the analyzed comparative datasets. Functional studies revealed diverse electron-donor utilization strategies supporting DNRA in plastisphere microorganisms. Evolutionary analyses showed that nrfA genes were distributed across different phyla through horizontal gene transfer, whereas purifying selection limited sequence divergence. These findings highlight a previously underappreciated genetic and transcriptional potential for DNRA in plastic-associated biofilms at the particle scale, with implications for nitrogen retention within plastisphere microhabitats.}, }
@article {pmid41962374, year = {2026}, author = {Zhou, LT and He, DH and Li, J and He, RX and Ma, SJ and Gong, GY and Zou, XS and Li, S and Zhou, YF and Hu, WJ}, title = {Dynamics and drivers of last-resort antibiotic resistance genes during pilot-scale aerobic fermentation of municipal sludge and subsequent bok choy pot trials.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141891}, doi = {10.1016/j.jhazmat.2026.141891}, pmid = {41962374}, issn = {1873-3336}, abstract = {Sludge from wastewater treatment plants may exacerbate environmental dissemination of last-resort antibiotic resistance genes (LARGs) when applied to land. However, LARG behavior during aerobic sludge fermentation and subsequent soil-plant transfer remains poorly understood. This study specifically targeted LARGs beyond common ARGs and coupled pilot-scale fermentation with bok choy cultivation to resolve their dynamics and compartmentalization. Using metagenomic sequencing with correlation and network analyses, we identified environmental drivers and inferred potential hosts. Optimized fermentation conditions (maintaining >50 °C for 10 days) reduced moisture to 30%, lowered the C/N ratio to 24.7, and achieved germination indices of 85%-90%. Fermentation promoted microbial succession, enhanced metal passivation and organic matter humification, and reduced antibiotic and ARG abundance, with total antibiotic degradation reaching 49.19% in the thermophilic phase. LARG abundance increased by 47.6% in the mesophilic phase due to cell lysis and MGE release, then declined by 9.7% in the thermophilic phase and 47.8% during maturation. Although fermentation stabilized sludge, specific genes (e.g., KPC-22 and poxtA) rebounded, driven by horizontal gene transfer and physicochemical changes. Subsequent planting demonstrated that a 10%-15% sludge application rate optimized bok choy agronomic performance and improved soil antibiotic degradation. Across soil, rhizosphere, and phyllosphere, LARGs exhibited distinct compartmentalization patterns. Network analysis further indicated that LARGs were primarily associated with indigenous soil taxa (e.g., Streptomyces) rather than potential pathogens (e.g., Klebsiella). Consequently, the impact on the core transmission network was minor, suggesting that appropriately fermented sludge application presents a controllable ecological risk and supports its safe utilization under the studied conditions.}, }
@article {pmid41963033, year = {2026}, author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I}, title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105049}, doi = {10.1016/j.fm.2026.105049}, pmid = {41963033}, issn = {1095-9998}, mesh = {*Cheese/microbiology/classification/analysis ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Animals ; Milk/microbiology ; Phylogeny ; Greece ; }, abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.}, }
@article {pmid41963036, year = {2026}, author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y}, title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105055}, doi = {10.1016/j.fm.2026.105055}, pmid = {41963036}, issn = {1095-9998}, mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Phylogeny ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Seeds/microbiology ; Microbiota ; Metagenome ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; }, abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.}, }
@article {pmid41963043, year = {2026}, author = {Liu, G and Zhong, J and Yang, D and Zeng, Y and Cao, R and He, S and Bai, W and Qu, C}, title = {The mechanisms underlying ester enhancement and higher alcohol reduction in Chi-flavor base liquor brewing via Limosilactobacillus fermentum fortification: A multi-omics investigation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105070}, doi = {10.1016/j.fm.2026.105070}, pmid = {41963043}, issn = {1095-9998}, mesh = {Fermentation ; *Limosilactobacillus fermentum/metabolism/genetics/isolation & purification ; *Alcoholic Beverages/microbiology/analysis ; *Esters/metabolism/analysis ; *Flavoring Agents/metabolism/analysis ; Saccharomyces cerevisiae/metabolism/genetics ; Acetates/metabolism/analysis ; *Alcohols/metabolism/analysis ; Ethanol/metabolism/analysis ; Lactates/metabolism/analysis ; Taste ; Bacteria/genetics/classification/isolation & purification/metabolism ; Multiomics ; }, abstract = {Chi-flavor Baijiu is a unique liquor in the Pearl River Delta region. Ethyl lactate is the key flavor with low content in base liquor, affecting qualities of Chi-flavor Baijiu. To address this issue, Limosilactobacillus fermentum Y8 (Y8) isolated from sour mash, was used to fortify the fermentation. Results showed that contents of ethyl acetate and ethyl lactate reached to 663.55 mg/L and 604.25 mg/L, increased by 334.97% and 331.26%, respectively, with that of ethanol unchanged and main higher alcohols reduced significantly. Metagenomic analysis revealed that Lactiplantibacillus, Limosilactobacillus, Pediococcus, Levilactobacillus, and Lactobacillus were the top five abundance species. Metatranscriptomic data indicated that Saccharomyces cerevisiae, Lactobacillus brevis and L. fermentum were the dominant active species, the succession of which was significantly influenced by Y8 addition. Correlation analysis revealed that L. fermentum was positively related to reducing sugar, total acid and esters, while negatively to higher alcohols. Based on metatranscriptomic analysis, a new pathway for lactate synthesis from lactaldehyde was found with Y8 fortification, along with acyl-CoA thioester hydrolase gene ybgC upregulated significantly, providing more precursors for ester synthesis. At the same time, enzymes related to ester synthesis were upregulated with that of higher alcohols downregulated. Collectively, Y8 fortification could affect the succession of microbiota and promote the synthesis of ester precursors and ester synthesis pathway, and decrease higher alcohols synthesis pathway. This study not only provides a strain to fortify Chi-Flavor Baijiu brewing with improved qualities but also reveals mechanisms of flavor modulation and microbial community succession during the brewing process.}, }
@article {pmid41963048, year = {2026}, author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M}, title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105075}, doi = {10.1016/j.fm.2026.105075}, pmid = {41963048}, issn = {1095-9998}, mesh = {Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Animals ; Swine ; Food Storage ; *Meat Products/microbiology/analysis ; Cooking ; *Microbiota ; Food Microbiology ; Food Handling ; }, abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.}, }
@article {pmid41963049, year = {2026}, author = {Zhai, WT and Zhao, H and Chai, LJ and Zhang, W and Zhang, XJ and Lu, ZM and Gao, CQ and Si, GR and Zhang, WQ and Wang, ST and Shen, CH and Xu, ZH}, title = {Microbial and environmental determinants of 1-propanol biosynthesis in Jiang-flavor Baijiu fermentation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105076}, doi = {10.1016/j.fm.2026.105076}, pmid = {41963049}, issn = {1095-9998}, mesh = {Fermentation ; *Flavoring Agents/metabolism ; *1-Propanol/metabolism ; *Wine/microbiology/analysis ; *Yeasts/metabolism/genetics/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Saccharomyces cerevisiae/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {1-Propanol is a crucial flavor compound in Jiang-flavor Baijiu, yet the key microbial pathways and environmental factors controlling its synthesis have not been systematically investigated. Using an integrated approach of metagenomics and culture-dependent techniques, this study identified the key microbes, pathways, and factors controlling 1-propanol synthesis. The highest 1-propanol level was detected in first-round base Baijiu, with rapid accumulation during early pit fermentation. Metagenomics revealed the propanoate pathway as the dominant route, primarily contributed by Limosilactobacillus, while Pichia and Saccharomyces were key providers of pyruvate decarboxylase in the citramalate and threonine pathways. Pure-culture validation confirmed that L. panis MR32 predominantly utilizes 1,2-propanediol as the precursor, while yeasts such as P. kudriavzevii 2J2 and S. cerevisiae LB7A prefer the 2-ketobutyrate pathway. Environmental tests revealed optimal 1-propanol production by L. panis MR32 at pH 5.5 and increasing yields with temperature (25-45 °C). In contrast, most yeasts produced the most 1-propanol at 30 °C, beyond which yields declined, with only P. kudriavzevii 2J2 and I. orientalis IO tolerating high lactic acid. Our findings clarify the microbial division of labor and environmental drivers of 1-propanol formation, enabling targeted fermentation control.}, }
@article {pmid41963512, year = {2026}, author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y}, title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47830-x}, pmid = {41963512}, issn = {2045-2322}, abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.}, }
@article {pmid41963805, year = {2026}, author = {Roslan, MF and Saad, MFM and Pau, SSN and Basir, S and Aziz, H and Akbar, MA and Bunawan, H}, title = {Bacterial community profiling of Malaysian drinking water reservoirs using metagenomic amplicon sequencing.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01422-w}, pmid = {41963805}, issn = {2730-6844}, }
@article {pmid41963968, year = {2026}, author = {Zhou, N and Liu, J and Zhang, X and Xiao, G and Zhang, M}, title = {Vitamin K2 emerges as the key mediator: Cetobacterium somerae ZNN-1 increases muscle protein deposition and improves liver health in Nile tilapia (Oreochromis niloticus).}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41963968}, issn = {1674-9782}, support = {32373145//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Cetobacterium somerae (C. somerae) is a common indigenous bacterium in the intestine of freshwater fish. Studies have shown that it has the potential to promote protein deposition, but the underlying mechanisms remain unclear.
RESULTS: Nile tilapia were fed with C. somerae ZNN-1 (10[8] CFU/g feed), which significantly increased the carcass ratio, reduced the hepatosomatic index, and decreased whole-body lipid content. Supplementation of C. somerae ZNN-1 significantly increased the crude protein content in muscle, promoted glucose uptake and utilization in muscle tissue, and activated the phosphorylation of S6K/S6 in muscle tissue. C. somerae ZNN-1 supplementation significantly decreased hepatic total lipid, triglyceride, and free fatty acid contents. Further analysis revealed that C. somerae ZNN-1 supplementation markedly activated the phosphorylation of hepatic AMPK and upregulated the expression of genes involved in hepatic lipolysis and fatty acid β-oxidation. Integrated serum metabolomic, bacterial genomic, and gut metagenomic analyses revealed that C. somerae ZNN-1 synthesized chorismate (CHA), which serves as a precursor for gut microbiota to produce vitamin K2 (VK2). In vitro experiments demonstrated that VK2 activated the S6K/S6 pathway to promote protein synthesis, while stimulating AMPK phosphorylation and activating lipid catabolism to reduce fat accumulation.
CONCLUSIONS: These findings provide a theoretical basis for the application of C. somerae ZNN-1 in enhancing edible protein content and reducing fat deposition of aquatic animals.}, }
@article {pmid41964024, year = {2026}, author = {Sosef, NP and Boxman, ILA and Dirks, RAM}, title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03159-5}, pmid = {41964024}, issn = {1743-422X}, support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; }, abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.}, }
@article {pmid41964077, year = {2026}, author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ}, title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02395-9}, pmid = {41964077}, issn = {2049-2618}, support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; }, abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.
RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by ~1 order of magnitude, yielding decreased community growth efficiency (CGE = new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.
CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.}, }
@article {pmid41964107, year = {2026}, author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W}, title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2657047}, doi = {10.1080/19490976.2026.2657047}, pmid = {41964107}, issn = {1949-0984}, abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.}, }
@article {pmid41764595, year = {2026}, author = {Martínez-Murcia, A and Navarro, A and Miró-Pina, C and García-Sirera, A and Pérez, L and García-Román, V and Navarro-Gracia, JF}, title = {Early detection of nosocomial pathogens in air and surfaces using an innovative genetic approach for surveillance in healthcare settings.}, journal = {Antimicrobial resistance and infection control}, volume = {15}, number = {1}, pages = {}, pmid = {41764595}, issn = {2047-2994}, support = {INNCAD/2022/23//AVI/ ; }, abstract = {BACKGROUND: Healthcare-associated infections remain a major cause of morbidity, mortality, and financial burden worldwide, further exacerbated by the emergence of antimicrobial resistance. Environmental reservoirs of pathogens, including air and surfaces, play a critical role in nosocomial transmission. This study aimed to validate an integrated air and surface molecular surveillance system for the early detection of clinically relevant pathogens and resistance genes in hospital environments.
METHODS: Weekly air and surface samples were collected over 28 weeks from two hospitals in southeastern Spain. DNA and RNA were extracted and analysed by quantitative PCR (qPCR) targeting bacterial, fungal, and viral pathogens, as well as antimicrobial resistance genes. A subset of samples underwent shotgun metagenomic sequencing to confirm qPCR results and characterize microbial communities. Environmental findings were compared with clinical infection data from both hospitals.
RESULTS: Viral, bacterial and fungal pathogens were detected with similar patterns between air and surface samples and between hospitals. Carbapenem resistance genes showed distinct distribution profiles between hospitals. Respiratory viruses displayed strong temporal correlations with patient admissions, with viral RNA occasionally detected before clinical peaks.
CONCLUSIONS: This integrated molecular surveillance system allows sensitive detection of pathogens and resistance genes in hospital environments. Coupling air and surface sampling with qPCR provides a robust tool for identifying contamination sources and tracking temporal infection trends. Its scalability and adaptability make it suitable for implementation as an early warning system in infection prevention programmes, enhancing patient safety and supporting proactive control of nosocomial infections.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13756-026-01725-8.}, }
@article {pmid41771971, year = {2026}, author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J}, title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41771971}, issn = {2045-2322}, support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; }, abstract = {UNLABELLED: Ganoderma lucidum has a long-standing history of use as a medicinal mushroom, with its spore oil (GLSO) extracted from broken cell walls using CO2 supercritical extraction. However, there is a notable scarcity of experimental studies on the protective effects and underlying mechanisms of GLSO on immune function impairment. The present study aims to explore the characteristics that GLSO contributes to protecting immune functions in cyclophosphamide-induced immunocompromised mice through a multi-omics analysis approach. GLSO administration significantly improved serum hemolysin levels, macrophage phagocytosis, and NK cell activity in immunosuppressed mice. Metagenomics, metabolomic, and proteomic analyses revealed that the immune protection mediated by GLSO was associated with structural rearrangements within gut microflora and shifts in microbial diversity. Specifically, there was an increase in beneficial microorganisms and a decrease in pathogenic organisms, accompanied by various alterations in metabolites and protein expressions. The identified 5 metabolites (propionic acid, beta-glycyrrhetinic acid, 3-aminosalicylic acid, creatine, and 2-phenylacetamide) and 5 proteins (Slc9a9, Blm, Hk3, AP1M2, and J chain) might serve as potential mediators of GLSO to alleviate immune dysfunction collectively caused by CYP in immunosuppressed mice.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40137-x.}, }
@article {pmid41935036, year = {2026}, author = {Larsson, DGJ and Flach, CF and Kristiansson, E}, title = {Antibiotic resistance gene analyses in microbial communities: challenges and opportunities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41935036}, issn = {2041-1723}, support = {2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; }, abstract = {Culture-independent antibiotic resistance gene analyses enable broad explorations of microbial communities but often fail to link such genes to bacterial hosts and genetic contexts. This makes assessing prevalence of resistant pathogens and likelihood of further transmission or resistance evolution uncertain.}, }
@article {pmid41952168, year = {2026}, author = {Shen, Y and Qu, S}, title = {Ganciclovir for severe neonatal varicella pneumonia when acyclovir is unavailable: a case report.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03142-0}, pmid = {41952168}, issn = {1743-422X}, abstract = {BACKGROUND: Perinatal varicella is a rare and severe condition with a high mortality rate, particularly when it leads to complications such as pneumonia in neonates. Acyclovir is the standard treatment for varicella-zoster virus (VZV) infections; however, limited options exist when it is unavailable. This case report describes the successful treatment of neonatal varicella pneumonia with ganciclovir and provides insights into its potential as an alternative therapy. A female Asian neonate was admitted to our hospital on the 9th day of life with a rash, fever, and respiratory distress. Her mother developed varicella at 39 weeks of pregnancy, four days before delivery. The infant was diagnosed with VZV pneumonia based on clinical presentation and confirmed by detection of VZV DNA in blood(metagenomic next-generation sequencing detected 109,491 sequences with 100% relative abundance and 99% confidence).
INTERVENTION: Ganciclovir 5 mg/kg every 12 h for 8 days; intravenous immunoglobulin 400 mg/kg once daily for 3 days.
OUTCOME: The infant was successfully weaned off mechanical ventilation, with normalized blood gas parameters (PaO₂/FiO₂ ratio 346) and inflammatory markers (CRP decreased from 29.44 mg/L to 2.87 mg/L). She was discharged home with stable breathing and crusted skin lesions. Telephone follow-up at 2 and 4 weeks post-discharge confirmed the infant remained well with no respiratory symptoms or developmental concerns.
CONCLUSION: Ganciclovir may serve as a life-saving alternative for severe neonatal VZV pneumonia when acyclovir is unavailable. This case highlights the need for further research to establish its safety, optimal dosing, and efficacy in this population.}, }
@article {pmid41953110, year = {2026}, author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J}, title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101380}, pmid = {41953110}, issn = {2352-7714}, abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.}, }
@article {pmid41953529, year = {2026}, author = {Brown, JR and Ross, CS and Worth, A and Merve, A and Storey, N and Hacohen, Y and Mankad, K and Kaliakatsos, M and Shendi, HM and Atkinson, L and Gilmour, K and Hatcher, J and Lennon, A and Bamford, A and Kusters, M and Elfeky, R and Núñe, A and Brown, IH and Reid, SM and Cooper, J and Byrne, AMP and James, J and Lean, FZ and Banyard, AC and Breuer, J}, title = {Identifying virulent avian paramyxovirus type-1: A paediatric case of progressive encephalitis diagnosed by clinical metagenomics with case series review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02555}, pmid = {41953529}, issn = {2214-2509}, abstract = {BACKGROUND: Immunocompromised patients presenting with encephalitis can present a diagnostic conundrum as infection can be caused by a broad range of pathogens, many of which are not detected by standard of care testing pathways. Untargeted metagenomics has proven utility in the diagnosis of such infections, particularly for immunocompromised patients.
METHODS: An immunosuppressed adolescent presented with idiopathic progressive muscle weakness resulting in respiratory failure, 16 years after haematopoeitic stem cell transplant for familial haemophagocytic lymphohistiocytosis type 5. Clinical and radiological findings suggested a diagnosis of isolated central nervous system haemophagocytic lymphohistiocytosis, however the patient demonstrated no improvement on immunosuppressive therapy. Untargeted metagenomics was performed on brain biopsy tissue.
RESULTS: Clinical metagenomics detected avian paramyxovirus 1 (APMV-1) in the brain tissue 12 days after biopsy, confirmed by targeted PCR and immunohistochemistry. The metagenomics results guided treatment; immunosuppression was stopped and medication with potential activity against RNA viruses started. The patient died 8 months after symptom onset.
CONCLUSIONS: We describe the third published case of fatal encephalitis caused by APMV-1, detectable only in brain parenchyma and only by clinical metagenomics, demonstrating the utility of brain biopsy and metagenomics when investigating encephalitis in immunocompromised patients. Case series review suggests profoundly immunocompromised patients are at risk of severe infection caused by AMPV-1.}, }
@article {pmid41953658, year = {2026}, author = {Song, J and Li, Y and Wang, L and Zhang, J and Shi, C and Zhong, L and Liu, C and Song, M and Yu, X and Zhang, W and Wen, P}, title = {Comparative study of the physicochemical properties, volatile compounds, and bacterial microbiota in commercial and traditional yak yogurt from the Qinghai-Tibet plateau.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103771}, pmid = {41953658}, issn = {2590-1575}, abstract = {This study aimed to elucidate differences between the commercial starter culture (CK) and traditional starters from different Tibetan regions (Gannan (GN), Qinghai (QH), Tibet (XZ)) in fermenting yak yogurt by physicochemical properties, flavor, and bacterial community. Results indicated acidity, proline, arginine, alanine, and C6:0 contents were significantly higher in the traditional starter culture than CK (P < 0.05). Gas chromatography-ion mobility spectrometry analysis found the traditional starter culture group was dominated by alcohols and esters, whereas CK exhibited richer ketones. Metagenomic analysis revealed Lactobacillus delbrueckii (49.56% in XZ, 24.86% in GN) and Streptococcus spp. (18.30% in CK, 17.21% in QH) as the dominant. Moreover, pH and titratable acidity were primary factors affecting microbial diversity. Meanwhile, glutamic acid modulated ester biosynthesis like ethyl acetate, while C16:0 fatty acids inhibited off-odor ketones such as 2-pentanone. This study offers valuable insights into developing specialized fermentation agents and standardizing the quality of yak yogurt.}, }
@article {pmid41953764, year = {2026}, author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF}, title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41953764}, issn = {2312-0541}, abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.
METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.
RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in α- and β-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.
CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.}, }
@article {pmid41954112, year = {2026}, author = {Banerjee, M and Lahiri, A and Basak, S and DAS, S and Mukhopadhyay, S and Banerjee, R and Basak, K}, title = {StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {41954112}, issn = {0973-7138}, mesh = {Humans ; Algorithms ; *Cross Infection/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; Autoencoder ; }, abstract = {As various technological innovations are assisting medical science in a considerable way, rendering a significant leap towards 'lab-to-land' delivery, in a similar vein, algorithm development and concomitant framework-based approaches help the field to enrich its patient care. Although antimicrobial drugs revolutionized this particular area, antimicrobial resistance is a pressing global health concern as microbial strains are becoming resistant to conventional antibiotics, undermining the efficacy of these drugs and leading to increased illness and healthcare costs. To tackle this menace, apart from technological innovations such as diagnostic kits, an informatics-based framework approach is the call of the day. Despite the emergence of several computational approaches, they lack in generalization, scope, and scalability. Here, we have developed a novel framework StaLAENet (stacked LSTM-nested deep-autoencoder network) to predict antibiotic-resistant gene drug classes targeting ESKAPE pathogens. This framework comprises two modules: a feature representation module comprising a stacked LSTM-nested deep autoencoder and a classification module that leverages a dense network using latent features. StaLAENet demonstrated an efficient performance - accuracy: 0.938±0.043, specificity: 0.888±0.061, precision: 0.912±0.020, and recall: 0.881±0.021 - for Enterococcus faecium using 4-mer data, with similar results for other organisms using various k-mer data. Comparative analysis confirmed its superiority over existing pipelines. Further, independent evaluation with non-redundant sequences (sourced from another database) and with a metagenomic dataset highlighted its generalizability, robustness, and capability to analyze complex microbial communities. StaLAENet can offer a robust solution for combating AMR, enabling an efficient way of antimicrobial stewardship and patient care.}, }
@article {pmid41954388, year = {2026}, author = {Zhao, P and Liu, H and Dong, J and Su, H and Jin, Q and Yang, F}, title = {From hepatitis misdiagnosis to zoonotic false alarms: a metagenomic blacklist framework for the parvo-like hybrid viral group.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0015726}, doi = {10.1128/spectrum.00157-26}, pmid = {41954388}, issn = {2165-0497}, }
@article {pmid41954393, year = {2026}, author = {Shukla, N and Budhbhatti, U and Puvar, A and Raval, I and Pandit, R and Chavda, P and Chauhan, A and Jhala, D and Shah, D and Shah, T and Raval, J and Prajapati, H and Patel, N and Upadhyay, K and Joshi, M and Patel, AK and Bondre, V and Kumar, N and Joshi, C}, title = {Genomic and evolutionary characterization of Chandipura virus: a cause of the 2024 outbreak in Gujarat, India.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0157825}, doi = {10.1128/spectrum.01578-25}, pmid = {41954393}, issn = {2165-0497}, abstract = {UNLABELLED: Acute encephalitis syndrome (AES) caused by Chandipura virus (CHPV) is a rapidly progressive and often fatal neurological illness predominantly affecting children in India. However, limited research on CHPV disease progression and viral genomics has hindered a comprehensive understanding of its transmission dynamics and evolutionary behavior. CHPV is endemic in India, with previous outbreaks (2003-2004) reported case fatality rates (CFRs) ranging from 56% to 75%. In the current (2024) outbreak, the CFR declined to 46%, with an overall test-positivity rate of 18.6%, possibly reflecting improvements in supportive care. Despite advances in genomics and sequencing technologies, only a limited number of CHPV genomes are publicly available. To address this gap, we performed whole-genome sequencing of CHPV isolated from a pediatric patient aged 12 years from Patan, Gujarat. Comparative genomic analysis with previously reported Indian strain revealed approximately 293 mutations, including 24 non-synonymous. The estimated evolutionary rate of CHPV was ~1.62 × 10[-2] substitutions/site/year. Furthermore, the selective pressure analysis showed that, despite the virus being under strong purifying (negative) selection, several non-synonymous changes were identified. Nonetheless, as the present analysis is based on the single genome, further sequencing, validation, and broader comparative analysis are required to draw a definitive inference. However, these findings suggest that even under purifying selection pressure, CHPV retains the ability to infect and cause severe disease in children. This highlights the continued need to investigate virus-host interactions, particularly host immune responses, to better understand CHPV pathogenesis and its ability to cause disease in children.
IMPORTANCE: Chandipura virus (CHPV) is an etiological agent of acute encephalitis syndrome (AES) in children, characterized by rapid neurological decline; yet the viral and host factors governing its neuropathogenesis and sudden outbreak dynamics remain poorly defined. Despite minimal genomic variation indicative of strong purifying selection, which supports the continued efficacy of existing molecular diagnostics and candidate therapeutics, CHPV re-emerges unpredictably in human populations, as exemplified by the 2024 AES cluster in Gujarat. This outbreak underscores the importance of continuous genomic surveillance to elucidate viral behavior and immune-evasion mechanisms. Moreover, it highlights the utility of both amplicon-based and metagenomic next-generation sequencing approaches for future CHPV detection and comprehensive genome characterization.}, }
@article {pmid41954722, year = {2026}, author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C}, title = {Correction: Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next‑generation sequencing.}, journal = {Infection}, volume = {}, number = {}, pages = {}, doi = {10.1007/s15010-026-02771-5}, pmid = {41954722}, issn = {1439-0973}, }
@article {pmid41954798, year = {2026}, author = {Liu, P and Zhang, J and Liu, X and Li, B and Peng, Y and Li, B and Lyu, X and Tan, L and Guo, Z and Li, Z and Hu, M}, title = {Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41954798}, issn = {1435-4373}, support = {Grant No.2023XQLH173//Central Universities of Central South University/ ; No. 82102499//National Natural Science Foundation of China/ ; No. 82270658//National Natural Science Foundation of China/ ; No. 2021JJ40840//the Hunan Natural Science Foundation/ ; No.202211003513//Scientific Research Project for Hunan Health Commission/ ; }, }
@article {pmid41954996, year = {2026}, author = {Prabhu, A and Rinke, C}, title = {ICTV Virus Taxonomy Profile: Krittikaviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {4}, pages = {}, doi = {10.1099/jgv.0.002239}, pmid = {41954996}, issn = {1465-2099}, mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure/isolation & purification ; Virion/ultrastructure/genetics ; DNA, Viral/genetics ; *Archaea/virology ; Virus Replication ; }, abstract = {The family Krittikaviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. These viruses have been identified through metagenomic analysis of brackish estuarine samples and are closely related to other 'magroviruses'. The family belongs to the order Magrovirales and includes the genus Velanvirus and the species Velanvirus brisbanense. Viruses in the family have a genome of about 80 kbp that includes modules for DNA replication and virion morphogenesis. Krittikavirids are predicted to form virions with an icosahedral capsid and helical tail, characteristic of viruses belonging to the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Krittikaviridae, which is available at ictv.global/report/krittikaviridae.}, }
@article {pmid41955630, year = {2026}, author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H}, title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.}, journal = {Infectious diseases (London, England)}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/23744235.2026.2654559}, pmid = {41955630}, issn = {2374-4243}, abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.
METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.
RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n = 18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.
CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.}, }
@article {pmid41955710, year = {2026}, author = {Sahu, TK and Rathored, J and Patil, P}, title = {Tri-layer microbiology for LMIC Hospitals: linking syndromic panels with reflex culture and targeted sequencing for real world care - a narrative review.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {30}, number = {3}, pages = {105808}, doi = {10.1016/j.bjid.2026.105808}, pmid = {41955710}, issn = {1678-4391}, abstract = {Rapid, syndromic molecular panels and high throughput sequencing have transformed the diagnostic landscape for sepsis, respiratory, gastrointestinal, and central nervous system infections, but their value in routine practice depends on how they are integrated with conventional microbiology and antimicrobial stewardship. This review synthesises recent high-quality evidence to propose a pragmatic three-tier hybrid framework. Tier 1 comprises syndrome specific rapid panels that provide organism and selected resistance markers within hours, primarily to accelerate early escalation or de-escalation rather than to replace culture. Tier 2 positions reflex culture and targeted adjunct tests as the non-negotiable specificity anchor, confirming molecular hits, distinguishing infection from colonisation or contamination, generating phenotypic susceptibility data and supplying isolates for infection prevention and public health surveillance. Tier 3 reserves targeted or metagenomic sequencing for a small, clinically critical subset of high suspicion, panel negative and culture negative cases, where additional breadth can realistically change management. Across sepsis/BSI, pneumonia, gastrointestinal infection and CNS disease, available data indicate that clinical benefit is driven less by any individual technology and more by disciplined implementation: clear indications, explicit reflex rules, close linkage to antimicrobial stewardship and systematic audit of key performance indicators such as time-to-targeted therapy, spectrum of antimicrobial use and cost per additional actionable diagnosis. The proposed tiered, syndrome wise algorithms provide a transferable conceptual scaffold that can be adapted to local resources, allowing laboratories in both high and low resource settings to introduce advanced diagnostics without abandoning culture-based anchors or stewardship accountability.}, }
@article {pmid41955799, year = {2026}, author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G}, title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141956}, doi = {10.1016/j.jhazmat.2026.141956}, pmid = {41955799}, issn = {1873-3336}, abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.}, }
@article {pmid41955854, year = {2026}, author = {Luo, M and Fan, J and Wang, X and Ge, Y and Feng, D and Cao, S and Wang, J and Deng, H and Luo, J and Zhao, Y and Ge, C and Bu, H}, title = {Microplastics drive the reconfiguration of microbial sulfur cycling pathways in seagrass bed sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128089}, doi = {10.1016/j.envpol.2026.128089}, pmid = {41955854}, issn = {1873-6424}, abstract = {Microplastics (MPs) pollution threatens marine biogeochemical cycles, but its impact on the sediment sulfur cycle remains unclear. A 112-day microcosm incubation experiment was conducted to investigate the effects of three common MPs, polylactic acid (PLA), polyethylene (PE), and polystyrene (PS), on sulfur speciation, microbial communities, and functional genes in seagrass bed sediments using integrated amplicon sequencing and metagenomics. MPs significantly altered sediment sulfur speciation, with PLA inducing the strongest shifts, including 111.2% accumulation of total inorganic sulfate (TIS) and a 163.3% increase in TIS/Sulfide ratios, indicative of enhanced sulfur oxidation, while PE and PS promoted sustained sulfide accumulation. Distinct polymer-specific changes in sulfur-cycling bacteria communities were observed, with PLA suppressing the dominant Bradymonas (31.3% decrease) while enriching heterotrophic Sulfitobacter (26.5% increase), PE driving a transition towards autotrophic pathways with Thiohalomonas increasing by 272.8%, and PS selectively enriching generalist sulfur-oxidizing genera such as Roseovarius and Methyloceanibacter. Metagenomic analysis highlighted a shift from assimilatory biosynthetic pathways to dissimilatory energy-generating processes. These findings suggest that MPs intensify sulfide stress and disrupt sulfur metabolism, thereby reducing sediment biogeochemical stability and potentially impairing carbon burial and ecosystem resilience. These results provide critical insights into the ecological consequences of MP exposure on biogeochemical cycles in seagrass bed sediments.}, }
@article {pmid41955934, year = {2026}, author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM}, title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.}, journal = {The Science of the total environment}, volume = {1030}, number = {}, pages = {181776}, doi = {10.1016/j.scitotenv.2026.181776}, pmid = {41955934}, issn = {1879-1026}, abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.
METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.
RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.
CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.}, }
@article {pmid41955982, year = {2026}, author = {Besharati Fard, M and Guo, H and De Vrieze, J and Wu, D}, title = {Chronic ciprofloxacin exposure reduces anaerobic digestibility of waste microalgal-bacterial aerobic granular sludge: Metagenomics and metatranscriptomics overview.}, journal = {Water research}, volume = {299}, number = {}, pages = {125876}, doi = {10.1016/j.watres.2026.125876}, pmid = {41955982}, issn = {1879-2448}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but its long-term sustainability depends on whether its waste biomass (WMB-AGS) can be effectively stabilized through anaerobic digestion, particularly under antibiotic stress. Here, we compared the digestibility and ciprofloxacin response of WMB-AGS and conventional waste activated sludge (WAS) using 21-day biochemical methane potential (BMP) tests, 3-day hydrolysis-acidogenesis assays, and 90-day semi-continuous digesters, supported by enzyme activity, extracellular polymeric substances (EPS) characterization, and multi-omics profiling. The WAS produced substantially higher methane yields (302 ± 7 mL CH4/g VS) than WMB-AGS (62 ± 4 mL CH4/g VS), confirming the superior digestibility of WAS. Ciprofloxacin effects were exposure-regime dependent, a single initial dose up to 1000 µg/L did not affect methane production in BMP assays. However, continuous ciprofloxacin exposure in semi-continuous digesters significantly reduced daily biogas production, from 114 ± 9 to 96 ± 6 mL/day in WAS and from 23 ± 1 to 15 ± 2 mL/day in WMB-AGS. During the hydrolysis-acidogenesis, ciprofloxacin promoted volatile fatty acid accumulation and inhibited key hydrolytic, acidogenic, and methanogenic enzymes. Biotransformation was the dominant ciprofloxacin removal mechanism. The EPS acted as an initial protective interface but also contributed to hydrolysis limitation. Multi-omics analyses showed that chronic ciprofloxacin exposure did not suppress core methanogenesis genes, but reconfigured upstream electron-transfer and methyl-transfer functions, with enrichment of Corynebacterium and Methanobacterium. Overall, WMB-AGS is inherently less digestible than WAS. These findings highlight the need to consider substrate-specific matrix effects and long-term antibiotic pressure when evaluating the downstream anaerobic valorization.}, }
@article {pmid41955988, year = {2026}, author = {Wang, X and Xue, T and Li, J and Zhang, C and Hao, G and Xing, Y and Tao, R and Guo, L and Zhang, H and Chai, S and Zheng, L}, title = {Novel photoelectron-driven nitrate reduction in anammox granules using photosensitive semiconductor iron mineral for wastewater treatment.}, journal = {Water research}, volume = {299}, number = {}, pages = {125862}, doi = {10.1016/j.watres.2026.125862}, pmid = {41955988}, issn = {1879-2448}, abstract = {The accumulation of nitrate byproducts and limited electron availability fundamentally constrain the efficacy of anaerobic ammonium oxidation (anammox) processes. While iron minerals regulate electron transfer, their potential to drive anammox via semiconductive photoexcitation remains underexplored. Here, we establish a novel "Photo-Chemo-Bio" strategy to overcome these thermodynamic bottlenecks using light-excited hematite (α-Fe2O3). Among tested minerals, hematite exhibited superior band-structure suitability, achieving a 3.65-fold photocurrent enhancement (4.06 μA·cm[-2]) upon bio-hybridization, facilitated by the active recruitment of photo-electrons via upregulated outer-membrane c-type cytochromes. Crucially, this photo-enhanced electron supply boosted the total nitrogen removal rate by 27.4% while suppressing nitrate yield by 42.8%. Kinetic analysis revealed a precise metabolic decoupling: solar irradiation did not accelerate ammonia oxidation but specifically diverted electron flow toward nitrate reduction pathways. Genome-resolved metagenomics unraveled the molecular basis of this synergy, identifying a "hardwired" cooperative network: flanking Desulfobacillus-like species, characterized by a specific metabolic truncation (absence of nor genes), act as obligate "net NO providers" to fuel the anammox core; concurrently, heterotrophic Casimicrobiaceae unexpectedly encode Photosystem II (psbA), functioning as auxiliary "energy antennas" to harvest photons. These findings demonstrate how mineral-microbe hybrids can orchestrate electron flux to close the nitrogen loop, offering a sustainable, carbon-free strategy for high-efficiency wastewater treatment.}, }
@article {pmid41956026, year = {2026}, author = {Sorgato, AC and Kim, B and Papillon, J and Nivala, J and Silveira, DD and Lapolli, FR and Forquet, N}, title = {Microbial fuel cells inoculated with French vertical flow treatment wetland sludge: A step towards clogging biodetector development.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {171}, number = {}, pages = {109297}, doi = {10.1016/j.bioelechem.2026.109297}, pmid = {41956026}, issn = {1878-562X}, abstract = {Clogging is considered an operational challenge in French vertical flow treatment wetlands (VFTWs), causing hydraulics and aeration problems. The available monitoring methods are labor intensive. Microbial fuel cells (MFCs) have emerged as real-time biosensors, including for treatment wetlands (TW) systems. In this study, French VFTW sludge was investigated as inoculum in MFCs, to assessing its adaptation into electrochemical environment as a step for clogging MFC-based biodetector implementation in such systems. The results show that the inoculum was successfully adapted, with stable current generation at 0.4 mA. The electrochemical impedance spectroscopy (EIS) demonstrated the establishment of a biofilm with electroactive characteristics and non-limiting anode. Metagenomic analysis showed that the French VFTW harbor electroactive species, and the MFC created a selective pressure on the VFTW sludge inoculum and significantly shaped the microbial community and function, stimulating the enrichment of electroactive bacteria (EAB), such Geobacterales (4.11% to 5.83%), with potential expression of cytochrome-c for extracellular electron transference (EET). This study illustrates the feasibility of developing electroactive biofilms from French VFTW and suggests its use as an inoculum, improving the integration of TW-MFC systems. Considering these results, the well-adapted anodic biofilm could enable the detection of aeration limitations via cathodic reactions in future studies.}, }
@article {pmid41956515, year = {2026}, author = {Rober, AR and Reese, LC and Brown, SP and McMahon, KD and Louca, S and Cieslik, J and Kane, ES and Turetsky, MR and Wyatt, KH}, title = {Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70300}, doi = {10.1111/1462-2920.70300}, pmid = {41956515}, issn = {1462-2920}, support = {MCB-2514370//National Science Foundation/ ; DEB-2141285//National Science Foundation/ ; DEB LTREB-2011286//National Science Foundation/ ; DEB LTREB-2011257//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; RJVA-PNW-01-JV-11261952-231//Pacific Northwest Research Station/ ; //USDA Forest Service/ ; }, mesh = {*Biofilms/growth & development ; *Ecosystem ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Cyanobacteria/genetics/classification ; Hydrology ; Droughts ; Floods ; Metagenomics ; }, abstract = {Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.}, }
@article {pmid41956535, year = {2026}, author = {Cui, T and Huang, M}, title = {Tuberculous Peritonitis Diagnosed by Metagenomic Next-Generation Sequencing Progressing to Fatal Encapsulating Peritoneal Sclerosis in a Peritoneal Dialysis Patient: A Case Report.}, journal = {Seminars in dialysis}, volume = {}, number = {}, pages = {}, doi = {10.1111/sdi.70022}, pmid = {41956535}, issn = {1525-139X}, support = {SZSM202411016//Sanming Project of Medicine in Shenzhen/ ; }, abstract = {A 40-year-old woman on peritoneal dialysis for 3 years presented with febrile peritonitis. Metagenomic next-generation sequencing (mNGS) confirmed Mycobacterium tuberculosis complex in ascitic fluid, leading to prompt anti-tuberculosis therapy. She initially improved but developed ultrafiltration failure 15 months later and transitioned to hemodialysis. At 18 months, she developed bowel obstruction, bloody ascites, and characteristic imaging and laparoscopic findings of encapsulating peritoneal sclerosis (EPS). Despite supportive care, she deteriorated and died 30 months after tuberculosis peritonitis diagnosis. This case highlights that mNGS enables rapid diagnosis of tuberculous peritonitis when conventional tests are inconclusive, and that tuberculosis peritonitis may serve as a potent inflammatory trigger for EPS even after peritoneal dialysis cessation. Early recognition and timely intervention may improve outcomes.}, }
@article {pmid41956809, year = {2026}, author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J}, title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336025}, pmid = {41956809}, issn = {1468-3288}, abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.
OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.
DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.
RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.
CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.}, }
@article {pmid41957175, year = {2026}, author = {Yang, S and Wang, X and Duan, J and Yang, S and He, J and Fang, C and Zhao, N and Huang, Y}, title = {Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47725-x}, pmid = {41957175}, issn = {2045-2322}, support = {2022YFD1901500, 2022YFD1901505//National Key R&D Program Project/ ; ZSYS[2025]035//Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform)/ ; grant number BQW[2024]009//Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province/ ; }, abstract = {Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (Ct) (p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (Ct/SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving "carbon-compensation" mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO3[-]-N), reshaped microbial community structure, up-regulated carbon-fixation genes (korA, facA, coxS), and suppressed carbon-degradation genes (pel, chi), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a "stoichiometry-community diversity" cascade significantly regulated SOC mineralization (p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.}, }
@article {pmid41957291, year = {2026}, author = {Yang, M and Fang, J and Liao, Q}, title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {41957291}, issn = {1434-9949}, }
@article {pmid41957365, year = {2026}, author = {Kan, J and Spotton, K and Morales-Amador, A and Hernandez, Y and Burian, J and Panfil, C and Ternei, MA and Boer, RE and Bhattacharjee, A and Brady, SF}, title = {Mode of action guided metagenomic natural product discovery reveals convergent evolution of a ClpP-targeting motif.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71586-7}, pmid = {41957365}, issn = {2041-1723}, support = {R35GM122559//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NIH T32 GM136640//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, abstract = {The discovery of natural products with specific modes of action from metagenomes remains challenging. Here, we present resistance-CONKAT-seq, a pipeline that links biosynthetic gene clusters (BGCs) to self-resistance genes, enabling identification of metabolites with desired molecular targets. Using clpP-directed resistance-CONKAT-seq, we identify the calprotamides, which activate native ClpP and enhance its activity. Cryo-EM and bioinformatic analyses reveal that the calprotamides' medium-chain N-acylphenylalanine substructure is a convergently evolved ClpP-targeting motif and identify additional BGCs predicted to encode this moiety, including some with co-localized clp genes. The synthesis of structures bioinformatically inspired by two such clp-linked BGCs, desmethyl jomthonic acid C and tuscamide, reveals that both enhance ClpP activity. Extending our bioinformatically guided synthesis study to additional BGCs lacking nearby clp genes shows that ClpP activity enhancement correlated with antibacterial activity, with the strongest enhancers exhibiting narrow-spectrum antibiotic activity. These findings establish N-acylphenylalanine as a previously unrecognized but common natural motif for targeting ClpP, which should help guide the discovery of both natural and synthetic ClpP modulators for antibiotic and anticancer development. Resistance-CONKAT-seq offers a scalable method for exploring biosynthetic dark matter for metabolites with desired modes of action.}, }
@article {pmid41947210, year = {2026}, author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J}, title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02403-y}, pmid = {41947210}, issn = {2049-2618}, support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; }, abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.
RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.
CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.}, }
@article {pmid41947478, year = {2026}, author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G}, title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.}, journal = {Phytotherapy research : PTR}, volume = {}, number = {}, pages = {}, doi = {10.1002/ptr.70205}, pmid = {41947478}, issn = {1099-1573}, support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; }, abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.}, }
@article {pmid41947790, year = {2026}, author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X}, title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1744020}, pmid = {41947790}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation & purification ; Metagenome ; Chronic Disease ; Aged ; }, abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.
METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.
RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable α-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.
CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.}, }
@article {pmid41948038, year = {2026}, author = {Howells, AEG and Santana, M and Cook, EM and Orrill, B and Boyer, G and Debes, RV and Fecteau, KM and Colman, DR and Boyd, ES and Shock, EL}, title = {Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1736896}, pmid = {41948038}, issn = {1664-302X}, abstract = {Methane oxidation in terrestrial geothermal systems is an understudied process contributing to carbon cycling in extreme environments. We combined geochemical analyses, 16S rRNA gene amplicon sequencing, shotgun metagenome sequencing, and [14]CH4 microcosm assays across 61 Yellowstone hot springs spanning pH 1.9-9.0 and temperatures of 28.6-92.2 °C to survey hydrothermal systems for methanotrophy. Bacterial aerobic methanotroph phylotypes were detected at multiple sites, including Verrucomicrobia (order S-BQ2-57) and Alphaproteobacteria, with the family Methylocystaceae having the highest relative abundance among bacterial methanotroph phylotypes. No known archaeal anaerobic methanotrophs were observed. Biological methane oxidation was widespread, occurring at 14 of 17 experimental sites under both ambient and air-amended conditions. Rates were highest at CH4-rich, NH3-poor sites dominated by bacterial methanotrophs, consistent with energy supply predictions integrating CH4/O2 and CH4/NH3 concentration ratios. Conversely, NH3-rich, energy-rich sites exhibited lower methane oxidation rates (MOR) and were dominated by archaeal ammonia oxidizers, primarily Candidatus Nitrosocaldus, suggesting chemical competitive inhibition of NH3 on methanotrophy. Remarkably, significant methane oxidation occurred at eight sites where no known methanotrophs were detected, including a site at 89.9 °C-well above the previously reported upper growth temperature limit for methanotrophs from continental geothermal and hydrothermal systems-pointing to uncharacterized thermophilic lineages. These results suggest that biological methane oxidation in Yellowstone hot springs is influenced by the interplay of substrate availability and energy supply. By linking energy supply calculations with microbial distributions, we identify both known methanotrophs (Verrucomicrobia, Alphaproteobacteria) and archaeal ammonia oxidizers as potential active contributors, while highlighting the potential for novel thermophilic lineages, thereby expanding the ecological and thermal boundaries of methane oxidation in extreme terrestrial ecosystems.}, }
@article {pmid41948759, year = {2026}, author = {Zhu, G and Zou, Z and Fang, Z and Xu, B}, title = {Rare but Critical: Severe Tropheryma Whipplei Pneumonia-Induced Cardiopulmonary Failure in a Young Immunocompromised Adult-A Case Report and Literature Review.}, journal = {Clinical case reports}, volume = {14}, number = {4}, pages = {e72448}, pmid = {41948759}, issn = {2050-0904}, abstract = {Tropheryma whipplei, traditionally linked to classic Whipple's disease with gastrointestinal involvement, is increasingly recognized as a cause of pneumonia. Reports of T. whipplei-associated pneumonia progressing to respiratory failure with concurrent acute cardiac failure remain extremely rare. A 38-year-old man with poorly controlled diabetes presented to the emergency department with acute chest tightness, dyspnea, and impaired consciousness. Laboratory findings indicated type II respiratory failure and elevated inflammatory markers. Imaging revealed scattered patchy hazy opacities and increased density bilaterally, prompting emergent intubation and transfer to the intensive care unit. Despite empirical antibiotics for severe pneumonia, he developed acute cardiac failure on day 3, manifesting as bloody sputum and diffuse moist rales with rhonchi on auscultation, alongside an LVEF of 49% and a markedly elevated serum BNP level of 3100 pg/mL. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected abundant T. whipplei sequences. He was administered targeted therapy with meropenem, supported by mechanical ventilation, diuresis, and glycemic control. Cardiopulmonary function improved, and he was discharged on oral doxycycline plus hydroxychloroquine. Follow-up endoscopy and biopsy showed no gastrointestinal involvement (Periodic Acid-Schiff negative), restored cardiac function (LVEF 58.6%), and no recurrence. This case underscores T. whipplei as a potential cause of isolated pneumonia with cardiopulmonary failure in functionally immunocompromised hosts and highlights the critical role of mNGS in guiding timely targeted therapy to improve outcomes.}, }
@article {pmid41949195, year = {2026}, author = {Saini, G and Yadav, R and Bagga, R and Sharma, N and Sethi, S}, title = {Cervicovaginal microbiota in female sex workers with bacterial vaginosis: A metagenomic perspective.}, journal = {Indian journal of dermatology, venereology and leprology}, volume = {}, number = {}, pages = {1-3}, doi = {10.25259/IJDVL_1199_2025}, pmid = {41949195}, issn = {0973-3922}, }
@article {pmid41949263, year = {2026}, author = {Marriott, L and Martinez-Lopez, A and Liga, A and Horiba, K and Warr, A and Phulusa, JN and Kumar, RS and Carey, L and Ito, Y and Parcell, BJ and Leslie, NR and Feasey, NA and Jacob, ST and Rylance, J and Kersaudy-Kerhoas, M}, title = {An automated and portable platform for rapid cell-free DNA isolation and its application in microbial DNA metagenomic sequencing from human blood samples.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5lc00876j}, pmid = {41949263}, issn = {1473-0189}, abstract = {The prompt identification of pathogens in human circulation in a clinically deployable format remains an unmet clinical need. The established test for infection diagnostics remains blood culture, which typically takes 2-4 days and is positive in less than 15% of cases, with many prevalent pathogens difficult or impossible to culture. While microbial cfDNA in blood could facilitate the diagnosis of sepsis, febrile and infectious conditions, sample preparation for cell-free DNA (cfDNA) analysis in decentralised settings presents challenges due to its complexity and the low concentration and fragmented nature of cfDNA in blood plasma. We developed a portable and automated platform and a consumable (CNASafe) for cfDNA isolation from human plasma samples. The platform-device performance was evaluated by comparing relative cfDNA yield against a reference (QIAGEN QIAamp Circulating Nucleic Acid Kit). cfDNA eluates from ten non-cultured blood samples from hospital patients were sequenced on a nanopore sequencer, and results compared to blood cultures. Extraction of cfDNA using the CNASafe device was completed in 40 minutes, compared to the 1 hour 15 min reference protocol. The device achieved an average relative cfDNA recovery of 100.5% over 333 unique extractions encompassing all parameter variations, demonstrating a performance equivalent to the reference kit. From the patient samples, a sufficient quantity of microbial cfDNA was extracted to either identify pathogens missed by blood cultures or confirm negative cultures. The CNASafe platform and real-time nanopore sequencing offer a promising solution for the rapid deployment of metagenomic diagnostics, enabling pathogen identification within a few hours in decentralised clinical environments.}, }
@article {pmid41949675, year = {2026}, author = {Chen, Y and Sun, N and Gan, B and He, Y and Luo, J and Pan, K and Zeng, Y and Jing, B and Zeng, D and Ni, X}, title = {Targeting Bifidobacterium animalis alleviates high-fluoride exposure-induced kidney injury in mice.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02031-7}, pmid = {41949675}, issn = {2191-0855}, support = {2025YFHZ0278//Sichuan Science and Technology Program/ ; }, }
@article {pmid41949810, year = {2026}, author = {Adolph, JE and Pentek, C and Bauch, T and Held, C and Brenner, T and Felderhoff-Müser, U and Grumaz, S and Horvatek, P and Steindor, M and Asar, L and Voigt, S and Dziobaka, J and Dohna-Schwake, C and Goretzki, SC}, title = {Next-generation sequencing of cell-free microbial DNA in blood samples of critically ill children: a single-center experience.}, journal = {Molecular and cellular pediatrics}, volume = {13}, number = {1}, pages = {}, pmid = {41949810}, issn = {2194-7791}, abstract = {BACKGROUND: Rapid and accurate pathogen detection is critical for optimizing outcomes in pediatric sepsis. Next-generation sequencing (NGS) of cell-free DNA (cfDNA) from blood enables culture-independent identification of microbial DNA from bacteria, viruses, fungi, and parasites. We evaluated the diagnostic yield and clinical impact of cfDNA-based NGS in critically ill and predominantly immunocompromised pediatric patients (≤ 18 years) with suspected infection. This retrospective single-center study included pediatric patients who underwent plasma cfDNA-NGS at a tertiary care hospital in Germany. Following computational removal of human DNA, remaining sequences were aligned to curated microbial reference databases. Diagnostic performance was compared with blood cultures and viral PCR, and clinical relevance was assessed by pediatric infectious disease specialists.
RESULTS: 111 tests in 78 pediatric patients, mostly with systemic inflammatory response syndrome of unknown etiology, were performed. Overall, 61 tests (54.5%) were positive for pathogenic cfDNA. Compared with conventional microbiological diagnostics, NGS demonstrated a sensitivity of 64.7% and specificity of 88.2% when blood cultures and viral PCR served as the reference standard. NGS identified additional pathogens in a substantial proportion (41.1%) of cases that remained negative by standard testing. Of those pathogens only found by NGS, over 60% were deemed clinically relevant. In 14.8% of positive NGS results, a pathogen-specific therapy was started, while 40.2% of tests led to a discontinuation of therapy (51.0% of negative tests). Out of all positive NGS, 38 (62.3%) were classified as clinically relevant. NGS testing also detected rare infections with fungi and parasites in four cases each.
CONCLUSION: Detection of pathogenic cfDNA through NGS from blood shows promising results as an additional diagnostic tool in critically ill pediatric patients with suspected infections. Clinical utility is currently still limited by its high cost, undetermined diagnostic validity and limitations in testing for resistances and restricted availability of raw sequencing data due to data-protection constraints.}, }
@article {pmid41949970, year = {2025}, author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A}, title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.}, journal = {La Tunisie medicale}, volume = {103}, number = {11}, pages = {1707-1717}, doi = {10.62438/tunismed.v103i11.6101}, pmid = {41949970}, issn = {2724-7031}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/therapy ; *Dysbiosis/therapy/microbiology/etiology ; *Gastrointestinal Microbiome/drug effects/physiology ; Probiotics/therapeutic use ; Hypoglycemic Agents/therapeutic use ; Insulin Resistance ; }, abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.}, }
@article {pmid41950191, year = {2026}, author = {Kador, SM and Shila, JF and Afrin, S and Jannat, J and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Hasan, MS and Sakib, N and Rahman, MS and Islam, OK and Islam, MT}, title = {Microbial diversity, functional genomics and antibiotic resistance in integrated chicken and fish farming systems of Bangladesh.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0344367}, doi = {10.1371/journal.pone.0344367}, pmid = {41950191}, issn = {1932-6203}, mesh = {Animals ; Bangladesh ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Aquaculture ; *Drug Resistance, Microbial/genetics ; *Fishes/microbiology ; Genomics ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Microbial Sensitivity Tests ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The integrated chicken and fish farming system in Bangladesh is widely practiced for its resource efficiency, yet its microbial structure, functional potential, and associated antimicrobial resistance risks remain poorly understood. This study investigated microbial communities, metabolic functions, and antimicrobial resistance profiles across multiple components of integrated farming systems, including chicken gut, chicken droppings, feed, fish intestine, and pond sediment. Microbial profiling was performed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, functional metagenomic prediction, and culture-based isolation, complemented by antimicrobial susceptibility testing. A total of 2,838 operational taxonomic units were identified, with bacteria constituting the vast majority of detected microorganisms. Microbial community composition was strongly shaped by sample type, reflecting distinct ecological niches within the farming system. Chicken gut samples were dominated by Firmicutes, feed samples by Cyanobacteria, and sediment samples exhibited the highest microbial diversity, including taxa involved in biogeochemical cycling. Functional analysis revealed that pathways related to amino acid and carbohydrate metabolism were most abundant across all samples, while sediment and feed were enriched in pathways associated with xenobiotic degradation, suggesting a role in environmental detoxification. Culture-based methods isolated clinically relevant bacteria, including Escherichia coli and Proteus mirabilis, although metagenomic analysis indicated that these organisms represented only a minor fraction of the overall microbial community. Antimicrobial susceptibility testing demonstrated notable resistance, particularly to tetracyclines and fluoroquinolones. Metagenomic analysis further identified multiple antimicrobial resistance genes, with several showing strong associations with specific bacterial genera. This study provides the first comprehensive characterization of microbial diversity, functional capacity, and antimicrobial resistance within integrated chicken and fish farming systems in Bangladesh, highlighting potential environmental reservoirs of resistance and underscoring the need for improved management strategies to enhance sustainability and reduce public health risks.}, }
@article {pmid41950533, year = {2026}, author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X}, title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128511}, doi = {10.1016/j.micres.2026.128511}, pmid = {41950533}, issn = {1618-0623}, abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.}, }
@article {pmid41950684, year = {2026}, author = {Cao, S and Liu, X and Tao, Y and Ren, J and Zhou, Z and Du, R}, title = {EPS-mediated mineralization drives granule densification and enhances denitratation-anammox coupling under alkaline conditions.}, journal = {Water research}, volume = {299}, number = {}, pages = {125888}, doi = {10.1016/j.watres.2026.125888}, pmid = {41950684}, issn = {1879-2448}, abstract = {The granular-based CANDAN (Complete Ammonium and Nitrate removal via Denitratation-Anammox over Nitrite) process offers a promising low-carbon and high-rate strategy for nitrogen removal; yet the mechanisms by which alkaline conditions regulate granule structure and functional coupling remain insufficiently understood. Here, a 9-L sequencing batch reactor (SBR) was operated for 130 days with stepwise pH elevation from 7.31 ± 0.03 to 8.52 ± 0.08 to elucidate alkaline condition-driven structural and functional adaptations in CANDAN granules. Moderate alkaline conditions significantly improved nitrogen removal, with total nitrogen removal efficiency increasing to 91.4 ± 0.1 %, accompanied by pronounced improvement in sludge settleability (sludge volume index after 30 min of settling, SVI30, decreased from 76.4 to 19.4 mL g[-1] SS) and stabilization of dominant granule sizes at 0.5-1 mm, accounting for approximately 69.8 % of the total granules, indicating progressive granule densification. Mineralogical analyses revealed that hydroxyapatite dominated the inorganic matrix, with co-precipitation of calcium carbonate (CaCO3) and transient magnesium ammonium phosphate formation reinforcing granule structure. Elevated pH also remodeled extracellular polymeric substances (EPS), increasing loosely bound EPS, raising the protein-to-polysaccharide ratio, and enriching tryptophan-like proteins that facilitated EPS-mediated mineral nucleation. Metagenomic analysis revealed streamlined carbon metabolism and enrichment of key nitrogen-cycling genes (napA, nosZ, hzsA), while downregulation of Ca[2+], Mg[2+], and phosphate transport genes favored extracellular mineral accumulation. Overall, moderately alkaline conditions drive EPS-mediated mineralization that densifies granules and stabilizes Denitratation-Anammox coupling, providing mechanistic insight for optimizing low-carbon nitrogen removal under alkaline wastewater conditions.}, }
@article {pmid41950685, year = {2026}, author = {Zuo, Z and Xing, Y and Qiao, L and Yang, S and Ren, D and Guo, M and Liu, Y and Huang, X}, title = {Unveiling in-pipe carbon-sulfur transformation and microbial function during urine transport for centralized management.}, journal = {Water research}, volume = {299}, number = {}, pages = {125840}, doi = {10.1016/j.watres.2026.125840}, pmid = {41950685}, issn = {1879-2448}, abstract = {Source-separated urine collection and centralized nutrient recovery at city-scale hold great potential for advancing sustainable resource management. As the critical link between urine collection systems and nutrient recovery facilities, urine-transporting sewer systems have recently been incorporated into life cycle assessments (LCA), yet their potential for biochemical transformations has not been explored. Here, for the first time, we experimentally unveil key pollutant transformations and microbial functions in a urine-fed bioreactor (representing urine transport), with a sewage-fed bioreactor serving as a control. Major urine nutrients (N, P, and K) remained largely stable during transport, whereas organic carbon and sulfate decreased markedly. Methane production was negligible over 160 days, while sulfide production initially declined but fully recovered by day 80, accompanied by elevated microbial activity and substantial sulfide accumulation in sediments. Microbial community analyses revealed that urine exposure reduced community richness and led to a pronounced community, with methanogenic archaea strongly inhibited and sulfate-reducing bacteria (SRB) becoming dominant under prolonged urine stress. A Desulfomicrobium-like SRB species was progressively enriched (∼35% of total metagenome-assembled genomes (MAGs)) and likely responsible for the sulfide rebound. Spatial heterogeneity of microbial communities in sediments further explains depth-specific sulfide accumulation. Overall, this study provides important insights into carbon-sulfur transformations and microbial adaptation in urine transport systems, informing improved system design, operation, and further LCA.}, }
@article {pmid41950966, year = {2026}, author = {Yan, S and Han, Q and Chen, L and Jin, D and Lu, Y and Zhou, J and Zhang, X}, title = {Simultaneous removal of Se(IV) and Cr(VI) from acidic wastewater using a Se(IV)-reducing internal circulation reactor: performance and microbial resistance mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134537}, doi = {10.1016/j.biortech.2026.134537}, pmid = {41950966}, issn = {1873-2976}, abstract = {Acidic wastewater contaminated with selenite (Se(IV)) and chromate (Cr(VI)) poses elevated environmental risks due to the combined toxicity of metal(liod) and acidity. Metal(loid)-resistant consortia, such as Se(IV)-reducing sludge (SeRS), provide a promising strategy for treating such wastewater by converting Se(IV) and Cr(VI) into less toxic Se(0) and Cr(III), respectively. In this study, an internal circulation (IC) reactor loaded with SeRS and granular activated carbon was constructed to evaluate its performance in treating such wastewater. In the absence of Cr(VI), the reactor achieved 94.6-98.5% Se(IV) removal at influent pH 4.5-8.0 with 1-3 mM Se(IV). At optimal pH 5.5, nearly complete removal of both oxyanions was achieved at Se(IV)/Cr(VI) molar ratio of 5.2-10.4. Alkalinity generation from acetate oxidation buffered influent acidity at influent pH 4.5-5.5 and sustained microbial activity. Cr(VI) stress selectively enriched Brucella, Trichlorobacter, and Seleniivibrio for Cr(VI) reduction, while Pseudomonas accounted for Se(IV) and Cr(VI) reduction. Integrated extracellular polymeric substances (EPS), glutathione reductase (GOR), and metagenomic analyses revealed microbial resistance to Cr(VI) stress likely relied on intracellular glutathione-related detoxification, enzymatic Se(IV)/Cr(VI) reduction and antioxidant defenses, while extracellular EPS protection declined. Overall, it was demonstrated that the developed IC reactor process enabled robust and efficient removal of both Se(IV) and Cr(VI) from acidic wastewater.}, }
@article {pmid41951175, year = {2026}, author = {Rana, N and Angrup, A and Tiewsoh, K and Ray, P}, title = {Automating Microbial Community Analysis (AMCA): Development and application of as amplicon based graphical pipeline in patients with Chronic Kidney Disease.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {101110}, doi = {10.1016/j.ijmmb.2026.101110}, pmid = {41951175}, issn = {1998-3646}, abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.
METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.
RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.
CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.}, }
@article {pmid41951362, year = {2026}, author = {Kariya, E and Tirard-Collet, P and Boulagnon-Rombi, C and Destras, G and Wallon, M and Menotti, J and Lapendry, A and Kaidi, N and Rabodonirina, M and Lievre, L and Depaquit, J and Villena, I and Trecourt, A and Huguenin, A}, title = {Integrated histomolecular diagnosis of mesenteric anisakiasis.}, journal = {Journal of clinical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1136/jcp-2026-210635}, pmid = {41951362}, issn = {1472-4146}, abstract = {A 49-year-old woman was admitted with gastrointestinal symptoms and imaging consistent with duodeno-ileitis. Her clinical course was complicated by mesenteric ischaemia, requiring resection of a 45-cm ileal segment. A pre-adult Anisakis spp. larva was identified within a mesenteric nodule through an innovative diagnostic approach combining histopathological analysis with shotgun metagenomic analysis.}, }
@article {pmid41951635, year = {2026}, author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S}, title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07154-x}, pmid = {41951635}, issn = {2052-4463}, abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.}, }
@article {pmid41951715, year = {2026}, author = {Wang, H and Wu, SH and Zhang, K and Chen, KH and Vilgalys, R and Liao, HL}, title = {Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09820-7}, pmid = {41951715}, issn = {2399-3642}, abstract = {Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.}, }
@article {pmid41951791, year = {2026}, author = {Somerville, TF and Kaye, SB}, title = {Comment on: 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections'.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {41951791}, issn = {1476-5454}, }
@article {pmid41951875, year = {2026}, author = {Wang, Y and Li, Y and Fang, J and Huang, Z and Zhang, C and Xu, B}, title = {A Novel Broad pH-Adaptive Bile Salt Hydrolase from Nomascus concolor Fecal Microbial Metagenome Facilitates the Cholesterol-Lowering Ability of Escherichia coli Nissle 1917.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41951875}, issn = {1867-1314}, support = {32360034//National Natural Science Foundation of China/ ; }, }
@article {pmid41943240, year = {2026}, author = {Zhu, W and Qian, J and Peng, M and Li, Y and Hu, J}, title = {Post-COVID-19 Area Postrema Syndrome With SARS-CoV-2 in CSF: A Dual-Case Report and Review of the Literature.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70421}, doi = {10.1002/iid3.70421}, pmid = {41943240}, issn = {2050-4527}, support = {ZDXM2024003//Wenshan Prefecture People's Hospital 2024 Annual Internal Scientific Research Key Projects/ ; }, mesh = {Humans ; Female ; *COVID-19/complications/cerebrospinal fluid/immunology ; *SARS-CoV-2 ; *Neuromyelitis Optica/cerebrospinal fluid/immunology/virology/etiology ; *Area Postrema/virology/pathology ; Middle Aged ; Adult ; Magnetic Resonance Imaging ; Immunoglobulin G/blood/cerebrospinal fluid ; Aquaporin 4/immunology ; Autoantibodies/blood ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune astrocytopathy characterized by inflammatory demyelinating lesions in the central nervous system. Area postrema syndrome (APS), marked by intractable nausea, vomiting, and hiccups, is a recognized but less common initial manifestation. Post-infectious autoimmunity triggered by SARS-CoV-2 has been increasingly associated with NMOSD pathogenesis; however, the clinical significance of direct viral neuroinvasion and its relationship to divergent patient outcomes remains poorly understood.
METHODS: We report two female patients who developed isolated APS shortly after COVID-19 infection. Both patients underwent comprehensive neurological evaluation, including brain and spinal magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis with metagenomic next-generation sequencing (mNGS), and serological testing for aquaporin-4 immunoglobulin G (AQP4-IgG), myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG), and glial fibrillary acidic protein immunoglobulin G (GFAP-IgG) using cell-based assays. Clinical outcomes were compared in the context of antibody serostatus and treatment strategies. A review of the relevant literature on post-COVID NMOSD was also performed.
RESULTS: Both patients presented with intractable vomiting and hiccups following SARS-CoV-2 infection, and MRI demonstrated isolated T2/FLAIR hyperintense lesions in the dorsal medulla consistent with area postrema involvement. SARS-CoV-2 RNA sequences were detected in the CSF of both patients via mNGS, suggesting direct viral neuroinvasion or blood-brain barrier compromise. Despite similar initial presentations, their outcomes diverged dramatically. Patient 1 was AQP4-IgG negative, responded well to immunotherapy with intravenous immunoglobulin and corticosteroids followed by mycophenolate mofetil maintenance, and remained relapse-free at 12-month follow-up with significant lesion regression on MRI. Patient 2 was AQP4-IgG positive in both serum and CSF, and despite acute treatment, experienced a fatal relapse 6 months later with longitudinally extensive transverse myelitis while on low-dose prednisone monotherapy.
CONCLUSIONS: Isolated APS may represent an important yet under-recognized manifestation of post-COVID-19 autoimmune neuroinflammation. Detection of SARS-CoV-2 in CSF supports a role for direct viral neuroinvasion as a localized inflammatory stimulus. AQP4-IgG serostatus serves as a critical prognostic determinant: seronegativity is associated with a benign, monophasic course, whereas seropositivity mandates prompt initiation of potent immunosuppressive therapy to prevent devastating relapses. Clinicians should maintain a high index of suspicion for NMOSD in patients with unexplained persistent vomiting following COVID-19, and perform urgent neuroimaging and antibody testing for early risk stratification.}, }
@article {pmid41943413, year = {2026}, author = {Liu, F and Xie, F and Zhong, Q and Lin, X and Yang, Q and Li, Y and Huang, C and Huang, Q and Xu, L and Zhong, J}, title = {Application Value of Metagenomic Next-Generation Sequencing Using Bronchoalveolar Lavage Fluid and Blood Samples in Patients with Severe Pneumonia Complicated with Bloodstream Infection.}, journal = {Polish journal of microbiology}, volume = {75}, number = {1}, pages = {75-83}, doi = {10.33073/pjm-2026-008}, pmid = {41943413}, issn = {2544-4646}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; Aged ; Bacteria/genetics/isolation & purification/classification ; *Pneumonia/microbiology/blood/complications/diagnosis ; Fungi/genetics/isolation & purification/classification ; Aged, 80 and over ; Adult ; *Sepsis/microbiology/diagnosis ; }, abstract = {This study was designed to systematically evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using blood and bronchoalveolar lavage fluid (BALF) samples in patients with severe pneumonia complicated by bloodstream infections. A retrospective analysis of 30 patients with severe pneumonia-bloodstream infection admitted to our hospital from January 2018 to December 2022 was conducted, and the potential pathogens in both BALF and blood samples were simultaneously detected by conventional microbial examination (traditional group) and mNGS tests (mNGS group), comparing the differences in pathogen species and detection rates between the two methods. There was no significant difference in the positivity of pathogen detection in BALF and blood samples using mNGS (p = 0.492). The proportion of bacteria (p = 0.005) and fungi (p = 0.037) detected by BALF mNGS was higher than that by blood mNGS, but there was no significant difference in the proportion of viruses (p = 0.121). In addition, the positive rate of pathogen detection by mNGS in BALF and blood samples was significantly higher than that by traditional methods (p < 0.01). BALF mNGS demonstrated superior diagnostic sensitivity for bacterial and fungal pathogen detection compared to blood mNGS and conventional culture methods. Notably, blood specimens retained distinct advantages in identifying specific viral infections. Future prospective studies with larger sample sizes are warranted to validate these findings.}, }
@article {pmid41943678, year = {2026}, author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J}, title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70843}, doi = {10.1111/gcb.70843}, pmid = {41943678}, issn = {1365-2486}, support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Biodiversity ; China ; *Soil/chemistry ; *Fungi/physiology ; Ecosystem ; *Sodium/analysis ; Salinity ; }, abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.}, }
@article {pmid41944124, year = {2026}, author = {Cai, S and Li, E and Sun, T and Huang, A and Zhang, Y and Xiong, X and Cheng, B and Chai, H and Zhang, J and Zhang, J and Hu, C and Zhang, W}, title = {Amine-Containing Micropollutants Exposure Reshapes Sludge Anaerobic Digestion via Enzymatic Inhibition and Stress-Mediated Alteration of Methanogenic Pathways.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10074}, pmid = {41944124}, issn = {1520-5851}, abstract = {Amine-containing micropollutants (AMPs), a class of structurally diverse polar compounds characterized by one or more amine functional groups, are frequently detected in wastewater sludge. However, the anaerobic transformation of these compounds and their impacts on microbial metabolism during anaerobic digestion (AD) remain poorly understood. In this work, six representative AMPs were selected to cover 16 structurally diverse primary, secondary, tertiary amine, and quaternary ammonium functionalities. α-C hydroxylation and N-acetylation were identified as the dominant initial reactions among the detected transformation products (TP), collectively accounting for 42.6% of all identified TPs. Furthermore, compound-specific differences in metabolic disturbance were observed. Quaternary ammonium compounds, N-dodecyl-N-benzyl-N,N-dimethylammonium chloride (DDBAC) and N,N-Didodecyl-N,N-dimethylammonium chloride (DDDAC) markedly reduced acetate kinase activity by 10.69 and 14.28%, respectively, and resulted in methane production yield reductions of 88.97 and 88.19%. The genome-centric metagenome revealed that exposure to AMPs prompted the reassembly of the microbial community, altered its functional attributes, and disturbed interspecies cross-feeding interactions. Specifically, AMPs triggered a shift in the methanogenic consortium from mixotrophic Methanosarcina flavescens to hydrogenotrophic Methanobacterium sp., owing to the latter's metabolic versatility, vigorous proliferation, and superior energy conservation. These findings indicated that the chemical properties of amine functional groups have effects on anaerobic biotransformation pathways and microbial energy metabolism, providing mechanistic insight into AMPs toxicity and guiding mitigation strategies to enhance the stability and resilience of full-scale AD systems.}, }
@article {pmid41944276, year = {2026}, author = {Feng, Z and Lu, JN and Wang, G and Li, M and Chen, D and Chen, C and Jiang, Y and Yu, H and Chao, Y and Tang, YT and Jin, C and Baker, AJM and Morel, JL and Xu, Z and Wang, S and Qiu, R}, title = {Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c13821}, pmid = {41944276}, issn = {1520-5851}, abstract = {Biological soil crusts (biocrusts) develop vertical redox-microbial-nutrient stratification that regulates hydrological and elemental cycles and contributes to ecological restoration in extreme environments, including mining regions. However, the roles of this heterogeneity in metal(loid) immobilization remain unclear, particularly in humid regions, where pronounced redox and microbial stratification may foster unrecognized stabilization mechanisms. We integrated physicochemical characterization with bioinformatic analysis to reveal stratified microbial communities and metabolic potentials in humid tailings biocrusts. Biocrusts exhibited stratified functionality through the upper photoautotrophic layer (PL) and the lower heterotrophic layer (HL). In the PL, Cyanobacteria and SWB02 formed a self-reinforcing oxygen barrier through clay-silt enrichment (2.8-fold higher than bare tailings sand) and extracellular polysaccharide accumulation (18-fold), which swelled upon hydration to physically hinder oxygen infiltration, confining Gammaproteobacteria-associated iron-manganese oxide immobilization to this layer. Beneath this barrier, the HL harbored sulfidogenic potential through microbes enriched in hydB (17.4-fold) and phsC (3.4-fold) genes, including Bacteroidota and Desulfobacterota, supporting a potential mechanism for metal(loid) sequestration via sulfide formation in underlying tailings, where sulfur occurred exclusively as sulfides at 5 cm depth. This barrier-mediated effect may outweigh metal(loid) immobilization within biocrusts. Our findings elucidate biocrust-mediated protection against metal(loid)s and provide theoretical support for remediation in humid mining regions.}, }
@article {pmid41944309, year = {2026}, author = {Wang, Z and Zhang, J and Lu, H and Ni, J and Yang, S and Shi, Y and Zhang, S and Zhang, P and Liu, L}, title = {Gemella morbillorum Promotes Colorectal Carcinogenesis: LPBDCP-Mediated Invasion Activates Ras Signaling and Destabilizes p53.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17245}, doi = {10.1002/advs.202517245}, pmid = {41944309}, issn = {2198-3844}, support = {82473713//National Natural Science Foundation of China/ ; 82173602//National Natural Science Foundation of China/ ; }, abstract = {Gut microbiota dysbiosis promotes colorectal cancer (CRC) tumorigenesis. A global fecal metagenomic analysis identified Gemella morbillorum as a key contributor to the CRC-associated microbiota. Fluorescence in situ hybridization revealed that Gemella morbillorum is enriched in CRC tumor tissues compared to adjacent normal tissues. In vitro and in vivo experiments elucidated the oncogenic effects of Gemella morbillorum on human CRC cell lines and mouse models. Multimodal imaging shows that Gemella morbillorum can internalize into host cells. RNA sequencing, co-immunoprecipitation, and mass spectrometry identified that Gemella morbillorum invades host cells via interaction between its LysM peptidoglycan-binding domain protein (LPBDCP) and host cell surface transmembrane protein TMEM140. This invasion triggers Ca[2] [+] influx, downregulates RASA4, and activates the PI3K-AKT-NF-κB and RAF-MEK-ERK signaling pathways. Following invasion, Gemella morbillorum secretes NAD-dependent protein deacetylase (NDPD), which induces p53 deacetylation and degradation. Collectively, these events accelerate cell proliferation, shorten the cell cycle, and inhibit apoptosis, thereby promoting malignant transformation. Genetic knockout of LPBDCP or TMEM140 effectively inhibits bacterial invasion and abrogates the oncogenic effects of Gemella morbillorum. In tumor-bearing mice, knockout of LPBDCP or NDPD eliminates the tumor-promoting effects of Gemella morbillorum. These results underscore Gemella morbillorum's role in CRC and pinpoint potential intervention targets.}, }
@article {pmid41946009, year = {2026}, author = {Sutaoney, P and Singh, P and Malakar, S and Arsi, L and Ghosh, P}, title = {Microbial lipases: Catalyzing sustainable solutions for industrial innovations.}, journal = {Enzyme and microbial technology}, volume = {198}, number = {}, pages = {110869}, doi = {10.1016/j.enzmictec.2026.110869}, pmid = {41946009}, issn = {1879-0909}, abstract = {Microbial lipases are multifaceted biological catalyst that have surfaced as a key driver in various industries and are both eco-friendly and cost efficient.In large scale applications, lipases produced from bacteria, fungi and yeasts function better than their equivalents generated from plants and animals due to their wide substrate specificity, catalytic efficacy and stability under physicochemical circumstances. Recent developments in microbial lipase research, including sources, screening techniques, assay procedures, production methods, purification tactics, and biochemical characterisation, are critically examined in this review.The structural and mechanistic elements that control lipase function-such as lid domains, interfacial activation, and catalytic triads-are given special attention since they all have an impact on the stability, specificity, and industrial performance of the enzyme.Large-scale screening is done to check for the production of lipase in Bacillus sp., Achromobacter sp., Alcaligenes sp., Arthrobacter sp., Pseudomonas sp., and Penicillium sp. Additionally, the combination of synthetic biology, metagenomics, CRISPR-Cas technologies, enzyme engineering, and AI-assisted modelling is emphasized as a revolutionary strategy for identifying and customizing lipases with desired characteristics, including extreme environment microbes and application-specific variants.The review also highlights the growing industrial uses of microbial lipases in the bio-fuel, food and beverage, detergent, textile, leather, pharmaceutical, and medical industries, highlighting their contribution to the development of economically feasible and ecologically safe bioprocesses. All things considered, microbial lipases are an important biotechnological tool for developing sustainable industrial innovation and green chemistry.}, }
@article {pmid41946242, year = {2026}, author = {Yang, Y and Wang, Y and Li, J and Long, Y and Xiao, X and Fang, C and Hu, L}, title = {Temperature-dependent demethylation of methylarsenic by methanogens: Linking carbon metabolism to arsenic speciation in landfills.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141986}, doi = {10.1016/j.jhazmat.2026.141986}, pmid = {41946242}, issn = {1873-3336}, abstract = {The environmental risk posed by arsenic (As) in landfills, driven by its high concentrations and mobility, is a significant concern. While inorganic arsenate [As(V)] and arsenite [As(III)] are dominant, the microbial-mediated conversion of these inorganic species into less toxic methylated arsenicals (MAs) is a key attenuation pathway. However, the reverse process-the demethylation of MAs back to more toxic inorganic forms-and its microbial drivers in landfills are not well understood. The availability of substrates and temperature are important growth factors and environmental factors that affect the activity and community structure of MA. This study investigated the demethylation of dimethylarsinic acid (DMAs) by methanogenic communities enriched from the leachate saturated zone (LSZ) under different thermal fields (15℃, 35℃, 55℃). We found that methylotrophic methanogens were the primary agents of DMAs demethylation, with the highest efficiency observed at mesophilic temperature (35℃), followed by thermophilic (55℃) and psychrophilic (15℃) conditions. Interestingly, methane (CH4) release exhibited a distinct trend (55℃ > 35℃ > 15℃), indicating an inconsistency between methanogenic activity and MAs demethylation efficiency at higher temperatures. A partial least squares path model (PLS-PM) revealed that both the abundance of methanogenic functional genes and CH4 release had a significant negative effect on As species (path coefficients of -0.615 and -0.376, respectively). Metagenomic analysis identified Methanosarcina as the dominant methylotrophic genus at 35℃, while Methanosarcina thermophila and JAULTD01 sp. were key drivers at 55℃. Our findings demonstrate that methanogens dynamically couple carbon metabolism to As speciation, and this coupling can be reshaped by temperature-mediated shifts in the dominant methanogens and their functional genes distribution.}, }
@article {pmid41946252, year = {2026}, author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP}, title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141985}, doi = {10.1016/j.jhazmat.2026.141985}, pmid = {41946252}, issn = {1873-3336}, abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.}, }
@article {pmid41946403, year = {2026}, author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y}, title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134561}, doi = {10.1016/j.biortech.2026.134561}, pmid = {41946403}, issn = {1873-2976}, abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.}, }
@article {pmid41946559, year = {2026}, author = {Campo-Beamud, C and Adan Ruiz, A and Bastante Quijano, J and Campo Beamud, E and Gómez-Romero, FJ and Fernández Ruíz, AJ and Copete, S}, title = {Publicly available multimodal large language models for ocular surface infections: benchmarking against corneal specialists in triage, diagnosis and treatment.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2025-328867}, pmid = {41946559}, issn = {1468-2079}, abstract = {BACKGROUND/AIMS: Ocular surface infections remain a major cause of visual loss worldwide, yet diagnosis often relies on slow or insensitive microbiological techniques. Artificial intelligence may complement emerging molecular tools by supporting rapid triage and diagnostic reasoning. This study benchmarked publicly available multimodal large language models (LLMs) against corneal specialists for the diagnosis, treatment and urgency triage of infectious keratitis and conjunctivitis.
METHODS: A single-centre diagnostic-accuracy study included 60 microbiologically confirmed infectious keratitis and conjunctivitis cases, each comprising a slit-lamp photograph and a paired clinical vignette. Six multimodal LLMs (GPT-4o, GPT-5, Gemini, Claude, Perplexity and Grok) were evaluated for diagnosis, treatment and urgency triage under three input conditions (image-only, text-only and image+text). Outputs were compared with two corneal specialists.
RESULTS: LLM performance depended strongly on input modality. Image-only accuracy was lowest (best GPT-5, 61.4%; κ=0.38) with frequent misclassification of fungal and Acanthamoeba keratitis and hallucinations confined to this setting. Text input improved results (GPT-5, 83.3%; κ=0.78), though accuracy remained below specialists (87-90%; κ≈0.8). Combined image+text achieved near-human accuracy without consistently surpassing corneal specialists (Perplexity 96.7%; κ=0.95; GPT-5 91.7%; κ=0.87). Treatment accuracy remained lower (81-85% vs 90-98%), while urgency triage matched experts in multimodal input.
CONCLUSION: Publicly accessible multimodal LLMs can approach expert-level performance in diagnosis and triage when provided with clinical context and slit-lamp images. Gaps in therapeutic reasoning and rare pathogen recognition underscore the need for targeted refinement and validation. These models may complement specialist care, supporting rapid triage and integration with molecular or metagenomic diagnostics, especially in resource-limited settings.}, }
@article {pmid41889817, year = {2026}, author = {Lu, T and Dietz, ZK and Ericsson, AC and Picking, WD and Picking, WL}, title = {Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41889817}, issn = {2692-8205}, abstract = {Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems.}, }
@article {pmid41937465, year = {2026}, author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT}, title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2508050}, doi = {10.4014/jmb.2508.08050}, pmid = {41937465}, issn = {1738-8872}, mesh = {*Petroleum/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Salinity ; Soil Microbiology ; Metagenomics/methods ; Biodegradation, Environmental ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Phylogeny ; }, abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.}, }
@article {pmid41937665, year = {2026}, author = {Sizikova, TE and Lebedev, VN and Borisevich, SV}, title = {The Mengla virus (Filoviridae: Dianlovirus).}, journal = {Voprosy virusologii}, volume = {71}, number = {1}, pages = {7-12}, doi = {10.36233/0507-4088-356}, pmid = {41937665}, issn = {2411-2097}, mesh = {Animals ; *Chiroptera/virology/genetics ; *Filoviridae/genetics/classification/pathogenicity/isolation & purification ; Humans ; Phylogeny ; Genetic Variation ; Genome, Viral ; *Filoviridae Infections/virology/epidemiology/genetics ; Asia, Southeastern/epidemiology ; Hemorrhagic Fever, Ebola/virology/genetics/epidemiology ; }, abstract = {INTRODUCTION: Filoviruses associated with various species of pteropodid bats (Chiroptera: Pteropodidae) are traditionally regarded as potential causative agents of hemorrhagic fevers with epidemic potential. The known agents of Ebola and Marburg fevers periodically cause sporadic cases and epidemic outbreaks in African countries. Recent discoveries of novel filoviruses associated with pteropodid bats in South and Southeast Asia highlight the necessity to investigate their genetic diversity and pathogenic potential. The aim of this study was to investigate the genetic diversity and pathogenic potential of new filoviruses associated with bats, based on literature data.
MATERIALS AND METHODS: This review is based on an analysis of published literature describing the detection and molecular characterization of novel filoviruses identified in different geographic regions, with a particular focus on filoviruses associated with pteropodid bats in South and Southeast Asia. The analyzed studies include data on virus discovery, genome organization, taxonomic classification, and experimental assessment of biological properties.
RESULTS: Several novel filoviruses have been identified by metagenomic RNA sequencing of tissues from pteropodid bats captured in South and Southeast Asia. Among them, Mengla virus was detected in tissues of pteropodid bats (Rousettus spp.) captured in Mengla County, Yunnan Province, People's Republic of China. Owing to a high level of genetic divergence, Mengla virus was classified as a representative of a new genus, Dianlovirus, within the family Filoviridae. Although a live isolate of Mengla virus has not yet been obtained, experimental studies using chimeric minigenome systems and virus-like particles suggest that the virus may exhibit tropism for tissues of various vertebrate hosts, including humans.
CONCLUSION: Members of the family Filoviridae are widely distributed within the geographic range of their natural reservoir-pteropodid bats-across South and Southeast Asia, including viruses evolutionarily related to Ebola and Marburg viruses. Although human disease caused by Mengla virus and other recently discovered filoviruses has not been documented, the potential for cross-species transmission and the emergence of novel filovirus infections in endemic regions remains.}, }
@article {pmid41937718, year = {2026}, author = {Chen, X and Xie, M and Feng, J and Zou, J and Shi, J and Xie, X}, title = {From Diet to Resistome: Habitat Fragmentation Rewires Gut Microbiomes To Elevate Antibiotic Resistance Gene Enrichment in a Horseshoe Crab Sentinel.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c17817}, pmid = {41937718}, issn = {1520-5851}, abstract = {Habitat fragmentation may amplify antibiotic resistance genes (ARGs), yet the ecological pathways linking landscape patterns to host resistomes in intertidal systems remain unclear. Macrobenthic organisms as potential reservoirs and dispersal nodes are ideal models. Focusing on the horseshoe crab (Tachypleus tridentatus), a food web hub and habitat indicator, we integrated landscape metrics, metagenomics, and path modeling (PLS-PM) to examine, across fragmented habitats, links among sediment physicochemistry, larval diet, gut microbiota, mobile genetic elements (MGEs), and ARGs. Results revealed that more fragmented habitats promoted individuals with higher ARG abundance and diversity, alongside stronger MGE enrichment and increased ARG-MGE co-occurrence, indicating enhanced mobility potential. Fragmentation also coincided with greater dietary diversity but higher among-individual convergence, selective assembly of gut microbiota with higher diversity, and tight ARG-MGE association. PLS-PM supported a diet-gut microbiota-MGE-ARG cascade, while the direct effects of sediment chemistry were not significant. Attributing ARG hosts at the MAG level, Enterobacteriaceae and Vibrionaceae dominated ARG abundance and enrichment, indicating lineage selectivity. Multidrug and polymyxin resistance was most prominent. These findings identify key AMR risk pathways and inform priority interventions for T. tridentatus and habitat conservation. The developed assessment framework is scalable and offers a paradigm for One Health management in mudflat systems.}, }
@article {pmid41937905, year = {2026}, author = {Cheng, Y and Peng, L and Liu, D and Zhong, L and Liu, Y and Yang, T}, title = {Case Report: A rare culprit of severe pulmonary infection in children: prevotella.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1782202}, pmid = {41937905}, issn = {2296-2360}, abstract = {BACKGROUND: To characterize the clinical features, diagnostic pitfalls, and treatment of severe pediatric pulmonary infection caused by Prevotella species.
METHODS: We retrospectively reviewed clinical data, the diagnostic workflow, antimicrobial regimens, and outcomes of two children with severe Prevotella pulmonary infection.
RESULTS: Case 1 was an 11-year-old boy with necrotizing pneumonia, and Case 2 was a 13-year-old boy with retained foreign-body aspiration. Both patients responded poorly to initial cephalosporin-based therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid identified Prevotella nanceiensis (sequence count 299,022; relative abundance 92.24%) and Prevotella oralis (210,449; 67.98%) within 24 h, whereas anaerobic culture (Case 1) became positive after 4 days. Based on mNGS results antibiotics were adjusted to metronidazole plus a carbapenem (meropenem for Case 1; imipenem-cilastatin for Case 2), and both children received adjunctive pulmonary rehabilitation before discharge. They subsequently recovered and were discharged.
CONCLUSION: Severe Prevotella pulmonary infection in children has non-specific manifestations and may respond poorly to conventional beta-lactam therapy, leading to delayed diagnosis. mNGS enables rapid pathogen identification and supports targeted anti-anaerobic treatment. For severe or complicated cases refractory to empirical therapy, metronidazole combined with a carbapenem may be an effective option.}, }
@article {pmid41937991, year = {2026}, author = {Halphen, J and Ahmadzade, M and Mankidy, B and Berenji, A and Ghasemi-Rad, M}, title = {Letter to the Editor: Evidence for a two-step species-level pulmonary nocardiosis diagnostic approach.}, journal = {World journal of radiology}, volume = {18}, number = {3}, pages = {118126}, pmid = {41937991}, issn = {1949-8470}, abstract = {Pulmonary nocardiosis, a rare and diagnostically challenging infection, usually presents with heterogeneous radiographic findings, compounded by the low sensitivity of traditional confirmatory cultures. In their most recent work, Wang et al analyzed 102 patients with pulmonary nocardiosis to address these concerns, investigating species-characteristic imaging patterns, pathological associations, and the role of metagenomic next-generation sequencing (mNGS) in the diagnostic approach. High-resolution computed tomography (CT) in adult patients with pulmonary infections caused by Nocardia wallacei was demonstrated to have a sensitive (85.71%) and specific (83.34%) presentation of bronchopneumonia in relation to the five Nocardia species in the sample with CT data. The authors also compared traditional cultures to mNGS, finding that traditional cultures and mNGS were concordantly positive in only 3.3% of cases. This letter supports a combined radiologic and molecular diagnostic approach, enabling earlier and more accurate species identification in pulmonary nocardiosis, thereby informing treatment decisions, and enhancing epidemiologic understanding.}, }
@article {pmid41938562, year = {2026}, author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F}, title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).}, journal = {Veterinary world}, volume = {19}, number = {2}, pages = {864-876}, pmid = {41938562}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.
MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), α- and β-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.
RESULTS: α-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, β-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.
CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.}, }
@article {pmid41938867, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R}, title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779554}, pmid = {41938867}, issn = {2235-2988}, mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.
METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.
RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.
DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.}, }
@article {pmid41939082, year = {2026}, author = {Turner, ML and Nguyen, MT and Kung, Y and Doan, T and Seitzman, GD}, title = {Rhizopus angle abscess, scleritis and endophthalmitis following Kahook Dual Blade goniotomy and phacoemulsification.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102572}, pmid = {41939082}, issn = {2451-9936}, abstract = {PURPOSE: To describe a rare case of Rhizopus angle abscess progressing to scleritis and endophthalmitis after routine cataract surgery with Kahook Dual Blade (KDB) goniotomy in an immunocompetent patient.
OBSERVATION: A 79-year-old male developed hyphema and anterior chamber fibrin three days after uncomplicated phacoemulsification with KDB. Despite intravitreal vancomycin and ceftazidime, inflammation worsened, and by postoperative day nine vision was count fingers with intraocular pressure of 29 mmHg. Slit-lamp exam showed an inferonasal corneal infiltrate with a purulent angle abscess at the goniotomy site and dense vitritis. Intravitreal and oral voriconazole were started for presumed fungal infection. Standard cultures and PCR were negative, but metagenomic RNA deep sequencing of aqueous fluid detected Rhizopus stolonifer. After two months of systemic and intravitreal voriconazole, the infection resolved and visual acuity improved to 20/70, leaving localized limbal thinning.
CONCLUSION AND IMPORTANCE: This case illustrates that Rhizopus angle abscess can occur in an immunocompetent host following anterior segment surgery and may masquerade as bacterial endophthalmitis. Early suspicion of fungal infection and use of metagenomic deep sequencing were critical for diagnosis and successful treatment, emphasizing the need to consider invasive fungal pathogens and advanced molecular diagnostics in culture-negative postoperative ocular infections.}, }
@article {pmid41939697, year = {2026}, author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M}, title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786817}, pmid = {41939697}, issn = {1664-302X}, abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.}, }
@article {pmid41939705, year = {2026}, author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP}, title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768977}, pmid = {41939705}, issn = {1664-302X}, abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.}, }
@article {pmid41939707, year = {2026}, author = {Li, X and Jin, S and Hu, H and Lan, Y and Ni, B and Su, J and Luo, S and Tan, L and Zhang, Y and Huang, H and Xu, Y and Yang, J and Zhou, C and Chen, K and Li, S and Liang, B and Bai, S and Zhang, K and Pan, H and Dong, X and Yan, D}, title = {Feeding Diqing Tibetan pigs with 50% of soybean meal replaced by walnut meal can reduce subcutaneous fat deposition and promote intramuscular fat accumulation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794046}, pmid = {41939707}, issn = {1664-302X}, abstract = {BACKGROUND: Protein feed resource shortage is a major constraint to the sustainable development of the livestock industry and a bottleneck problem hindering the growth of the Tibetan pig industry in China's Qinghai-Tibet Plateau region. Walnut meal, rich in protein, holds promise as a substitute for soybean meal. However, the effects and underlying mechanisms of walnut meal substitution on Tibetan pigs in Diqing remain unclear.
RESULTS: The study showed that substituting 50% of soybean meal with walnut meal in the diet of Diqing Tibetan pigs significantly reduced backfat thickness and increased intramuscular fat content (P < 0.05). Integrated multi-omics analyses, including metagenomics, transcriptomics, and lipidomics, revealed that walnut meal substitution significantly reduced the abundance of Clostridium butyricum in the cecum of Diqing Tibetan pigs. The reduction in Clostridium butyricum was linked to the lipolytic capacity of subcutaneous adipose tissue, potentially facilitating the breakdown of triglycerides into free fatty acids (FFAs), which are then released into the bloodstream. When these free fatty acids are transported to muscle tissue, the muscle exhibited inhibited oxidative metabolism (e.g., a decrease in acylcarnitine metabolites), while showing an upregulation in the expression of genes related to adipocyte differentiation (e.g., MEDAG, VDR) and triglyceride synthesis (e.g., PPARGC1A, ANGPTL4). Ultimately, these processes may contribute to the synthesis and storage of triglycerides in muscle, thereby facilitating intramuscular fat deposition.
CONCLUSION: This study reveals that walnut meal can serve as a substitute for soybean meal, and a 50% substitution ratio is conducive to intramuscular fat deposition in Diqing Tibetan pigs. The findings provide valuable insights for the development and application of unconventional protein feed resources, and offer new perspectives for the production of marbled pork.}, }
@article {pmid41939710, year = {2026}, author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J}, title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741638}, pmid = {41939710}, issn = {1664-302X}, abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.}, }
@article {pmid41939717, year = {2026}, author = {Navarro-Nieva, A and Martínez-Checa, F and Delgado, R and Párraga, J and Francino, MP and Jiménez-Hernández, N and Del Moral, A}, title = {Airborne microorganisms in muddy rain: microbe-mineral interactions and their ecosystem impact.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1772201}, pmid = {41939717}, issn = {1664-302X}, abstract = {The Sahara Desert and the Sahel region in North Africa contribute approximately 50-70% of global atmospheric dust emissions. Microorganisms can attach to dust particles and be dispersed into exogenous environments, being subsequently deposited by gravitational sedimentation (dry deposition) or through aqueous precipitation (wet deposition) also known as muddy rain. In the present work, five muddy rain samples were collected in Granada (Spain) during different episodes in 2021-2022. The SEM-EDX study demonstrated a high content of fine clay particles which may facilitate the atmospheric transport of microorganisms. The colonization of strategic microsites and the formation of mineral aggregates might be possible mineral-bacteria interactions. According to metagenomic analysis, Pseudomonadota (64%), Bacteroidota (13%), and Bacillota (6%) were the main phyla. At the genus level, extremophiles, plant-beneficial bacteria, and others involved in soil biogeochemical cycles have been described. Fourteen cultivable microorganisms were isolated and identified by means of 16S rRNA sequencing. Members of the phyla Pseudomonadota, Bacillota, Actinomycetota and Bacteroidota have been found. Among the isolates, Stenotrophomonas rhizophila and Brevundimonas bullata potentially exert beneficial effects at the ecosystem level. In general, muddy rain facilitates the transport and dispersal of microorganisms from different environments, with a potential positive influence on soils and vegetation in terrestrial ecosystems.}, }
@article {pmid41940150, year = {2026}, author = {Luo, H and Wang, Y and Hou, H and Yang, J and Liu, YX}, title = {Advances and applications in sequencing-based pathogen surveillance.}, journal = {aBIOTECH}, volume = {7}, number = {1}, pages = {100004}, pmid = {41940150}, issn = {2662-1738}, abstract = {The ongoing emergence of infectious diseases necessitates cutting-edge diagnostic methodologies. Traditional diagnostic methods are constrained by limited range, lengthy processing times, and inadequate sensitivity. High-throughput sequencing technologies, particularly multiplex polymerase chain reaction (PCR)-based targeted sequencing, have emerged as transformative tools for pathogen detection, offering enhanced sensitivity, specificity, and cost efficiency. However, challenges in primer design, such as dimerization and bias, limit the effectiveness of these approaches. This review explores advances in sequencing technologies, emphasizing the roles of culturomics, metagenomics, and metatranscriptomics in pathogen discovery. We spotlight innovative strategies for error-tolerant primer design that address existing limitations by balancing coverage and specificity, thereby optimizing the multiplex PCR process. Furthermore, integration of artificial intelligence enhances the precision and scalability of sequencing, enabling real-time diagnostics. Collectively, these advances offer promising pathways to bolster global health, food security, and ecological resilience through robust and sustainable pathogen-detection systems.}, }
@article {pmid41940273, year = {2026}, author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X}, title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.}, journal = {Current zoology}, volume = {72}, number = {1}, pages = {14-29}, pmid = {41940273}, issn = {1674-5507}, abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.}, }
@article {pmid41940285, year = {2025}, author = {Jeong, GH and Lim, KS}, title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.}, journal = {Journal of animal science and technology}, volume = {67}, number = {6}, pages = {1207-1214}, pmid = {41940285}, issn = {2055-0391}, abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.}, }
@article {pmid41940335, year = {2026}, author = {Buysse, M and Ballinger, MJ and Bruley, M and Amoros, J and Grillet, J and Farassat, N and Serr, A and Lagrèze, WA and Wennerås, C and Grankvist, A and Schön, T and Berglund, J and Bell-Sakyi, L and Sprong, H and Duron, O}, title = {A human-associated Spiroplasma ixodetis lineage responsible for infantile cataracts and adult febrile illness.}, journal = {iScience}, volume = {29}, number = {4}, pages = {115233}, pmid = {41940335}, issn = {2589-0042}, abstract = {Bacteria of the Spiroplasma ixodetis clade are well characterized as reproductive parasites and defensive endosymbionts of arthropods. Nevertheless, clinical evidence indicates that they can also infect humans, causing neonatal ocular disease and acute febrile illness in adults. Using metagenomic assembly and phylogenomic analyses of Spiroplasma ixodetis-related human infections (SiRHIs), combined with a systematic meta-analysis of public datasets, we identified 25 human cases across ten European countries. Despite the frequent detection of multiple S. ixodetis strains in ticks, our data provide no evidence implicating tick-associated strains in human infections. Instead, SiRHI constitute a distinct monophyletic lineage within the S. ixodetis clade, consistent with a shared evolutionary origin with arthropod-associated relatives. Notably, SiRHI genomes harbor horizontally acquired chaperone genes absent from most arthropod-associated Spiroplasma, while retaining conserved effector genes typical of endosymbionts, suggesting the preservation of ancestral symbiotic traits alongside newly acquired molecular adaptations.}, }
@article {pmid41940665, year = {2026}, author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X}, title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0191125}, doi = {10.1128/spectrum.01911-25}, pmid = {41940665}, issn = {2165-0497}, abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.
IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.}, }
@article {pmid41940696, year = {2026}, author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M}, title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0190325}, doi = {10.1128/aem.01903-25}, pmid = {41940696}, issn = {1098-5336}, abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.}, }
@article {pmid41940802, year = {2026}, author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , }, title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2653550}, doi = {10.1080/19490976.2026.2653550}, pmid = {41940802}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Mouth/microbiology ; Female ; *Bacteria/classification/isolation & purification/genetics ; Feces/microbiology ; Child, Preschool ; Saliva/microbiology ; Infant ; Cross-Sectional Studies ; *Bacterial Translocation ; *Growth Disorders/microbiology ; Child ; *Gastrointestinal Tract/microbiology ; Metagenomics ; }, abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.}, }
@article {pmid41940852, year = {2026}, author = {Jin, Z and Yuan, Q and Wang, J and Liao, H and Bol, R and Wu, D and Wu, Q and Tang, Y and Guo, W and Liu, Y and Chen, J}, title = {Recycling of Sedimentary Phosphorus Pools in Two Yunnan-Guizhou Plateau Lakes, Southwest China.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00162}, pmid = {41940852}, issn = {1520-5851}, abstract = {Applying phosphate oxygen isotopes (δ[18]OP) to identify sediment phosphorus (P) sources and its recycling is still challenging due to poor understanding in δ[18]OP variations of sediment P pools and their driving mechanisms. Here, we analyzed the δ[18]OP in inorganic P (Pi) pools of sediment cores and varied P sources from Lake Dianchi and Lake Erhai in the Yunnan-Guizhou Plateau, Southwest China. The δ[18]OP values of sediment detrital Pi (Det-Pi, nonbioavailable P) were consistent with those of watershed soils (within ∼0.4-0.6‰), indicating that the δ[18]OP of sediment Det-Pi inherits the δ[18]OP of soil Det-Pi. The δ[18]OP values of aluminum-bound Pi (Al-Pi) and authigenic Pi (Auth-Pi) in sediment were close to or within the δ[18]OP equilibrium (δ[18]OP-eq) ranges, implying oxygen isotopic exchange equilibrium between phosphate and ambient water prior to the formation of sediment Al-Pi and Auth-Pi. However, the δ[18]OP of iron oxide-bound Pi (Fe-Pi) in sediment was lighter (∼3‰) than δ[18]OP-eq, retaining the negative isotopic signal of organic P (Po) remineralization. Furthermore, [31]P NMR and metagenomic analysis indicated that microbial-mediated Po mineralization and Pi recycling are the driving factors for δ[18]OP changes in sediment Fe-Pi, Al-Pi, and Auth-Pi. These integrated insights deepen our understanding of the biogeochemical cycling for sedimentary P.}, }
@article {pmid41940893, year = {2026}, author = {Liao, Y and Wang, B and Li, Y and Ni, W and Li, X and Hu, S}, title = {Establishment of the chromid database and analysis of evolutionary research.}, journal = {Molecular genetics and genomics : MGG}, volume = {301}, number = {1}, pages = {}, pmid = {41940893}, issn = {1617-4623}, mesh = {*Evolution, Molecular ; Phylogeny ; *Genome, Bacterial/genetics ; *Databases, Genetic ; *Bacteria/genetics/classification ; Polymorphism, Single Nucleotide ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {In bacterial multireplicon genomes, in addition to the main chromosome, there is a widespread class of secondary replicons with a distinct evolutionary status known as chromids. These elements possess plasmid-like replication and partitioning systems, while their nucleotide composition and gene functions are highly similar to those of the main chromosome. Therefore, chromids are considered to play important roles in the evolution of bacterial genome architecture and in environmental adaptation. With advances in long-read sequencing technologies and breakthroughs in bioinformatics methods, metagenomic data resources have been greatly expanded. Using our previously developed automated tool, "Chromid-Finder", we systematically identified and collected chromid sequences from large-scale metagenomic assemblies. These data were then uniformly curated, classified, and centrally managed to construct a public database platform dedicated to chromids-Chromid Database. On this basis, we conducted comprehensive analyses of the evolutionary and genetic characteristics of chromids. Phylogenetic analyses revealed the overall evolutionary landscape of chromids. Variation analyses showed that SNP distributions on chromids exhibit clear and well-organized patterns, depicting a dynamic population that is continuously adapting to the environment through fine-scale sequence tuning and non-coding regulatory mechanisms. Structural variation analyses further identified several hotspot regions significantly enriched in key genes related to metabolic functions, nutrient acquisition, and antibiotic resistance. The distribution patterns of recombination events suggest that their occurrence is likely driven primarily by non-phylogenetic factors such as environmental conditions and ecological niches. In addition, systematic quantification of heritable mobile genetic elements indicated that the number of integrative and conjugative elements (ICEs) largely determines the overall mobile element burden within chromids.}, }
@article {pmid41941835, year = {2026}, author = {Hennen, J and Ifrach, J and Morse, C and Charcos, I and Godil, SS and Mossop, CM}, title = {First reported case of Lawsonella clevelandensis brain abscess in the setting of invasive cutaneous squamous cell carcinoma identified via bedside stereotactic aspiration: illustrative case.}, journal = {Journal of neurosurgery. Case lessons}, volume = {11}, number = {14}, pages = {}, doi = {10.3171/CASE25887}, pmid = {41941835}, issn = {2694-1902}, abstract = {BACKGROUND: Brain abscesses associated with malignant skull base invasion pose unique diagnostic and management challenges for neurosurgeons, particularly when routine cultures remain negative. The authors report the first documented intracranial infection caused by Lawsonella clevelandensis, a recently described anaerobe that mimics Nocardia or Mycobacterium sp., diagnosed using bedside stereotactic biopsy as well as metagenomic next-generation sequencing.
OBSERVATIONS: A 74-year-old woman with recurrent, locally invasive facial squamous cell carcinoma presented with recent-onset shaking of her lower extremity and a large right frontal mass extending through the calvarium and orbit. Imaging revealed ring-enhancing lesions consistent with abscess. Bedside stereotactic biopsy and drainage were performed, and metagenomic sequencing identified L. clevelandensis. Antibiotics were narrowed to ceftriaxone and metronidazole, stabilizing her condition, although repeat drainage was required for radiographic progression. She subsequently underwent multidisciplinary skull base resection and reconstruction, with operative cultures isolating Enterococcus faecium but no further Lawsonella sp.
LESSONS: This case represents the first documented intracranial L. clevelandensis infection and demonstrates the diagnostic value of molecular sequencing in culture-negative brain abscesses. It also highlights bedside stereotactic biopsy and drainage as a safe, minimally invasive strategy for managing intracranial infection in medically complex patients. https://thejns.org/doi/10.3171/CASE25887.}, }
@article {pmid41942049, year = {2026}, author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J}, title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.004}, pmid = {41942049}, issn = {2090-1224}, abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.
OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.
METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.
RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.
CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.}, }
@article {pmid41942192, year = {2026}, author = {Xia, Y and Kuda, T and Zhou, Q and He, Q}, title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118924}, doi = {10.1016/j.foodres.2026.118924}, pmid = {41942192}, issn = {1873-7145}, mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; *Microbiota/drug effects ; Antioxidants/pharmacology ; Animals ; *Fermented Foods/microbiology ; Humans ; Food Quality ; Taste ; }, abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.}, }
@article {pmid41942205, year = {2026}, author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H}, title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118955}, doi = {10.1016/j.foodres.2026.118955}, pmid = {41942205}, issn = {1873-7145}, mesh = {*Food Storage/methods ; *Prunus avium/microbiology ; *Metagenomics/methods ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; *Fruit/microbiology ; }, abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.}, }
@article {pmid41942425, year = {2026}, author = {Peña-Valencia, MF and Robaina-Estévez, S and Custer, GF and Turak, O and Sierra, F and Mendes, LW and Rubiano-Labrador, C and Gutiérrez, J and Vaksmaa, A and Dini-Andreote, F and Rosado, AS and Reyes, A and Jiménez, DJ}, title = {Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71548-z}, pmid = {41942425}, issn = {2041-1723}, abstract = {Mangroves are ecosystems located at land-sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.}, }
@article {pmid41942856, year = {2026}, author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT}, title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04996-8}, pmid = {41942856}, issn = {1471-2180}, support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; }, }
@article {pmid41942925, year = {2026}, author = {Maimaitiming, A}, title = {Metagenomic next-generation sequencing (mNGS) for severe cat bite infections with negative aerobic culture: a single-center retrospective study in a rabies vaccination center.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13222-9}, pmid = {41942925}, issn = {1471-2334}, }
@article {pmid41943157, year = {2026}, author = {Bruna, P and Barra, PJ and García, M and Liachko, I and de la Luz Mora, M and Dutilh, BE and Abanto, M}, title = {Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00887-7}, pmid = {41943157}, issn = {2524-6372}, support = {2023-21230832//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT Regular 1241293//Agencia Nacional de Investigación y Desarrollo/ ; 1230084//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; FONDECYT Regular 1251164//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; Consolidator grant 865694/ERC_/European Research Council/International ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.
RESULTS: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.
CONCLUSIONS: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.}, }
@article {pmid41764528, year = {2026}, author = {Zhang, W and Su, Q and Shi, H and Sun, Y and Li, X and Li, M and Wang, H and Yu, J and Wong, N and Chan, FKL and Zhang, J and Ng, SC}, title = {Discovery and characterization of Christensenella hongkongensis as a novel bacterium in the adenoma-carcinoma progression.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41764528}, issn = {1479-5876}, abstract = {BACKGROUND: Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and commonly starts from a pre-cancerous stage. This study aimed to identify potential fecal bacterial candidates associated with progression of CRC from the adenoma-carcinoma sequence and to explore underlying mechanisms of carcinogenesis.
METHODS: Publicly metagenomic datasets were analyzed using MaAsLin2 to identify bacterial species enriched in CRC patients compared to healthy controls. Additionally, we established a large cohort in mainland China, consisting of 686 subjects, including 285 CRC patients, 73 advanced adenoma patients (AA), 134 non-advanced adenoma patients (nAA), and 194 healthy controls (NC). Fecal samples from this cohort were analyzed by duplex quantitative polymerase chain reaction (qPCR) to validate the abundance of key bacterial candidate and its association with tumor node metastasis (TNM) stages. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic performance of Christensenella hongkongensis (C. hongkongensis) alone and in combination with fecal immunochemical test (FIT) across different CRC stages. In vitro experiments and transcriptome sequencing were performed to explore the effects of C. hongkongensis and its mechanisms in CRC progression.
RESULTS: MaAsLin2 analysis identified seven bacterial species were significantly more abundant in fecal samples of CRC patients than in healthy controls (p < 0.05). Among them, C. hongkongensis, an obligately anaerobic, catalase-positive, motile, non-sporulating, gram-positive coccobacillus was distinguished by its lowest abundance in healthy controls and significant enrichment in CRC patients. Validation in our recruited cohort showed that the abundance of C. hongkongensis progressively increased from non-advanced adenomas to advanced adenomas and CRC. For classifying AA from nAA, C. hongkongensis yielded an area under the ROC curve (AUC) of 0.60 (95% CI 0.53–0.68), with 45.2% sensitivity and 85.8% specificity. A combined model integrating C. hongkongensis abundance and FIT further improved diagnostic performance, increasing AUCs from 0.77 to 0.81 for AA vs NC (p < 0.05) and from 0.76 to 0.82 for AA vs nAA (p < 0.001). Linear regression analysis revealed a significant positive association between C. hongkongensis and TNM stages in CRC. In vitro experiments showed that C. hongkongensis promoted CRC cell proliferation, inhibited apoptosis, and enhanced the growth of patient-derived CRC organoids. RNA-seq analysis identified activation of the Wnt/β-catenin signaling pathway, which was further validated by elevated protein levels of active β-catenin, reduced phosphorylation of GSK3β, and the upregulation of downstream targets c-Jun and Cyclin-D1.
CONCLUSIONS: Our findings suggest that C. hongkongensis promotes colorectal tumorigenesis via Wnt/β-catenin activation, and highlight its potential as a novel non-invasive bacterial marker for early detection and monitoring of CRC progression.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07886-9.}, }
@article {pmid41935438, year = {2026}, author = {Bai, Y and Zhao, J and Wang, Z and Zheng, J and Zhu, X and Shao, Y and Zhang, X}, title = {A case of Rickettsia felis caused pneumonia and diagnosed by clinical analysis and Targeted Next-Generation Sequencing (tNGS) using Bronchoalveolar Lavage Fluid (BALF): A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {5}, pages = {103217}, doi = {10.1016/j.jiph.2026.103217}, pmid = {41935438}, issn = {1876-035X}, abstract = {Feline rickettsia pneumonia is a rare lung disease caused by feline R. felis infection, which is mainly transmitted by feline fleas. A 57-year-old male patient was hospitalized with pain in the back of the sternum. Chest CT showed bilateral diffuse interstitial lung disease with multiple nodules. After the empirical anti-infection treatment was ineffective, the second-generation meta-genome sequencing (mNGS) of bronchoalveolar lavage (BALF) was diagnosed as feline rickettsia infection. In terms of treatment, inject tegacycline intravenously and then sequentially take minocycline. The patient's symptoms were relieved quickly, and the imaging improved significantly. This report summarizes the clinical and imaging characteristics and diagnosis and treatment experience of the case, aiming to provide reference for the early identification and treatment of such rare infections.}, }
@article {pmid41935631, year = {2026}, author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , }, title = {Alcohol-Related Liver Disease Disrupts Bile Acid Homeostasis and Gut Microbial Bile Acid Metabolism.}, journal = {JHEP reports : innovation in hepatology}, volume = {}, number = {}, pages = {101848}, doi = {10.1016/j.jhepr.2026.101848}, pmid = {41935631}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.
METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n=462), alongside matched healthy controls (n=148), and validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.
RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F=69.9, p=8.6e-66) and feces (inprimis, cholic acid: F=5.5, p=1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multi-step dehydroxylation pathway (e.b. baiB) increased, whereas those in the reduction arm (baiN) were depleted. In ALD patients, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.
CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.
CLINICAL TRIAL NUMBER: GALAXY main cohort: Danish Data Protection Agency nos. 13/8204, 16/3492 and 18/22692; and Odense Patient Data Exploratory Network under study identification nos. OP_040 and OP_239 Validation cohort 1: EudraCT number 20214-001856-51 Validation cohort 2: ClinicalTrial.gov ID NCT03863730 IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive alcohol-related liver disease progression. Additionally, our study identifies specific bacterial species influencing bile acid concentrations in alcohol-related liver disease using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating alcohol-related liver disease.}, }
@article {pmid41935814, year = {2026}, author = {Sambucci, KM and Samaš, P and Ssebide, B and Petrželková, KJ and Okello, RO and Nizeyimana, F and Bukamba, N and Smiley-Evans, T and Gilardi, K and Pafčo, B and Červená, B}, title = {Shifts in strongylid communities associated with chronic wasting in mountain gorillas.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {104848}, doi = {10.1016/j.ijpara.2026.104848}, pmid = {41935814}, issn = {1879-0135}, abstract = {Host-parasite relationships are typically maintained in a dynamic equilibrium, but disruptions to this balance can lead to clinical disease and population-level health impacts. Chronic wasting, characterized by chronic loss of body condition, alopecia, a browning hair coat and pot belly, is an emerging health concern in mountain gorillas of Bwindi Impenetrable National Park, Uganda. Deworming of suspected cases has led to marked short-term health improvements, implicating intestinal helminths. To investigate, we analysed faecal samples from human-habituated gorillas collected in 2018 and 2021, and unhabituated gorillas in 2018, using high-throughput sequencing of strongylid nematodes (ITS-2) and gut bacteria (16S). Strongylid community composition varied with chronic wasting occurrence, with Oesophagostomum emerging as a key taxon driving this difference, while bacterial communities remained relatively stable. Strongylid diversity increased between 2018 and 2021, and habituated gorillas exhibited reduced strongylid genetic diversity, higher relative abundance of Oesophagostomum and lower relative abundance of Murshidia compared to unhabituated gorillas. These results suggest that a higher abundance of Oesophagostomum is associated with chronic wasting in mountain gorillas due to either a causative association or because of other genetic, immunological or environmental causes allowing Oesophagostomum, a common member of the gut eukaryote community of the Bwindi gorillas, to overpopulate.}, }
@article {pmid41935918, year = {2026}, author = {Lazarevic, V and Ruppé, E and Schrenzel, J}, title = {10th International Conference on Clinical Metagenomics (ICCMg10): meeting report.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.008}, pmid = {41935918}, issn = {1878-4380}, abstract = {The 10th International Conference on Clinical Metagenomics (ICCMg10) brought together clinicians, microbiologists, bioinformaticians, and industry partners to review progress and challenges in translating metagenomics into routine clinical practice. Discussions focused on advances in sequencing technologies, automation, clinically oriented workflows, and computational and reporting strategies. Clinical sessions addressed diagnostic implementation across infectious syndromes, including respiratory, prosthetic joint, bloodstream, and deep-seated infections, with attention to cell-free DNA assays, long-read sequencing, and antimicrobial resistance detection. Broader applications of metagenomics, spanning microbiota research and environmental systems, reflected the expanding scope of the field. Overall, ICCMg10 underscored the importance of multidisciplinary collaboration, harmonized practices, and clinically meaningful interpretation to support the broader implementation of clinical metagenomics.}, }
@article {pmid41936200, year = {2026}, author = {Uematsu, S}, title = {Programming systemic and mucosal immunity through co-adjuvant-based prime-boost vaccination.}, journal = {Current opinion in virology}, volume = {76}, number = {}, pages = {101525}, doi = {10.1016/j.coviro.2026.101525}, pmid = {41936200}, issn = {1879-6265}, abstract = {The development of effective mucosal vaccines has been limited by the limited availability of mucosal adjuvant approaches with established clinical track records and an incomplete understanding of how systemic and mucosal immunity are coordinated. Recent studies indicate that the priming phase of vaccination plays a decisive role in programming the quality, durability, and anatomical distribution of subsequent immune responses. This review discusses emerging evidence that co-adjuvant-based priming strategies can establish long-lasting immune programs that enable adjuvant-free mucosal boosting. Focusing on the combination of CpG DNA and curdlan as a prototypical example, this review highlights how coordinated activation of innate immune receptors during priming imprints dendritic cells, B cells, and T cells to support robust mucosal IgA and tissue-resident immunity. This review further discusses translational advances demonstrating that this immune programming paradigm can be maintained using translationally oriented formulations designed with clinical development in mind and validated in non-human primates. Independent studies using mRNA and protein-based vaccines support the general principle that the quality of priming, rather than the boosting modality, determines successful mucosal immunity. Together, these findings redefine vaccine adjuvants as tools for immune programming and provide a conceptual framework for next-generation vaccine design.}, }
@article {pmid41936930, year = {2026}, author = {Zhou, Z and Song, Y and Zhou, Y}, title = {Metagenomic Next-Generation Sequencing Profiling of Primary versus Iatrogenic Osteoarticular Infections: Unveiling Distinct Pathogen Spectra and Diagnostic Implications.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108688}, doi = {10.1016/j.ijid.2026.108688}, pmid = {41936930}, issn = {1878-3511}, abstract = {OBJECTIVE: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus microbial culture in primary osteoarticular infection (POI) and iatrogenic osteoarticular infection (IOI), and to analyze pathogen spectrum differences and clinical implications.
METHODS: Ninety-two patients with confirmed osteoarticular infection (POI, n=42; IOI, n=50) were retrospectively analyzed. All specimens were tested using both mNGS and conventional culture. The pathogen detection rates, pathogen spectrum composition, detection of mixed infections, and concordance of results between the two methods were compared.
RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (72.83% vs. 43.48%; P < 0.001), particularly in IOI (78.00% vs. 34.00%; P < 0.001). Pathogen profiling showed predominance of Staphylococcus aureus in POI, whereas IOI exhibited greater microbial diversity with increased detection of Staphylococcus epidermidis (31.03%) and anaerobes (13.79%). Polymicrobial infections were more frequently identified by mNGS (14.13% vs. 4.35% by culture; P = 0.024), primarily in the IOI group. Concordance between mNGS and culture was substantial in POI (κ = 0.66; 95% CI: 0.42-0.89) but only slight in IOI (κ = 0.12; 95% CI: -0.12 to 0.35), largely attributable to the high rate of mNGS-exclusive positives in IOI (48.00%).
CONCLUSION: mNGS improves pathogen detection in osteoarticular infections, especially in IOI where it identifies complex and polymicrobial infections more effectively than culture, providing critical support for guiding antimicrobial therapy.}, }
@article {pmid41936935, year = {2026}, author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F}, title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134553}, doi = {10.1016/j.biortech.2026.134553}, pmid = {41936935}, issn = {1873-2976}, abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.}, }
@article {pmid41936957, year = {2026}, author = {Ghaly, TM and Shah, BS and Coleman, NV and Elbourne, LDH and Le Roux, JJ and Gillings, MR and Paulsen, IT and Tetu, SG}, title = {Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124428}, doi = {10.1016/j.envres.2026.124428}, pmid = {41936957}, issn = {1096-0953}, abstract = {Humans are a major evolutionary force, yet our impacts on the evolution of Earth's microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2,500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase (Nar) were specific to Burkholderiales, a major group of denitrifying bacteria. Nar protein regions under positive selection flanked the enzyme's substrate channel, favouring smaller amino acids, likely resulting in the widening of the channel entrance. We present a novel hypothesis that this channel widening could increase rates of substrate turnover, which we propose would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant nitrate reducers globally, such evolutionary consequences of agriculture on this lineage could have cascading environmental impacts, including increased nitrous oxide emissions. These findings indicate that anthropogenic selection might be altering protein-level evolution of vital microbial biogeochemical processes.}, }
@article {pmid41937023, year = {2026}, author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H}, title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.}, journal = {Travel medicine and infectious disease}, volume = {}, number = {}, pages = {102978}, doi = {10.1016/j.tmaid.2026.102978}, pmid = {41937023}, issn = {1873-0442}, abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.
METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.
RESULTS: In total, 3,770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1,021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).
CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.}, }
@article {pmid41937144, year = {2026}, author = {Bočaj, V and Pongrac, P and Likar, M}, title = {Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00890-y}, pmid = {41937144}, issn = {2524-6372}, support = {P1-0212//The Slovenian Research and Innovation Agency/ ; P1-0212//The Slovenian Research and Innovation Agency/ ; P1-0212//The Slovenian Research and Innovation Agency/ ; }, abstract = {BACKGROUND: Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.
RESULTS: The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log2 fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.
CONCLUSION: Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.}, }
@article {pmid41937169, year = {2026}, author = {Mullin, CE and Louca, S}, title = {Effects of heat-assisted sample desiccation on microbiome surveys.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00889-5}, pmid = {41937169}, issn = {2524-6372}, abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.}, }
@article {pmid41857392, year = {2026}, author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J}, title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41857392}, issn = {1432-184X}, support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science & Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; }, abstract = {UNLABELLED: Cold seep is a distinctive deep-sea environment mainly formed by methane-rich fluids leaking on the seafloor, gaps remain regarding the influence of seepage on microorganisms inhabiting water column across vertical and horizontal dimensions. Site F cold seep, located at 1,120 m depth on the northern South China Sea (SCS) slope, is one of the most active cold seeps in SCS. We performed 16S rRNA gene and metagenomic sequencing on samples collected by Niskin bottles mounted on Conductivity-Temperature-Depth profiler and Remote Operated Vehicle to analyze the structure and metabolic potentials of microbial communities throughout the water column at Site F. Microbial abundance generally decreased with depth at all sampling spots and was higher at sites adjacent to the seepage compared to those farther away, indicating a potential vertical and horizonal influence of methane seepage on water microbial community. High microbial abundance at deeper depths may attribute to a higher proportion of Gammaproteobacteria, comprised mainly of Alcanivoracaceae, Alteromonadaceae, Marinobacteraceae, methylotrophs represented by Methylophagaceae and Methylococcales (mainly Methylomonadaceae), and sulfur-oxidizing bacteria represented by SUP05 and Ectothiorhodospiraceae. Consistently, the aerobic methane oxidation gene pmoA was more prevalent in the deeper water and was found in four bacterial classes in addition to Gammaproteobacteria. Sulfur-oxidizing genes also exhibited higher abundances at depths and were primarily affiliated with Rhodobacteraceae. These microbes likely play important roles in aerobic oxidation of methane and sulfur, contributing to methane depletion during upward diffusion. By integrating sampling across vertical and horizontal dimensions, we demonstrate that seepage shapes the microbial community and biogeochemical functions in the water column at Site F.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02722-5.}, }
@article {pmid41933601, year = {2026}, author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y}, title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134536}, doi = {10.1016/j.biortech.2026.134536}, pmid = {41933601}, issn = {1873-2976}, abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.}, }
@article {pmid41933710, year = {2026}, author = {Huang, S and Zhang, S and Chen, Y and Su, X and Lu, X and Song, X and Li, W and Guo, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Wang, X and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of CRESS-DNA viruses in six wild herbivorous mammal species from the Qinghai-Tibet plateau.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105932}, doi = {10.1016/j.meegid.2026.105932}, pmid = {41933710}, issn = {1567-7257}, abstract = {As natural reservoirs for diverse viruses, mammals harbor complex and highly diverse viral communities. The Qinghai-Tibet Plateau, recognized as the "Third Pole" of Earth, exerts substantial evolutionary pressure on virions through its extreme environmental conditions characterized by high altitude, hypoxia, intense ultraviolet radiation, and dramatic diurnal temperature variation. Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses represent a ubiquitous group of small viruses that play crucial roles in maintaining global ecological equilibrium. Through viral metagenomic analysis of 741 fresh fecal samples collected from six wild herbivorous mammal species across three geographical regions of the Qinghai-Tibet Plateau, we systematically characterized their virome composition, revealing distinct interspecies variations in viral community structure. Focusing on CRESS-DNA viruses, we identified 180 complete viral sequences containing intact replication-associated protein (Rep) genes, including: Circoviridae (2 sequences, 1 novel), Genomoviridae (48 sequences, 38 novel), Smacoviridae (106 sequences, 103 novel), and Unclassified CRESS-DNA viruses (24 sequences, 20 novel), collectively representing an 86% discovery rate of novel viral virus. These viral sequences exhibited remarkable genetic divergence, with the majority (73%) failing to cluster within established taxonomic units, suggesting the plateau may constitute an evolutionary hotspot for novel CRESS-DNA viruses. Our findings not only expand current understanding of CRESS-DNA viral diversity but also indicate potential long-term symbiotic virus-host relationships rather than purely pathogenic interactions in this extreme ecosystem. Notably, high viral detection rates in species such as the Pseudois nayaur suggest their potential role as key transmission vectors. These discoveries provide novel insights into virus-host coevolution mechanisms under extreme environmental conditions and establish a scientific foundation for early warning systems of viral transmission risks in high-altitude ecosystems.}, }
@article {pmid41933826, year = {2026}, author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D}, title = {The Health Threat of Wild Animals by Rank I ARGs from Habitat Soils: Metagenomic and Metabolomic Evidence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128041}, doi = {10.1016/j.envpol.2026.128041}, pmid = {41933826}, issn = {1873-6424}, abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.}, }
@article {pmid41934012, year = {2026}, author = {Moraïs, S and Mizrahi, I}, title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.005}, pmid = {41934012}, issn = {1878-4380}, abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.}, }
@article {pmid41934196, year = {2026}, author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ}, title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.}, journal = {Molecular nutrition & food research}, volume = {70}, number = {7}, pages = {e70450}, doi = {10.1002/mnfr.70450}, pmid = {41934196}, issn = {1613-4133}, support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; }, mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; }, abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.}, }
@article {pmid41934511, year = {2026}, author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM}, title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41934511}, issn = {1572-9699}, mesh = {*Chitosan/administration & dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; }, abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.}, }
@article {pmid41934651, year = {2026}, author = {Zhang, N and Li, L and Chen, F and Kang, X and Liu, L and Kuang, D}, title = {Rapid Cavitary Pneumonia and Reversible Hepatic Injury in Burkholderia pseudomallei ST271 Infection.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951729}, doi = {10.12659/AJCR.951729}, pmid = {41934651}, issn = {1941-5923}, mesh = {Humans ; Male ; *Melioidosis/drug therapy/diagnosis/complications/microbiology ; Middle Aged ; *Burkholderia pseudomallei/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; }, abstract = {BACKGROUND Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease endemic to tropical and subtropical regions that displays highly variable clinical presentations, ranging from localized abscesses to severe septicemia. Sequence type (ST) 271 has been rarely reported; data concerning its clinical and epidemiological characteristics remain limited. This report describes a rare case of ST271 infection presenting with rapidly progressive cavitary pneumonia and reversible hepatic injury. CASE REPORT A previously healthy 50-year-old male construction worker from Haikou, China, presented with a 2-week history of intermittent fever, hemoptysis, and persistent cough. Chest computed tomography revealed a thick-walled cavitary mass in the right upper lobe. Laboratory findings demonstrated substantially elevated liver enzymes, indicating acute hepatic injury. Metagenomic sequencing of bronchoalveolar lavage fluid identified B. pseudomallei, and whole-genome sequencing classified the isolate as ST271. The strain was sensitive to imipenem, ceftazidime, and trimethoprim-sulfamethoxazole; preliminary in vitro bacteriophage susceptibility also was observed. After initiation of intravenous ceftazidime followed by oral trimethoprim-sulfamethoxazole, the patient showed rapid clinical improvement that included robust resolution of the pulmonary lesion and normalization of liver enzymes, consistent with reversible hepatic injury. CONCLUSIONS This case highlights the aggressive clinical course of the rare B. pseudomallei ST271 strain, characterized by rapidly progressive cavitary pneumonia and concurrent hepatic injury in an immunocompetent host. Early identification using sequencing techniques facilitated timely targeted therapy and a favorable recovery. The observed in vitro phage susceptibility may provide preliminary insight for future research into alternative management strategies for resistant strains.}, }
@article {pmid41934839, year = {2026}, author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B}, title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141959}, doi = {10.1016/j.jhazmat.2026.141959}, pmid = {41934839}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.}, }
@article {pmid41934858, year = {2026}, author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F}, title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141965}, doi = {10.1016/j.jhazmat.2026.141965}, pmid = {41934858}, issn = {1873-3336}, abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.}, }
@article {pmid41935109, year = {2026}, author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J}, title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46434-9}, pmid = {41935109}, issn = {2045-2322}, support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; }, abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.}, }
@article {pmid41935274, year = {2026}, author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S}, title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03152-y}, pmid = {41935274}, issn = {1743-422X}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.
METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.
RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.
CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.}, }
@article {pmid41935328, year = {2026}, author = {Li, XX and Li, BY and Fu, GW and Zhao, H and Li, J and Zhou, YH and Zhang, X and Zhao, YC}, title = {Clinical impact of metagenomic next-generation sequencing on pathogen detection and outcomes in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-12702-2}, pmid = {41935328}, issn = {1471-2334}, }
@article {pmid41935339, year = {2026}, author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R}, title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00885-9}, pmid = {41935339}, issn = {2524-6372}, abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.
RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.
CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.}, }
@article {pmid41928235, year = {2026}, author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE}, title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.}, journal = {BMC medical genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12920-026-02359-w}, pmid = {41928235}, issn = {1755-8794}, }
@article {pmid41928361, year = {2026}, author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S}, title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02392-y}, pmid = {41928361}, issn = {2049-2618}, support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; }, abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.
RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.
CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.}, }
@article {pmid41928791, year = {2026}, author = {Bajaj, J and Sommer, A and Auch, B and Khoruts, A}, title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9142184/v1}, pmid = {41928791}, issn = {2693-5015}, abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.}, }
@article {pmid41929040, year = {2026}, author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ}, title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.714183}, pmid = {41929040}, issn = {2692-8205}, abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.
IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.}, }
@article {pmid41929113, year = {2026}, author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R}, title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714056}, pmid = {41929113}, issn = {2692-8205}, abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.}, }
@article {pmid41929272, year = {2026}, author = {Biesheuvel, MM and Barkema, HW and Morley, PS and Pinnell, LJ and Doster, E and Valeris-Chacin, R}, title = {In silico performance of a targeted enriched metagenomics approach to infer Mycoplasma bovis strains in milk.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1770245}, pmid = {41929272}, issn = {2297-1769}, abstract = {Strain variation plays a key role in the microbial epidemiology of Mycoplasma bovis, yet its true diversity remains incompletely characterized, partly due to limitations of culture-based methods. This study evaluated the in silico suitability of a targeted enrichment (TE) shotgun sequencing approach to detect and classify M. bovis strains in milk metagenomic samples. As a proof of concept, the accuracy of this approach was assessed using milk-derived M. bovis strains. A total of 620 M. bovis whole-genome sequences were downloaded from NCBI, of which 162 (26.1%) originated from milk samples. Genomes were grouped into Genomically Clustered Sequence Variants (GSVs) using MashTree and TreeCluster to enable strain-level classification. To simulate TE sequencing data, genomes from different milk-associated GSVs were randomly selected and fragmented in silico into 150-bp reads. Mock milk samples were generated by sampling reads with replacement from these genomes. Sequencing depth was modeled using a Poisson distribution, while mixed-strain DNA samples were simulated by including 1, 3, 6, or 9 GSVs per sample. Enrichment proportions were set at 0.3, 0.5, 0.7, and 0.9. Two classification tools, Kraken2 and Themisto/mSWEEP, were evaluated for their ability to detect and classify the simulated TE reads. Themisto/mSWEEP consistently outperformed Kraken2, achieving an average read classification accuracy of 84.9% compared with 1.4% for Kraken2. Sensitivity for Themisto/mSWEEP was 100% with a single spiked GSV and declined slightly to 97.0% with nine GSVs, whereas Kraken2 achieved sensitivities of only 17.3% and 4.7%, respectively. Positive predictive value (PPV) showed a similar pattern: 98% for Themisto/mSWEEP vs. 4.7% for Kraken2 with a single GSV, and 65.5% vs. 10% with nine GSVs. While Kraken2's PPV increased slightly with additional GSVs, Themisto/mSWEEP's PPV decreased. Both methods maintained high specificity and negative predictive value (>91%) across all scenarios. Enrichment proportion had no measurable effect on performance. Overall, Themisto/mSWEEP demonstrated superior accuracy for GSV-level identification of M. bovis strains. Enrichment to at least 30% of total reads was sufficient to recover strain-level data. Further work is needed to assess the biological relevance and practical applications of these genomic clusters.}, }
@article {pmid41929449, year = {2026}, author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ}, title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1725666}, pmid = {41929449}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Male ; *Periodontitis/therapy/microbiology ; Female ; Middle Aged ; *Mouth/microbiology ; Longitudinal Studies ; Adult ; Bacteria/classification/genetics/isolation & purification ; *Lung/physiology ; Metagenomics ; Aged ; }, abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.
METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.
RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.
DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.}, }
@article {pmid41929455, year = {2026}, author = {Geng, Y and Yuan, Y and Lin, X and Wei, J and Zhang, Q and Mao, X and Zhang, X and Zhang, X and Zhang, Y and Zhao, J and Guo, F and Zheng, P}, title = {Distinct characteristics on mixed infection of SARS-CoV-2 variants and other respiratory pathogens among patients with acute COVID-19 in central China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1653022}, pmid = {41929455}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/virology/epidemiology ; China/epidemiology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/genetics/isolation & purification/classification ; *Coinfection/virology/epidemiology/microbiology ; Aged ; Adult ; Risk Factors ; Mycoplasma pneumoniae/isolation & purification ; Severity of Illness Index ; Hospitalization ; High-Throughput Nucleotide Sequencing ; Pneumonia, Mycoplasma/epidemiology ; Respiratory Tract Infections ; }, abstract = {BACKGROUND: Reports on mixed infection with different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in China remain scarce. In this study, we analyzed the clinical characteristics of mixed infections involving different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in central China.
METHODS: Nested polymerase chain reactions and metagenomic next-generation sequencing were employed to identify severe acute respiratory syndrome coronavirus 2 variants. Clinical data, including hospitalization days, severity classification, outcomes, and laboratory data, were collected and analyzed.
RESULTS: Seven patients had mixed infections with different severe acute respiratory syndrome coronavirus 2 variants in samples collected on different dates. Overall, 54.6% (83/152) of patients had co-existing respiratory pathogen infection. The most common co-existing respiratory pathogen was Mycoplasma pneumoniae. Longer hospital stays, intensive care unit admission, and prolonged duration from admission to positive severe acute respiratory syndrome coronavirus 2 sample detection were independent risk factors for acute coronavirus disease infection with different respiratory pathogens. Severity classification, mixed infection, cerebral fraction, and fever were independent risk factors for failed treatment. Early detection of white blood cell count, procalcitonin, and D-dimer concentrations can help predict mixed respiratory infections and treatment outcomes.
CONCLUSIONS: The phenomenon of mixed infection with different variants in patients with coronavirus disease may have been underestimated. Therefore, active surveillance of severe acute respiratory syndrome coronavirus 2 variants should be performed in older patients with comorbidities.}, }
@article {pmid41929479, year = {2026}, author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X}, title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760881}, pmid = {41929479}, issn = {1664-3224}, mesh = {Male ; *Dysbiosis/complications/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Asthenozoospermia/metabolism/etiology/microbiology ; Humans ; Mice ; Case-Control Studies ; Fecal Microbiota Transplantation ; Adult ; Fatty Acids, Volatile/metabolism ; Butyrates/metabolism ; Sperm Motility ; Metabolomics ; Testis/metabolism ; }, abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.
MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.
RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.
CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.}, }
@article {pmid41929693, year = {2026}, author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z}, title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729476}, pmid = {41929693}, issn = {1664-302X}, abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.
METHODS: Vaginal swabs (sPTB, n = 37; term, n = 62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.
RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p < 0.05), and distinct community structure (PERMANOVA p < 0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC = 0.82), and a multi-metabolite model improved classification (AUROC = 0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.
CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.}, }
@article {pmid41929767, year = {2026}, author = {Peng, W and Yang, W and Ma, L and Wang, Q and Yang, R and Ji, A and She, M and Wang, T and Gong, W and Yan, L}, title = {Flower vinegar prepared from Yunnan large-leaved tea tree prevents high-fat diet-induced obesity in mice by regulating gut microbiota.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1749951}, pmid = {41929767}, issn = {2296-861X}, abstract = {Obesity and its metabolic complications are major public health concerns. The gut microbiota plays a pivotal role in regulating host adiposity. Fermented products from Camellia sinensisvar. Assamica (Yunnan large-leaved tea) flowers, a novel food ingredient, may offer therapeutic potential, but their effects on obesity and gut microbiota remain unexplored. We investigated the anti-obesity effects of vinegar fermented from Camellia sinensisvar. Assamica flowers (TTFV) in a high-fat diet (HFD)-induced obese mouse model. Body weight, glucose and lipid metabolism, hepatic injury, steatosis, inflammation, and oxidative stress were assessed. Metabolomic analysis and metagenomic sequencing of gut microbiota were performed. Key metabolic pathways were analyzed. TTFV supplementation significantly attenuated HFD-induced body weight gain, improved glucose and lipid profiles, alleviated hepatic steatosis and injury, and reduced systemic inflammation and oxidative stress. TTFV modulated host metabolite profiles and related metabolic pathways. Crucially, TTFV reshaped the gut microbiota structure: it increased the relative abundance of Bacteroidota and decreased the Firmicutes/Bacteroidota ratio at the phylum level. At the family level, it promoted beneficial bacteria (Oscillospiraceae, Eubacteriaceae) and suppressed potentially harmful ones (Erysipelotrichaceae). Metabolic pathway analysis indicated TTFV's positive role in maintaining cellular homeostasis and regulating metabolic disturbances. Our findings demonstrate that TTFV exerts protective effects against HFD-induced obesity in mice. These benefits are closely associated with the remodeling of gut microbiota composition and the modulation of key metabolic pathways. This study is the first to report the anti-obesity potential and microbiota-regulating effects of TTFV, suggesting its promise as a functional food ingredient for promoting intestinal health and mitigating obesity-related metabolic disorders.}, }
@article {pmid41929953, year = {2026}, author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE}, title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.}, journal = {Journal of Alzheimer's disease reports}, volume = {10}, number = {}, pages = {25424823261436287}, pmid = {41929953}, issn = {2542-4823}, abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.
OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.
METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.
RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (ε4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.
CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.}, }
@article {pmid41930262, year = {2025}, author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C}, title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1757196}, pmid = {41930262}, issn = {1664-302X}, abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.}, }
@article {pmid41930266, year = {2026}, author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J}, title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag041}, pmid = {41930266}, issn = {2730-6151}, abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.}, }
@article {pmid41930333, year = {2026}, author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T}, title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.}, journal = {MedComm}, volume = {7}, number = {4}, pages = {e70705}, pmid = {41930333}, issn = {2688-2663}, abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.}, }
@article {pmid41930475, year = {2026}, author = {Tan, Y and Zou, D and Ni, C and Zeng, Q and Li, M}, title = {From Field Metagenomes to Mutant Genomes: Coevolution of Cyanophages and Synechococcus in Estuarine Ecosystems.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12277}, pmid = {41930475}, issn = {1520-5851}, abstract = {Picocyanobacteria, represented by Prochlorococcus and Synechococcus, are major photosynthetic organisms in aquatic ecosystems, and their viruses (cyanophages) significantly impact cyanobacterial ecology and evolution. Here, we combined metagenomics of Synechococcus communities along four representative estuaries in China and whole-genome analyses of laboratory-evolved Synechococcus mutants to link viral diversity to host adaptation and evolution. We assembled 83 cyanophage genomes (mainly cyanomyoviruses), with expanded auxiliary metabolic genes encoding glycosyltransferases and radical S-adenosyl methionine proteins involved in amino acid and lipopolysaccharide metabolism. Metagenome-assembled cyanobacterial genomes revealed mutations predominantly in membrane-associated functions linked to phage infection. In parallel, we identified genetic pathways conferring phage resistance in 18 evolved Synechococcus mutant strains that are resistant to phage infection. Notably, mutations in carbohydrate (rfbA) and photosynthetic energy transfer (cpeT) of Synechococcus mutants recurred in both cultured isolates and recovered metagenomes. These results indicate that cyanophages in estuaries leverage broader metabolic toolkits, while Synechococcus repeatedly evolves resistance. Together, these findings outline a reciprocal adaptive landscape that helps explain the persistence and turnover of picocyanobacterial populations in estuarine environments.}, }
@article {pmid41930516, year = {2026}, author = {Wang, W and Li, M and Liu, X and Li, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Anaerobic antimony oxidation by mine groundwater bacteria: The energy-detoxification trade off governed by carbon source and Sb concentration.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141926}, doi = {10.1016/j.jhazmat.2026.141926}, pmid = {41930516}, issn = {1873-3336}, abstract = {Microorganisms drive anaerobic antimony (Sb) oxidation and detoxification in groundwater, how carbon source (organic vs. inorganic) regulates this process and shapes microbial adaptive strategies remains unclear. To fill this knowledge gap, microcosms were conducted with groundwater from Xikuangshan mining-area, integrating with hydrochemistry, genes quantification, and metagenomics. The results demonstrated efficient anaerobic Sb(III) oxidation coupled with NO3[-] reduction, regulated synergistically by Sb concentration and carbon sources. The concentration of 0.5 mM Sb(III) served as a critical threshold that triggered changes in bacterial diversity, composition, and Sb(III)-oxidation behavior. Below this, NaHCO3 promoted higher oxidation rates (P < 0.05), linked to enrichment of Hydrogenophaga, Aquabacterium, Acidovorax, and aioA genes (Sb-oxidizing gene). Above 0.7 mM Sb(III), Na-lactate activated aioA and narrowed the rate gap, accompanied by increases in both abundance and niche of Dechloromonas. In addition, elevated Sb stress reshaped the metabolic networks across microcosms. The communities prioritized energy allocation to nitrogen fixation (nifH) with multiple benefits over redundant carbon fixation (cbbL). This research expands the known range of Sb and carbon drive microbial metabolic remodeling, advancing our predictive understanding of Sb biogeochemical cycling in contaminated aquifers.}, }
@article {pmid41930813, year = {2026}, author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S}, title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158039}, doi = {10.1016/j.phymed.2026.158039}, pmid = {41930813}, issn = {1618-095X}, abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.
PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.
METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-γ-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.
RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-κB signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-κB signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.
CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-κB signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.}, }
@article {pmid41931872, year = {2026}, author = {Ren, Z and Wen, Y and Ma, Y and Li, M and Wang, L and Yu, R and Wu, L}, title = {Species-specific salinity adaptation mechanisms drive niche partitioning of nitrite-dependent anaerobic methane oxidation bacteria in a natural wetland gradient.}, journal = {Water research}, volume = {298}, number = {}, pages = {125791}, doi = {10.1016/j.watres.2026.125791}, pmid = {41931872}, issn = {1879-2448}, abstract = {Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a key process regulating methane emissions from wetland ecosystems. However, the species-specific mechanisms that enable N-DAMO bacteria to adapt and occupy distinct niches along environmental gradients (such as salinity) remain largely unknown. This makes it difficult to predict the ecological function of these bacteria. In this study, the structure, functional diversity, and species-specific salinity adaptation mechanisms of N-DAMO bacterial community in the Ulansuhai Wetland along a natural salinity gradient were investigated. An integrated approach combining metagenomic sequencing, isotopic tracer experiment, quantitative PCR, and biogeochemical measurements was employed for this research. The results show that salinity significantly reshaped the community structure and diversity of N-DAMO bacteria, while their potential activity remained functionally stable. This functional resilience was underpinned by distinct niche partitioning among four dominant species of Candidatus Methylomirabilis, species. Each species exhibited unique genomic potential for exopolysaccharide biosynthesis, osmoregulation, and stress response. Furthermore, the N-DAMO process constituted a significant methane sink, representing 39.5% of the observed anaerobic methane oxidation activity. Path analysis further explained that salinity regulated N-DAMO bacterial communities directly and through indirect pathways mediated by soil carbon and nitrogen pools. This research provides the first mechanistic framework linking species-specific genomic traits of N-DAMO bacteria to salinity adaptation and niche partitioning. The study offers novel insights for predicting wetland methane emissions.}, }
@article {pmid41931886, year = {2026}, author = {Xiao, S and Han, Z and Tang, Y and Wu, X and Huang, J and Zeng, W}, title = {Dual roles of tetracycline-degrading bacteria in pollutant detoxification and resistome reshaping under tetracycline-copper co-contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141951}, doi = {10.1016/j.jhazmat.2026.141951}, pmid = {41931886}, issn = {1873-3336}, abstract = {Combined contamination of soils with antibiotics and heavy metals represents a growing environmental challenge, yet remediation strategies addressing their synergistic toxicity remain limited. In this study, the bioremediation potential of a tetracycline-degrading bacterial consortium (Raoultella sp. XY-1 and Pandoraea sp. XY-2) was evaluated in tetracycline-copper (TC-Cu) co-contaminated soils by integrating chemical, biological, and ecological assessments. Soil column experiments demonstrated that bioaugmentation significantly enhanced TC degradation (48.57-53.71% after 90 days) compared to uninoculated controls (<12%), while simultaneously reducing copper bioavailability by shifting acid-extractable and reducible fractions toward more stable oxidizable forms. Inoculation further alleviated the strong inhibition of soil enzymatic activities (sucrase, urease, phosphatase), reflecting improved soil functional recovery. Metagenomic sequencing revealed that TC-Cu co-contamination reshaped microbial community composition, particularly increasing the relative abundance of Actinomycetota and Campylobacterota. Bioaugmentation further facilitated the establishment of Raoultella and indirectly stimulated indigenous resistant taxa through community interactions. Correlation network analysis further revealed that Raoultella was a highly connected genus in co-occurrence networks of antibiotic resistance gene (ARG)- and metal resistance gene (MRG)-hosting genera. LC-MS detection of intermediate products during TC microbial degradation proposed three microbial degradation pathways and inferred microbial resistance mechanisms under TC-Cu coexistence. Collectively, these findings highlight that TC-degrading bacteria not only reduce pollutant toxicity but also reshape microbial and genetic landscapes in co-contaminated soils, potentially suppressing the diffusion risk of resistance genes at low TC-Cu level. This work provides novel insights into the ecological trade-offs of bioremediation and supports the development of targeted, sustainable strategies for complex antibiotic-metal pollution scenarios.}, }
@article {pmid41931897, year = {2026}, author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y}, title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141890}, doi = {10.1016/j.jhazmat.2026.141890}, pmid = {41931897}, issn = {1873-3336}, abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.}, }
@article {pmid41932005, year = {2026}, author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A}, title = {A survey of bacterial and fungal communities of table olives.}, journal = {International journal of food microbiology}, volume = {455}, number = {}, pages = {111759}, doi = {10.1016/j.ijfoodmicro.2026.111759}, pmid = {41932005}, issn = {1879-3460}, abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.}, }
@article {pmid41932427, year = {2026}, author = {Bao, C and Ren, Y and Tang, C and Su, Y and Yue, H and Chen, X}, title = {Viral Isolation and Genomic Characteristics of the First Bovine Parainfluenza Virus Type 3 Isolated from Water Buffaloes (Bubalus bubalis) in China.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106655}, doi = {10.1016/j.tvjl.2026.106655}, pmid = {41932427}, issn = {1532-2971}, abstract = {Bovine parainfluenza virus type 3 (BPIV3) is an important pathogen associated with bovine respiratory disease. In this study, we report the isolation and genomic characterization of BPIV3 from a water buffalo with respiratory symptoms in China. Virus isolation was performed using susceptible cell cultures, followed by identification via RT-qPCR, transmission electron microscopy, and indirect immunofluorescence. Metagenomic sequencing of the near-complete genome showed that the isolate shared 89.9%-91.1% nucleotide identity with BPIV3 genotype A strains. Notably, several distinct mutations were identified in the structural protein genes, and phylogenetic analysis demonstrated that the isolate formed a separate cluster within genotype A, suggesting that it may represent a novel subtype within this genotype. To our knowledge, this is the first report describing the isolation and genomic characterization of BPIV3 from water buffaloes in China. These findings provide baseline molecular data for further studies on the genetic diversity and evolution of BPIV3.}, }
@article {pmid41932524, year = {2026}, author = {Qian, J and Li, X and Xu, X and Zhang, D and Xiang, G and Wang, Z and Zhang, Z and Liu, M and Hao, W and Wu, D}, title = {Thiosulfate-Driven redox buffering enables efficient nitrogen removal and norfloxacin degradation in mixed denitrifying systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134550}, doi = {10.1016/j.biortech.2026.134550}, pmid = {41932524}, issn = {1873-2976}, abstract = {Wastewaters often contain both conventional pollutants and recalcitrant antibiotics, posing challenges to biological treatment. This study investigated a mixed autotrophic-heterotrophic denitrification system driven by sodium acetate and sodium thiosulfate for simultaneous nitrate and norfloxacin removal. A sequencing batch reactor was operated in four stages, culminating in norfloxacin exposure (0.5 mg/L). Results showed stable nitrogen removal (>95%) and norfloxacin degradation (>90%) under sustained antibiotic stress. Batch tests confirmed that the co-presence of thiosulfate and acetate enhanced norfloxacin biodegradation via co-metabolic pathways, with negligible abiotic removal. Three-dimensional excitation-emission matrix spectroscopy revealed a shift toward humic-like extracellular polymeric substances under norfloxacin, supporting biofilm integrity. 16S rRNA sequencing and metagenomics indicated dynamic microbial restructuring, with persistent core taxa (Thauera, Desulfofustis) and enrichment of stress-tolerant groups (norank_o_SJA-15). Functional analysis showed upregulation of carbon metabolism (pta, ackA), denitrification (nirS, nosZ), and sulfur oxidation (SUOX, SoxX, SoxA) genes, alongside oxidative stress mitigation genes (catB, gst) and xenobiotic degradation genes (HGD, E1.13.11.4). Antibiotic resistance gene profiles shifted toward multidrug (>29%), peptide resistance (14.0%→15.4%), and glycopeptide resistance (7.0%→9.4%), dominated by multidrug efflux and target alteration mechanisms, enabling community resilience while minimizing energetically costly defenses. This work elucidates the synergistic roles of dual electron donors in pollutant co-removal and stress mitigation, offering a robust, sustainable strategy for treating antibiotic-laden wastewater.}, }
@article {pmid41932525, year = {2026}, author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J}, title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134546}, doi = {10.1016/j.biortech.2026.134546}, pmid = {41932525}, issn = {1873-2976}, abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-l-Proline, l-Histidine, and Hypaphorin, with l-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.}, }
@article {pmid41932647, year = {2026}, author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L}, title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2026.03.023}, pmid = {41932647}, issn = {1673-8527}, abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.}, }
@article {pmid41932883, year = {2026}, author = {Silva, RMB and Slyvka, A and Lee, YJ and Guan, C and Lund, SR and Raleigh, EA and Skowronek, K and Kuska, MS and Bochtler, M and Weigele, PR}, title = {A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70671-1}, pmid = {41932883}, issn = {2041-1723}, support = {FNP, POIR.04.04.00-00-5D81/17-00//Fundacja na rzecz Nauki Polskiej (Foundation for Polish Science)/ ; }, abstract = {Nucleic acid modifying enzymes drive diverse defense and counter-defense measures in the evolutionary arms race between viruses and their cellular hosts. Abundant and widespread bacterial viruses (bacteriophage or phage) encode for biosynthetic pathways that install elaborate DNA hypermodifications which protect their genomic DNA from host endonucleases. Here, we establish the molecular basis for the multistep biosynthesis of 6-aminocarboxymethyl-2'-deoxyadenosine (6-NcmdA), a nucleobase hypermodification found in the virion DNA of bacteriophage Mu that leads to restriction evasion in the context of phage-host conflicts. In the first step, we show that Mu-encoded Mom enzyme catalyzes the formation of 6-NcmdA by transferring glycine from charged tRNA[Gly] to the N6 position of adenine within double-stranded DNA. We uncover a second step where the glycyl-dA intermediate undergoes an on-base rearrangement to form 6-NcmdA. Examination of the proposed reaction pathways by quantum chemical calculations confirms the instability of acyl exocyclic groups at N6-adenine and reveals an energetically favorable orientation of 6-NcmdA that restores canonical base pairing. An X-ray structure confirms Mom is a member of the GNAT superfamily and suggests binding sites for both tRNA and DNA. Guided by the Mom structure and patterns of sequence conservation across metagenomic space, we show residues R111 and S124 are essential for catalysis. This work demonstrates that the Mom enzyme defines a new category of acetyltransferases utilizing charged tRNA to modify DNA.}, }
@article {pmid41932890, year = {2026}, author = {Zhao, L and Zheng, J and Shen, Y and Xu, X and Liu, X and Yu, J and Li, J and Yang, B and Chen, L and Wang, F and Liu, S and Peng, X and Du, J and Dong, R}, title = {Composite polyphenols mitigate microplastic exposure-related immune disturbances: a two-phase population trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71167-8}, pmid = {41932890}, issn = {2041-1723}, abstract = {Microplastics (MPs) are widespread, making it urgent to elucidate their toxicity and identify intervention strategies. Here, we designed a two-phase population trial, comprising a baseline pilot population (n = 151) and a 28-day randomized, double-blind, placebo-controlled trial (n = 98). Primary outcomes include fecal MP concentration and blood parameters (complete blood count, glycemic and lipid, and cytokines), with exploratory outcomes comprising fecal metagenomics and plasma metabolomics. The median MP concentration in 151 participants' fecal samples is 158.28 μg/g dry weight, correlating with levels of 7 inflammatory indexes, 4 cytokines, and 2 lipid indicators. Composite polyphenols (CP) significantly reduced plasma levels of IL-1β (P = 0.045, effect sizes = -0.463), IL-6 (P = 0.023, effect sizes = -0.576) and IL-8 (P = 0.022, effect sizes = -0.529). 507 differentially expressed microbiotas (DEMs; P < 0.05) and 144 significantly different metabolites (SDMs; P-FDR < 0.25, VIP ≥ 1) are observed between the high and low MP exposure groups; 108 DEMs and 85 SDMs are identified following CP intervention. Notably, CP could mitigate the pro-inflammatory effects of high MP exposure by modulating gut microbiota and up-regulating glycerophospholipid metabolism and arginine biosynthesis. The gut bacteria Staphylococcus and the plasma metabolite PC (22:5/0:0) are identified as potential mediators in this protective effect. Trial registration: ClinicalTrials.gov: NCT06437119.}, }
@article {pmid41932913, year = {2026}, author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M}, title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00976-y}, pmid = {41932913}, issn = {2055-5008}, abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.}, }
@article {pmid41933095, year = {2026}, author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W}, title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44972-w}, pmid = {41933095}, issn = {2045-2322}, abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.}, }
@article {pmid41933201, year = {2026}, author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB}, title = {Unbinned contigs expand known diversity in the global microbiome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41933201}, issn = {2058-5276}, support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.}, }
@article {pmid41933302, year = {2026}, author = {Wu, L and Pu, J and Xi, X and Bao, Y and Luo, L}, title = {Streptomyces morookaense spinal suppurative infection: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13238-1}, pmid = {41933302}, issn = {1471-2334}, support = {2025M781412//The China Postdoctoral Science Foundation/ ; }, abstract = {PURPOSE: Streptomyces species are ubiquitous soil actinomycetes and a major source of antibiotics, but invasive human infection with spinal involvement is exceedingly rare and may mimic tuberculous or fungal spondylodiscitis. We report a thoracic suppurative vertebral infection caused by Streptomyces morookaense and highlight an integrated diagnostic approach.
METHODS: A 66-year-old woman with no known immunodeficiency developed progressive thoracic back pain one month after severe trauma with open wounds. CT/MRI showed osteolytic endplate destruction at T3-T4 with paravertebral abscess formation. Fluoroscopy-guided percutaneous biopsy of the T4 vertebral body was performed for histopathology, culture, and metagenomic next-generation sequencing (mNGS).
RESULTS: Histopathology demonstrated fibrinous exudate, necrosis, and inflammatory granulation tissue with fragmented trabeculae, without granuloma or caseous necrosis; acid-fast staining was negative. Vertebral tissue culture grew Streptomyces spp, and mNGS identified high-abundance sequences matching S. morookaense. Intravenous piperacillin/tazobactam led to rapid pain relief and normalization of inflammatory markers within one week, and no recurrence was observed during follow-up.
CONCLUSION: This case suggests that Streptomyces morookaense has the potential to involve the thoracic spine in immunocompetent individuals. For unexplained spinal infections with negative routine tests, percutaneous vertebral sampling with integrated interpretation of pathology, culture, and mNGS can improve detection of rare pathogens and help avoid inappropriate empirical therapy.}, }
@article {pmid41933424, year = {2026}, author = {Zhao, Y and Wang, Z and Fan, D and Zhang, J and Tu, Y and Diao, Q and Cui, K}, title = {Gut microbiota-driven IL-17/PPAR axis mediates epigallocatechin-induced intestinal repair in weaned lambs.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41933424}, issn = {1674-9782}, support = {2024YFD1300204//National Key Research and Development Program of China/ ; 32172764//National Natural Science Foundation of China/ ; 25036//Agricultural Science Technology Project of Shijiazhuang/ ; }, abstract = {BACKGROUND: Early weaning is a key strategy to improve lamb production efficiency; however, it inevitably compromises intestinal barrier integrity and function. This study aimed to investigate the effects of epigallocatechin (EGC) on growth performance and intestinal barrier function in weaned lambs, using metagenomics, metabolomics, and intestinal transcriptomics to elucidate the underlying mechanisms.
RESULTS: Weaning induced oxidative stress, inflammation, and metabolic disruptions in the jejunum. Supplementation with 12.5 mg/kg EGC (LE) significantly improved growth performance, reduced diarrhea incidence (P < 0.05), enhanced mucosal antioxidant capacity (P < 0.001), and strengthened anti-inflammatory ability (P < 0.001). Metagenomic analysis showed that the LE intervention enriched Ruminococcus spp. and reduced the abundance of Slackia. This microbial shift was associated with elevated luminal concentrations of valeric acid and microbial metabolites derived from EGC. Transcriptomic profiling revealed that the intervention upregulated the PPAR signaling pathway, which supports nutrient metabolism and barrier repair. Concurrently, it attenuated aberrant IL-17 signaling and promoted the restoration of mucosal immune homeostasis, indicating a resolution of excessive inflammatory responses.
CONCLUSIONS: Supplementation with 12.5 mg/kg EGC alleviates weaning stress by fostering a beneficial gut microbiota and promoting the production of specific metabolites. These changes reactivate PPAR mediated epithelial repair and dampen pathological immune activation. Low-dose EGC is an effective nutritional strategy to improve intestinal health and growth in weaned ruminants.}, }
@article {pmid41542635, year = {2026}, author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA}, title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41542635}, issn = {2692-8205}, support = {F31 DK138748/DK/NIDDK NIH HHS/United States ; R21 AI173448/AI/NIAID NIH HHS/United States ; F31 HD117458/HD/NICHD NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI055449/AI/NIAID NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; }, abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS carriage in the vaginal tract is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D paired with vaginal GBS colonization to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokine profiles at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to an array of eight pro-inflammatory cytokines post-GBS infection. Pairing cytokine observations with GBS colonization outcomes revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS vaginal colonization. Supplementation with intravaginal rIL-1α was sufficient to resolve GBS burden differences between diabetic mice and non-diabetic controls, confirming that deficient vaginal cytokine responses contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention in the susceptible diabetic population.}, }
@article {pmid41663924, year = {2026}, author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y}, title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.}, journal = {BMC microbiology}, volume = {26}, number = {}, pages = {}, pmid = {41663924}, issn = {1471-2180}, support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; }, abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling.
RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P < 0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P < 0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P < 0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI.
CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04788-0.}, }
@article {pmid41666437, year = {2026}, author = {Kohsar, M and Haar, M and Schmidt-Chanasit, J and Ramharter, M and Buchholz, BM and Krasemann, S and Bernreuther, C and Cadar, D and Omansen, TF and Wichmann, D and Ko, LM and Jordan, S}, title = {Fatal Dengue Fever in a Traveler Returning from Togo to Germany.}, journal = {The American journal of tropical medicine and hygiene}, volume = {114}, number = {4}, pages = {720-723}, pmid = {41666437}, issn = {1476-1645}, mesh = {Humans ; *Travel ; *Dengue/complications/diagnosis ; Fatal Outcome ; Germany ; Togo ; Male ; *Liver Failure, Acute/virology ; Adult ; }, abstract = {A previously healthy traveler of Togolese origin visiting friends and relatives presented with severe dengue complicated by acute liver failure. Despite intensive care management and listing for high-urgency liver transplantation, the patient succumbed to the disease. This case highlights the risk for life-threatening travel-related complications of dengue.}, }
@article {pmid41736110, year = {2026}, author = {Pirolo, M and Sherwani, MK and Espinosa-Gongora, C and Eriksen, EØ and Tassinato, C and Alberdi, A and Guardabassi, L}, title = {Faecal microbiome profiling uncovers putative biomarkers for piglets resilient to post-weaning diarrhoea.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41736110}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a major health and economic concern in intensive pig production. In this study, we hypothesized that the faecal microbiome, sampled before disease onset, could provide early prognostic markers of PWD risk and applied a machine-learning framework to identify biomarkers predictive of piglet susceptibility or resilience to PWD. At two Danish commercial farms experiencing PWD outbreaks, four pens per farm were monitored for 14 days post-weaning, with daily clinical assessments and rectal swabs collected every other day. In a nested case–control design, we profiled 140 samples from 41 piglets that developed PWD and 82 samples from 16 piglets that remained healthy by 16S rRNA sequencing. Additionally, we performed shotgun metagenomics on 56 pre-diarrhoeic samples from susceptible piglets and 47 from resilient piglets. A random-forest classifier with recursive feature elimination identified metagenome-assembled genomes (MAGs) predictive of resilience or susceptibility, trained and cross-validated independently within each farm. Negative binomial zero-inflated mixed (NBZIM) models assessed associations with known PWD risk factors (e.g. birth/weaning weights, weaning age and dam parity).
RESULTS: Prior to diarrhoea onset, microbial community structures differed significantly between resilient and susceptible piglets at both farms (PERMANOVA, p < 0.05). Feature-reduced models achieved high accuracy (AUC = 0.94 and 0.82 in Farm A and Farm B, respectively) and identified 10 and 13 MAGs enriched in resilient piglets, and one and two MAGs enriched in susceptible piglets from the two farms, respectively. All MAGs were farm-specific, highlighting the multifactorial aetiology of PWD. NBZIM models indicated that most predictive MAGs were independent of established PWD risk factors. Temporally, these MAGs peaked in relative abundance early after weaning (day 4 in Farm A; day 0 in Farm B). In the farm with unclear aetiology, functional analysis showed that susceptibility-associated MAGs were depleted for arginine/ornithine and vitamin (cobalamin, thiamine) biosynthesis and lactate production traits, suggesting metabolic dysbiosis.
CONCLUSIONS: Our findings indicate that pre-diarrhoeic faecal microbiome signatures predict PWD risk and provide a foundation for early prognostic tools and targeted interventions, including probiotic development, to mitigate PWD and reduce reliance on antimicrobials in pig production.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00522-3.}, }
@article {pmid41742048, year = {2026}, author = {Zhang, Y and Wangjia, P and Yang, S and Liu, P and Xu, X and Han, H}, title = {Bartonella quintana endocarditis presenting with severe coombs-positive anemia: a case report.}, journal = {BMC cardiovascular disorders}, volume = {26}, number = {1}, pages = {}, pmid = {41742048}, issn = {1471-2261}, support = {XZ202501ZR0145//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402030(W)//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402105(W)//Natural Science Foundation of Tibet Autonomous Region/ ; }, abstract = {BACKGROUND: Bartonella quintana is a recognized cause of blood culture-negative endocarditis, often associated with predisposing social factors or pre-existing valvulopathy. Diagnosis is challenging and relies on advanced microbiological techniques.
CASE PRESENTATION: A 17-year-old Tibetan herdsman from a high-altitude region presented with a two-week history of fever, dyspnea, and lower limb edema. He had no history of homelessness or alcoholism but lived in poor sanitary conditions. Laboratory investigations revealed severe Coombs-positive hemolytic anemia and serological markers suggestive of systemic lupus erythematosus (SLE). Transthoracic echocardiography showed vegetations on both aortic (bicuspid) and mitral valves with severe regurgitation and rapid hemodynamic progression. All blood cultures were negative. Metagenomics Next-Generation Sequencing (mNGS) of peripheral blood identified B. quintana as the causative pathogen. Antibiotic therapy was adjusted to doxycycline (9 weeks) and gentamicin (3 weeks). Concurrently, immunomodulatory therapy with methylprednisolone and intravenous immunoglobulin was administered for the hemolytic anemia. Given the severe valvular insufficiency, the patient successfully underwent urgent aortic and mitral valve replacement. His clinical condition improved significantly post-operatively.
CONCLUSION: This case highlights the diagnostic utility of mNGS in confirming B. quintana endocarditis in a culture-negative scenario, especially when clinical presentation is complicated by concomitant autoimmune features mimicking Libman-Sacks endocarditis. A treatment strategy combining targeted antibiotics for the infection and immunomodulation for the hematologic complication, followed by definitive surgery, led to a successful outcome. It underscores that B. quintana infection should be considered in patients from disadvantaged backgrounds with endocarditis, even in the absence of classic risk factors.}, }
@article {pmid41749306, year = {2026}, author = {Liu, Z and Liu, M and Chen, H and Li, S and Zheng, N and Xing, G and Zhang, Y and Xu, J and Li, M and Xiao, C and Lu, T and Yan, Q and Lei, Z and Feng, M and Li, Y}, title = {Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancer.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41749306}, issn = {1479-5876}, abstract = {BACKGROUND: The gut microbiota is a key modulator of immune checkpoint inhibitor (ICI) efficacy, yet the contribution of the gut virome remains poorly defined, particularly in advanced non–small cell lung cancer (NSCLC). Here, we characterized the gut virome and explored its potential role in shaping response to PD-1 blockade.
METHODS: We performed metagenomic virome profiling of fecal samples from 338 advanced NSCLC patients treated with PD-1 inhibitors and evaluated model generalizability in an independent external cohort (n = 30). Viral diversity, taxonomic composition, and functional potential were analyzed. Virus–bacteria co-occurrence networks were constructed, and random forest classifiers were developed to predict treatment response.
RESULTS: Viral Shannon diversity decreased progressively with poorer clinical response, and β-diversity analyses revealed distinct virome community structures between responders (R) and non-responders (NR). Differential abundance analysis identified 194 NR-enriched vOTUs, predominantly assigned to Peduoviridae and Inoviridae, and 594 R-enriched vOTUs, mainly from Herelleviridae and Microviridae. Host prediction indicated that NR-enriched vOTUs frequently targeted bacterial genera such as Clostridium_M, Bacteroides, and Escherichia, whereas R-enriched vOTUs targeted beneficial genera such as Faecalibacterium and Roseburia. Network analyses further revealed response-specific virus–bacteria interaction modules. Functional profiling showed that NR-enriched vOTUs were associated with metabolic functions, including K01689 (eno; enolase). A virus-only random forest model outperformed a bacterium-only model in predicting response (area under the curve [AUC] = 0.768 vs. 0.664) and maintained superior performance in the external cohort (AUC = 0.742). In addition, Akkermansia muciniphila positivity was associated with a higher-diversity, responder-favorable virome configuration.
CONCLUSIONS: The gut virome undergoes marked remodeling during anti–PD-1 therapy in advanced NSCLC and displays distinct taxonomic, ecological, and functional signatures associated with clinical outcome. These findings support the gut virome as a strong predictor of ICI response and highlight its potential as both a biomarker and a therapeutic target.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07900-0.}, }
@article {pmid41761072, year = {2026}, author = {Costa, J and Pascoal, F and Baptista, MS and Hop, H and Assmy, P and Wold, A and Magalhães, C and Duarte, P}, title = {Comparative analysis of prokaryotic communities, hydrography, and biogeochemistry in Atlantic vs non-Atlantic influenced Svalbard fjords.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41761072}, issn = {1471-2180}, abstract = {BACKGROUND: Fjords in Svalbard are undergoing significant changes due to climate warming. Those along the west coast of Spitsbergen are particularly affected by the increasing influence of “warm” Atlantic Water (AW), a process known as Atlantification. We compared Kongsfjorden, a relatively “warm” fjord on the west coast, with Rijpfjorden, a typical cold Arctic fjord on the north coast of Nordaustlandet, combining physical and biogeochemical data with 16S rRNA gene amplicon and shotgun metagenomic sequencing. We hypothesize that differences in fjords’ water masses and prokaryotic communities provide insight into the effects of Atlantification as it expands eastwards along the shelf north of Svalbard.
RESULTS: We found that warm AW dominated in Kongsfjorden, whereas Rijpfjorden was dominated by cold Arctic Water and Winter Cooled Water. Our results suggest that the Atlantic-influenced Kongsfjorden is a nutrient sink, whereas Rijpfjorden showed similar behavior only in 2016, a particularly warm year, otherwise no clear sink/source role could be identified. Analysis of 16S rRNA gene sequences revealed that Proteobacteria had higher relative abundances in Kongsfjorden while Bacteroidota dominated in Rijpfjorden. Ammonium and nitrite-oxidizing prokaryotes were most prevalent in deeper water masses of both fjords. The archaeal taxa of the ammonia-oxidizing community, mainly Nitrosopumilus and Nitrosopelagicus, were consistently more dominant than ammonium and nitrite-oxidizing bacteria. Denitrification and nitrogen fixation genes differed between the fjords, with Kongsfjorden having a higher coverage of diazotroph genes.
CONCLUSIONS: Kongsfjorden and Rijpfjorden displayed distinct hydrographic conditions, with Kongsfjorden being under a stronger influence of Atlantification. Our results suggest that warmer water masses are linked to higher nutrient uptake. The clear association between microbial communities and water masses offers insight into changes driven by Atlantification.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04821-2.}, }
@article {pmid41862737, year = {2026}, author = {Liu, L and Yu, QQ and Zhang, YL and Zhou, JT and Jin, Y and Jiang, CH and Zhuang, S and Wei, J and Li, P and Miao, H and Zhao, YY}, title = {Renal fibrosis is induced by hyperactive Wnt/β-catenin pathway via microbial-mediated tryptophan metabolism-driven AhR signaling in rodents and humans.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41862737}, issn = {1420-9071}, support = {82274079//National Natural Science Foundation of China/ ; 82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Key Science and Technology Program of Shaanxi Province/ ; }, abstract = {UNLABELLED: Renal fibrosis is a common pathological endpoint in progressive chronic kidney disease (CKD). Clinical evidence indicates that a decline in renal function is more closely associated with tubulointerstitial fibrosis (TIF) than with glomerular injury. Recent advances in multi-omics technologies have provided powerful tools for uncovering unrecognized disease molecular mechanisms. Metagenomic and metabolomic analyses were performed to profile the fecal microbiota and serum metabolites, respectively, and to identify tubulointerstitial damage (TID)-related bacterial taxa and metabolites. Identified serum metabolites were also determined in healthy controls and tubulointerstitial nephropathy (TIN) patients. The expression of aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling–related genes and proteins was evaluated in obstructed kidney of unilateral ureteral obstruction (UUO) rats and AhR shRNA-treated UUO mice as well as in 1-hydroxypyrene (HP)-stimulated HK-2 cells untreated or treated with AhR shRNA. UUO induced progressive TID and TIF in rats. Alterations in gut microbiota composition, particularly changes in Enterocloster aldenensis (E. aldenensis) and Lactobacillus acidipiscis (L. acidipiscis), were strongly correlated with TID. In parallel, microbial-derived tryptophan catabolites (MDTCs), including tryptamine, indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), indole-3-acrylic acid, indole-3-aldehyde (IAld), and indoxyl sulfate were strongly associated with TID severity. Linear regression analyses revealed correlation coefficients exceeding 0.80 between E. aldenensis and IAA, ILA, and IPA, and between L. acidipiscis and IAld, indicating close relationships with progressive TIF. Similarly, the changes of 14 MDTCs were further demonstrated in TIN patients and they could separate TIN patients form healthy controls. Some MDTCs showed strongly correlation with estimated glomerular filtration rate in TIN patients and high values of area under the curve, sensitivity and specificity. These microbial and metabolic alterations were accompanied by activation of the AhR–Wnt/β-catenin signaling pathway. By contrast, AhR shRNA treatment inhibited mRNA expression of AhR and its downstream target genes, including cytochrome P450 family 1 subfamily A member 1 (CYP1A1), CYP1A2, CYP1B1 and cyclooxygenase-2 accompanied by suppressing nuclear AhR localization, retarded protein expression of Wnt1, β-catenin and Twist, enhanced E. aldenensis and L. acidipiscis abundances and reversed MDTC dysregulation in UUO mice. Bioactivity-directed isolation and identification demonstrated that polyporusterone A (PPA) from Polyporus umbellatus increased abundance of E. aldenensis and L. acidipiscis and normalized dysregulated MDTCs in UUO rats. PPA treatment suppressed intrarenal AhR signaling and Wnt1/β-catenin pathway. Consistent effects were observed in HP-induced HK-2 cells treated with PPA; however, AhR knockdown partially attenuated these inhibitory effects. Taken together, this study first demonstrated that the enrichment of pathogenic bacteria and depletion of probiotics-mediated dysregulation of MDTCs is closely linked to the activation of the AhR–Wnt/β-catenin signaling axis in UUO rat model. Targeting GM may represent a promising therapeutic strategy for CKD and renal fibrosis.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06176-3.}, }
@article {pmid41923365, year = {2026}, author = {Merritt, B and Ratcliff, JD and Ta, S and Osis, G and Mauldin, MR and Thielen, PM}, title = {TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag119}, pmid = {41923365}, issn = {1367-4811}, abstract = {MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score.
RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest.
Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41923466, year = {2026}, author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC}, title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70324}, pmid = {41923466}, issn = {1758-2229}, support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; }, mesh = {*Phytophthora/genetics/isolation & purification ; *Soil Microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Forests ; *Microbiota ; Plant Diseases/microbiology/parasitology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Nucleic Acid Amplification Techniques ; Phylogeny ; }, abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.}, }
@article {pmid41923582, year = {2026}, author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A}, title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.}, journal = {Journal of diabetes research}, volume = {2026}, number = {1}, pages = {e9317962}, pmid = {41923582}, issn = {2314-6753}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/complications/blood ; Pilot Projects ; Middle Aged ; *Dyslipidemias/microbiology/blood ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Adult ; Bacteria/genetics/classification ; }, abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.}, }
@article {pmid41923636, year = {2026}, author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK}, title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.011}, pmid = {41923636}, issn = {1934-6069}, abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.}, }
@article {pmid41923798, year = {2026}, author = {Ibisanmi, TA and Jiang, X and Willcox, M and Kumar, N}, title = {Recent advances in computational antimicrobial peptide discovery through big data, modeling, and artificial intelligence and their interplay in ushering the next golden era of drug development.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1749404}, pmid = {41923798}, issn = {2673-7647}, abstract = {The accelerating antimicrobial resistance (AMR) crisis continues to render more and more conventional antibiotics ineffective. Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics due to their broad-spectrum activity, diverse mechanisms of action, and lower propensity for resistance. Traditional discovery approaches face limitations arising from the vast sequence space and the challenge of balancing efficacy with low toxicity. Addressing these challenges is critical for developing next-generation antimicrobial agents, and computational methods are increasingly driving progress. Public repositories, and techniques such as molecular docking enable in silico evaluation of peptide target interactions, identifying candidates with strong binding potential. Molecular dynamics (MD) simulations offer deeper insights into how AMPs disrupt membranes, form pores, or act synergistically, while Steered MD extends this to probing membrane penetration. Artificial intelligence (AI) methods, including machine learning and deep learning, capture complex sequence activity relationships, predict novel AMPs from genomic and metagenomic data, and design new peptides de novo using generative models. Despite rapid advances, most existing reviews treat these approaches in isolation, leaving a fragmented understanding of their interplay. This paper addresses that gap by unifying computational strategies, highlighting synergies, and critiquing limitations. Ultimately, integrating these methodologies offers a path toward more efficient AMP discovery to fight AMR.}, }
@article {pmid41923934, year = {2026}, author = {Dhawi, F and Alsanie, SI}, title = {Contrasting leaf transcriptomic responses to drought and heat stress in the desert CAM species Mesembryanthemum forsskalii.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1805066}, pmid = {41923934}, issn = {1664-462X}, abstract = {INTRODUCTION: Dryland ecosystems are increasingly exposed to extreme heat and prolonged water limitation. Facultative crassulacean acid metabolism (CAM) enables certain desert plants to enhance water-use efficiency and adjust carbon assimilation under stress conditions. Mesembryanthemum forsskalii Hochst. ex Boiss. (Aizoaceae; locally known as Samh) is a hyper-arid adapted species native to Saudi Arabia, yet genomic and transcriptomic resources for this plant remain scarce. This study aimed to generate foundational genomic resources and characterize transcriptional responses to drought and heat stress.
METHODS: We integrated rhizosphere metagenomics and leaf transcriptomics. A genome-resolved rhizosphere metagenome was generated from mature field-grown plants. In parallel, micropropagated plants were exposed under controlled conditions to progressive drought (17 days without irrigation) or acute heat shock (55 °C for 120 min), each compared with well-watered controls. RNA sequencing generated 123.77 Gb raw data and 121.96 Gb clean reads after quality filtering. Differential gene expression was identified using thresholds of |log2FC| ≥ 2 and FDR ≤ 0.05, followed by transcription factor profiling and KEGG pathway annotation.
RESULTS: Heat stress induced substantially broader transcriptional reprogramming than drought. A total of 1,348 genes were differentially expressed under heat stress, compared with 84 genes under drought. Heat exposure strongly increased the expression of transcription factor families including B3 (20.00-fold relative to drought), bHLH (22.65-fold), and bZIP (8.94-fold). KEGG pathway analysis revealed expanded representation of metabolic pathways under heat, including secondary metabolite biosynthesis, ribosome function, carbon metabolism, and endoplasmic reticulum protein processing. Rhizosphere binning recovered archaeal and bacterial genomes affiliated with stress-tolerant lineages, providing the first microbial genomic framework associated with M. forsskalii.
DISCUSSION: These results demonstrate a heat-dominant transcriptional response in M. forsskalii and provide the first integrated transcriptomic and rhizosphere metagenomic resources for this desert facultative CAM species. Heat-inducible transcription factors, particularly B3 and NAC families, emerge as promising targets for improving thermotolerance and water-use efficiency in crops.}, }
@article {pmid41924127, year = {2026}, author = {Booker, AE and Fei, C and Amin, SA and Custer, J and Watkins, K and Yaeger, W and Ahn, SH and Vidyarathna, NK and Burns, A and Klass, S and Glibert, PM and Heil, CA and Schulz, F and Martínez Martínez, J}, title = {Complex viral interactions revealed for the harmful bloom-forming dinoflagellate Karenia brevis.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag051}, pmid = {41924127}, issn = {2730-6151}, abstract = {Karenia brevis regularly forms harmful blooms along the West Florida Shelf that negatively affect marine and terrestrial organisms through toxin production. These blooms impose economic and environmental hardship, driving the need for research to understand the factors influencing their dynamics and to mitigate their impacts. A mostly unresolved issue is the potential role of viruses in bloom termination. We conducted an experiment incubating K. brevis cultures with size-fractionated bloom water samples. Flow cytometry revealed giant virus-like populations (VLPs) in replicate cultures with <1 μm-filtered and <0.2 μm-filtered bloom water. The VLPs' abundance was paralleled by declines in photoefficiency and culture lysis. Metagenomic analyses of the lysates revealed 11 giant virus genomes (35%-100% complete) representing 7 viral operational taxonomic units (vOTUs) within the order Imitervirales (Nucleocytoviricota). Ten of these vOTUs were more abundant in the incubations with <0.2 μm-filtered bloom water, coinciding with the absence or low abundance of algicidal bacteria. The vOTUs and K. brevis cell abundances showed a positive correlation at a coastal site during bloom and nonbloom periods. The most apparent association was to vOTU6, which may owe its competitive advantage to the presence of the auxiliary metabolic genes bacteriorhodopsin, carbonic anhydrase, and dinoflagellate viral nucleoprotein. The metagenomes also contained polinton-like virus (PLV) genomes. Since many PLVs are hypothesized to depend on co-infection with Nucleocytoviricota viruses for their propagation, our results suggest complex viral interactions within K. brevis blooms. Future research to elucidate virus-bacteria-K. brevis interaction mechanisms may be key to understanding bloom dynamics and developing management tools.}, }
@article {pmid41924306, year = {2026}, author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D}, title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2622259}, pmid = {41924306}, issn = {2993-3935}, abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.}, }
@article {pmid41924310, year = {2026}, author = {Chen, X and Wang, N and Jiang, C and Luo, S and Cheng, M and Chu, D and Hu, C and Zhang, P and Chen, K and Yang, F and Xiong, J and Ning, K and Miao, W}, title = {Data Mining of Sediment Microbiomes of the Tibetan Plateau Revealed a Genomic Repository of Ancient Lineages and Adaptive Evolution of Asgardarchaeota.}, journal = {Research (Washington, D.C.)}, volume = {9}, number = {}, pages = {1213}, pmid = {41924310}, issn = {2639-5274}, abstract = {The extreme climatic conditions of the Tibetan Plateau foster unique microbial communities, especially in the sediment ecosystem. A thorough understanding of these communities could facilitate revealing their microbial diversity, biological resources, and response to climate change. Here, we have constructed the Tibetan Plateau Microbial Catalog of Sediment (TPMC-S) based on 248 metagenomic sediment samples from the Tibetan Plateau. We identified 511,056,752 nonredundant genes and recovered 13,696 metagenome-assembled genomes with enormous phylogenetic novelty (over 90% novel species), far exceeding other contemporary Tibetan microbial catalogs and expanding the microbial functional diversity. We also revealed that similarities of sediment microbial communities followed the distance-decay relationship. Furthermore, sediments contained a high proportion of evolutionarily "possible ancient species (PAS)" compared with paired aquatic samples, especially ancient archaeal lineages, suggesting a microbial "sedimentary archive" in sediment. Finally and most importantly, Asgardarchaeota, including 2 potentially novel genera, were identified from the sediments, and their latest divergence predated the uplift of the Tibetan Plateau, while they still gained functions to adapt to extreme environments. Our findings positioned the Tibetan Plateau as both a genomic repository of microbial antiquity, especially Asgardarchaeota, and an active arena for modern extremophile innovation, providing insights for deciphering microbial resilience strategies in climate-sensitive ecosystems and informing novel bioprospecting efforts.}, }
@article {pmid41924424, year = {2026}, author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Sangtian, M and Panmontha, W and Bunlungsup, S and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sriswasdi, S and Viangteeravat, T}, title = {Correction: Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1817909}, doi = {10.3389/fcimb.2026.1817909}, pmid = {41924424}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2026.1751074.].}, }
@article {pmid41924426, year = {2026}, author = {Pan, Y and Du, N and Liu, Y and Wu, M and Hao, S and He, Y and Jiang, Y}, title = {Clinical features of Tropheryma Whipplei in pediatric pneumonia: an mNGS and tNGS-based case-control study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1753963}, pmid = {41924426}, issn = {2235-2988}, mesh = {Humans ; Case-Control Studies ; Male ; Female ; *Tropheryma/genetics/isolation & purification ; Child, Preschool ; Child ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; *Whipple Disease/microbiology/pathology ; *Pneumonia/microbiology ; Mycoplasma pneumoniae/isolation & purification ; Coinfection/microbiology ; Adolescent ; }, abstract = {INTRODUCTION: Tropheryma whipplei (TW), which causes Whipple disease, has recently been associated with respiratory diseases, particularly pneumonia. To understand its role in pediatric pneumonia, this study analyzed the clinical and pathogenetic characteristics of TW in pediatric pneumonia patients.
METHODS: We utilized metagenomic and targeted next-generation sequencing (mNGS/tNGS) data from 3,759 pediatric bronchoalveolar lavage fluid (BALF) samples (2023-2024). This case-control study included 103 TW-positive pediatric pneumonia patients (59 with severe pneumonia, SPTW+; 44 with mild pneumonia, MPTW+), along with 206 TW-negative pneumonia patients as controls (118 with severe pneumonia, SPTW-; 88 with mild pneumonia, MPTW-).
RESULTS: Through inter-group comparisons, the results showed that TW-positive patients were younger and had lower BMIs than controls, with shorter hospital stays and milder inflammation. Severe TW-positive cases showed more localized right-lung lesions, less pleural effusion, and more bronchial involvement. Mycoplasma pneumoniae co-detection was frequent (86.4%), along with Moraxella catarrhalis, human bocavirus type 1, and rhinovirus A.
DISCUSSION: TW-positive pediatric pneumonia presents with milder symptoms, suggesting that TW may act as a colonizer rather than a primary pathogen. Consequently, antimicrobial treatment specifically targeting TW may not be immediately warranted at detection. These results provide important insight for the individualized treatment of pediatric pneumonia with TW positive.}, }
@article {pmid41925105, year = {2026}, author = {Zu, S and Yu, X and Song, J and Xiao, Y and Yi, H and Li, H}, title = {The Role of Gut Microbiota and Their Derived Metabolites in Chemotherapy-Induced Nausea and Vomiting in Ovarian Cancer.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71752}, doi = {10.1002/cam4.71752}, pmid = {41925105}, issn = {2045-7634}, support = {2023QH1193//Startup Fund for Scientific Research, Fujian Medical University/ ; YCXH 22-10//Nursing Research Special Fund of Fujian Maternal and Child Health Hospital/ ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Animals ; Humans ; Rats ; Middle Aged ; *Ovarian Neoplasms/drug therapy ; Rats, Sprague-Dawley ; *Vomiting/chemically induced/microbiology/metabolism ; *Nausea/chemically induced/microbiology/metabolism ; Dysbiosis/microbiology ; *Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Cisplatin/adverse effects/administration & dosage ; Metabolomics ; Fecal Microbiota Transplantation ; Aged ; Carboplatin/adverse effects/administration & dosage ; Feces/microbiology ; Paclitaxel/adverse effects/administration & dosage ; Metabolome ; Adult ; }, abstract = {OBJECTIVE: This study aimed to investigate the relationship between gut microbiota and chemotherapy-induced nausea and vomiting (CINV) in patients with ovarian cancer undergoing platinum-based chemotherapy (carboplatin or cisplatin combined with paclitaxel).
METHODS: Clinical data and fecal samples were collected from patients with ovarian cancer after admission but prior to the initiation of their first chemotherapy cycle. Patients were divided into the CINV (n = 25) and non-CINV (n = 25) groups on the basis of symptoms occurring after chemotherapy. No additional samples were collected during chemotherapy. Integrated metagenomic sequencing and untargeted metabolomic profiling identified CINV-associated microbial taxa and metabolites. Additionally, fecal microbiota transplantation (FMT) in SD rats validated causal links between gut dysbiosis and CINV pathogenesis.
RESULTS: Bacteroides caccae, Corynebacteriales, and Corynebacterium were significantly enriched in the CINV group. KEGG enrichment revealed upregulated pathways in CINV, including focal adhesion, lysosome function, and eukaryotic cellular communities. Metabolomic analysis identified 19 significantly increased metabolites in the fecal samples of CINV patients versus 10 in non-CINV controls. KEGG enrichment revealed that the pentose phosphate pathway, glutathione metabolism, and lipoic acid metabolism were significantly implicated in CINV pathogenesis. Multi-omics integration revealed Bacteroides sp. A1C1 strongly correlated with hesperetin, arbutin, orciprenaline, and myristolic acid. In rats, cisplatin-induced CINV models showed higher kaolin consumption versus controls (p < 0.05). FMT from non-CINV donors reduced kaolin consumption in cisplatin-treated rats (p < 0.05). The expression of 5-HT3R, NK1R, and NK2R in the medulla oblongata and colon was significantly increased in the cisplatin model group (p < 0.05) and partially reversed by non-CINV FMT (p < 0.05).
CONCLUSIONS: Gut microbiota dysbiosis directly contributes to CINV pathogenesis. Bacteroides sp. A1C1 and its putatively identified metabolites (hesperetin, arbutin, orciprenaline, and myristolic acid) represent potential diagnostic biomarkers for CINV.}, }
@article {pmid41925202, year = {2026}, author = {Leibovitzh, H and Krongauz, D and Schlesinger, Y and Cohen, NA and Hirsch, A and Ron, Y and Thurm, T and Godneva, A and Weinberger, A and Segal, E and Maharshak, N}, title = {Phage-display immunoprecipitation sequencing reveals distinct antibody signatures against bacterial flagellins associated with treatment response in Crohn's disease.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000001030}, pmid = {41925202}, issn = {2155-384X}, abstract = {OBJECTIVES: Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.
METHODS: Thirty-nine patients with active CD (Harvey-Bradshaw Index [HBI]>4 or fecal calprotectin [FCP]>150μg/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22 and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.
RESULTS: Using PhIP-Seq analysis, only the anti-flagellin antibodies library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (HBI≤4 and FCP≤150) versus non-remission at all time points (p<0.05). Of the 55 anti-flagellin antibodies analyzed, 15 showed consistent >1.5-fold over-representation in non-remission samples, with high conservation of amino-acid sequences and targeting of Clostridiales, Lachnospiraceae, or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while non-remission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semi-essential amino acids biosynthesis (q<0.05).
CONCLUSIONS: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.}, }
@article {pmid41925227, year = {2026}, author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y}, title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag068}, pmid = {41925227}, issn = {1751-7370}, abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/LPMO-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.}, }
@article {pmid41926886, year = {2026}, author = {Hoang, HG and Chacha, WE and Binh, QA and Mukherjee, S and Jiang, Y and Zhang, T and Van Tung, T and Tran, HT and Naidu, R}, title = {Biotechnologies for removal of per- and polyfluoroalkyl substances (PFAS) in biosolids: Current status and challenges.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129237}, doi = {10.1016/j.jenvman.2026.129237}, pmid = {41926886}, issn = {1095-8630}, abstract = {Per- and polyfluoroalkyl substances (PFAS), widely recognized as "forever chemicals," pose significant environmental management challenges due to their persistence, mobility, and bioaccumulative behavior. Biosolids derived from wastewater treatment plants represent an important pathway for PFAS redistribution into terrestrial environments, particularly through land application. This review provides a comprehensive assessment of the global distribution, environmental behavior, toxicity, and biodegradation potential of PFAS in biosolids. A bibliometric analysis was conducted using the Web of Science database, and keyword co-occurrence mapping with VOSviewer was applied to evaluate research trends from 2018 to 2024. The findings indicate that research activity is concentrated in China (31%), Europe (30%), and North America (16%), with limited data available from South America, Oceania, and Africa, highlighting regional knowledge gaps. The environmental fate of PFAS in biosolids is governed by pH, temperature, redox conditions, and organic matter content, which influence sorption-desorption processes, mobility, and long-term persistence in soils. Biodegradation pathways include anaerobic reductive defluorination and aerobic oxidative transformation. Certain bacterial genera, such as Dehalobacter spp. and Gordonia spp., have demonstrated degradation efficiencies approaching 80-90% under optimized laboratory conditions. Fungal-mediated oxidative processes may further promote partial mineralization through enzymatic defluorination. In phytoremediation systems, long-chain PFAS preferentially accumulate in plant roots, whereas short-chain compounds exhibit greater mobility and translocation potential. Emerging remediation strategies integrating metagenomics, functional gene characterization, and enzyme-based treatments show promise for enhancing PFAS attenuation. However, substantial uncertainties remain regarding long-term bioaccumulation, biomagnification, and regulatory risk thresholds. Addressing these gaps is essential for developing science-based management strategies for PFAS-contaminated biosolids and protecting environmental and human health.}, }
@article {pmid41926891, year = {2026}, author = {Duan, P and Guan, Y and Zhang, J and Han, Z and Li, H and Wang, S and Kong, F and Cui, Y}, title = {Enhanced performance and mechanism of nano-iron-nickel modified substrate in the treatment of compound antibiotic wastewater in constructed wetland.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129455}, doi = {10.1016/j.jenvman.2026.129455}, pmid = {41926891}, issn = {1095-8630}, abstract = {Nano zero-valent iron nickel (nZVI/Ni) was loaded on the walnut shell activated carbon (AC) and its spheres (ACS) to prepare nZVI/Ni-ACS and nZVI/Ni/AC-SAS composites. These were applied in constructed wetlands (CWs) to construct a "substrate-microorganism" synergistic system for treating tetracycline (TC) and sulfamethoxazole (SMX) in livestock and poultry wastewater. Adsorption experiments determined the optimal mass ratios were ACS:Fe:Ni = 2:1:0.05; AC:Fe:Ni = 1:1:0.05; nZVI/Ni/AC:SA = 6:1. At 500 μg/L influent concentrations, TC and SMX removal efficiencies in CWs with modified substrates (CW-LA: 86.96%/87.79%; CW-LB: 89.88%/86.94%) significantly exceeded gravel (CW-G: 26.07%/55.28%) and ACS (CW-Z: 39.90%/67.56%) systems. Mechanistically, the modified substrates strongly adsorbed TC and SMX, while Fe and Ni acted as electron donors and catalysts to drive their chemical reduction and stimulate biological co-metabolism. Metagenomic analysis revealed that the TC/SMX removal mechanisms were associated with an increased abundance of antibiotic-resistant microorganisms (Methanothrix, Desulfobacter, Thauera, Geobacter, Pseudomonas), which benefited efficient antibiotic degradation, while their immobilization within the tightly bound EPS (TB-EPS) matrix effectively minimized ecological risks. This study provided critical data for the enhanced CW treatment of TC and SMX in livestock and poultry wastewater by modified substrates.}, }
@article {pmid41927118, year = {2026}, author = {Huang, H and Liu, Z and Liu, X and Li, Q and Yang, X and Chen, L and Ye, W}, title = {Coinfection of Human Cytomegalovirus and Pneumocystis jirovecii Caused Severe Pneumonia in a Non-HIV Elderly Patient: A Case Report.}, journal = {Annals of clinical and laboratory science}, volume = {56}, number = {1}, pages = {122-129}, pmid = {41927118}, issn = {1550-8080}, mesh = {Humans ; *Pneumocystis carinii/isolation & purification ; *Cytomegalovirus Infections/complications/virology/drug therapy ; *Pneumonia, Pneumocystis/microbiology/complications/drug therapy ; *Coinfection/virology/microbiology ; *Cytomegalovirus/isolation & purification ; Male ; Aged ; *Pneumonia ; }, abstract = {OBJECTIVE: To present a case of a non-human immunodeficiency virus (HIV)-infected patient with human cytomegalovirus (HCMV) viremia and severe Pneumocystis jirovecii (PJ) pneumonia.
CASE REPORT: The patient was admitted in June 2024 for chronic dry cough and dyspnea. Sputum-targeted next-generation sequencing (tNGS) and blood pathogen metagenomic detection were used to identify concurrent infections of sputum HCMV and PJ, along with blood HCMV. The extensive treatment included intravenous ganciclovir, in conjunction with caspofungin and oral sulfamethoxazole, augmented by glucocorticoids and breathing assistance. After three weeks, the patient's oxygenation index markedly improved, accompanied by the significant resolution of imaging lesions, leading to patient discharge in June 2024.
CONCLUSION: This case underscores the diagnostic efficacy of tNGS on several opportunistic infections for older people with several comorbidities.}, }
@article {pmid41927536, year = {2026}, author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J}, title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.}, journal = {Nutrition & diabetes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41387-026-00418-w}, pmid = {41927536}, issn = {2044-4052}, abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.
METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.
RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs > 0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.
CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.}, }
@article {pmid41927550, year = {2026}, author = {Oki, H and Takebe, K and Bonsu, A and Fujii, K and Masuda, R and Henderson, N and Mima, T and Koide, T and Moradi, M and Matsushita, O and Sakon, J and Kawahara, K}, title = {Bacterial collagenase harnesses collagen geometry for processive cleavage.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71099-3}, pmid = {41927550}, issn = {2041-1723}, support = {24K10218//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K14519//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K06545//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 2218054//Armenian National Science and Education Fund (Armenian National Science & Education Fund)/ ; GM103429 and GM151696//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria secrete collagenases that unwind the collagen triple helix and processively trim Gly-X-Y triplet repeats, yet the molecular basis of this process has remained obscure. Here, cryo-electron microscopy reveals how Hathewaya histolytica collagenase ColH engages its substrate and exploits the helix's architecture for catalysis. ColH encircles a single collagen triple helix in a closed-ring conformation and, through dynamic domain motions, dehydrates and destabilises it. The enzyme undergoes substrate-assisted twisting to adopt a rigid ratcheted conformation, in which one chain is bent into a tripeptide-long 'bight' and threaded into the active site for cleavage, while two uncut strands are partitioned to non-catalytic sites. Release of the bight appears to reset the enzyme, with the uncut strands serving as guiding tracks. Repeated cycling between dynamic and rigid states likely enables triplet-by-triplet translocation, allowing ColH to harness collagen's geometry for processive degradation. These findings reveal a bacterial strategy for collagen unwinding and cleavage distinct from that of mammalian collagenases, highlighting divergent evolutionary solutions for degrading one of nature's most intractable substrates.}, }
@article {pmid41927589, year = {2026}, author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, Č and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H}, title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71145-0}, pmid = {41927589}, issn = {2041-1723}, abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.}, }
@article {pmid41927746, year = {2026}, author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA}, title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46933-9}, pmid = {41927746}, issn = {2045-2322}, support = {SRUG2204254606//National Research Foundation/ ; }, abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.}, }
@article {pmid41736165, year = {2026}, author = {Wei, C and Chen, Z and Wang, Y and Huang, L and Chen, C}, title = {Large-scale genomic analysis of jumbo phages: coevolution, genome architecture, and host interaction mechanisms.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41736165}, issn = {2524-4671}, support = {32272831//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Jumbo phages are phages with comparatively large genome sizes. Jumbo phages have been identified in various microbial communities. However, their diversity, genome structure, potential function, and their interactions with hosts and other phages are largely unknown due to insufficient genomic data.
RESULTS: We collected 59,652,008 putative viral genomes from seven habitats by using 38 public metagenome datasets, an integrated public viral genome database (IGN), and pig gut viral genome databases. We obtained 10,754 jumbo phage genomes with sizes ranging from 200 to 831 kb. Most (94.64%) of these jumbo phage genomes were classified into Caudoviricetes, and the results have expanded the known diversity of Caudoviricetes. We found 2,389 species-like operational genome clusters that contained 3,727 (34.69%) genomes without any known viral genomes in the IGN, suggesting potential novel species-like genomes. Genome analysis suggested the potential coevolution of jumbo phages with habitat types and highlighted the utilization of alternative genetic codes and their corresponding suppressor tRNAs for recoding stop codons. CRISPR spacer analysis revealed potential bacterial or archaeal hosts of jumbo phages and uncovered competitive networks among jumbo phages. Habitat type had an important effect on the variation in phage auxiliary metabolic genes.
CONCLUSIONS: This study provides an important resource and new knowledge for future studies on the interaction between jumbo phages and their bacterial or archaeal hosts.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00534-z.}, }
@article {pmid41917792, year = {2026}, author = {Karnachuk, OV and Lukina, AP and Avakyan, MR and Panova, IA and Kadnikov, VV and Beletsky, AV and Mardanov, AV and Novikov, AA and Scherbakova, VA and Ravin, NV}, title = {A Novel Slowly Evolving Lineage of the Desulforudis Clade From the Deep Subsurface.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70293}, doi = {10.1111/1462-2920.70293}, pmid = {41917792}, issn = {1462-2920}, support = {24-14-00396//Russian Science Foundation/ ; 22-14-00178-Р//Russian Science Foundation/ ; }, mesh = {Phylogeny ; Genome, Bacterial ; Siberia ; RNA, Ribosomal, 16S/genetics ; Evolution, Molecular ; DNA, Bacterial/genetics ; }, abstract = {Endemic to the deep subsurface biosphere sulphate-reducing 'Desulforudis audaxviator' has been called a living microbial fossil due to the high nucleotide sequence identity of its genomes across continents. Evolutionary stasis of this bacterium was established based on the analysis of metagenome assembled genomes, single cell genomes and a single axenic culture. The lack of high-quality reference genomes necessitates efforts to cultivate and isolate pure cultures that could shed light on the hypothetical slow evolution of Desulforudis-clade bacteria deep underground. Molecular signatures demonstrated the presence of Desulforudis-like phylotypes in subsurface environments worldwide. Here we report the isolation of four novel strains of the Desulforudis-clade, all belonging to Desulfosceptrum tomskiensis gen. nov. sp. nov. Four strains of the new species were isolated from deep boreholes in Western Siberia, separated by hundreds of kilometres. Genome comparisons revealed minimal differences between these strains, with average nucleotide sequence identity (ANI) values above 99.9%, low number of SNPs, and near-identical CRISPRs. The bacterium, together with Desulforudis audaxviator BYF[T] gen. nov. sp. nov., deposited in international culture collections, provides a bases for understanding the slow evolution of Bacillota endemic to the deep biosphere.}, }
@article {pmid41918091, year = {2026}, author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J}, title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04921-z}, pmid = {41918091}, issn = {1471-2180}, support = {2022YFC26023002//National Key Research and Development Program of China/ ; }, }
@article {pmid41918132, year = {2026}, author = {Gao, L and Fang, BZ and Yang, J and Lian, ZH and Chen, Y and Mohamad, OAA and Xu, QY and Liu, YH and Wu, D and Yuan, Y and Abdugheni, R and Li, MM and Wang, P and Ortúzar, M and Li, XY and Huang, JR and Liu, L and Jiang, HC and Shu, W and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02361-5}, pmid = {41918132}, issn = {2049-2618}, support = {2022B0202110001//Guangdong S&T Program/ ; }, abstract = {BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood.
RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis.
CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.}, }
@article {pmid41918376, year = {2026}, author = {Yuan, H and Guan, T and Yuan, Q and Zeng, Q and Yu, J and Cai, Y and Liu, E and Li, Q and Wang, Y}, title = {Molecular-Microbial Cascades Regulate Organic Phosphorus Mineralization in Lake Sediments.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15353}, pmid = {41918376}, issn = {1520-5851}, abstract = {Organic phosphorus (Po) mineralization is a major internal source of soluble reactive phosphorus (SRP) in lakes, yet the molecular and microbial mechanisms governing this transformation remain poorly understood. Here, we aim to elucidate these mechanisms by integrating excitation-emission fluorescence spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), and metagenomics across two contrasting ecological niches in Taihu Lake, namely the Cyanophyta-dominated and macrophyte-dominated regions. We also supplement our results with the findings from a global meta-analysis. We found that fulvic-associated Po (Fu-Po) dominated sedimentary Po inventories, whereas Po extracted with NaHCO3 (NaHCO3-Po) and microbial biomass Po (biomass-Po) exhibited higher decomposition potential. Fluorescence indices indicated increasing lability with depth, and humic-like materials exhibited a higher tendency to be decomposed under anoxia, accompanied by the accumulation of fulvic-like fractions. FT-ICR-MS revealed proteins and lignins as key constituents of humic-associated Po and Fu-Po, supporting their bioavailability, while NaHCO3-Po was enriched in compounds with lipid-like CHOSP formulas, suggesting greater lability. Metagenomics identified phoD as the most abundant phosphatase-encoding gene, with rare but highly connected phoD-harboring taxa emerging as potential keystone regulators alongside abundant functional groups. Across global lake sediments, alkaline phosphatase activity, Po content, and phoD abundance were found to covary positively, and structural equation modeling highlighted Fu-Po as a disproportionate indirect driver of SRP replenishment via phoD-mediated phosphatase activity. These findings reveal a mechanistic cascade linking molecular composition to phoD-mediated enzymatic potential in Po mineralization, identifying Po bioavailability, rather than inorganic phosphorus pools alone, as a critical driver for reducing internal loading. Targeting this pathway could modulate Po mineralization mechanisms in sediments worldwide, offering valuable insights into the management of lake eutrophication under accelerating nutrient pressures.}, }
@article {pmid41918527, year = {2026}, author = {Yang, K and Huang, Y and Gu, L and Li, J and Ma, Y and Gao, P and Qiu, W and Liu, K and Zhang, Y and Liu, H and Xu, J and Xu, J and Liu, T}, title = {Er-Chen Decoction ameliorates metabolic dysfunction-associated steatotic liver disease via gut microbiota-barrier axis-driven hepatic metabolic reprogramming.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768664}, pmid = {41918527}, issn = {1664-302X}, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) constitutes a critical global health challenge, with gut-liver axis dysfunction and metabolic endotoxemia serving as key drivers. The traditional Chinese medicinal formula Er-Chen Decoction (ECD) has proven effective in treating metabolic disorders, yet the specific mechanisms by which it modulates gut-liver crosstalk have not been fully elucidated.
METHODS: A mouse model of MASLD was established via a high-fat diet (HFD). The therapeutic effects of ECD were evaluated using the glucagon-like peptide-1 (GLP-1) receptor agonist semaglutide (SE) as a positive control. A comprehensive analysis of the underlying mechanisms of ECD treatment was conducted by integrating fecal metagenomic sequencing, untargeted serum metabolomic profiling, hepatic transcriptomic analysis, and molecular biology assays.
RESULTS: Treatment with ECD markedly ameliorated hepatic steatosis, insulin resistance, and hyperlipidemia, demonstrating a therapeutic efficacy comparable to that of SE. Fecal metagenomic analysis indicated that whereas SE predominantly enriched the genus Akkermansia, the relative abundance of Bifidobacterium and Lactobacillus was markedly and specifically elevated following ECD treatment. Serum metabolomic profiling revealed that ECD specifically activated the tryptophan-indole metabolic pathway, as evidenced by elevated concentrations of indoleacrylic acid and indole-3-acetic acid. Correlation analyses established a strong positive correlation between these indole derivatives and the bacterial genera enriched by ECD. Mechanistically, our findings suggest that elevated indoles activate the aryl hydrocarbon receptor (AHR) in the colon, upregulating tight junction proteins ZO-1 and Occludin and restoring intestinal barrier integrity, thereby significantly reducing serum lipopolysaccharide (LPS) levels. In hepatic tissue, the diminished LPS influx alleviated the suppression of DNA methyltransferase 3B (DNMT3B), thereby promoting the epigenetic silencing of the lipid droplet fusion protein CIDEA and inhibiting pathological hepatic lipogenesis.
CONCLUSION: Our findings elucidate a novel mechanism through which ECD may ameliorate MASLD via the distinctive "gut microbiota-indole-barrier" axis. In contrast to SE, ECD modulates gut microbiota composition to boost indole production and subsequently activate AHR signaling. This activation inhibits endotoxin translocation and induces hepatic DNMT3B-mediated epigenetic reprogramming to reverse hepatic steatosis. These results offer scientific evidence supporting the potential of ECD as an effective therapeutic strategy for MASLD.}, }
@article {pmid41918743, year = {2026}, author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F}, title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1745166}, pmid = {41918743}, issn = {1664-3224}, mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/microbiology/urine ; Middle Aged ; Adult ; *Neutrophils/immunology/metabolism ; Aged ; Biomarkers ; Pyelonephritis/immunology/urine ; Bacteriuria/immunology ; }, abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.
METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.
RESULTS AND DISCUSSION: On average, 23.29% ± 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% ± 17.88%), pyelonephritis (22.75% ± 12.91%), asymptomatic bacteriuria (18.17% ± 17.14%)] and 30.63% ± 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% ± 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.}, }
@article {pmid41918857, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M}, title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20990}, pmid = {41918857}, issn = {2167-8359}, mesh = {*Peptides/genetics/pharmacology ; *Antineoplastic Agents/pharmacology ; *Metagenome ; Humans ; *Genome, Microbial ; *Software ; High-Throughput Nucleotide Sequencing ; Algorithms ; Computational Biology/methods ; }, abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.
METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.
RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.}, }
@article {pmid41918874, year = {2026}, author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D}, title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1782744}, pmid = {41918874}, issn = {2235-2988}, mesh = {Humans ; Female ; *Probiotics/administration & dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; }, abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.
METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.
RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-α and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.
DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.}, }
@article {pmid41918946, year = {2026}, author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG}, title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41918946}, issn = {2312-0541}, abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.
METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32 weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and α-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).
CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.}, }
@article {pmid41919078, year = {2026}, author = {Fan, Y and Qin, H and Liu, J and Abbas, M and Yang, C and Cheng, H and Dong, X}, title = {Lactobacillus acidophilus alleviates slow transit constipation by modulating 5-HT pathway and gut microbial composition.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1775405}, pmid = {41919078}, issn = {2296-861X}, abstract = {INTRODUCTION: Slow transit constipation (STC) is a chronic disease characterized by delayed intestinal transit and weakened spontaneous contractions of colonic smooth muscle. Current pharmacological treatments are often associated with adverse effects, highlighting the need for safe and more effective therapeutic strategies. This study investigated the potential role of Lactobacillus acidophilus (L. acidophilus) in regulating intestinal motility and alleviating STC, as well as the underlying mechanism.
METHODS: A humanized mouse model was established by intragastric administration of fecal bacterial suspension from STC patients on alternate days, in order to evaluate the effect of L. acidophilus on constipation. The regulatory effect of L. acidophilus on intestinal motility was evaluated using defecation parameters. Colon histopathology was assessed by hematoxylin-eosin (H&E) staining. Immunohistochemistry (IHC), RT-qPCR, ELISA, and in vitro cell experiments were performed to examine the inflammatory cytokine levels and changes in the 5-hydroxytryptamine (5-HT) signaling pathway. In addition, metagenomic sequencing was used to analyze changes in the intestinal microbial community.
RESULTS: The results showed L. acidophilus treatment significantly enhanced intestinal peristalsis and maintained the intestinal barrier by up-regulating Occludin expression and down-regulating inflammatory cytokines, including TNF-α and IL-1β, thereby suppressing inflammatory responses. Both in vivo and in vitro experiments showed that L. acidophilus affected the synthesis and release of 5-HT by regulating the expression of TPH1 and the mechanosensitive ion channel Piezo1. Additionally, L. acidophilus reshaped the intestinal microbial community structure and altered the inter-bacterial interaction network, which was closely associated with improved intestinal motility.
CONCLUSION: Our current research reveals that constipation symptoms by L. acidophilus through the gut microbiota composition, intestinal barrier, and the 5-HT signaling pathway. These findings provide a strong theoretical basis for the development of L. acidophilus as a potential therapeutic strategy for the treatment of STC.}, }
@article {pmid41919237, year = {2026}, author = {Zheng, D and Li, L and Qi, H and Jiao, XF and Wang, K}, title = {Successful azithromycin treatment of Chlamydia psittaci pneumonia in second-trimester pregnancy resulting in term delivery: a case report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1780706}, pmid = {41919237}, issn = {1663-9812}, abstract = {Psittacosis pneumonia is a zoonotic infection caused by Chlamydia psittaci (C. psittaci), primarily transmitted via contact with infected avian species. Diagnostic challenges arise from the inherent difficulties of pathogen culture and serological testing, frequently resulting in misdiagnosis or underdiagnosis. Gestational psittacosis, in particular, is a rare but life-threatening condition, with delayed diagnosis conferring risk of severe maternal and fetal complications. We present a case of C. psittaci pneumonia in a 24-week pregnant woman, with the diagnosis confirmed by metagenomic next-generation sequencing (mNGS). Empirical intravenous azithromycin (0.5 g daily) was promptly initiated for 3 days, leading to rapid symptomatic resolution. After a 2-day interruption, targeted oral azithromycin (0.5 g daily) was restarted for an additional 3 days following pathogen confirmation via mNGS. The patient was successfully discharged after a 10-day hospital stay under multidisciplinary management. She finally gave birth to a healthy baby girl at 40 weeks and 3 days of gestation, with favorable maternal and neonatal outcomes. To our knowledge, this represents one of the few reported cases of full-term delivery following azithromycin monotherapy for gestational psittacosis. It provides valuable insights into the diagnosis and management of gestational psittacosis, emphasising the importance of multidisciplinary involvement in preserving maternal and fetal safety.}, }
@article {pmid41919563, year = {2026}, author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W}, title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.70091}, pmid = {41919563}, issn = {1522-7278}, abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.}, }
@article {pmid41919955, year = {2026}, author = {Pan, W and Tang, S and Wanek, W and Liu, X and Zhou, J and Gregory, AS and Marsden, KA and Chadwick, DR and Liang, Y and Wu, L and Jones, DL and Ma, Q}, title = {Organic Fertilization Promotes the Microbial Formation of Moderately Active Soil Phosphorus Pools to Sustain Phosphorus Availability: Insights from 180 years of Fertilization.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12810}, pmid = {41919955}, issn = {1520-5851}, abstract = {Phosphorus (P) fertilization is essential for crop production, but most applied P is rapidly fixed into mineral-associated forms. Although fertilization regulates P distribution in soils, its effects on microbe-mediated processes that regulate P availability and stabilization remain unclear. Here, we investigated P transformations under organic fertilization (FYM), inorganic fertilization (NPK), and no fertilization (NIL) using the 180 year Broadbalk experiment. Through [33]P isotopic tracing, metagenomics, and enzymatic profiling, we found that FYM and NPK stimulate distinct P transformation pathways. FYM, through sustained organic carbon inputs, enhanced microbial immobilization and phosphatase activity, causing a 41% reduction in stable P formation and 47% increase in moderately active P levels and shifting P dynamics toward more bioavailable forms. NPK fertilization reduced pH and limited microbial carbon availability; 33% of [33]P was recovered in the stable P fraction, indicating abiotic immobilization into inorganic P pools. The microbial community under NPK adapted to P fixation by enriching P-cycling-related genes and acid-tolerant taxa, enhancing P turnover relative to NIL but preventing long-term immobilization less effectively than FYM. Thus, organic fertilization maintains P in more biologically available forms and mitigates abiotic P fixation; our research provides a mechanistic foundation for more efficient and resilient P management in agroecosystems.}, }
@article {pmid41919968, year = {2026}, author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C}, title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0039226}, doi = {10.1128/aem.00392-26}, pmid = {41919968}, issn = {1098-5336}, abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.}, }
@article {pmid41920399, year = {2026}, author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Rahman, MS and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT}, title = {Rooftop and surface garden soils in Bangladesh harbor diverse resistome profiles.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {4}, pages = {}, pmid = {41920399}, issn = {1573-2959}, support = {Grant ID: Proc-451-05//This work was conducted as part of the CGIAR Research Initiative on Resilient Cities Through Sustainable Urban and Peri-urban Agri-food Systems and is supported by contributors to the CGIAR Trust Fund (https://www.cgiar.org/funders)./ ; }, mesh = {*Soil Microbiology ; Bangladesh ; Soil/chemistry ; *Environmental Monitoring ; *Drug Resistance, Microbial/genetics ; Gardens ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Despite the growing expansion of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles (i.e., resistome) of microbial communities in rooftop and surface garden soils in Bangladesh remain insufficiently characterized, limiting our understanding of their potential role as reservoirs and disseminators of AMR. In this study, shotgun metagenome sequencing was applied to 27 soil samples, including 7 from Dhaka rooftop gardens (DRG), 6 from Dhaka surface gardens (DSG), 8 from Gazipur rooftop gardens (GRG), and 6 from Gazipur surface gardens (GSG) to comprehensively characterize their resistome profiles. We identified 88 antibiotic resistance genes (ARGs), of which 19 (21.6%) were shared across all sites, and found significant differences in resistome composition by garden type (p = 0.04). Rooftop soils harbored more ARGs (DRG, 50; GRG, 48) than surface soils (DSG, 40; GSG, 41) and were dominated by glycopeptide resistance genes, collectively representing 62.43-74.07% of ARGs. Rooftop garden soils were also enriched in efflux pumps (adeF, 45.21% of rooftop ARGs) and ribosomal-protection-related oxazolidinone resistance gene O23S (62.13% in GRG). Conversely, surface soils featured a higher abundance of genes mediating antibiotic inactivation, such as CATA (11.64% in DSG) and fosBx1 (5.94% of surface ARGs), as well as those conferring co-resistance to biocides (qacG) and metals. The efflux pump gene adeF also remained a significant component of the surface resistome (24.33% of surface ARGs). Geographic location also modulated resistome composition. Garden soils from Gazipur emerged as notable hotspots, characterized by extremely high abundances of tetracycline efflux pumps (TET45) and multiple copper resistance genes and regulators (e.g., COPA, YCNJ, CSOR). Key ARG carriers included Bacillus licheniformis, B. paralicheniformis, Pseudomonas sabulinigri, and Paenibacillus spp. Spearman correlation analyses revealed strong positive associations (r = 1.0) between specific taxa and resistance mechanisms, as well as co-occurrence patterns among antibiotic, biocide, and metal resistance genes. Collectively, these results indicate that garden soils represent important reservoirs of ARGs, with resistome architecture influenced by both garden type and location, highlighting the necessity for sustainable management practices and a One Health approach to environmental resistome surveillance.}, }
@article {pmid41921236, year = {2026}, author = {Lu, D and Ping, C and Jia, D and Liu, J and Wang, H and Song, Y and Cai, X}, title = {Mechanism of Legionella pneumophila-induced liver injury via gut microbiota translocation under immunosuppression.}, journal = {Pathology, research and practice}, volume = {282}, number = {}, pages = {156456}, doi = {10.1016/j.prp.2026.156456}, pmid = {41921236}, issn = {1618-0631}, abstract = {Legionnaires' disease presents substantial clinical challenges in immunocompromised patients, with the pathogenesis of multi-organ dysfunction remaining poorly understood. Through an immunosuppressed guinea pig model, we demonstrate that Legionella pneumophila (Lp) infection triggers a systemic pathological cascade that extends beyond pulmonary damage. Our results show that Lp infection not only induces severe pulmonary inflammation and endothelial barrier disruption but also initiates gut-liver axis injury mediated by intestinal microbiota dysbiosis. Metagenomic sequencing revealed specific enrichment of Anoxybacillus kestanbolensis and Geobacillus vulcani in both intestinal and hepatic tissues post-infection, indicating microbial translocation. This bacterial dissemination was associated with enhanced hepatocyte apoptosis and exacerbated liver injury. Mechanistically, we demonstrate that Lp infection compromises intestinal epithelial integrity, promotes translocation of enteric pathogens, and subsequently activates hepatic apoptotic pathways, thereby aggravating systemic inflammation and multi-organ failure. These findings elucidate the gut microbiota-gut-liver axis as a pivotal mechanism in Lp-induced systemic damage and suggest potential therapeutic targets for severe Legionnaires' disease in immunocompromised hosts.}, }
@article {pmid41921318, year = {2026}, author = {Wang, F and Shi, C and Zhang, W and Chen, Y and Chen, Z and Yang, S and Zhang, J and Liu, W and Cao, W}, title = {Fresh-seawater interface shapes nitrogen fate in a subtropical estuary: Insights from multi-isotopic and metagenomic analyses.}, journal = {Water research}, volume = {298}, number = {}, pages = {125836}, doi = {10.1016/j.watres.2026.125836}, pmid = {41921318}, issn = {1879-2448}, abstract = {Estuaries, the key transitional interface between freshwater rivers and saline seas, are hotspots of nitrogen (N) cycling processes. In this study, we integrated multi-isotope and metagenomic sequencing techniques to characterize nitrate (NO3[-]) sources, mixing and transformation processes, and the regulatory roles of microbial functional genes in different seasons and subzones in the Jiulong River estuary, a typical subtropical estuary. NO3[-]-N was the dominant form of dissolved inorganic N (70.31-91.70 %), with significantly lower concentrations in the seaward subzone than those in other subzones. Hydrochemical parameters, dual-isotope (δ[15]N-NO3[-] and δ[18]O-NO3[-]) signatures, and MixSIAR model indicated that soil N was the largest contributor to NO3[-] (44.7 %), followed by M&S and groundwater in the riverward subzone. The upstream inflow from the riverward subzone accounted for 64.6 % of NO3[-] sources in the mixing subzone. Extensive aquaculture activities in the estuary were the dominant NO3[-] source (44.8 %), followed by M&S and the upstream inflow from the mixing subzone in the seaward subzone. Nitrate reduction genes dominated the N-cycling functional genes and mediated the primary NO3[-] transformation pathways. The PLS-PM model indicated dissimilatory nitrate reduction to nitrite (DNRN) genes had a significant positive effect (0.892) on NO3[-] concentrations and influenced competition between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification for substrates through the C/N ratios. The lower nosZ/narG ratios and higher nitrous oxide concentrations in the riverward and mixing subzones led to more susceptibility to incomplete denitrification, whereas the higher DNRA/DNRN ratios and the significant positive correlation between DNRA and the C/N ratios favored DNRA in the seaward subzone. The lower temperatures and river flows in winter were significantly lower than those in other seasons, which constrained N transforming capacity and resulted in the lowest dissolved nitrous oxide concentration. Therefore, salinity and temperature regulated the primary N-cycling processes by reshaping the composition of functional genes. Overall, this study clarifies the N sources and transformation pathways and provides a systematic theoretical foundation for the development of subzone-based management strategies for estuarine ecosystems.}, }
@article {pmid41921321, year = {2026}, author = {Sudarshan, AS and Konstantinidis, KT and Pinto, AJ}, title = {Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems.}, journal = {Water research}, volume = {298}, number = {}, pages = {125784}, doi = {10.1016/j.watres.2026.125784}, pmid = {41921321}, issn = {1879-2448}, abstract = {A recent metagenomic survey of drinking water systems revealed that a highly prevalent and dominant uncultured bacterial genus (Raskinella) was represented globally by a single species (Raskinella chloraquaticus). R. chloraquaticus comprises of two sub-species groups, Lineages 1 and 2, the former representing a globally prevalent genomovar. The objective of this study was to perform comparative analysis of the gene content of R. chloraquaticus to characterize the gene-level diversity and determine factors shaping the diversity of this species. Pangenome analysis revealed that R. chloraquaticus possesses a core set of genes that constitute a major portion (87.74%) of the known gene content of the genome. Furthermore, most of the gene diversity of R. chloraquaticus is associated with Lineage 2 organisms, which consists of at least four distinct genomovars. Lineage 1 organisms consist of a higher proportion of identical genes than would have been expected if changes primarily occurred through random mutations and thus is potentially indicative of recombination. In contrast, Lineage 2 organisms appear to have emerged through random mutations and display stronger geographic preference. These results indicate that homologous recombination and geographic isolation likely shape the genetic repertoire of R. chloraquaticus. Further, the high level of gene conservation in R. chloraquaticus may be reflective of highly selective environment in drinking water systems. Thus, R. chloraquaticus may represent a model organism to probe selective pressures shaping the drinking water microbiome.}, }
@article {pmid41921326, year = {2026}, author = {Liu, X and Li, C and Zhao, Y and Li, X and Zhang, Q and Zhang, L and Peng, Y}, title = {A novel approach for achieving high enrichment of anammox and nitrogen removal rate in municipal wastewater treatment: A pure biofilm process.}, journal = {Water research}, volume = {298}, number = {}, pages = {125838}, doi = {10.1016/j.watres.2026.125838}, pmid = {41921326}, issn = {1879-2448}, abstract = {Against the backdrop of global carbon neutrality goals and increasingly stringent pollutant discharge standards, the anammox nitrogen removal process has gained significant attention due to its high efficiency, energy-saving, and environmentally friendly characteristics. The current mainstream wastewater treatment technologies still encounter challenges in enriching anaerobic ammonium-oxidizing bacteria (AnAOB) and managing the disposal of substantial amounts of residual sludge. The pure biofilm process has garnered significant attention as the primary focus for autotrophic nitrogen removal transformation in wastewater treatment plants (WWTPs), owing to its ability to efficiently enrich AnAOB and produce low amounts of sludge. This study innovatively proposed a novel pure biofilm process and explored the self-enrichment mechanism of AnAOB in this system. Over 200 days of municipal wastewater treatment under a low C/N ratio (average of 3), the effluent ammonia nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (NRE) achieved 97.72 ± 1.50 % and 94.27 ± 2.92 %, respectively. Long-term operation and batch experiments revealed that carbon source regulation is crucial for the performance of pure biofilm systems. Furthermore, the pure biofilm system demonstrates greater resilience to organic loading shocks compared to floc sludge and hybrid systems. QPCR and 16S rRNA sequencing confirmed the successful enrichment of AnAOB (pre-anoxic:8.94 %, post-anoxic:8.61 %), with anammox contributing to an impressive 81.10 % of nitrogen removal. Additionally, fluorescence in situ hybridization combined with confocal laser scanning microscopy (FISH-CLAM) technology demonstrated a spatially uniform distribution of AnAOB within the system, in contrast to hybrid systems. Metagenomic sequencing revealed the carbon and nitrogen metabolic pathways of functional bacteria in the pure biofilm system, showing that AnAOB's metabolic diversity and ecological niche adaptation within the biofilm structure drove their self-enrichment. Finally, microelectrode measurements of N2O production in the pure biofilm system confirmed its substantial potential for emission reduction. This work offers a practical solution for WWTPs aiming to reduce energy consumption and transition from heterotrophic to autotrophic nitrogen removal processes.}, }
@article {pmid41921531, year = {2026}, author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, QL}, title = {Feasibility of Low-Biomass Exhaled Breath Microbiome Sequencing Using a PDC-Sampler in Febrile and Healthy Individuals.}, journal = {Journal of breath research}, volume = {}, number = {}, pages = {}, doi = {10.1088/1752-7163/ae5a51}, pmid = {41921531}, issn = {1752-7163}, abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated by Pseudomonadota, Bacillota, Bacteroidota, and Actinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.}, }
@article {pmid41921761, year = {2026}, author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S}, title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113232}, doi = {10.1016/j.diabres.2026.113232}, pmid = {41921761}, issn = {1872-8227}, abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.}, }
@article {pmid41921901, year = {2026}, author = {Möller, T and Kreft, A and Dennebaum, M and Hess, G and Michel, C and Kriege, O}, title = {Disseminated Strongyloides stercoralis Infection Diagnosed by Metagenomic Next-Generation Sequencing of a Cell-Free DNA blood sample in a Patient with Hematologic Malignancy in Germany: A Case Report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108668}, doi = {10.1016/j.ijid.2026.108668}, pmid = {41921901}, issn = {1878-3511}, abstract = {BACKGROUND: Rare infections that are atypical for Central Europe are increasingly relevant due to global migration, climate change, and the widespread use of immunosuppressive therapies. Diagnosing such infections is often delayed or missed entirely because conventional testing relies on prior clinical suspicion and region-specific test panels. Hypothesis-free metagenomic next-generation sequencing (mNGS) offers a promising diagnostic strategy in these cases.
CASE PRESENTATION: We report a case of disseminated Strongyloides stercoralis (S. stercoralis) infection with hyperinfection syndrome in a man undergoing B-cell-depleting lymphoma therapy. The patient presented with gastrointestinal and pulmonary symptoms, weight loss, and eosinophilia. Conventional microbiological and serological testing failed to identify a cause. Diagnosis and relevant bacterial and fungal coinfection was established using mNGS (DISQVER®) from blood-derived cell-free DNA. Treatment with ivermectin and albendazole led to rapid clinical improvement, and the patient recovered completely.
CONCLUSION: This case illustrates the diagnostic challenges posed by rare infections in immunocompromised patients in non-endemic regions. It highlights the growing need for broad, rapid, and hypothesis-independent diagnostic tools such as mNGS, which can play a key role in identifying unexpected pathogens and guiding early targeted therapy in high-risk populations.}, }
@article {pmid41921920, year = {2026}, author = {Yang, MT and Qin, Y and Xu, C and Leng, X and Li, XM and Hou, QY and Sun, YZ and Zhao, Q and Liu, S and Tang, LY and Ma, H and Chen, BN and Zhang, XX and Li, ZY and Ni, HB}, title = {Virulence and Antimicrobial Resistance Profiling of Klebsiella pneumoniae Isolated from Foxes in Northern China.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108476}, doi = {10.1016/j.micpath.2026.108476}, pmid = {41921920}, issn = {1096-1208}, abstract = {Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.}, }
@article {pmid41922261, year = {2026}, author = {Adebayo, AA and Babalola, OO}, title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70325}, doi = {10.1111/1758-2229.70325}, pmid = {41922261}, issn = {1758-2229}, support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {*Daucus carota/microbiology/growth & development ; *Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation & purification/metabolism ; }, abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.}, }
@article {pmid41922337, year = {2026}, author = {Doni, L and Trinanes, J and Bosi, E and Vezzulli, L and Martinez-Urtaza, J}, title = {Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71231-3}, pmid = {41922337}, issn = {2041-1723}, abstract = {Long-range dispersals of marine bacteria in the oceans have remained largely indecipherable, which is particularly relevant for Vibrio, responsible for global epidemics in humans and animals. Here, we combine the analysis of 40 terabases of metagenomic data and satellite-tracked surface drifter data, from across the globe revealing that Vibrio are abundant members of the ocean surface and show a strong association with microplankton, which appears to govern their distribution and connectivity at a global scale. We identify long-distance biological corridors connecting Vibrio communities, including potentially pathogenic Vibrio. These corridors allow movement over thousands of kilometres in a fairly short time, with estimates of less than 1.5 years to cross an ocean basin. These findings have deep implications for the demography and community dynamics of Vibrio species and the epidemiology of associated diseases.}, }
@article {pmid41922358, year = {2026}, author = {Korchagina, MV and Mullin, CE and Soufi, HH and Lambert, S and Moran, IG and Porch, R and Albright, SE and Doran, AS and Jones, LM and Malamud, N and Jin, Q and Wood, AM and Louca, S}, title = {Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07139-w}, pmid = {41922358}, issn = {2052-4463}, abstract = {Hot springs are natural laboratories for studying microbial diversity, evolution, and adaptation to extreme environments. Despite their abundance across the Western US, information about the functional and genomic structure of inhabiting microbial communities is restricted to a handful of locations. Here we present a dataset of 500 deep metagenomes, totaling 3.38 terabasepairs and collected from 56 remote hot springs across the US Great Basin and Yellowstone, with 25 of the hot springs surveyed annually over 4 consecutive years. Additionally, we present 780 bacterial and archaeal metagenome-assembled genomes (MAGs) binned from these metagenomes, with completeness ≥80% and contamination ≤5%, of which 149 are considered "high quality". Many of the MAGs likely represent entirely novel genera and even families, relative to the Genome Taxonomy Database. Our spatiotemporally extensive dataset yields insight into the microbial functional structure at dozens of previously unstudied locations, substantially expands our repertoire of extremophile microbial genomes, provides a new resource for high-temperature biotechnology, and enables future phylogenomic studies of these communities through space and time.}, }
@article {pmid41913289, year = {2026}, author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P}, title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00828-2}, pmid = {41913289}, issn = {1757-4749}, abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.}, }
@article {pmid41913691, year = {2026}, author = {Erens, J and Heine, C and Lötters, S and Krehenwinkel, H and Crawford, AJ and Rueda-Solano, LA and Plewnia, A}, title = {A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70122}, doi = {10.1111/1755-0998.70122}, pmid = {41913691}, issn = {1755-0998}, support = {//Ministerium für Wirtschaft, Verkehr, Landwirtschaft und Weinbau Rheinland-Pfalz/ ; //Deutsche Gesellschaft für Herpetologie und Terrarienkunde/ ; //Forschungsfonds of Trier University/ ; //Forschungsinitiative Rheinland-Pfalz through Trier University/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; *Amphibians/classification/genetics ; *DNA, Environmental/genetics ; Workflow ; *Metagenomics/methods ; }, abstract = {Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots-particularly in remote and resource-limited tropical regions-to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.}, }
@article {pmid41913730, year = {2026}, author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A}, title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.}, journal = {Open research Europe}, volume = {6}, number = {}, pages = {65}, pmid = {41913730}, issn = {2732-5121}, abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.}, }
@article {pmid41913758, year = {2026}, author = {Chin, D and Campbell, B and Petersen, J and Lim, SJ and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {131}, pmid = {41913758}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Anodontia alba (buttercup lucine; Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1 862.85 megabases. Most of the assembly (99.28%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.48 kilobases. Gene annotation of this assembly by Ensembl identified 12 083 protein-coding genes. From the metagenome data, we recovered four bins, of which three were high-quality MAGs.}, }
@article {pmid41913906, year = {2026}, author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y}, title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {590621}, pmid = {41913906}, issn = {1178-7074}, abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.}, }
@article {pmid41914171, year = {2026}, author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN}, title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {18}, number = {1}, pages = {39439}, doi = {10.31083/FBE39439}, pmid = {41914171}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.
METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.
RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).
CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.}, }
@article {pmid41914631, year = {2026}, author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS}, title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0219825}, doi = {10.1128/spectrum.02198-25}, pmid = {41914631}, issn = {2165-0497}, abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.}, }
@article {pmid41914733, year = {2026}, author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D}, title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0235725}, doi = {10.1128/aem.02357-25}, pmid = {41914733}, issn = {1098-5336}, abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.}, }
@article {pmid41914849, year = {2026}, author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y}, title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0035926}, doi = {10.1128/aem.00359-26}, pmid = {41914849}, issn = {1098-5336}, abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.}, }
@article {pmid41915015, year = {2026}, author = {Sun, Y and Wu, X and Zanina, OG and Rivkina, EM and Lloyd, KG and Löffler, FE and Vishnivetskaya, TA}, title = {Incomplete Denitrifying Bacteria Drive N2O Fluxes in Ancient Siberian Permafrost Microcosms.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag034}, pmid = {41915015}, issn = {1574-6941}, abstract = {Nitrous oxide (N2O) contributes to stratospheric ozone depletion and global warming. Knowledge about microbial formation and consumption of N2O in old permafrost remains limited. Permafrost samples collected on the East Siberian Sea coast of Russia from a single borehole at depths of 5.4 and 16.9 m, which showed presence of nitrogen substances and nitrogen cycling genes, were used to establish microcosms supplemented with NO3-- and N2O to assess denitrification and N2O consumption at 4 and 20°C. Rapid N2O formation was observed in NO3--supplemented microcosms, but N2O consumption was slow and incomplete over a 1-year incubation in all microcosms. Twenty-three qualified metagenome-assembled genomes (MAGs) harboring genes involved in NO3- and/or N2O reduction were recovered from both NO3-- and N2O-supplemented microcosms. Twenty MAGs represent novel taxa. Four MAGs, two of each from NO3-- and N2O-supplemented microcosms, contained nosZ genes indicating N2O consumption potential, however the complete denitrification (i.e., NO3-→N2) gene sets were not detected in these MAGs. Though, N2O production exceeded N2O consumption in NO3--supplemented microcosms at 4°C. Our microcosm experiments suggest N2O formation surpasses its consumption in newly-thawed ~120 kyr old permafrost, emphasizing the importance of using integrated approaches to assess and predict N turnover in response to permafrost degradation.}, }
@article {pmid41915265, year = {2026}, author = {Volk, A and Mills, M and Chae, S and Lee, J}, title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41915265}, issn = {1614-7499}, abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.}, }
@article {pmid41915324, year = {2026}, author = {Varshney, A and Sarethy, IP}, title = {Metagenome-based insights into bacteriophage diversity of an urban river ecosystem.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41915324}, issn = {1573-4978}, }
@article {pmid41915473, year = {2026}, author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C}, title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117166}, doi = {10.1016/j.celrep.2026.117166}, pmid = {41915473}, issn = {2211-1247}, abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.}, }
@article {pmid41915526, year = {2026}, author = {Xiao, Z and Wei, A and Jia, Y and Zhao, W and Jiang, X}, title = {Semantic fusion of dual perspectives on genomic sequences and quorum sensing for bacteriophage lifestyle prediction.}, journal = {IEEE journal of biomedical and health informatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/JBHI.2026.3679001}, pmid = {41915526}, issn = {2168-2208}, abstract = {As the most ubiquitous and abundant viral community, bacteriophages (phages for short) play a vital role in regulating the ecological balance by infecting bacteria and archaea. Phages can be classified into two types based on their lifestyles: virulent phages and temperate phages, which are closely related to their functional characteristics and influence their interaction patterns with hosts. Therefore, identifying phage lifestyle is critical for understanding the mechanisms by which phages infect bacteria and represents a key step in mastering their functions and potential applications. In this paper, we propose a novel method for phage lifestyle identification by considering two perspectives. One perspective is based on the genomic sequences of phages, in which both local and global semantic features are integrated. The other perspective focuses on the host quorum sensing phenomena that influence phage lysogen-lysis decisions. Specifically, we first capture local sequence variation patterns by extracting the relative positional information of nucleotide fragments at different intervals, which enables robust representation of local genomic semantics. Secondly, the pretrained nucleotide language model DNABERT is applied to capture the semantics of genome sequences by considering the global contextual information. Finally, combined with quorum sensing signals from the bacterial host, a final fusion representation is obtained, which is fed into a predictive model to identify the phage's lifestyle. Experimental results show that our method has excellent and stable performance in both phage complete genome and short contigs from metagenomic data. We also investigate early-life viral colonization in the human gut metagenome, further validating the model's generalizability and real-world applicability.}, }
@article {pmid41915541, year = {2026}, author = {Yue, Y and Kang, YJ and Wang, H and Jiang, H and Zhou, H and Jiang, W and Li, K}, title = {Diagnosis of Cat-Scratch Disease by Metagenomic Next-Generation Sequencing.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {15303667261435870}, doi = {10.1177/15303667261435870}, pmid = {41915541}, issn = {1557-7759}, abstract = {Cat-scratch disease caused by Bartonella henselae is a worldwide distributed zoonotic disease. Cats are the major reservoirs of B. henselae, and human infection cases are usually resulted from contact with pet cats. In this study, a 49-year-old woman presented to the hospital after 10 days of fever. She also complaint lymph node enlargement and pain. Laboratory tests indicated liver dysfunction and inflammation. Pathological examination of the lymph node suggested the possibility of cat-scratch disease, and then doxycycline was used. Metagenomic next-generation sequencing showed that 59496 sequences of B. henselae were identified, confirming the diagnosis of cat-scratch disease. Meanwhile, Acinetobacter towneri and Epstein-Barr virus were also identified. Doxycycline therapy was continued, and the enlargement of lymph node was apparently alleviated. Epidemiological investigation showed that she had a pet cat, and she was possibly infected through direct contact with the cat. Cat-scratch disease in China may be an underestimated disease. Although multiple methods for detecting B. henselae have been established, low bacteremia is still a key challenge to molecular diagnosis. mNGS is a preferable choice for the diagnosis of cat-scratch disease due to its feasibility, sensitivity, and timeliness.}, }
@article {pmid41916285, year = {2026}, author = {Makumbi, JP and Leareng, SK and Bezuidt, OK and Coelho, LP and Makhalanyane, TP}, title = {Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum.}, journal = {Cell reports}, volume = {}, number = {}, pages = {117128}, doi = {10.1016/j.celrep.2026.117128}, pmid = {41916285}, issn = {2211-1247}, abstract = {Inadequate wastewater treatment can drive the spread of antimicrobial resistance (AMR), threatening ecosystems and human health. Extracellular DNA (exDNA) stabilizes antimicrobial resistance genes (ARGs) in the environment and facilitates horizontal gene transfer, yet its taxonomic structure and influence on AMR ecology remain poorly understood, especially in African aquatic systems. We profile exDNA-associated resistomes across nine South African wastewater treatment plants and receiving rivers, comparing single-stage activated sludge process (ASP-only) and combined ASP-biofilter systems. exDNA harbors high-risk mobile ARGs conferring resistance to last-resort antibiotics, with enrichment in effluents and downstream rivers. Surprisingly, upstream river samples also carry abundant ARGs, indicating cumulative inputs from multiple environmental reservoirs. ARGs are mainly associated with Pseudomonadota and Bacteroidota, suggesting that exDNA constitutes an ecologically distinct AMR reservoir dominated by key taxa. These findings underscore the need to integrate exDNA into AMR surveillance and highlight its broader role in microbial adaptation within freshwater environments.}, }
@article {pmid41917109, year = {2026}, author = {Foresto, L and Radaelli, E and Leuzzi, D and Palladino, G and Scicchitano, D and Bejaoui, S and Turroni, S and Rampelli, S and Santolini, C and Pari, A and Marcellini, F and Danovaro, R and Corinaldesi, C and Candela, M}, title = {Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45229-2}, pmid = {41917109}, issn = {2045-2322}, }
@article {pmid41917329, year = {2026}, author = {Sun, Y and Hu, X and Han, J and Wang, Y and Luo, J and Yu, J and Duan, Y and Wang, X and Liu, J}, title = {Rapid and noninvasive artificial intelligence-assisted diagnostic method for oral squamous cell carcinoma.}, journal = {NPJ digital medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41746-026-02527-3}, pmid = {41917329}, issn = {2398-6352}, support = {Grant No. 82272815//The National Natural Science Foundation of China/ ; Grant No. 62322114//The National Natural Science Foundation of China Outstanding Youth Fund/ ; Grant No. YG2023LC06//The Medical Engineering Cross Foundation of Shanghai Jiao Tong University/ ; }, abstract = {Oral squamous cell carcinoma (OSCC) remains the most common head and neck malignancy, for which early detection is critical yet challenging with current invasive methods. This study aimed to establish a comprehensive diagnostic framework for OSCC by integrating proton transfer reaction-time-of-flight mass spectrometry (PTR-TOF-MS) breath analysis and metagenomic sequencing with artificial intelligence (AI). Exhaled breath and saliva samples were collected from participants in a discovery cohort (n = 222) and an external validation cohort (n = 83). Samples were analyzed using PTR-TOF-MS and metagenomic sequencing, and multimodal diagnostic models were constructed and trained on the discovery cohort data. We identified OSCC-specific biomarkers, including methanethiol and Fusobacterium nucleatum, and developed an interactive online platform (https://bio.futurecnn.com/) enabling real-time predictions and biomarker interpretability. The AI-driven diagnostic model achieved excellent accuracy (ROC-AUC: 0.92) in distinguishing OSCC patients from healthy controls in the external set. This approach offers a practical, noninvasive solution for OSCC screening and establishes an adaptable framework for other breath-based diagnostics.}, }
@article {pmid41907005, year = {2026}, author = {Jeunen, GJ and Mills, S and Bailie, M and Mauvisseau, Q and Lamare, M and Mariani, S and Pearman, W and Zavodna, M and Treece, J and Ferreira, S and Gemmell, NJ}, title = {Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70132}, doi = {10.1111/1755-0998.70132}, pmid = {41907005}, issn = {1755-0998}, support = {MFP-UOO2116//Royal Society of New Zealand Marsden Fast-Start Fund/ ; ANTA1801//Ministry of Business, Innovation, and Employment/ ; //University of Otago Research Grant (UORG)/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *Metagenomics/methods ; *Specimen Handling/methods ; RNA, Ribosomal, 16S/genetics ; *Preservation, Biological/methods ; Fishes/genetics ; }, abstract = {Recent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. In this proof-of-concept study, we evaluated the feasibility of extracting historical eDNA from the ethanol preservative used to store museum specimens. We compared a variety of extraction methods (centrifugation, evaporation, filtration, and precipitation) using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a bryozoan, a demosponge, and a glass sponge. Comparative analyses with tissue biopsies revealed that 10 mL ethanol filtration performed equal to or, in some instances, outperformed tissue biopsies for all three specimens when examining the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (α-diversity) and community characterisation (β-diversity). This initial study demonstrates the potential of ethanol preservative as a valuable, non-destructive source of historical eDNA from museum-stored filter-feeding specimens. These findings highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic, metagenomic, and metabarcoding research.}, }
@article {pmid41907295, year = {2026}, author = {Liu, J and Zhou, Y and Xu, F and Liu, W and Chen, H and Yan, Q and Guo, J and Lai, L}, title = {Case Report: Cavitary Legionella pneumophila pneumonia in a kidney transplant recipient: mNGS-guided diagnosis and prolonged combination therapy.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1697062}, pmid = {41907295}, issn = {2296-858X}, abstract = {Legionella pneumophila is an uncommon but potentially life-threatening cause of pneumonia in solid organ transplant (SOT) recipients. Diagnosis is challenging due to nonspecific features and the limited sensitivity of conventional assays. Metagenomic next-generation sequencing (mNGS) offers unbiased detection and may be particularly valuable in immunocompromised hosts with refractory pneumonia. We report the first documented case in Asia of cavitary Legionella pneumonia in a kidney transplant recipient. A 60-year-old man presented with fever and bilateral pulmonary nodules 5 months post-transplant. Despite empirical antifungal and antibacterial therapy, his condition progressed radiologically to cavitary disease. Bronchoalveolar lavage fluid mNGS identified abundant L. pneumophila reads, confirming the diagnosis. Initial azithromycin monotherapy achieved transient improvement but failed to prevent radiological progression. Escalation to prolonged dual therapy with azithromycin and levofloxacin resulted in rapid symptomatic relief, progressive cavity regression on serial computed tomography, and preserved allograft function. Sequential blood-based mNGS demonstrated declining pathogen reads paralleling recovery. This brief research report emphasizes three practice points for SOT recipients with refractory pneumonia: (1) early mNGS can shorten time-to-diagnosis when routine tests are inconclusive; (2) Legionella infection may manifest with atypical cavitary lesions in immunocompromised hosts, warranting scheduled imaging even when symptoms improve; and (3) prolonged macrolide-fluoroquinolone combination therapy may be required for severe or non-resolving cases. Together with our literature review, this case expands understanding of the radiological spectrum, diagnostic strategies, and therapeutic considerations of Legionella pneumonia in transplant populations.}, }
@article {pmid41907709, year = {2024}, author = {Nirmalkar, K and Patel, J and Kang, DW and Bellinghiere, A and Bowes, DA and Qureshi, F and Adams, JB and Krajmalnik-Brown, R}, title = {Bimodal distribution of intestinal Candida in children with autism and its potential link with worse ASD symptoms.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2358324}, pmid = {41907709}, issn = {2993-3935}, abstract = {The gastrointestinal (GI) tract harbors a complex and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e. mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. This work aimed to elucidate the gut mycobiota in a cohort of 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants, autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We performed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota, Saccharomyces cerevisiae was significantly lower (relative abundance) in the ASD fecal samples compared to TD children. Candida and C. albicans demonstrated a bimodal distribution among children with ASD. The small subset of children with elevated C. albicans or decreased S. cerevisiae had increased Autism Treatment Evaluation Checklist (ATEC) scores. Our findings suggest that a deficit of S. cerevisiae, and an overgrowth of C. albicans in a subset of children is associated with worse autism severity. Future work employing shotgun metagenomics with a larger cohort is encouraged to advance understanding of the functional role of fungi, and their possible interplay with GI symptoms and autism severity in children with ASD.}, }
@article {pmid41907719, year = {2024}, author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G}, title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2438621}, pmid = {41907719}, issn = {2993-3935}, abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.}, }
@article {pmid41908157, year = {2024}, author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F}, title = {Diversity and composition of gut protist in young rural Zimbabwean children.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1399160}, pmid = {41908157}, issn = {2813-4338}, abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.
METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.
RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).
SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.}, }
@article {pmid41908294, year = {2026}, author = {Schulz, S and Börner, S and Bitter, K and Gheit, H and Partsakhashvili, J and Ukkat, J and Misiak, D and Reichert, S}, title = {Possible association between the microbiota in subgingival and atherosclerotic plaque in a cohort of patients with carotid stenosis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2648325}, pmid = {41908294}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontal pathogens have been implicated in systemic diseases, including atherosclerosis. This study investigates the relationship between subgingival and microbial colonization of carotid plaque in patients undergoing carotid endarterectomy (DRKS00021598).
METHODS: Microbial samples from both subgingival and carotid plaques were collected from 25 hospitalized patients. Preoperative all patients underwent periodontal examination. The microbial composition was assessed using metagenomics sequencing of 16S rRNA gene (V3/V4 regions).
RESULTS: Bacterial DNA was detected in both subgingival and carotid plaque samples. The microbial composition differed between both communities. Alpha diversity was significantly higher in subgingival samples than in carotid plaques (p = 0.039). Beta diversity analysis, (including unweighted UniFrac (p < 0.001), linear discriminant analysis, principal component analysis) confirmed significant differences between subgingival and carotid plaque microbiota. The study revealed overlaps in a few individual cases.
CONCLUSIONS: These findings show that carotid plaque microbiota differ from subgingival communities and are not exclusively of oral origin, suggesting additional systemic sources.}, }
@article {pmid41908297, year = {2026}, author = {Shantha, JG and Chen, C and Hinterwirth, A and Gonzales, JA and Acharya, NR and Lietman, TM and Doan, T}, title = {Integrated metagenomic sequencing and phage display-based immunoprecipitation sequencing for presumptive viral infection: a case report.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102561}, pmid = {41908297}, issn = {2451-9936}, abstract = {PURPOSE: To report a case of uveitis in which unbiased metagenomic sequencing (MDS) and phage immunoprecipitation sequencing (PhIP-Seq) were performed on intraocular fluid.
OBSERVATIONS: A female patient with a past medical history of human immunodeficiency virus (HIV-1) who presented with chronic active anterior and intermediate uveitis with cystoid macular edema in the left eye. She had a previous ocular history of viral retinitis presumed to be secondary to cytomegalovirus (CMV). An anterior chamber tap was performed for viral polymerase chain reactions (PCRs), MDS, and pathogen PhIP-Seq. PCR testing and MDS were negative for pathogen genetic materials. PhIP-Seq detected antibody enrichment of CMV, as well as HIV-1 andSARS-CoV-2.
CONCLUSIONS: The combination of MDS and PhIP-Seq has the potential to provide additional insights into the pathogenesis and the ocular microenvironment of uveitis patients.}, }
@article {pmid41908958, year = {2026}, author = {Song, Y and Pu, X and Liu, Q and Hou, S and Zou, D and Xiang, Y and Gu, S and Chu, M}, title = {Dietary energy alters jejunal microbial function without changing its structure in small-tailed Han sheep.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1730873}, pmid = {41908958}, issn = {2297-1769}, abstract = {Dietary energy levels typically influence the structure and functional profile of the gastrointestinal microbial community. In this study, thirty 6-month-old Small-tailed Han (STH) sheep were randomly divided into three groups and fed corn-based diets with different energy levels for 150 days. Jejunal contents were then collected and analyzed using metagenomic sequencing to assess microbial alpha diversity and taxonomic composition. Functional annotation and enrichment analysis were performed using the KEGG database. Principal coordinate analysis (PCoA) and alpha diversity indices (Chao1, Shannon, Simpson and good coverage) revealed no significant changes in the overall structure or macro-ecological characteristics of the jejunal microbial community in response to dietary energy levels. At the phylum level, Bacillota was the absolutely dominant phylum, while at the genus level, Methanobrevibacter was the most abundant genus. The abundances of these core microbial taxa did not differ significantly among groups. However, KEGG functional enrichment analysis revealed significant differences in microbial functions between groups. The low-energy group exhibited enrichment in pathways related to energy deficiency and stress adaptation, whereas the high-energy group showed significant enrichment in pathways associated with active growth and anabolic metabolism. In conclusion, although dietary energy levels did not significantly alter the microbial community structure in the jejunum of STH sheep, they profoundly influenced its functional potential. These findings suggest that dietary energy may modulate host nutrient acquisition and health status by regulating the functional characteristics of the jejunal microbiota.}, }
@article {pmid41909054, year = {2025}, author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M}, title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.}, journal = {Applied microbiology (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {}, pmid = {41909054}, issn = {2673-8007}, abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.}, }
@article {pmid41909251, year = {2026}, author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y}, title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1735540}, pmid = {41909251}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.
METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.
RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).
DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.}, }
@article {pmid41909254, year = {2026}, author = {Pan, K and Zhang, Z and Feng, L and Wu, X and Yang, X and He, X and Xiao, Y and Yang, D and Duan, C and Wang, Q}, title = {Biochar regulates putative keystone microbial taxa to drive phosphorus cycling and increase availability in urban greenspace soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786258}, pmid = {41909254}, issn = {1664-302X}, abstract = {The quality of soil in urban green spaces often deteriorates due to poor design practices, insufficient maintenance, and environmental pressures associated with urbanization. Although biochar, as an effective soil additive, can significantly improve the soil quality in greenspace, it significantly influences the phosphorus (P) cycling processes through functional regulation of microbial community; however, further analysis is essential to validate this mechanism. Therefore, this study reported pot experiments using Euonymus kiautschovicus, a typical urban greenspace plant, followed by metagenomic analysis for investigating microbial-driven P cycle mechanisms. Four treatment groups were established according to the dosage of biochar, including 0% (CK), 4% (BC4), 8% (BC8), and 12% (BC12). Biochar application significantly increased soil available P (AP) and total P (TP) content, with BC12 demonstrating maximum AP and TP content of 21.79 mg kg[-1] and 0.62 g kg[-1], respectively. On the one hand, biochar serves as a direct source of P. On the other hand, it enhances AP by regulating P-cycling functional microorganisms. Random forest model identified phnP, phoA, relA, ppnK, pstA, phnD, and pstS as the putative keystone genes regulating soil P cycling. Microbial co-occurrence network analysis and partial least squares path modeling (PLS-PM) demonstrated that the biochar application improved soil AP by regulating putative keystone microbial taxa (Modules 1 and 2) involved in P cycling. This study elucidates the microbial mechanisms underlying biochar-mediated P cycling in greenspace soils, providing a scientific basis for biochar application for improved soil quality in urban greenspace.}, }
@article {pmid41909264, year = {2026}, author = {Li, L and Zhao, D and Du, R and Tang, K and Zhang, Y}, title = {Niche adaptation of particle-associated ammonia-oxidizing archaea sustains nitrification under marine deoxygenation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773718}, pmid = {41909264}, issn = {1664-302X}, abstract = {Marine deoxygenation is restructuring coastal microbial niches and metabolic networks, with cascading effects on biogeochemical cycles, a key component of which is the nitrogen cycle. Particles constitute a critical ecological interface that mediates microbial niche partitioning and oxygen-sensitive balance between nitrogen loss and retention in deoxygenating coastal waters. However, the niche-dependent metabolic partitioning of microbial communities and its influence on the nitrogen cycle under deoxygenation remains poorly constrained. We conducted a 22-day field investigation of the deoxygenated water column off the Zhoushan coast, China, combining temporal [15]N-tracer-based nitrification rate measurements with size-fractionated metagenomic sequencing during the day of the most severe bottom-water oxygen depletion. Our data revealed a nitrification hotspot in the low-oxygen waters below the pycnocline, with persistently elevated rates and an enriched abundance of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria. Notably, particle-associated AOA exhibited significantly enriched genomic potential for coupled nitrogen cycling and carbon fixation, while the dominant groups adapted to low-oxygen particles via distinct metabolic strategies. Nitrosomarinus-like AOA exhibited higher gene counts (amoA-normalized) for ammonia (amt) and high-affinity phosphate (pst) transporters, whereas their Water column group A-like counterparts were enriched in low-affinity phosphate transporters (pit). Urease gene enrichment in both major AOA clades implicates urea as an ecologically relevant alternative nitrogen source for ammonia acquisition in coastal waters. Furthermore, particle-associated AOA may couple nitrite production and consumption via co-enriched ammonium monooxygenase (amoA) and nitrite reductase (nirK), potentially increasing nitrogen loss through local nitrite utilization. Collectively, our findings demonstrate that differential adaptation across clades underpins the pivotal role of AOA in nitrogen cycling under deoxygenation.}, }
@article {pmid41909265, year = {2026}, author = {Nagy, Á and Tóth, GE and Sály, P and Pereszlényi, CI and Babinszky, GC and Makrai, L and Somogyi, BA and Gyuranecz, M}, title = {Development of Nanopore amplicon sequencing method for culture-free genotyping of Bacillus anthracis strains directly from environmental samples.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771578}, pmid = {41909265}, issn = {1664-302X}, abstract = {Fast and accurate genetic subtyping of pathogens is required to respond appropriately to biological events caused by natural outbreaks or bioattacks involving anthrax. In this study, we developed and validated a culture-free genotyping method that combines a multiplex PCR-based amplicon sequencing method on the Nanopore platform with in silico multiple-locus variable-number tandem repeat analysis (MLVA) of 31 loci to identify an unknown Bacillus anthracis strain directly from environmental samples. The novel method accurately identified repeat numbers for all loci in 12 different MLVA genotype Bacillus anthracis strains analyzed in the study, matching 100% with the reference capillary electrophoresis and Sanger sequencing results. The detection limit of the method, at which all 31 variable-number tandem repeat loci were successfully identified, was found to be 10[4] CFU spores/sample for pure spore samples and at 10[6] CFU spores/sample for spiked environmental samples from three matrices (soil, swab, and muddy water). Specificity tests yielded negative results for samples containing only non-Bacillus anthracis members of the Bacillus cereus group, which produced sequencing reads for 15 loci but were non-specific to Bacillus anthracis. To validate the method, we genotyped 11 Bacillus anthracis strains originating from a historical collection of Hungarian isolates. The MLVA31 typing scheme classified the strains into five groups, four of which fell into the A.Br.008/009 Trans-Eurasian (TEA) group within the clade A, and one into the B.Br.CNEVA group within the clade B. The largest group within clade A comprises six strains that are assumed to be members of the dominant Bacillus anthracis population in Hungary. Our results demonstrate that PCR-based amplicon sequencing using the portable MinION device is highly effective for on-site genotyping of pathogens directly from environmental samples. This establishes the NGS-based MLVA genotyping as a valuable tool for biodefense laboratories in preliminary forensic investigations of bioterrorism-related anthrax outbreaks. Furthermore, our results provide new insights into the genetic diversity of Bacillus anthracis in a region (Hungary, Central Europe) that is underrepresented in research and has limited scientific data.}, }
@article {pmid41909643, year = {2026}, author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O}, title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.}, journal = {Biofilm}, volume = {11}, number = {}, pages = {100357}, pmid = {41909643}, issn = {2590-2075}, abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.}, }
@article {pmid41909838, year = {2026}, author = {Zhang, B and Wang, L and Wang, J and Qi, D and Zhang, N}, title = {Comparative diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture in spinal infections: a systematic review and meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1689254}, pmid = {41909838}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Spinal Diseases/diagnosis/microbiology ; *Microbiological Techniques/methods ; }, abstract = {BACKGROUND: Spinal infections are relatively uncommon but clinically serious conditions that require timely and accurate diagnosis to prevent severe complications. Traditional microbial culture methods remain the gold standard but suffer from low sensitivity and prolonged turnaround times. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool offering broad-spectrum pathogen detection. However, its diagnostic performance in spinal infections remains unclear.
OBJECTIVE: To systematically evaluate and compare the diagnostic accuracy of mNGS and conventional microbial culture in detecting pathogens in spinal infections.
METHODS: This systematic review and meta-analysis adhered to the 2020 PRISMA guidelines and was registered in PROSPERO. A comprehensive literature search of PubMed, Cochrane Library, Web of Science, and Scopus was performed up to July 2025. Studies involving suspected spinal infection patients tested by both conventional microbiological methods and metagenomic next-generation sequencing (mNGS) were included. Data extraction and quality assessment were independently conducted by two reviewers using standardized tools. Meta-analyses were performed to pool diagnostic accuracy metrics, and publication bias was assessed.
RESULTS: A total of 14 studies involving 1,353 patients were included after screening 4,132 records. All studies originated from China, with sample sizes ranging from 17 to 301. Quality assessment showed generally high methodological rigor with low risk of bias. Conventional meta-analysis demonstrated that mNGS had significantly better positive agreement (OR = 0.46, p < 0.00001), higher sensitivity (OR = 0.45, p < 0.00001), and superior negative predictive value (OR = 0.36, p < 0.00001) compared to traditional methods, while specificity and positive predictive value were comparable. Diagnostic meta-analysis revealed pooled sensitivity and specificity of 0.86 and 0.90, respectively, with an AUC of 0.90, indicating high diagnostic accuracy. Fagan nomogram analysis showed that with a 50% pre-test probability, positive and negative mNGS results corresponded to post-test probabilities of 89% and 13%, respectively. No significant publication bias was detected.
CONCLUSIONS: mNGS exhibits superior sensitivity and overall diagnostic accuracy compared to traditional microbial culture in spinal infections, supporting its use as a valuable complementary diagnostic tool. Further prospective, multicenter studies are warranted to validate these findings and promote standardized clinical implementation.
PROSPERO, identifier CRD420251114975.}, }
@article {pmid41909845, year = {2026}, author = {Wang, C and Min, M and Dai, Z and Wang, G and Wang, Y and Hu, T and Ma, Y and Zhang, S and Wu, C and Zhou, R}, title = {Diagnostic value of metagenomic next-generation sequencing in patients with febrile lung cancer with negative conventional microbiological tests and without neutropenia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1715563}, pmid = {41909845}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/complications/microbiology/diagnosis ; Retrospective Studies ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Aged ; *Fever/microbiology/diagnosis/etiology ; Aged, 80 and over ; }, abstract = {INTRODUCTION: Fever in nonneutropenic lung cancer often remains microbiologically unresolved because of the limitations of conventional microbiological tests (CMT). We assessed whether plasma metagenomic next-generation sequencing (mNGS) improves diagnostic yield and accelerates defervescence in these patients.
METHODS: We retrospectively analyzed 53 CMT-negative febrile lung cancer patients (August 2023-October 2024). Patients were classified into high-suspicion infectious fever (HSIF) or high-suspicion tumor fever (HSTF) groups based on mNGS results, and clinical management was adjusted accordingly.
RESULTS: mNGS identified pathogens in 69.8% (37/53) of patients, commonly including Epstein-Barr virus, Mycobacterium tuberculosis, and Candida albicans. Patients in the HSIF group showed significantly higher baseline inflammatory markers than those in the HSTF group. Importantly, following mNGS-guided antimicrobial therapy, the HSIF group achieved significantly higher defervescence rates at 48 h (73.0% vs. 37.5%; p = 0.029) and 96 h (89.2% vs. 68.8%; p = 0.027) compared to the HSTF group.
DISCUSSION: In conclusion, in CMT-negative, nonneutropenic febrile lung cancer, plasma mNGS significantly increases pathogen detection and informs antimicrobial decisions associated with earlier defervescence, although interpretation is limited by the retrospective design and lack of an independent gold standard.}, }
@article {pmid41909847, year = {2026}, author = {Huang, Y and Cai, Q and Chen, Y and Amutijiang, D and Lu, Y and Huang, W and Li, L}, title = {Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779296}, pmid = {41909847}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Bacteriophages/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing ; Sputum/virology/microbiology ; Bronchoalveolar Lavage Fluid/virology/microbiology ; *Respiratory Tract Infections/virology/microbiology ; Male ; Female ; Middle Aged ; Bacteria/virology/genetics ; Aged ; Computational Biology ; Adult ; Virome ; }, abstract = {BACKGROUND: Respiratory tract infections are common infectious diseases, with microbial dysbiosis closely linked to clinical outcomes in the host. As key regulators of bacteria, phages can influence the structure and stability of microbial communities by infecting host bacteria. Metagenomic next-generation sequencing (mNGS) enables comprehensive analysis of phage community characteristics in clinical samples.
METHODS: This study included 6,404 clinical samples, comprising 4,837 bronchoalveolar lavage fluids (BALF) and 1,567 sputum samples, for metagenomic next-generation sequencing (mNGS), while collecting patient demographics, sample types, mNGS results, and clinical outcomes. Host-derived sequences were removed post-sequencing and aligned against viral reference databases. Phage community structures across sample types were assessed using alpha and beta diversity metrics. Spearman correlation analysis explored associations between phages and bacteria. Further bioinformatics analysis was performed on 194 samples, including viral sequence assembly and identification using SPAdes, VirSorter2, and PhaMer; CD-HIT clustering and redundancy removal; CheckV quality assessment; PhaTYP lifestyle prediction; Prodigal protein gene annotation; and BLASTP alignment against the CARD database to screen for phage resistance genes.
RESULTS: The sputum and BALF groups exhibited comparable richness, diversity, and evenness, yet their community structures differed significantly. Intensive Care Unit (ICU) admission status was closely associated with reduced phage community diversity and significant alterations in community structure, and the abundance distribution of several phage families (Peduoviridae, Autoscriptoviridae, Casjensviridae, Demerecviridae) also changed significantly. Additionally, the phage community structure in sputum samples was significantly associated with patient clinical outcomes. Correlation analysis demonstrated that the Aliceevansviridae family in sputum samples had extensive positive associations with various bacteria. After assembly, 69.5% of pOTUs were predicted to be temperate phages, and 28.9% were predicted to be virulent phages; moreover, the vast majority (99.2%) of phage sequences showed low similarity to antibiotic resistance genes.
CONCLUSION: This study identifies distinct phage community characteristics across respiratory sample types and reveals that ICU patients exhibit reduced phage diversity and markedly altered community structures. Furthermore, the phage composition in upper respiratory tract samples shows a clear relationship with patient prognosis, providing new insights into respiratory infection microecology.}, }
@article {pmid41909891, year = {2025}, author = {Manzoor, H and Kayani, MUR}, title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2483446}, pmid = {41909891}, issn = {2993-3935}, abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.}, }
@article {pmid41909892, year = {2025}, author = {Montenegro-Borbolla, E and Wakim El-Khoury, J and Bertelli, C and Schoepfer, A and Guery, B and Galperine, T}, title = {Resolution of long-term severe irritable bowel syndrome following fecal microbiota transplantation: A case report and microbiota analysis.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2487905}, pmid = {41909892}, issn = {2993-3935}, abstract = {The diagnosis and management of irritable bowel syndrome (IBS) is challenging due to its complex symptoms and inconsistent treatment responses. Given the important role of gut microbiota in gastrointestinal health, fecal microbiota transplantation (FMT) is a promising intervention. We describe the case of a 55-y-old woman without prior gastrointestinal issues who, following severe depression, developed multiple gastrointestinal symptoms, including abdominal pain, fluctuating bowel habits, and a persistent burning sensation in her mouth and upper gastrointestinal tract. At Lausanne University Hospital, she was diagnosed with IBS resistant to multiple lines of treatment and a multidisciplinary team proposed multiple oral FMTs. One-month post-FMT, her gastrointestinal symptoms significantly improved and remained better after a year, with only the burning sensation persisting. Analysis of pre- and post-FMT samples and donor material, using 16S rRNA amplicon metagenomics, revealed a 90% genus-level taxonomic overlap between the patient and the donor. The observed changes in the relative abundance of these genera, including the enrichment of beneficial gut commensals, as well as the elimination of IBS-associated genera likely supported her recovery. Overall, FMT led to substantial improvement in her long-standing gastrointestinal symptoms.}, }
@article {pmid41909896, year = {2025}, author = {Yasuda, T and Takagi, T and Naito, Y and Inoue, R and Mizushima, K and Asaeda, K and Hashimoto, H and Kitae, H and Uchiyama, K and Ouchi, N and Adachi, A and Kamitani, T and Matoba, S and Itoh, Y}, title = {Sarcopenia-related gut microbiota in the elderly: Insights from the longevity region of Kyotango and its nutritional associations.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2591561}, pmid = {41909896}, issn = {2993-3935}, abstract = {Sarcopenia is influenced by the gut microbiota and dietary habits; however, the underlying mechanisms remain elusive. This study investigated the gut microbiota composition of elderly individuals in a healthy longevity region and examined its association with sarcopenia and dietary habits. Fecal metagenomic analysis was used to identify gut microbiota taxonomy. Sarcopenia was diagnosed on the basis of grip strength, gait speed, and muscle volume. Japanese dietary habits were assessed using a brief-type self-administered diet history questionnaire. A total of 318 elderly individuals from Kyotango were recruited, 5.7% of whom were diagnosed with sarcopenia. Individuals with sarcopenia exhibited a lower abundance of a genus belonging to the family Lachnospiraceae, and a higher abundance of Megasphera. Several butyrate-producing bacteria, including Lachnospira and Coprococcus showed a positive correlation with sarcopenia related factors, whereas Dorea and Streptococcus were negatively correlated. Hierarchical cluster analysis revealed that these beneficial genera were also positively associated with the frequent intake of traditional Japanese dietary components. These findings suggest that the observed microbial and dietary associations may provide a mechanistic basis for potential protective effects against sarcopenia. Our findings suggest that butyrate-producing bacteria associated with Japanese dietary patterns play a protective role against sarcopenia.}, }
@article {pmid41909897, year = {2025}, author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M}, title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2527766}, pmid = {41909897}, issn = {2993-3935}, abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.}, }
@article {pmid41909909, year = {2025}, author = {Wang, H and Yu, S and Zhao, K and Hu, T and Wu, Z and Liang, H and Lin, X and Cui, L and Yao, J and Liu, X and Tong, X and He, N and Xiao, L and Kristiansen, K and Li, S and Zou, Y}, title = {Faecalibacterium longum alleviates high-fat diet-induced obesity and protects the intestinal epithelial barrier in mice.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2459599}, pmid = {41909909}, issn = {2993-3935}, abstract = {Numerous studies have indicated that depletion of Faecalibacterium is related to obesity. Here we show that Faecalibacterium longum CM04-06 out of 29 strains of the Faecalibacterium genus annotated in CGR2 exhibited the strongest inverse correlation with body mass index (BMI) in a cohort of 1120 han Chinese individuals. Administration of F. longum CM04-06 to mice prevented high-fat diet (HFD)-induced obesity, improved glucose tolerance, reduced adipose tissues mass, and liver steatosis. Supplementation with F. longum CM04-06 reduced the level of pro-inflammatory cytokines in liver, colon, and circulation. F. longum CM04-06 protected the intestinal epithelial barrier increasing the expression of tight junction proteins. Metagenomic sequencing indicated that F. longum supplementation did not change the overall composition of the gut microbiota in mice, but selectively increased the relative abundance of Staphylococcus xylosus and Staphylococcus nepalensis. In conclusion, our results point to a potential therapeutic potential of F. longum CM04-06.}, }
@article {pmid41909910, year = {2025}, author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J}, title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2570502}, pmid = {41909910}, issn = {2993-3935}, abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.}, }
@article {pmid41909911, year = {2025}, author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO}, title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2589861}, pmid = {41909911}, issn = {2993-3935}, abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.}, }
@article {pmid41910132, year = {2026}, author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A}, title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019126}, doi = {10.1128/msystems.00191-26}, pmid = {41910132}, issn = {2379-5077}, abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.
IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.}, }
@article {pmid41910137, year = {2026}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0418725}, doi = {10.1128/spectrum.04187-25}, pmid = {41910137}, issn = {2165-0497}, abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.
IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20°C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25°C and 30°C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.}, }
@article {pmid41910214, year = {2026}, author = {Zhang, F and Xu, W and Zeng, R and Chen, J and Huang, J}, title = {Limosilactobacillus reuteri normalizes gut microbiota dysfunction and social deficits of rat offspring associated with prenatal exposure to stress.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649440}, doi = {10.1080/19490976.2026.2649440}, pmid = {41910214}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Pregnancy ; *Limosilactobacillus reuteri/physiology ; Rats ; *Prenatal Exposure Delayed Effects/microbiology ; Male ; Social Behavior ; Oxytocin/metabolism ; Fecal Microbiota Transplantation ; *Stress, Psychological/microbiology ; Rats, Sprague-Dawley ; *Probiotics/administration & dosage ; Paraventricular Hypothalamic Nucleus/metabolism ; Behavior, Animal ; }, abstract = {Prenatal stress (PS) is a potential risk factor for social behavior impairment in offspring. Here, we demonstrate that PS induces gut microbiota alterations that are associated with impaired sociability and social novelty preference in rat offspring. In addition, we found that these behavioral deficits could be partially rescued through either cohousing with normal offspring or fecal microbiota transplantation from control donors. Metagenomic analysis identified Limosilactobacillus reuteri (L. reuteri) as a key species based on the considerable difference in its abundance between the PS and control offspring. Subsequent investigations revealed that supplementing L. reuteri during critical neurodevelopmental windows restored oxytocin levels in the paraventricular nucleus (PVN) and rescued dopamine reward pathway function, thereby ameliorating PS-induced social deficits. Notably, these beneficial effects were completely abolished by either treatment with an oxytocin receptor antagonist or subdiaphragmatic vagotomy. Thus, both oxytocin signaling and vagal afferent pathways play essential roles in the observed benefits of L. reuteri. Our findings indicate that social behavior impairments in offspring exposed to prenatal maternal stress can be explained by a novel mechanism involving the gut microbiota-brain axis: whereby PS-induced depletion of specific commensal bacteria (particularly L. reuteri) disrupts vagus nerve-mediated oxytocinergic modulation of PVN-to-VTA dopaminergic circuits, ultimately leading to social behavior impairments in offspring.}, }
@article {pmid41910252, year = {2026}, author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y}, title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0252325}, doi = {10.1128/aem.02523-25}, pmid = {41910252}, issn = {1098-5336}, abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.}, }
@article {pmid41910273, year = {2026}, author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P}, title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0179025}, doi = {10.1128/msystems.01790-25}, pmid = {41910273}, issn = {2379-5077}, abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.
IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.}, }
@article {pmid41910342, year = {2026}, author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D}, title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0085625}, doi = {10.1128/msphere.00856-25}, pmid = {41910342}, issn = {2379-5042}, abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.
IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.}, }
@article {pmid41910375, year = {2026}, author = {Sprenger, GA and Gee, JE and Elrod, MG and Weiner, ZP and Gulvik, CA}, title = {Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent Burkholderia pseudomallei for rapid public health response events.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0292625}, doi = {10.1128/spectrum.02926-25}, pmid = {41910375}, issn = {2165-0497}, abstract = {Shotgun metagenomics, when sufficient read depth exists for each taxon, enables capturing metagenome-assembled genomes (MAGs) directly from a microbial community. In 2021, an aromatherapy spray contaminated with Burkholderia pseudomallei caused an outbreak of melioidosis in the United States. Metagenome-assembled genome binning depends in part on different nucleotide compositions, and the contaminated aromatherapy spray contained other bacteria, including related species (e.g., Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia multivorans, Burkholderia pseudomultivorans, Cupriavidus pauculus, and Pseudomonas aeruginosa with average nucleotide identity (ANI) to B. pseudomallei being 84.2%, 84.4%, 84.7%, 84.8%, 75.7%, and 72.3%, respectively, and AAI being 79.5%, 79.8%, 80.5%, 80.4%, 62.5%, and 52.9%, respectively). We performed metagenomic sequencing on the contaminated aromatherapy spray to determine if a public metagenomic pipeline (https://github.com/nf-core/mag) can form a MAG of B. pseudomallei. Upon completion of the pipeline, inter- and intracontig comparisons revealed few potential contaminants of related taxa. Conservative removal of those contigs was especially valuable, ultimately obtaining an ANI of 99.9% between the B. pseudomallei MAG and the genome of an isolate from the aromatherapy spray. This underscores the importance of quality checking recovered MAGs (e.g., for congeneric chimerism) for high-resolution objectives such as outbreak pathogenomics. Importantly, our analysis revealed that the identical conclusion was made possible with the B. pseudomallei MAG (as with its corresponding isolate genome), which was that the aromatherapy B. pseudomallei originated from South Asia (specifically India). Because rapid read-based (k-mer) taxonomic classification methods often report false positives, this operational framework could be valuable for rapid biothreat radar detection systems in public health surveillance.IMPORTANCEIn 2021, an imported aromatherapy spray caused a U.S. outbreak of melioidosis after contamination with Burkholderia pseudomallei. Using shotgun metagenomics, we reconstructed a near-complete genome of the pathogen directly from the product, despite the presence of other related microbes. The assembled genome showed 99.9% similarity to a cultured isolate. This work demonstrates that metagenomics can recover high-quality pathogen genomes from complex samples, supporting outbreak investigations and enhancing public health surveillance.}, }
@article {pmid41910449, year = {2026}, author = {Santos, JCE and Go, DJL and Unciano, RD and Yu, PK and Lao, AR and Enriquez, MLD and Espiritu, LM and Shrestha, AMS}, title = {Investigating the resistome, taxonomic composition, and mobilome of bacterial communities in hospital wastewaters of Metro Manila using a shotgun metagenomics approach.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0396325}, doi = {10.1128/spectrum.03963-25}, pmid = {41910449}, issn = {2165-0497}, abstract = {We profiled antibiotic resistance genes, bacterial communities, and mobile genetic elements in untreated hospital wastewater from three tertiary hospitals in Metro Manila using shotgun metagenomic sequencing. The resistome analysis revealed high abundances of genes known to confer resistance against sulfonamides (sul1, sul2), aminoglycosides (aadS), and macrolides/streptogramins (msrE, mphE). High-risk resistance genes were also detected, including those known to confer resistance to β-lactams (blaOXA, blaTEM, blaGES, blaNDM, blaKPC), colistins (mcr-5), and tetracyclines [tet(C), tet(A), tet(L), tet(M)]. Comparisons with hospital wastewater resistome profiles from regional neighbors and other lower-and-middle-income countries indicated broadly similar relative abundances of dominant resistance genes, with differences largely driven by low-abundance resistance genes. The bacterial community was dominated by the phylum Pseudomonadota, with high relative abundances of the genera Stenotrophomonas, Rhodococcus, and Pseudomonas, while ESKAPEE pathogens were detected at lower levels. A diverse array of mobile genetic elements-many known to be associated with resistance to multiple drug classes and disinfectants-was also observed. Overall, this study provides a valuable preliminary evidence base for future antimicrobial resistance and epidemiological surveillance efforts in the Philippines, particularly those employing wastewater-based approaches.IMPORTANCEAntimicrobial resistance (AMR) is a growing public health threat caused by pathogenic bacteria that are no longer controlled by commonly used treatments. Infections caused by these resistant bacteria may lead to prolonged illness, more severe symptoms, or even death. Hospitals are critical hotspots for the emergence and spread of AMR. Their wastewater, which contains antibiotics, medical and human waste, and diverse microbial communities, can support the persistence and dissemination of resistant bacteria. The significance of this research lies in identifying and characterizing these bacterial communities and the resistance genes they carry. Such information can provide an indication of the resistance burden faced by patients and serve as an early warning system to strengthen infection prevention and control measures, support national surveillance efforts, and inform the development of more effective treatment and management strategies in healthcare settings.}, }
@article {pmid41910593, year = {2026}, author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , }, title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.}, journal = {Pancreas}, volume = {}, number = {}, pages = {}, doi = {10.1097/MPA.0000000000002618}, pmid = {41910593}, issn = {1536-4828}, abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.
OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).
METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.
RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.
CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.}, }
@article {pmid41910796, year = {2026}, author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D}, title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41910796}, issn = {1573-7446}, }
@article {pmid41910951, year = {2026}, author = {Dasgupta, S}, title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261419483}, doi = {10.1177/15578100261419483}, pmid = {41910951}, issn = {1557-8100}, abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.}, }
@article {pmid41911008, year = {2026}, author = {Hosen, ME and Horwood, PF and Sarker, S}, title = {Integrating metagenomics and metatranscriptomics into Orthoflavivirus diagnosis: a transformative approach for clinical virology.}, journal = {The Journal of general virology}, volume = {107}, number = {3}, pages = {}, doi = {10.1099/jgv.0.002247}, pmid = {41911008}, issn = {1465-2099}, mesh = {*Metagenomics/methods ; Humans ; *Flaviviridae Infections/diagnosis/virology ; *Flaviviridae/genetics/isolation & purification ; Transcriptome ; *Gene Expression Profiling/methods ; Virology/methods ; }, abstract = {Diagnostic inaccuracies are a major yet often overlooked threat to global health, leading to delayed treatment, preventable harm and systemic gaps in disease control. Among the most affected domains are Orthoflavivirus infections, which pose ongoing diagnostic challenges due to antigenic cross-reactivity, overlapping clinical symptoms and the narrow temporal sensitivity of standard tools such as serology and reverse transcription polymerase chain reaction. These constraints have led to widespread misdiagnoses and underreporting, ultimately hampering both effective clinical management and public health response. Recent advances in metagenomic and metatranscriptomic sequencing offer a transformative solution by enabling unbiased, simultaneous pathogen detection and real-time profiling of viral and host transcriptomics. In this review, we assess the diagnostic performance and translational value of these approaches in resolving Orthoflavivirus infections, with case examples from clinical settings in countries like the USA, UK, China and Germany which have already implemented these approaches into routine diagnosis in some settings. We examine key methodological considerations, including optimal sample timing, sample types and processing, sequencing strategy selection and the diagnostic performance of various platforms. We highlight the growing use of metatranscriptomics for detecting active infections, profiling viral and host responses, identifying coinfections and supporting real-time surveillance. We also discuss the key challenges such as technical expertise, lack of standardization, cost, turnaround time and regulatory approval that currently limit global implementation. Finally, we highlight emerging international efforts to integrate sequencing-based diagnostics into routine hospital workflows. Together, these innovations mark a critical shift toward precision diagnostics for Orthoflavivirus infections, with broad implications for clinical settings.}, }
@article {pmid41911519, year = {2026}, author = {Zhang, H and Cao, Z and Zha, X and Wang, W and Jashenko, R and Hu, H and Ji, R}, title = {Host intestinal microbiota adaptive changes following Paranosema locustae infection and mechanism of chronic pathogenesis.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/jisesa/ieag027}, pmid = {41911519}, issn = {1536-2442}, support = {2023D01D08//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; TSYCLJ0016//Tianshan Talent Training Program/ ; 32260254//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Male ; *Orthoptera/microbiology ; Bacteria/classification ; }, abstract = {Paranosema locustae infection reduces the abundance and diversity of the intestinal bacteria in locusts, although the microbial adaptive changes and the underlying mechanism of chronic pathogenesis remain unclear. In this study, the intestinal microbial changes in Calliptamus italicus (Linnaeus, 1758) (Orthoptera: Acrididae) were analyzed with metagenomic sequencing after P. locustae infection. Results showed that the diversity of intestinal microbial communities in C. italicus declined after P. locustae infection, while the abundance of infection-specific taxa in C. italicus in the experimental groups was significantly higher than those in the control groups, irrespective of sex (P<0.05). The populations of opportunistic pathogenic bacteria such as Klebsiella aerogenes and Enterococcus faecalis increased significantly (P < 0.05). Meanwhile, the abundances of probiotics such as Pediococcus acidilactici and Enterobacter hormaechei increased significantly (P <0.05), which could inhibit the pathogenicity of P. locustae. The results suggested that the interplay of changes in the species and quantities of probiotics and pathogenic bacteria in the intestine of C. italicus after P. locustae infection was an important factor contributing to the difficulty of P. locustae in quickly breaching the host defense system and to its chronic pathogenicity.}, }
@article {pmid41912071, year = {2026}, author = {Zhang, PP and Cui, MY and Shen, Y and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF}, title = {Ophiopogon japonicus Polysaccharide Ameliorates Pulmonary Fibrosis via Gut Microbiota-Metabolite Crosstalk.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108464}, doi = {10.1016/j.micpath.2026.108464}, pmid = {41912071}, issn = {1096-1208}, abstract = {Despite the clinical application of Ophiopogon japonicus in idiopathic pulmonary fibrosis (PF), its key anti-fibrotic components and underlying mechanisms remain poorly defined. Using a bleomycin-induced murine PF model, we systematically compared the efficacy of the total extract (OJTE), polysaccharides (OJTP), saponins (OJTS), and flavonoids (OJTF). The active component was further investigated via integrated metagenomics and metabolomics (serum/feces) to decipher the gut-lung axis mechanism. All O. japonicus components attenuated lung injury and collagen deposition, with OJTP demonstrating the most potent efficacy (reducing lung hydroxyproline content by 42.12% (p < 0.01) compared to the model group). Multi-omics analysis revealed that OJTP remodeled the gut microbiota, notably enriching probiotic strains such as Muribaculaceae bacterium (log2FC = 2.17) and Duncaniella muricolitica (log2FC = 2.06), as well as the polysaccharide-utilizing species Prevotella sp. MGM2 (log2FC = 2.79). Concomitantly, OJTP significantly altered host metabolism, upregulating key metabolites including urobilinogen (p < 0.0001) and 5-amino valeric acid betaine (5-AVAB, p < 0.002). These metabolites are implicated in porphyrin and amino acid metabolism, respectively. Correlation networks further established strong associations between these OJTP-modulated microbes and metabolites. Our study first identifies OJTP as the primary bioactive component of O. japonicus against PF. We propose a novel trans-organ mechanism wherein OJTP ameliorates PF via orchestrating a "gut microbiota-metabolite" axis, highlighting the therapeutic potential of targeting polysaccharide-probiotic synergy.}, }
@article {pmid41912361, year = {2026}, author = {Rathwell, C and Fuchsman, CA and Rocap, G}, title = {Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70274}, doi = {10.1111/1462-2920.70274}, pmid = {41912361}, issn = {1462-2920}, support = {DGE-2140004//National Science Foundation/ ; DEB-1542240//National Science Foundation/ ; OCE-2022911//National Science Foundation/ ; }, mesh = {Pacific Ocean ; *Bacteria/virology/genetics/classification/metabolism ; Phylogeny ; *Chlorophyll/metabolism/analysis ; *Microbiota ; *Seawater/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {Oxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.}, }
@article {pmid41912389, year = {2026}, author = {Wang, YY and Zhang, Q and Zhao, ZF and Zhao, YX and He, Y and Liu, PL and Li, YH}, title = {[Coexistence of lung cancer, brucellosis, and tuberculosis in a single patient: a case report].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {4}, pages = {421-424}, doi = {10.3760/cma.j.cn112147-20260105-00006}, pmid = {41912389}, issn = {1001-0939}, support = {H2024206551//Hebei Natural Science Foundation/ ; 20260411//Hebei Medical Research Project/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Lung Neoplasms/complications/diagnosis ; *Brucellosis/complications/diagnosis ; *Tuberculosis, Pulmonary/complications/diagnosis ; Mycobacterium tuberculosis/isolation & purification ; *Carcinoma, Squamous Cell/complications/diagnosis ; Coinfection ; }, abstract = {Lung cancer, pulmonary tuberculosis, and brucellosis are common clinical diseases. They share overlapping clinical manifestations and pulmonary imaging findings, and all may involve multiple organ systems, making differential diagnosis challenging. We reported a rare case of lung cancer, and co-infection with pulmonary tuberculosis and brucellosis. A 57-year-old male was admitted to our hospital, presenting with intermittent fever for 7 months and cough accompanied by shortness of breath for 1 month. He had previously sought medical care at multiple hospitals, where he was diagnosed with brucellosis and suspected of having pulmonary tuberculosis. Despite receiving anti-tuberculosis and anti-brucellosis treatments, his pulmonary imaging abnormalities and dyspnea progressively worsened. Pathological examination of mucosal biopsies obtained via bronchoscopy and cervical lymph node biopsy at our hospital confirmed squamous cell lung carcinoma. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid detected Mycobacterium tuberculosis. Although his pulmonary condition temporarily improved following standardized anti-tuberculosis treatment and chemotherapy for lung cancer, the lung cancer subsequently progressed, and the patient ultimately died.}, }
@article {pmid41912482, year = {2026}, author = {Shao, Y and Wang, J and Liu, Y and Ni, Y and Liu, Z and Li, Y and Jia, Q and Li, Q and Wang, X and Li, T and Liu, M and Zhang, S and Guo, Y and Guo, X and Wang, D and Liu, Y and Liu, C and Cai, H and Ning, Y and Zhang, J and Xu, G and Le, W}, title = {Distinct metabolomic and proteomic signatures in Parkinson's disease patients with REM sleep behavior disorder.}, journal = {Signal transduction and targeted therapy}, volume = {11}, number = {1}, pages = {}, pmid = {41912482}, issn = {2059-3635}, support = {82271524//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401742//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024RY003//Dalian Science and Technology Bureau/ ; No. 2023-MS-262//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Humans ; *Parkinson Disease/genetics/metabolism/complications/microbiology/pathology/blood ; Female ; Male ; *REM Sleep Behavior Disorder/genetics/metabolism/pathology/blood/complications/microbiology ; *Metabolomics ; Middle Aged ; Aged ; *Proteomics ; Gastrointestinal Microbiome/genetics ; }, abstract = {Rapid eye movement sleep behavior disorder (RBD) is the most specific prodromal marker of Parkinson's disease (PD), affecting 40-50% of PD patients. PD with RBD (RBD-PD) represents a clinically aggressive subtype characterized by more severe motor and nonmotor symptoms, prominent autonomic dysfunction, and accelerated disease progression; however, its underlying pathogenesis remains poorly understood. Here, we integrated multiplatform metabolomics and proteomics with precise clinical phenotyping to delineate molecular signatures in plasma across different PD subtypes. Our analyses demonstrated that PD patients exhibit significant metabolic reprogramming, characterized by a shift in energy metabolism from the tricarboxylic acid cycle toward glycolysis, a dysregulated urea cycle, and lipid remodeling, as well as extensive activation of inflammatory and immune responses involving the PI3K-Akt, IL-17, NF-kappaB, MAPK and TNF signaling pathways. Notably, the RBD-PD subgroup exhibited distinctive metabolic disturbances characterized by the accumulation of gut microbiota-derived toxic aromatic amino acid catabolites. Importantly, these alterations were also observed in idiopathic RBD (iRBD) patients, representing the prodromal stage of PD. By integrating metagenomic profiles, we further revealed that gut microbial dysbiosis in RBD-PD and iRBD drives a functional shift away from dietary fiber fermentation and toward enhanced degradation of protein, aromatic amino acids, glycine, and intestinal mucin glycans. This metabolic reprogramming is associated with exacerbated oxidative stress, neuroinflammation, and accelerated pathological progression. These findings provide multiomic evidence that clarifies the molecular heterogeneity in PD and highlights gut microbiota-driven dysfunction as a key contributor to both the iRBD and RBD-PD subtypes.}, }
@article {pmid41912529, year = {2026}, author = {Achudhan, AB and Narayanan, R and Madhavan, T}, title = {Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07068-8}, pmid = {41912529}, issn = {2052-4463}, abstract = {Plastic pollution is an escalating environmental concern, particularly in coastal regions where sediments serve as long-term sinks for plastic debris. Despite this, the microbial communities inhabiting plastic-contaminated sediments remain poorly characterized in highly polluted hotspots. In this study, we conducted a genome-resolved metagenomic investigation of sediment sample from plastic pollution hotspot in India. Using Illumina short-read sequencing and three high-performing binning tools we reconstructed 52 non-redundant metagenome-assembled genomes (MAGs) from 2,374 initial bins. All MAGs met the MIMAG criteria with 15% reaching near-complete genomes. Taxonomic classification revealed diverse representation of 18 different phyla. Interestingly, 90% of the MAGs could only be classified at intermediate taxonomic levels in the Genome Taxonomy Database (GTDB), suggesting the presence of novel microbial lineages. Taxonomic novelty was further confirmed using the Type Strain Genome Server (TYGS), which identified 3 novel orders, 16 families, and 28 genera. This study provides the first comprehensive genomic insight into microbial communities from plastic-polluted coastal sediments in India and lays the groundwork for exploring their ecological functions.}, }
@article {pmid41913056, year = {2026}, author = {Marques, LL and Pinho, AJ and Pratas, D}, title = {FALCON2: compression-based metagenomic classification of ancient viruses.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag155}, pmid = {41913056}, issn = {1367-4811}, abstract = {MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples.
RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC = 0.625), Kraken2 (AUPRC = 0.184), and CLARK-S (AUPRC = 0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40 bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8 GB RAM for typical analyses.
AVAILABILITY: FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41704740, year = {2026}, author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C}, title = {Integrated metagenomic and metabolomic analysis reveals regional style differences in Maotai-flavour Baijiu.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100558}, pmid = {41704740}, issn = {2666-5174}, abstract = {This research focused on Maotai-flavour Baijiu from three representative production regions in the Chishui River Basin, namely Maotai Town (MT), Jinsha (JS), and Renhuai (RH). By integrating metabolomics and macrogenomics techniques, the study analyzed the differences in volatile flavor compounds and microbial community structures in the fourth-round fermented grains and base liquor. Additionally, it explored the associative mechanism between microorganisms and flavor metabolism. The findings indicate that the microbial community compositions of fermented grains vary significantly across different production areas. The production area of Maotai Town mainly consists of Saccharomyces and Lactobacillus, with the highest content of ester substances. The fungal community in Jinsha is extremely stochastic, abundant in Mucoromycota, and has elevated contents of aldehydes and phenols. The distribution of microorganisms and flavor substances in the Renhuai production area lies between the two. The sensory evaluation of the base liquor indicates that the Jinsha production area features prominent floral and fruity aromas, the Maotai Town exhibits significant sour and sauce aromas, and the Renhuai production area has a well-balanced flavor. The correlation analysis shows that yeasts such as Saccharomyces and Pichia are positively correlated with esters such as ethyl acetate, while bacteria such as Limosilactobacillus are closely associated with short-chain fatty acid metabolism. This research reveals the microbiological basis for the differences in the Maotai style among different production regions and provides a theoretical foundation for regional characteristic production and process optimization.}, }
@article {pmid41704794, year = {2025}, author = {Basu, U and Ahanger, SA and Gai, X and Hu, X}, title = {Longitudinal metagenomics reveals continuous restructuring of soil pathobiome under persistent Phytophthora pressure.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1749879}, pmid = {41704794}, issn = {1664-462X}, abstract = {Soil borne pathogen, Phytophthora nicotianae causes black shank disease in tobacco, present a pervasive threat to global agriculture, with conventional control strategies often proving inadequate. A critical gap exists in our understanding of the long-term, dynamic interplay between the pathogen and the soil microbiome. To address this, we conducted a six-year longitudinal metagenomic study in a monocultured tobacco field, revealing a pathobiome in constant, non-equilibrium adaptation. Our analysis uncovered profound microbial restructuring, beginning with cumulative transcriptional reprogramming of highly significant genes. Functional profiling showed a critical metabolic shift toward anabolic capacity, with a 66.7% increase in KEGG orthologs and enrichment of amino acid biosynthesis (+8.9%), ribosomes (+13.0%), and quorum sensing (+11.0%). The soil resistome underwent dramatic succession, featuring an initial coordinated defense (R[2]=0.825), a comprehensive collapse in Year 3-4 (917 downregulated genes), and a resilient recovery that drove a net increase in antibiotic resistance, indicating a lasting ecosystem alteration. Virulence factor evolution revealed strategic trade-offs, with flagella systems dominating (2,583 occurrences) while more costly energy consuming secretion systems declined, and 87 core virulence factors persisted across time. Crucially, we observed a widespread decoupling between genetic potential and functional expression; key categories for defense and signal transduction declined in abundance (slopes of -150.4 and -264.9, respectively) despite stable gene counts, suggesting a systemic, energy conserving survival strategy. Concurrently, the community experienced progressive diversity loss (Shannon index slope = -0.0464/yr at genus level) despite maintained species richness (717 species), indicating restructuring was driven by shifting evenness rather than species loss. Our findings exhibit that persistent pathogen pressure drives the soil microbiome into a continuous state of adaptive restructuring, prioritizing coordinated defensiveness and metabolic efficiency over stability. This time resolved framework challenges static views of soil ecosystems and provides a foundational dataset for developing predictive, microbiome informed strategies to manage soil borne diseases sustainably.}, }
@article {pmid41704809, year = {2026}, author = {Zhang, M and Jiao, T and Li, W}, title = {Allergic bronchopulmonary aspergillosis in a patient without history of asthma: a case report.}, journal = {Medical mycology case reports}, volume = {51}, number = {}, pages = {100770}, pmid = {41704809}, issn = {2211-7539}, abstract = {Allergic bronchopulmonary aspergillosis (ABPA) is a pulmonary hypersensitivity disease triggered by Aspergillus fumigatus. While the standard first-line therapy per International Society for Human and Animal Mycology (ISHAM) guidelines is glucocorticoids or itraconazole alone, combination therapy may be used briefly for rapid symptom control. We present a 39-year-old man without asthma who presented with cough and sputum. Chest computed tomography (CT) revealed diagnostic findings of central bronchiectasis and high-attenuation mucus, later confirmed as mucus plugs by bronchoscopy. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) detected a high load of A. fumigatus. Markedly elevated total IgE, A. fumigatus-specific IgE, and eosinophils confirmed ABPA. Although initial voriconazole monotherapy failed, adding oral glucocorticoids led to rapid clinical and radiographic improvement. No recurrence was observed on CT 7 months post-treatment, reinforcing that asthma is not a prerequisite for ABPA diagnosis.}, }
@article {pmid41704848, year = {2025}, author = {Nayak, D and Behera, P and Singh, S and Tripathy, PS and Dash, SS and Dasgupta, M and Mohanty, S and Sahoo, MR and Satapathy, CR and Sasmal, A and Sahu, S}, title = {Sucrose supplementation influences gut microbial diversity and functional shifts in Apis cerana indica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1733283}, pmid = {41704848}, issn = {1664-302X}, abstract = {Honeybee colonies are increasingly threatened by nutritional scarcity and biotic stressors, underscoring the need to understand the role of gut microbiota in mitigating these challenges. This study examined the gut microbial composition of Apis cerana indica under two dietary regimes: sucrose-fed and sucrose-unfed, to assess how nutrition influences microbial diversity and metabolic potential following metagenomics. Metagenomic sequencing of gut samples revealed 147,146 contigs, with the longest and shortest contigs measuring 615,154 kb and 200 kb, respectively. Comparative analysis indicated a higher relative abundance of Bacillus spp. in sucrose-fed bees, whereas Enterococcus was more dominant in unfed populations. Sucrose feeding significantly enhanced gut microbial diversity (Shannon index: 2.59; Simpson's index: 0.87) compared to unfed bees (Shannon: 1.91; Simpson: 0.68). Key genera, including Gilliamella, Bacillus, and Lactobacillus, were consistently present but showed varying relative abundances. Functional annotation via KEGG pathway analysis revealed elevated activity of glycolysis and the pentose phosphate pathway in sucrose-fed bees, with exclusive detection of key metabolic enzymes, hexokinase and enolase. Additionally, elevated sucrose metabolism and proteolytic enzyme activity were noted, reflecting enhanced metabolic versatility. Our findings highlight the importance of sucrose dietary supplementation in shaping gut microbial structure and function, their diversity, and metabolic capacity, suggesting its potential as a practical nutritional intervention to sustain honeybee health during a period of floral dearth. The outcome of the study encourages exploring the long-term ecological and physiological impacts of dietary strategies on colony resilience and productivity.}, }
@article {pmid41704904, year = {2025}, author = {Av, EZ and Greenberg, A and Knaan, T and Melanson, EL and Youngster, I and Dubnov-Raz, G and Borenstein, E and Gepner, Y}, title = {The associations between physical activity, microbiome and metabolic adaptation in sedentary overweight adults.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1722274}, pmid = {41704904}, issn = {2296-861X}, abstract = {Despite well-established benefits of exercise on metabolic regulation and the gut microbiome (GM), its impact on body composition is inconsistent and often attenuated by metabolic adaptation. This compensation mechanism adjusts energy expenditure including total daily energy expenditure (TDEE) and resting metabolic rate (RMR). Intra-individual variation in exercise response remains unclear, but might be explained by the GM. In this well-controlled study, we investigated the relationship between aerobic exercise, GM composition, and metabolic adaptation in a cohort of 16 sedentary overweight adults (ages 21-45, 50% female) over a 12-week moderate-intensity intervention (65-75% HRmax; 20 kcal/kg/week). Pre- and post-intervention RMR was measured via whole-room calorimetry, TDEE by doubly labeled water, and GM composition via shotgun metagenomics. While body composition did not change at the group-level, a subset of participants ("responders") showed improved body composition and aerobic capacity. Using machine learning, we identified bacterial species, including Faecalibacterium prausnitzii species, whose abundance pre-training is predictive of response. Additionally, we found that responder GM communities are more compositionally cohesive and post-training increases in GM diversity are associated with higher TDEE and RMR. These findings highlight the complex interaction between exercise, metabolism and the GM, and suggest that baseline GM characteristics may contribute to individual variability in metabolic adaptation. This insight may help guide microbiome-informed strategies to enhance exercise efficacy. Clinical trial registration: ClinicalTrials.gov, identifier NCT04460040.}, }
@article {pmid41704957, year = {2026}, author = {Zhu, J and Xia, T and Wang, L and Yin, X and Ma, Y and Shen, J}, title = {Investigating the benefits of metagenomic next-generation sequencing for patients experiencing infections after total hip replacement surgery: a retrospective cohort study with a minimum of one year of follow-up.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1735867}, pmid = {41704957}, issn = {2235-2988}, mesh = {Humans ; Male ; Middle Aged ; *Arthroplasty, Replacement, Hip/adverse effects ; Female ; Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/microbiology/diagnosis/drug therapy ; Aged, 80 and over ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Follow-Up Studies ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) technology in diagnosing and treating periprosthetic joint infection (PJI) following total hip arthroplasty (THA).
METHODS: From September 2018 to September 2024, 15 patients with periprosthetic infection after total hip arthroplasty were admitted. There were 11 males and 4 females; ages ranged from 28 to 87 years old, with an average of 63 years old. Infection occurred 6 to 42 months after total hip arthroplasty, with an average of 22.7 months. The infection lasted between 15 and 115 days, averaging 37.6 days. After being admitted to the hospital, joint fluid was collected for bacterial culture and mNGS. Following admission, joint fluid was collected for bacterial culture and mNGS, and antibiotics were adjusted based on the results, with surgery used to control the infection if needed.
RESULTS: Bacterial culture method was positive in 10 cases (66.7%), with a total of 12 pathogenic bacteria types detected. MNGS was positive in 15 cases (100.0%), with a total of 19 pathogenic bacteria types detected. There was a statistically significant difference in the positive rate between the two methods (P < 0.05). Out of the 10 patients, 5 who tested positive using both the bacterial culture method and mNGS test showed identical pathogenic bacterial types, resulting in a 50.0% compliance rate. The testing time (from sample delivery to results) was (3.07 ± 0.96) days for bacterial culture method and (1.67 ± 0.49) days for mNGS test, and the difference was statistically significant (t=5.03, P<0.001). The patients were followed up for 13 to 82 months, with a mean of 40.7 months. In one patient, the infection returned three months after undergoing one-stage revision surgery, while the other 14 patients showed no signs of infection, resulting in an infection control rate of 93.3%.
CONCLUSION: MNGS can detect the pathogenic bacteria of postoperative PJI after THA more quickly and accurately than the bacterial culture method, which is crucial for guiding antibiotic and surgical treatment combinations for patients with postoperative PJI after THA.}, }
@article {pmid41705163, year = {2026}, author = {}, title = {Correction to: Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag020}, doi = {10.1093/ismeco/ycag020}, pmid = {41705163}, issn = {2730-6151}, abstract = {[This corrects the article DOI: 10.1093/ismeco/ycaf183.].}, }
@article {pmid41705261, year = {2026}, author = {Fentie, EG and Lim, K and Andargie, YE and Park, S and Shin, JH}, title = {Preserving fermented-foods microbial diversity through systematic culturomics for the discovery of multi-strain probiotic candidates.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101318}, pmid = {41705261}, issn = {2665-9271}, abstract = {Fermented foods (FFs) represent complex living ecosystems that deliver viable microbes and bioactive metabolites linked to human health benefits. However, many probiotic strains isolated from FFs fail to reproduce these effects in vivo, likely due to the disruption of their natural ecological synergy during isolation. Here, we employed a systematic, ecology-aware culturomics framework to transform the Kimchi microbiome into genome-vetted, multi-species probiotic candidates while preserving ecological fidelity. Specifically, 56 distinct enrichment culture conditions were established using six liquid media (In-situ, MRS, NB, TSB, BHI, BB) across varied redox states (aerobic, anaerobic, microaerophilic), incubation periods (12 h, 66 h), and selective suppressants (CHIR-090, nalidixic acid). Results indicated that In-situ and MRS media under microaerophilic conditions effectively preserved the lactobacilli core, whereas generalist media and aeration expanded taxonomic breadth to include rare taxa. Furthermore, extended incubation (66h) successfully unlocked 107 unique taxa compared to the limited diversity of short incubation (12h). Shotgun metagenomic mining further revealed promising functional properties, including acid tolerance, adhesion modules, and diverse bacteriocin-skewed biosynthetic gene clusters. Crucially, the collection exhibited a strong safety profile: only 1 % of identified risk factors were antibiotic resistance genes (ARGs) on mobile genetic elements (MGEs), and only 4 % represented colocalized ARGs, virulence factors, and MGEs. Systematic-culturomic isolation later yielded over 90 strains, including Weissella, Bacillus, and Lactococcus, significantly expanding beyond standard lactobacilli-centric portfolios. Overall, this study confirms that ecology-aware culturomics captures the functional diversity of the Kimchi microbiome, providing a scalable model for realizing the full therapeutic potential of FFs.}, }
@article {pmid41705811, year = {2026}, author = {Paietta, EN and Kraberger, S and Gordon, M and Ehmke, E and Yoder, AD and Varsani, A}, title = {Metagenome-assembled genomes of anelloviruses in crowned lemur and aye-aye swabs.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0147325}, pmid = {41705811}, issn = {2576-098X}, abstract = {Two circular, complete genomes of anelloviruses were identified from a crowned lemur anal swab and an aye-aye skin swab from individuals at the Duke Lemur Center (Durham, NC, USA). The anelloviruses represent two species in the Anelloviridae family and expand a developing lemur-associated anellovirus lineage.}, }
@article {pmid41705822, year = {2026}, author = {Guo, Z and Xiao, Y and Zhao, J and Tang, Z and Lin, Y and Yang, K}, title = {MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0242225}, pmid = {41705822}, issn = {1098-5336}, support = {22176133//National Natural Science Foundation of China/ ; }, mesh = {*Metagenome ; *Anti-Bacterial Agents/pharmacology ; Microbiota ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Computational Biology/methods ; }, abstract = {The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.}, }
@article {pmid41705858, year = {2026}, author = {Teixeira Martins, C and Gombert, AK and Venturini, AM}, title = {Lactobacillus and Limosilactobacillus MAGs from alcoholic fermentation in sugarcane biorefineries.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0070525}, pmid = {41705858}, issn = {2576-098X}, support = {2022/15256-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/10728-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306190/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {We recovered and characterized four bacterial MAGs from two Brazilian sugarcane biorefineries, with the aim of investigating the microbial environment during fuel ethanol production. MAGs belonged to Lactobacillus amylovorus and Limosilactobacillus fermentum, both known lactic acid bacterial contaminants. Genomic analyses revealed key functional traits but no resistance or virulence genes.}, }
@article {pmid41705859, year = {2026}, author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM}, title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0134625}, pmid = {41705859}, issn = {2576-098X}, support = {2020/11534-0, 2022/15112-8, and 2017/03172-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 88887.514375/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.}, }
@article {pmid41706260, year = {2026}, author = {Matsumoto, M and Shiotani, A and Osawa, M and Handa, O and Matsumoto, H and Umegaki, E and Yonezawa, H and Osaki, T}, title = {Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.}, journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association}, volume = {29}, number = {2}, pages = {338-346}, pmid = {41706260}, issn = {1436-3305}, support = {Research Project Grant//Kawasaki Medical School/ ; }, }
@article {pmid41707175, year = {2026}, author = {Huang, X and Deng, K and Zhu, G and Huang, W and Gong, G and Liu, H and Yang, T and Gui, Y and Li, W}, title = {Dynamics of soil microbiome throughout the cultivation life cycle of Phallus rubrovolvatus.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-14}, doi = {10.1139/cjm-2025-0279}, pmid = {41707175}, issn = {1480-3275}, mesh = {*Soil Microbiology ; *Microbiota ; China ; Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Metagenomics ; Metagenome ; }, abstract = {Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of Phallus rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during Phallus rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.}, }
@article {pmid41707285, year = {2026}, author = {Du, Z and Li, Z and Chen, X and Liu, M and Feng, L and Li, Q and Chen, Z and Chen, Q}, title = {Laboratory-scale simulation study on the bioremediation of marine oil pollution by phosphate-solubilizing bacteria Bacillus subtilis PSB-1.}, journal = {Marine pollution bulletin}, volume = {226}, number = {}, pages = {119422}, doi = {10.1016/j.marpolbul.2026.119422}, pmid = {41707285}, issn = {1879-3363}, abstract = {Phosphate-solubilizing bacteria (PSB) are well-known for their ability to convert nonbioavailable phosphates into bioavailable forms, however, research on PSB that possess both phosphate solubilization and crude oil degradation capabilities in marine environments has not yet been explored, and the role of these bacteria in microbial remediation of petroleum contamination in seawater needs be investigated. In this study, laboratory simulated marine oil spill bioremediation experiment was carried out to explore the role of PSB with crude oil degradation capabilities (A strain of PSB-1 used in this study) in petroleum hydrocarbon degradation by indigenous microorganisms in marine environment. It was found that PSB-1 significantly enhanced crude oil removal, with a degradation efficiency of 60% achieved after 30 days at a crude oil concentration of 1 g/L, Concurrently, the concentration of soluble phosphate in seawater increased to 47.36 mg/L, reflecting a 170% increase compared to the control. Metagenomic analysis further indicated that the phosphate-solubilizing activity of PSB-1 not only augmented phosphate availability but also stimulated the growth and succession of indigenous hydrocarbon-degrading microorganisms, thereby altering the microbial community structure and improving overall degradation capacity. These findings highlight the ecological significance of PSB-1 in facilitating crude oil biodegradation in marine environments and offer novel insights into bioremediation strategies for crude oil-contaminated seawater.}, }
@article {pmid41707316, year = {2026}, author = {Yang, J and Meng, X and Zhang, H and Sun, W and Yang, L and Li, S}, title = {Mobile genetic elements drive the assembly of high-risk resistance and virulence configurations at the riverine water-sediment interface.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {124055}, doi = {10.1016/j.envres.2026.124055}, pmid = {41707316}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; *Interspersed Repetitive Sequences ; *Rivers/microbiology ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/pathogenicity ; Virulence/genetics ; Water Pollutants, Chemical ; Virulence Factors/genetics ; }, abstract = {Riverine ecosystems are major conduits and repositories for microplastics, heavy metals and antibiotics yet how these co-occurring stressors jointly shape resistance and virulence risks across water and sediments remains unclear. Here we combined shotgun metagenomics with pollutant profiling along a representative rural-to-urban gradient during the dry season to resolve the distribution, mobility and drivers of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), virulence factors (VFs) and mobile genetic elements (MGEs) in paired surface waters and surficial sediments. Bacterial communities were dominated by Pseudomonadota and Actinomycetota while fungal communities were dominated by Ascomycota and Uroviricota respectively with stronger land-use effects observed in water than in sediments. Across all samples we detected 36 ARG classes and 1589 subtypes where multidrug and efflux or target alteration mechanisms predominated. Furthermore ARG richness, abundance and diversity increased from rural to urban reaches in both media. MGEs were dominated by transposases where ARG-MGE co-localization on 1474 contigs revealed dense transposase-centered networks in urban sediments that linked multidrug, peptide, glycopeptide and tetracycline resistance. Crucially we identified contigs co-harboring ARGs, MRGs, and VFs as multi-trait risk gene carriers. Urban reaches hosted diverse carrier lineages whereas rural reaches were dominated by the high abundance of specific carriers. SourceTracker and partial least squares path modeling together indicated that rural sediments are the principal upstream sources of microbes and risk genes while MGEs in urban sediments translate multi-pollutant stress into enlarged and more mobile risk gene pools. These findings highlight the need to jointly manage agricultural inputs and urban sediments under multi-stressor conditions.}, }
@article {pmid41707391, year = {2026}, author = {Werid, GM and Hemmatzadeh, F and Batterham, T and Miller, D and Edwards, R and Trott, DJ and Petrovski, K}, title = {Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease.}, journal = {Veterinary microbiology}, volume = {315}, number = {}, pages = {110926}, doi = {10.1016/j.vetmic.2026.110926}, pmid = {41707391}, issn = {1873-2542}, mesh = {Animals ; Cattle ; *Lung/microbiology/virology ; *Cattle Diseases/microbiology/virology ; Metagenomics ; *Dysbiosis/veterinary/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Virome ; Microbiota ; Australia ; *Bovine Respiratory Disease Complex/microbiology/virology ; Bacteriophages/genetics ; }, abstract = {Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.}, }
@article {pmid41707423, year = {2026}, author = {Francés, Á and López, M and González-Raurich, M and Cobo-Díaz, JF and Prieto, M and Allende, A and Gil, MI and Truchado, P and Alvarez-Ordóñez, A and Oliveira, M}, title = {Characterization of microbial diversity, chemical hazards and antimicrobial resistant bacteria in wash water from a fresh-cut vegetable processing plant.}, journal = {International journal of food microbiology}, volume = {452}, number = {}, pages = {111667}, doi = {10.1016/j.ijfoodmicro.2026.111667}, pmid = {41707423}, issn = {1879-3460}, mesh = {*Bacteria/drug effects/genetics/isolation & purification/classification ; *Vegetables/microbiology ; *Drug Resistance, Bacterial ; *Water Microbiology ; Food Handling ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Pesticides/analysis ; Microbial Sensitivity Tests ; }, abstract = {This study investigated the quality of process wash water (PWW) in an industrial fresh-cut produce facility. Traditional microbiological and physico-chemical parameters, such as aerobic mesophilic counts, coliforms, molds and yeasts, pH, free chlorine, oxidation-reduction potential, and organic matter indicators, were monitored to contextualize water quality dynamics across the workday. Additionally, untargeted analyses were performed to characterize the microbiome and resistome and identify chemical hazards in PWW, highlighting the occurrence of antimicrobial-resistant bacteria and the presence of some pesticides at low levels, including chlorantraniliprole, cyprodinil, fludioxonil, and propyzamide, in a real-world processing environment. Antimicrobial susceptibility tests and whole genome sequencing of twelve coliform isolates revealed multidrug-resistant strains, including Enterobacter mori, Enterobacter ludwigii, and Klebsiella oxytoca, carrying resistance genes such as oqxB, fosA, and blaACT-12, as well as the plasmid-borne blaOXY-2-2. Metagenome analyses revealed a microbial community dominated by the genus Pseudomonas, together with high abundance of Rheinheimera mangrovi and Pantoea agglomerans. Moreover, resistome analysis disclosed that 83% of detected antimicrobial resistance genes were associated with beta-lactam resistance. Additionally, the efficacy of chlorine against one K. oxytoca isolate obtained from PWW using a dynamic system simulating a produce washing operation confirmed that maintaining pH at 6.5 and stable free chlorine levels of 6 mg/L was sufficient for complete inactivation. These findings demonstrate the importance of implementing proper wash water management practices in fresh produce processing, including preventing excessive organic matter accumulation through adequate water replenishment and maintaining chemical parameters within the validated operational range, supported by systematic verification and monitoring.}, }
@article {pmid41707490, year = {2026}, author = {Jian, Z and Zhao, R and Zi, X and He, S and He, X and Ye, Y and Wang, K and Ge, C and Jia, J and Hu, Y and Dou, T}, title = {Sustainable antibiotic reduction in poultry production with Pulsatilla saponins and herbal supplementation.}, journal = {Poultry science}, volume = {105}, number = {5}, pages = {106562}, pmid = {41707490}, issn = {1525-3171}, abstract = {The prolonged use of antibiotics in poultry production promotes the accumulation and spread of antibiotic resistance genes (ARG), raising concerns for animal health and public safety. Developing effective antibiotic alternatives that support performance while limiting resistance risk is therefore a priority. Using broiler chickens as a model, this study evaluated the effects of Pulsatilla saponins, alone or combined with a compound herbal formulation, on growth performance, immune responses, cecal microbiota, and the intestinal resistome, with an antibiotic-treated group as reference. Growth and immune parameters were integrated with shotgun metagenomic sequencing to characterize microbial and ARG responses to dietary interventions. Compared with antibiotic supplementation, the combination of 0.5% herbal medicine and 0.6% Pulsatilla saponins (ZBZ) combination significantly enhanced immune traits, including spleen index and serum IgA and IgM levels, while increasing cecal microbial diversity and reshaping community composition. Metagenomic analyses showed that antibiotic treatment enriched efflux pump and target modification associated ARG, indicative of a multidrug resistance profile. In contrast, ZBZ markedly reduced the abundance and diversity of multidrug resistance-related ARG. Notably, ZBZ supplementation enriched short-chain fatty acid-producing taxa that were negatively correlated with multiple ARG classes, suggesting that improvements in the intestinal metabolic environment and colonization resistance constrained the expansion of resistant bacteria. Overall, the combined use of Pulsatilla saponins and a compound herbal formulation improved growth and immune performance while reducing intestinal ARG burden through coordinated modulation of the cecal microbiota-resistome axis, providing a sustainable nutritional strategy for antibiotic-reduced poultry production.}, }
@article {pmid41707528, year = {2026}, author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y}, title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119865}, doi = {10.1016/j.ecoenv.2026.119865}, pmid = {41707528}, issn = {1090-2414}, mesh = {China ; *Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; Mining ; *Environmental Monitoring ; Manganese/analysis ; Agriculture ; Soil/chemistry ; Bacteria/genetics/classification ; *Microbiota ; Genes, Bacterial ; }, abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.}, }
@article {pmid41707775, year = {2026}, author = {Yu, S and Jin, Y and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J}, title = {Capacitive bimetallic redox cycles and ligand-to-metal charge transfer to Boost denitrification with Ni[II]/Fe[II]-Gallic acid phenolic networks.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134237}, doi = {10.1016/j.biortech.2026.134237}, pmid = {41707775}, issn = {1873-2976}, mesh = {*Denitrification ; Oxidation-Reduction ; Ligands ; Nitrates ; *Gallic Acid/chemistry ; *Nickel/chemistry ; *Iron/chemistry ; Water Purification/methods ; Wastewater/chemistry ; }, abstract = {Biological denitrification is limited by slow nitrate (NO3[-]) reduction due to low electron transfer efficiency, unsatisfactory community functional efficiency and insufficient metabolic activity of microbial communities. To overcome these challenges, Ni[2+] and Fe[2+] were incorporated with gallic acid (GA) to form bimetallic polyphenol networks (NiFeGA BPNs) with low-cost and high-biocompatibility. NiFeGA BPNs exhibited capacitive Ni(II)/Fe(II) redox cycles and excellent ligand-to-metal charge transfer capabilities to enable complete degradation of 200 mg/L NO3[-] within 8 h. All these improvements could be ascribed to that NiFeGA BPNs significantly improved electron transfer efficiency and stimulated microbial metabolic activity, which were proved by extracellular polymeric substances electrochemical analysis and electron transport chain inhibitors experiments. More importantly, metagenomic sequencing analysis confirmed that NiFeGA BPNs improved community structure by directionally enriching Pseudomonas. Consequently, NiFeGA BPNs significantly improving denitrification, which provides both theoretical guidance and technical frameworks for the continuous and efficient treatment of nitrate in wastewater.}, }
@article {pmid41707923, year = {2026}, author = {do Nascimento, AC and de Albuquerque, TMR and de Oliveira, DG and de Oliveira, AP and da Costa, PCT and de Sales, LCS and da Silva, JYP and Lins, JDS and E Silva, AL and da Silva, EF and do Nascimento, YM and Tavares, JF and Lima, MDS and Bezerra, TKA and de Oliveira, MEG and El-Bacha, T and Alves, JLB and de Souza, EL}, title = {Integrated metagenomic and metabolomic profiling in an in vitro colonic fermentation study to assess the impacts of conventional, unconventional, and whole edible beet (Beta vulgaris L.) parts on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals.}, journal = {The Journal of nutritional biochemistry}, volume = {153}, number = {}, pages = {110316}, doi = {10.1016/j.jnutbio.2026.110316}, pmid = {41707923}, issn = {1873-4847}, abstract = {Beet (Beta vulgaris L.) has been widely studied as a functional food, particularly for its bioactive compounds. This study evaluated the physicochemical characteristics, nutritional composition, antioxidant capacity, and the impacts of freeze-dried beet root (FDBR), freeze-dried beet stems and leaves (FDBSL), and freeze-dried whole beet (FDWB) on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals. FDBR, FDBSL, and FDWB had high nutritional value. FDWB had the highest protein content (10.6/100 g), while FDBSL had the highest total dietary fiber content (46.6/100 g). Twenty-eight phenolic compounds were identified, and the antioxidant capacity reached up to 60.6 µmol Trolox/g in FDBR. 16S rRNA amplicon sequencing analysis demonstrated that colonic fermentation of FDBR, FDBSL, and FDWB with fecal inoculum from hypertensive individuals decreased the Firmicutes/Bacteroidetes ratio, decreased or maintained the bacterial diversity, increased the relative abundance of Bifidobacteriaceae, Lactobacillaceae, and Enterobacteriaceae, and decreased Lachnospiraceae, Oscillospiraceae, and Peptostreptococcaceae. Colonic fermentation of FDBR mainly increased the abundance of Bifidobacterium (1.18-7.63%), while FDBSL increased the abundance of Phocaeicola. FDBR, FDBSL, and FDWB decreased the pH values (6.74-5.09) and altered the metabolic profile during colonic fermentation by consuming sugar and producing several metabolites associated with health-promoting properties, while maintaining antioxidant capacity. FDBR, FDBSL, and FDWB may be circular resources with beneficial effects on the composition and metabolic responses of the intestinal microbiota in hypertensive individuals and could be exploited as dietary adjuvant strategies in the management of arterial hypertension.}, }
@article {pmid41708005, year = {2026}, author = {Lin, CC and Uno, H and Yamada, C and Terada, T and Lu, TJ and Fushinobu, S}, title = {Structural insights into glycoside hydrolase family 1 β-glucosidase: Selective oligosaccharide hydrolysis, synthesis, and product profiling.}, journal = {The Journal of biological chemistry}, volume = {302}, number = {4}, pages = {111293}, pmid = {41708005}, issn = {1083-351X}, abstract = {β-Glucosidases are essential enzymes in plant cell wall metabolism and have diverse biotechnological applications, including cellulose degradation and prebiotic oligosaccharide synthesis. Td2F2, a glycoside hydrolase family 1 (GH1) β-glucosidase derived from a compost metagenome, exhibits a unique preference for sophorose. However, the molecular basis of this specificity remains unclear. In this study, we determined high-resolution crystal structures of Td2F2 in complex with sophorose (1.64 Å) and laminaribiose (1.16 Å) using sodium malonate as a cryoprotectant. Structural analysis, complemented by molecular dynamics simulations, revealed a distinct subsite +1', where Asn223, Thr225, Glu296, and Arg325 form hydrogen bonds with the reducing-end glucose of sophorose, stabilizing an alternative, nonproductive binding mode adjacent to the catalytic subsites. Site-directed mutagenesis confirmed that residues in subsite +1' are critical for substrate specificity. Guided by structural insights, we designed T225N and E296D mutants, which exhibited enhanced hydrolytic activity toward sophorose. To further investigate the transglycosylation potential of Td2F2, we characterized its dynamic product profile, ranging from disaccharides to tetrasaccharides, using porous graphitic carbon liquid chromatography-orbitrap tandem mass spectrometry. When p-nitrophenyl β-D-glucopyranoside and glucose were used as substrates, Td2F2 preferentially formed β-1→2 and β-1→3 linkages. These findings provide structural evidence that the subsite +1' is a "waiting position" in the GH1 β-glucosidase, offering novel insights into its role in hydrolysis and transglycosylation selectivity. This structural and functional framework paves the way for future GH1 enzyme engineering and expanded biotechnological applications.}, }
@article {pmid41708187, year = {2026}, author = {Fang, M and He, J and Zhou, S and Hong, P and Ke, L and Wu, H and Shu, Y}, title = {Pleurotus ostreatus polysaccharides improve microcystin-LR-induced intestinal damage in tadpoles by regulating the interaction between microbiota and intestine.}, journal = {Harmful algae}, volume = {153}, number = {}, pages = {103056}, doi = {10.1016/j.hal.2026.103056}, pmid = {41708187}, issn = {1878-1470}, mesh = {Animals ; *Intestines/drug effects/microbiology ; *Microcystins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Pleurotus/chemistry ; *Polysaccharides/pharmacology ; Larva/drug effects/microbiology ; *Ranidae ; Marine Toxins ; Oxidative Stress/drug effects ; }, abstract = {Exposure to microcystins (MCs) can cause severe intestinal damage. This study aimed to assess the efficacy of Pleurotus ostreatus polysaccharide in alleviating intestinal damage induced by microcystin-leucine-arginine (MC-LR) in tadpoles. Over a 30-day period, tadpoles (Pelophylax nigromaculatus) received daily exposures to MC-LR and were provided with diets either supplemented with or devoid of P. ostreatus polysaccharide. Results revealed that feeding P. ostreatus polysaccharide conferred protection against MC-LR-induced intestinal damage by mitigating barrier damage, lowering intestinal permeability, and reducing the tissue burden of MC-LR. The LPS/TLR4 pathway response was attenuated, reducing inflammation, and oxidative stress-mediated apoptosis response was also diminished. Gram-negative bacteria (e.g., Bacteroides) in the intestine show a positive correlation with LPS content and the transcription of key genes in the LPS/TLR4 pathway. Metagenomic and metabolite analysis of intestinal contents revealed increased abundance of the alanine-glyoxylate aminotransferase gene (agxt)-the key enzyme converting glyoxylic acid to glycine-and elevated glycine content in the MC-LR-exposed group fed polysaccharide. Results from the corresponding fecal microbiota transplantation experiment aligned with the trends observed in the exposure experiment. Therefore, polysaccharide alleviates MC-LR-induced intestinal damage by enhancing intestinal microbiota-mediated glycine synthesis, supplying raw materials for intestinal GSH production, reducing oxidative stress levels, and simultaneously dampening the LPS/TLR4 pathway response. Moreover, feeding polysaccharides might also regulate the intestine's defense against pathogens after MC-LR exposure by enhancing lysozyme activity. There is no evidence of intestinal damage in the P. ostreatus exopolysaccharide group. This study highlights for the first time the role of P. ostreatus polysaccharides in mitigating MC-LR-induced intestinal tissue damage, potentially offering novel insights for their application in aquaculture.}, }
@article {pmid41708296, year = {2026}, author = {Huang, J and Zhang, J and Liang, H and Fang, P and Tang, A and Klümper, U and Guo, J and Berendonk, TU and Honda, R and Lin, L and Li, X and Li, B}, title = {Antibiotics or Heavy Metals in Livestock Wastewater: Which One Is the Main Driver for the Development and Spread of Antibiotic Resistance under Coexposure?.}, journal = {Environmental science & technology}, volume = {60}, number = {8}, pages = {6510-6524}, doi = {10.1021/acs.est.5c06042}, pmid = {41708296}, issn = {1520-5851}, mesh = {*Wastewater ; Livestock ; *Anti-Bacterial Agents ; *Metals, Heavy ; Animals ; *Drug Resistance, Microbial/genetics ; Phylogeny ; Enrofloxacin ; }, abstract = {Antibiotics and heavy metals are widely used in livestock farming to promote animal health and growth, leading to their frequent co-occurrence as contaminants in livestock wastewater. However, their relative contributions to shaping the antibiotic resistome in treatment systems remain unclear. In this study, we simulated an aerobic activated sludge process treating livestock wastewater containing enrofloxacin and heavy metals (Cu[2+] and Zn[2+]) to evaluate the development of antibiotic resistance using metagenomic and metatranscriptomic approaches. We observed a diverse and transcriptionally active resistome with over half of the detected antibiotic resistance genes (ARGs) showing expression. ARG profiles under coexposure to enrofloxacin and heavy metals more closely resembled those under heavy metal exposure alone than those under enrofloxacin exposure alone. Zn[2+] exposure resulted in the highest absolute ARG abundance, nearly double that of the control group. Both enrofloxacin and heavy metals significantly altered the abundance and phylogenetic composition of the antibiotic-resistant bacteria (ARB). The exposure to Zn[2+] enhanced the relative abundance and expression level of both metal resistance genes (MRGs)-carrying ARB and the ARGs-carrying plasmids. Phylogenetic analysis of ARG flanking sequences revealed high homology across various genetic contexts. Among mobile genetic elements, plasmids had a greater influence on ARG profiles than did phages or integrative and conjugative elements (ICEs). Transcriptional profiles of microbial physiological adaptations suggested that modulation of cell membrane permeability, promotion of conjugative transfer, and formation of biofilm might play roles in enhancing antibiotic resistance. These findings suggest at environmentally relevant concentrations, heavy metals such as Zn[2+] may present a stronger selective pressure than enrofloxacin for the propagation of antibiotic resistance in aerobic activated sludge process treating livestock wastewater.}, }
@article {pmid41708335, year = {2026}, author = {Hkimi, C and Yaiche, H and Kamoun, S and Ben Aissa-Haj, J and Boujemaa, M and Abdelhak, S and Ghedira, K and Hamdi, Y}, title = {OMICs data from Tunisian population: challenges and opportunities in the era of precision medicine.}, journal = {Personalized medicine}, volume = {23}, number = {1}, pages = {23-33}, doi = {10.1080/17410541.2026.2632096}, pmid = {41708335}, issn = {1744-828X}, mesh = {Humans ; Tunisia ; *Precision Medicine/methods/trends ; *Genomics/methods ; Proteomics/methods ; Metabolomics/methods ; Metagenomics/methods ; Exome Sequencing/methods ; }, abstract = {OBJECTIVE: The transition to precision medicine (PM) is revolutionizing healthcare by enabling diagnostics and treatments tailored to individual molecular and genetic profiles, with omics sciences at its core. In Tunisia, growing interest is seen through initiatives such as Personalized Medicine in North Africa (PerMediNA).
METHODS: This study assesses Tunisia's readiness for PM by mapping publicly available omics datasets and related publications using Tunisian human data. A structured search across PubMed and major repositories covered studies published between 2010 and 2023 involving high-throughput technologies.
RESULTS: A total of 11 omics datasets were found, mainly genomic, alongside 104 publications, of which 96 focused on genomics. Whole exome sequencing (n = 46) and targeted gene panels (n = 37) were the most used approaches. Only six proteomics, one transcriptomics, and one metagenomics studies were identified; no epigenomics or metabolomics datasets were found. Research centered mainly on cancers, including breast, colorectal, and leukemia. While Tunisia shows progress in genomics, major gaps exist in other omics domains.
CONCLUSIONS: Advancing PM in Tunisia requires establishing a national omics data repository with ethical governance, promoting North - South collaborations to build capacity in non-genomic omics fields, and fostering public - private partnerships to strengthen infrastructure, data sharing, and sustainable research development.}, }
@article {pmid41708851, year = {2026}, author = {Appler, KE and Lingford, JP and Gong, X and Panagiotou, K and Leão, P and Langwig, MV and Greening, C and Ettema, TJG and De Anda, V and Baker, BJ}, title = {Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41708851}, issn = {1476-4687}, abstract = {Asgard archaea were pivotal in the origin of complex cellular life[1]. Heimdallarchaeia (a class within the phylum Asgardarchaeota) are inferred to be the closest relatives of eukaryotes. Limited sampling of these archaea constrains our understanding of their ecology and evolution[2,3], including their role in eukaryogenesis. Here we use massive DNA sequencing of marine sediments to obtain 404 Asgardarchaeota metagenome-assembled genomes, including 136 new Heimdallarchaeia and several novel lineages. Analyses of their global distribution revealed they are widespread in marine environments, and many are enriched in variably oxygenated coastal sediments. Detailed metabolic reconstructions and structural predictions suggest that Heimdallarchaeia form metabolic guilds that are distinct from other Asgardarchaeota. These archaea encode hallmark proteins of an aerobic lifestyle, including electron transport chain complex (IV), haem biosynthesis and reactive oxygen species detoxification. Heimdallarchaeia also encode novel clades of respiratory membrane-bound hydrogenases with additional Complex I-like subunits, which potentially increase proton-motive force generation and ATP synthesis. Thus, we propose an updated Heimdallarchaeia-centric model of eukaryogenesis in which hydrogen production and aerobic respiration may have been present in the Asgard-eukaryotic ancestor. This expanded catalogue of Asgard archaeal genomic diversity suggests that bioenergetic factors influenced eukaryogenesis and constitutes a valuable resource for investigations into the origins and evolution of cellular complexity.}, }
@article {pmid41708882, year = {2026}, author = {K-Jánosi, K and Sztojka, A and Kis, IE and Biksi, I and Bakos, Z and Kaszab, E and Mag, T and Albert, E}, title = {Characterisation of Salmonella Typhimurium from a fatal equine nosocomial outbreak and retrospective analysis of equine clinic salmonellosis cases (2010-2025).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41708882}, issn = {2045-2322}, abstract = {UNLABELLED: In 2024, a highly fatal outbreak of equine salmonellosis occurred in a Hungarian equine referral hospital, resulting in the death or euthanasia of four out of five affected horses. Salmonella (S.) enterica subsp. enterica serovar Typhimurium was identified as the primary causative agent from equine faecal, reflux, and post-mortem intestinal content samples, while one case involved S. Coeln. Extensive environmental sampling during the outbreak also yielded multiple Salmonella serovars. Whole-genome sequencing revealed a high degree of genetic relatedness among the S. Typhimurium isolates, confirming nosocomial transmission. The source of the isolated S. Typhimurium was most likely a 3-year-old gelding imported immediately before the admission to the hospital. The isolates belonged to sequence type ST376 and exhibited multidrug resistance, including extended-spectrum β-lactamase and fluoroquinolone resistance genes. Retrospective analysis of microbiological records from 2010 to mid-2024 identified 23 Salmonella-positive equine cases involving eight serovars and three probable nosocomial clusters preceding the 2024 outbreak. Following the outbreak, enhanced passive surveillance was implemented between October 2024 and August 2025. During this period, 56 at-risk horses were examined using selective bacteriological testing of clinical and post-mortem samples, of which 11 (19.6%) were Salmonella-positive, representing eight different serovars. A distinct cluster of S. Martonos was detected, and six of the surveillance-associated cases resulted in fatal outcomes. These findings demonstrate that Salmonella is repeatedly introduced into the equine hospital environment and that serovars differ markedly in virulence and transmission dynamics. The exceptionally high case fatality observed during the 2024 outbreak underscores the importance of integrated genomic surveillance, rapid diagnostics, and sustained infection control measures to mitigate the risk of severe nosocomial salmonellosis in equine clinics.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40617-0.}, }
@article {pmid41708925, year = {2026}, author = {Wawina-Bokalanga, T and Makangara-Cigolo, JC and Ola-Mpumbe, R and Lokilo, E and Mwakisenda-Tshakotsho, F and Delphine, M and Kahindo, I and Tshonaka-Nkololo, A and Vakaniaki, EH and Loman, N and Houben, S and Lumembe-Numbi, R and Kinganda-Lusamaki, E and Ponga-Museme, A and Mukota-Nungu, Y and Kumar, A and Meris, M and Wilkinson, S and Colquhoun, R and Kenye, KM and Akil-Bandali, P and Amuri-Aziza, A and Martinez, GS and Kelvin, DJ and Dijkman, R and Hensley, LE and Kasita, C and Kafua-Wemba, F and Mwamba, D and Subissi, L and Hoff, NA and Peeters, M and Rimoin, AW and Mokili, JL and Lunguya-Metila, O and Nkwembe, E and Rambaut, A and Liesenborghs, L and Low, N and Kindrachuk, J and Vercauteren, K and Edwards, R and Kelly, JN and Mbala-Kingebeni, P and Ahuka-Mundeke, S and Mumba, D and Muyembe-Tamfum, JJ}, title = {Deciphering the etiology of the 2024 outbreak of undiagnosed febrile illness in Panzi, Democratic Republic of the Congo.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41708925}, issn = {1546-170X}, abstract = {In late 2024, an outbreak of over 400 cases of undiagnosed febrile illness, predominantly presenting as fever and cough, was reported in Panzi Health Zone, southwestern Democratic Republic of the Congo. Here we conducted an epidemiological and laboratory investigation to determine the etiology of the outbreak. Clinical data and specimens were prospectively collected from 108 individuals, of whom 59/108 (54.6%) were female. Children aged <5 years were the most affected (47/108, 43.5%); 14/32 (43.7%) were malnourished. Oro/nasopharyngeal swabs from 96/108 individuals were PCR tested; 26 blood samples were sequenced. Plasmodium falciparum was detected in 56/108 (51.8%) individuals. Co-infections were also detected, with influenza A(H1N1)pdm09 virus in 16/56 (28.6%) and severe acute respiratory syndrome coronavirus 2 in 10/56 (17.9%) individuals. No novel pathogens were detected via metagenomics. Our findings suggest that the outbreak was primarily associated with a surge in malaria cases, with concurrent viral respiratory infections. Increasing decentralized laboratory capacity and strengthening broader health systems remain crucial for faster outbreak detection and investigation.}, }
@article {pmid41709052, year = {2026}, author = {Idris, H and Hairi, HH and Ahmad, A and Danish-Daniel, M and Zin, NM and Sanderson, RA and Raja Yahya, MFZ and Majhool, AA and Hassan, MY and Azman, MAZ}, title = {Revealing actinobacterial diversity inhabiting Malaysian Beach Ridges Interspersed with Swales (BRIS) soil : insights from culture-dependent and metagenomic approaches.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {29}, number = {3}, pages = {301-313}, pmid = {41709052}, issn = {1618-1905}, abstract = {The discovery of novel antibiotics remains a pressing global challenge as many known microorganisms continue to yield compounds already present in existing drugs. To overcome this limitation, bioprospecting in underexplored and extreme environments using both culture-dependent and culture-independent strategies has become essential. In this study, we investigated the microbial diversity of Beach Ridges Interspersed with Swales (BRIS) soil from Setiu, Terengganu, Malaysia—an environment characterized by poor nutrient retention, low water-holding capacity, and acidic conditions with lack information available on their microbial community composition. Therefore, this study was conducted with the main objectives to investigate actinomycetes community composition in BRIS soil using metagenomics and culture-dependent approaches. To address these objectives, a dual approach was employed: (i) culture-dependent isolation of actinomycetes using selective media, followed by morphological and 16S rRNA gene-based phylogenetic analysis, and (ii) culture-independent high-throughput sequencing of the 16S rRNA gene (Illumina MiSeq) to characterize the broader microbial community. Results from the selective isolation yielded 180 actinomycete isolates grouped into 69 colour-based categories, with 15 representatives identified by 16S rRNA sequencing as belonging predominantly to Streptomyces, alongside the rare genus Dermacoccus. In contrast, metagenomic analysis revealed a far richer microbial landscape comprising 4719 OTUs, 32 bacterial phyla, and 380 genera, including a high proportion of uncultured taxa. Notably, actinobacterial diversity was dominated by Acidothermus, whereas Streptomyces predominated in culture-dependent isolation, highlighting the complementary nature of both approaches. These findings confirm that BRIS soil harbours unique microbial communities shaped by its physicochemical conditions, with potential as a reservoir for rare actinomycetes and novel bioactive compounds. The study provides the first combined culture-dependent and metagenomic insight into BRIS soil microbiota and underscores its promise for future pharmaceutical and biotechnological exploration.}, }
@article {pmid41709267, year = {2026}, author = {Baquer, F and Grillon, A}, title = {Interaction between tick and host microbiotas: a four-step waltz.}, journal = {Parasites & vectors}, volume = {19}, number = {1}, pages = {}, pmid = {41709267}, issn = {1756-3305}, mesh = {Animals ; *Microbiota ; Humans ; *Tick-Borne Diseases/microbiology/transmission ; *Ticks/microbiology ; Symbiosis ; Skin/microbiology/immunology ; *Host Microbial Interactions ; Host-Pathogen Interactions ; }, abstract = {Tick-borne diseases represent a growing public health concern worldwide, yet the microbial factors that govern pathogen transmission remain incompletely understood. Over the past decade, high-throughput metagenomics and functional studies have revealed that two distinct microbial communities-the vertebrate host's skin microbiota and the tick's own microbiome-act synergistically as key modulators of pathogen acquisition, persistence within the vector, and successful transmission to the vertebrate host. At the feeding site, the skin microbiota orchestrates local cutaneous immunity, influences inflammatory responses, and can either hinder or inadvertently facilitate dermal establishment of tick-borne pathogens such as Borrelia burgdorferi sensu lato (s.l.), Anaplasma phagocytophilum, Rickettsia species, Babesia spp., and tick-borne encephalitis virus. Tick feeding itself induces rapid and sometimes long-lasting dysbiosis of the skin microbial community, creating temporal windows of vulnerability for pathogen invasion. Concurrently, within the tick vector, a core set of endosymbiotic bacteria, including Rickettsia buchneri, Midichloria mitochondrii, Coxiella-like, and Francisella-like endosymbionts, engage in complex mutualistic, competitive, and facilitative interactions. These symbionts regulate vector competence through nutrient provisioning (especially B-vitamins), direct competition for niche space, and immune priming or suppression of the tick's innate immune system. Such interactions ultimately determine the maintenance, abundance, and transmissibility of tick-borne pathogens. By integrating these dual host-vector microbiome perspectives in a comprehensive review, we highlight emerging mechanistic insights into transmission ecology and biologically grounded targets for the prevention and control of tick-borne diseases, including anti-microbiota vaccines and paratransgenic and microbiome-based approaches.}, }
@article {pmid41709323, year = {2026}, author = {Yin, S and Xiao, Z and Yu, Z and Zhou, C and Jian, J and Xiao, Y and Yang, H}, title = {Iterative enrichment cultivation and multiomic analysis reveal potential endophytic bacteria affecting the sinomenine synthesis in Sinomenium acutum.}, journal = {Microbial cell factories}, volume = {25}, number = {1}, pages = {}, pmid = {41709323}, issn = {1475-2859}, mesh = {*Endophytes/metabolism/genetics ; *Morphinans/metabolism ; *Sinomenium/metabolism/microbiology ; *Bacteria/metabolism/genetics/classification ; }, abstract = {Endophytes play important roles in plant metabolite synthesis, and certain strains were capable of producing bioactive compounds identical to those of their hosts. However, it remains unknown whether culturable endophytes of S. acutum can synthesize intermediate metabolites for the plant principal bioactive compound-sinomenine (SIN) or the compound itself. In this study, we investigated the successions of the culturable bacterial community and the alkaloid profiles within S. acutum endophytes across ten iterative enrichment cultivations using Czapek-Dox and Gause's No. 1 chemically defined media. The results demonstrated significant alterations in the composition and structure of the endophytic consortium and metabolites of the endophytic consortium during iterative cultivation. Priestia aryabhattai dominated the community in the first generation, whereas Microbacterium paraoxydans and Bacillus velezensis became dominant by the tenth generation. SIN was detected at the first and the fifth generation, with declining concentrations, and was absent at the tenth generation. Correlation network analysis revealed a strong positive correlation between the relative abundance of P. aryabhattai and the SIN content. Furthermore, a specific strain, L15, identified as P. aryabhattai, was isolated from the iterative culture. UPLC-MS/MS analysis of P. aryabhattai L15 metabolites confirmed the presence of SIN, alongside other alkaloids including cyclanoline, N-methylhigenamine-7-O-glucopyranoside, and isoquinoline. Further metagenomic analysis also indicated that the relative abundance of P. aryabhattai was significantly (p < 0.05) positively correlated with the SIN content in plant tissues. This study systematically elucidated the role of endophytic bacteria and provides potential strains for the synthesis of bioactive compounds and pharmaceutical research.}, }
@article {pmid41709890, year = {2026}, author = {Dai, L and Zhan, W and Huang, X and Lyu, L and Jiang, S and Zhou, P}, title = {Refractory multiple brain abscesses caused by Prevotella loescheii and Porphyromonas gingivalis: successful endoscopic lavage and drainage: a case report and review of the literature.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1736006}, pmid = {41709890}, issn = {2296-858X}, abstract = {BACKGROUND: Brain abscesses represent life-threatening conditions, with management complexities significantly heightened in cases involving multiple lesions that are refractory to standard empirical therapies. Prevotella loescheii and Porphyromonas gingivalis, anaerobic bacteria typically residing within the oral flora, are infrequent yet formidable pathogens responsible for intracranial abscess formation. The fastidious nature of these microorganisms often results in delayed diagnosis and initiation of targeted treatment.
CASE PRESENTATION: A 25-years-old male presented with a 1-month history of cough, sputum production, and persistent high-grade fever reaching 41 °C. Initially diagnosed with a brain abscess at a local hospital, he received empirical treatment with ceftriaxone, acyclovir, and mannitol, which failed to yield clinical improvement. His condition subsequently deteriorated, characterized by disturbances in consciousness and dysarthria. The antimicrobial regimen was escalated to include vancomycin and meropenem. Despite these efforts, the patient's neurological status continued to decline, with imaging studies revealing the development of multiple new intracranial abscesses and diffuse intracranial hypertension. Surgical intervention was undertaken, involving abscess excision and decompressive craniectomy. Postoperative imaging 1 week later showed further abscess expansion and the onset of right-sided hemiplegia. Upon admission to our institution, metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid identified the presence of Prevotella loescheii and Porphyromonas gingivalis. The antimicrobial regimen consisting of vancomycin and meropenem was maintained, and the patient underwent endoscopic intracranial abscess lavage with burr hole external drainage. This integrated approach led to significant radiographic resolution of the abscesses and a gradual improvement in the patient's level of consciousness. The refractory infection was traced back to an oropharyngeal source.
CONCLUSION: This case highlights the critical diagnostic value of mNGS in detecting fastidious oral anaerobic pathogens in culture-negative refractory brain abscesses. It illustrates that a combination of targeted antibiotic therapy and minimally invasive surgical intervention-specifically, endoscopic lavage and drainage-can be highly effective in managing complex, multi-loculated abscesses caused by Prevotella loescheii and Porphyromonas gingivalis. Maintaining a high index of suspicion for an odontogenic or oropharyngeal origin is crucial in the diagnostic evaluation of such infections.}, }
@article {pmid41710035, year = {2026}, author = {John, J and Ortiz, M and Ramond, P and Campbell, BJ}, title = {Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag021}, pmid = {41710035}, issn = {2730-6151}, abstract = {Functional redundancy (FRed) is expected to buffer ecosystems against change, yet it has rarely been characterized in natural systems. How changes in microbial metabolisms, activity, and FRed in ecosystems are influenced by temporal, spatial, and environmental patterns is especially unclear. Here, we analyzed paired metagenomic and metatranscriptomic datasets from surface water samples collected in the Chesapeake and Delaware Bays, USA. These adjacent estuaries experience similar climatic conditions but differ in nutrient availability, salinity, and other environmental factors. We reconstructed 345 high quality metagenome assembled genomes and assessed their metabolic flexibility, and the extent of gene encoded (potential) and expressed (realized) FRed as a function of environmental drivers, microbial lifestyle (free living vs. particle attached), and gene function. The microbiomes exhibited high metabolic flexibility, reflecting their potential, and in many cases, realized gene expression, to exploit diverse energy sources, ranging from organic carbon substrates to trace gases. Potential and expressed FRed varied across seasons, lifestyles, and gene functions, and was structured within each bay by environmental factors such as temperature, salinity, and concentrations of phosphate, silicate, and chlorophyll a. These findings highlight variability in community-level metabolism, and FRed across estuarine microbiomes, shaped by environmental conditions, seasonality, and lifestyle, and provide insights into how these communities may respond to future perturbations.}, }
@article {pmid41710165, year = {2026}, author = {Stevenson, Z and Schultz, DL and Chamberlain, M and Rico, K and Anbar, A and Dekas, AE and Swanner, ED}, title = {Lowering the Mo limit for nitrogen fixation by Mo-nitrogenase.}, journal = {Communications earth & environment}, volume = {7}, number = {1}, pages = {169}, pmid = {41710165}, issn = {2662-4435}, abstract = {Archean ocean marine primary productivity may have been limited by biologically available nitrogen. Due to low molybdenum abundances, early biological nitrogen fixation is thought to have relied on alternative nitrogenases that incorporate vanadium or iron instead of molybdenum. Here, we examine nitrogen fixation in a Cyanobacteria-dominated, ferruginous, low-sulfate, low-molybdenum lake, which replicates biological and chemical conditions relevant to early marine primary productivity. Nitrogen fixation occurs even when molybdenum is <1 nM, 100x less than the abundance in modern oceans. Molybdenum additions did not increase nitrogen fixation rates, indicating that diazotrophs were not molybdenum limited. Only the molybdenum-iron nitrogenase was detected in metagenomes and metatranscriptomes, indicating that the alternative nitrogenases were not required. We suggest that low sulfate (<1 μM) and/or efficient uptake mitigated molybdenum limitation. These results indicate that molybdenum bioavailability may be strongly controlled by sulfate and that alternative nitrogenases are not essential for nitrogen fixation at low molybdenum.}, }
@article {pmid41710374, year = {2026}, author = {He, L and Li, F}, title = {Clinicopathologic Features of Genitourinary Malakoplakia and Analytical Utility of the MetaPath Assay.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {582917}, pmid = {41710374}, issn = {1178-6973}, abstract = {PURPOSE: To describe the clinicopathological spectrum of genitourinary malakoplakia (MPL) and to evaluate the feasibility and clinical impact of metagenomic pathogen detection (MetaPath) performed on archival formalin-fixed paraffin-embedded (FFPE) tissue.
PATIENTS AND METHODS: Clinical imaging, histopathology, immunohistochemistry, special stains and MetaPath results were retrospectively analysed in five MPL cases diagnosed between January 2019 and August 2025.
RESULTS: The cohort comprised four men and one woman with a median age of 65.4 years. Four lesions arose in the prostate and one in the bladder. Histology showed chronic granulomatous inflammation with numerous eosinophilic histiocytes containing 5-10 µm targetoid Michaelis-Gutmann bodies. CD68 and CD163 were diffusely positive; PAS and iron stains highlighted the inclusions. MetaPath identified pathogens in 3/5 (60%) FFPE specimens (Escherichia coli in two, Pseudomonas aeruginosa in one). Antibiotic regimens were adjusted according to MetaPath results. After a median follow-up of 6 months (range 4-8) all patients remained symptom-free.
CONCLUSION: MPL is frequently misdiagnosed as malignancy. MetaPath can reliably detect pathogens in archival tissue and guide targeted antimicrobial therapy, representing a valuable adjunct to conventional culture.}, }
@article {pmid41711070, year = {2025}, author = {Beauvais, M and Schatt, P and Soulié, T and Lambert, S and Montiel, L and Gaudin, M and Chaffron, S and Logares, R and Bouget, FY and Galand, PE}, title = {Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41711070}, issn = {1751-7370}, support = {ANR-24-CE02-7681//French Agence Nationale de la Recherche/ ; }, mesh = {*Vitamin B 12/metabolism ; *Seawater/microbiology/chemistry ; Seasons ; *Thiamine/metabolism ; Mediterranean Sea ; *Microbiota ; Metagenomics ; *Bacteria/metabolism/genetics/classification ; Metagenome ; }, abstract = {Marine microbial communities are fundamental to nutrient and biogeochemical cycling, with intricate networks of metabolic interdependencies influencing their structure and dynamics. Among these, vitamins B1 (thiamin) and B12 (cobalamin) play crucial roles as enzymatic cofactors in central metabolic pathways. Despite their importance, the temporal dynamics of vitamin production, bioavailability, and associated microbial interactions remain poorly understood. Using a 7-year monthly metagenomic time series from the NW Mediterranean Sea (SOLA station), we found that vitamin B1/B12 auxotrophs (need for an exogenous vitamin source) were present throughout the year. Among B1 auxotrophs, those requiring the thiamin precursor pyrimidine were the most prevalent, with peak abundances in summer. Distinct metagenome-assembled genome co-abundance patterns between B1 and B12 producers/auxotrophs across seasons suggested mutualistic relationships. Double B1/B12 vitamin complementarities were more common in summer, and single vitamin complementarity was dominant in winter. As previously shown for vitamin B12, which is limiting during winter, bioassays revealed variable availability of vitamin B1 in winter seawater despite the abundance of its producers, suggesting potential transfer of vitamin B1 among microorganisms. Finally, microcosm experiments showed that B1 and B12 amendments significantly influenced the composition of microbial communities, with temporal variations in their impact. In some cases, B12 and B1 amendments favored both vitamin auxotrophs and producers, highlighting complex interdependencies between B1 and B12 producers and consumers. Our findings highlight the complexity of B vitamin-mediated metabolic interactions that shape microbial community dynamics and underscore the need for long-term, high-resolution studies to better understand vitamin-driven ecological processes in marine systems.}, }
@article {pmid41711071, year = {2026}, author = {Boeckel, C and Lisovski, S and Stoof-Leichsenring, KR and Weiß, JF and Liu, S and Harms, L and Herzschuh, U}, title = {DNA virus-host patterns in lake and marine environments over the last glacial cycle.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag025}, pmid = {41711071}, issn = {1751-7370}, abstract = {Viruses are integral to population dynamics, biogeochemical cycling, and host evolution, making them essential for ecosystem function. We explore long-term virus-host interactions mainly within microbial ecosystems in lake and marine environments across the late Pleistocene and Holocene. Sedimentary ancient DNA (sedaDNA) from five Siberian lakes and three Subarctic/Antarctic marine cores were analysed to infer past DNA virus taxa from metagenomic sequences. Viruses accounted for 357 161 reads (0.089% of total mapped reads), distributed across 2084 unique viral taxa. Virus communities differ between lakes and marine sites, with lakes dominated by Caudoviricetes and marine environments featuring Caudoviricetes and Algavirales. Each time series shows compositional changes from the Pleistocene to the Holocene, supporting sedaDNA as a tool to reconstruct time-resolved ancient viral assemblages. Among the most abundant viruses, we identified 83 virus-host pairs documented in published literature, spanning bacterial, archaeal, and eukaryotic hosts, and assessed their associations based on co-occurrence correlations. Over millennia, virus-host co-variations are particularly stable in marine systems, especially for phytoplankton-infecting viruses. However, in the Bering Sea, we find a lack of virus-host correlation, likely because an Arctic Pelagibacter strain expanded after the Bering Strait opened, potentially due to absent viral infection, although database limitations prevent clear interpretation. Antagonistic patterns also appear between bacteriophages and hosts, possibly linked to shifts between lytic and lysogenic cycles in response to environmental changes. This study demonstrates that sedaDNA time-series can reveal ancient viral community structures and long-term ecological patterns, highlighting the value of ancient viromes in understanding ecosystem-specific responses to environmental change.}, }
@article {pmid41711085, year = {2026}, author = {Hart, LN and Errera, R and Godwin, C and Loftin, KA and Laughrey, ZR and Katona, LR and Johnson, EC and Cory, RM and Kiledal, EA and Den Uyl, P and Kharbush, JJ and Sherman, DH and Dick, GJ}, title = {Diverse Cyanopeptides Follow Distinct Temporal Succession Patterns in Freshwater Harmful Algal Blooms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag026}, pmid = {41711085}, issn = {1751-7370}, abstract = {Toxic cyanobacterial harmful algal blooms (cyanoHABs) threaten freshwater resources globally and are intensifying with increasing eutrophication. Bloom toxicity is strongly influenced by intraspecific variation in the biosynthetic repertoires of toxic cyanobacteria, yet few studies examine the diversity of cyanobacterial cyanopeptides beyond hepatotoxic microcystins. To understand the dynamics and drivers of cyanopeptide diversity in cyanoHABs, we analyzed temporal patterns of cyanobacteria, metabolites, and their biosynthetic gene clusters (BGCs) in western Lake Erie using a seven-year time series (2016-2022) of metagenomic and metabolomic data. Our findings demonstrate that shifts from Microcystis to Dolichospermum occur later in the bloom season, coinciding with lower temperatures. Modules of co-varying BGCs (biosynthesis modules) from these genera were identified with hierarchical clustering, with uncharacterized BGCs among the most abundant. Biosynthesis modules rich in nonribosomal peptide synthetases (NRPS) peaked in early August, coinciding with elevated levels of inorganic nitrogen, warmer temperatures, and high Microcystis abundance. In contrast, modules rich in polyketide synthases (PKS) and ribosomally synthesized and post-translationally modified peptides (RiPPs) peaked following the Microcystis maximum in mid-August. Metabolomic analyses confirmed that metabolites followed shared seasonal patterns with their associated biosynthesis modules, forming three phases characterized by (1) microcystins, (2) anabaenopeptins and aeruginosins, and (3) aerucyclamides. These phases co-varied with bottom-up and top-down pressures, with later phases coinciding with increased microbially processed organic nitrogen and reduced detection of grazers. This study demonstrates consistent seasonal patterns of cyanobacterial metabolite succession and co-occurrence beyond microcystins, suggesting tradeoffs between biosynthetic resource demands and ecological controls.}, }
@article {pmid41711914, year = {2026}, author = {Demin, K and Onasenko, K and Beletskaya, A and Tsoy, A and Boyko, M and Kulikov, M and Kulikova, D and Prazdnova, E}, title = {Studying organosulfonate metabolism in southern Russia chernozem soil microbial community: ubiquity of the desulfonation pathways and possible mixotrophy in common soil heterotrophs.}, journal = {Archives of microbiology}, volume = {208}, number = {4}, pages = {201}, pmid = {41711914}, issn = {1432-072X}, support = {SP-12-23-04//Priority 2030/ ; }, }
@article {pmid41711928, year = {2026}, author = {Farias, LABG and Viana Neto, OM and Lima Sobrinho, EP and de Melo, AGND and Pontes, IM and Gonçalves, BBS and Benevides, HP and Maia, SPO and Rodrigues, JLN and Perdigão Neto, LV}, title = {Streptococcus suis infection as an emerging zoonotic threat in Brazil: a One Health-based review.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {68}, number = {}, pages = {e19}, pmid = {41711928}, issn = {1678-9946}, mesh = {*Streptococcus suis/genetics/isolation & purification ; Brazil/epidemiology ; Animals ; *Streptococcal Infections/epidemiology/transmission/microbiology/diagnosis/veterinary ; Humans ; Swine ; One Health ; *Communicable Diseases, Emerging/epidemiology/microbiology ; *Bacterial Zoonoses/epidemiology/microbiology ; *Zoonoses/microbiology ; *Swine Diseases/microbiology/epidemiology ; }, abstract = {Streptococcus suis infection is an emerging zoonotic pathogen of growing concern in Brazil, particularly in the Northeast-a region lacking swine-focused surveillance. Although human contamination remains rare, they have been increasingly reported among individuals exposed to pigs or pork products, and most commonly present as central nervous system infections. Diagnostic challenges persist, especially related to culture-based methods, highlighting the need for advanced molecular tools like polymerase chain reaction and metagenomic Next-Generation Sequencing. Veterinary data reveal a high diversity of serotypes and concerning rates of antimicrobial resistance. These studies remain scarce in regions with reports of human infection. This review highlights the clinical, epidemiological, and microbiological aspects of S. suis in Brazil and underscores the importance of One Health approaches to enhance detection and prevention.}, }
@article {pmid41712385, year = {2026}, author = {Hong, J and Xue, W and Wang, T}, title = {Universal gene-level bimodality in natural microbial communities.}, journal = {Cell reports}, volume = {45}, number = {3}, pages = {117013}, doi = {10.1016/j.celrep.2026.117013}, pmid = {41712385}, issn = {2211-1247}, mesh = {Humans ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; }, abstract = {Bimodality-the coexistence of two peaks in trait distributions-is common in natural ecosystems. In microbiomes, bimodality of species abundances is known. However, whether this pattern applies to community functionality remains unclear. Here, we systematically investigate the abundance distributions of individual genes in different microbiomes, from human gut to ocean, revealing widespread gene-level bimodality. The bimodal genes are enriched in niche-specific pathways, suggesting their roles in ecological adaptation of the community. Based on their abundances, we develop a framework for microbiome functional typing, offering a gene-centric alternative to the taxonomy-based paradigm. Applied to the human gut, our approach identifies eleven genes exhibiting robust bimodality across western countries. These genes are associated with diseases such as liver cirrhosis. Machine learning models leveraging these genes are predictive of these diseases, underscoring their potential as clinically relevant biomarkers. Our work provides critical insights for microbiome functional architecture and has implications for microbiome-based diagnostics.}, }
@article {pmid41712566, year = {2026}, author = {Bedoya-Urrego, K and Peñuela-Martínez, AE and Alzate, JF}, title = {Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0332370}, pmid = {41712566}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; Fermentation ; *Coffee/microbiology ; Phylogeny ; *Yeasts/genetics/classification ; Metagenome ; Biodiversity ; Genome, Fungal ; }, abstract = {Yeasts play a pivotal role in coffee fermentation, shaping microbial succession and contributing to the development of final flavor profiles. Despite their importance, yeast taxonomy in this context remains poorly resolved. Traditional classification methods often result in misidentifications due to the limited resolution of classical microbiological techniques and the rapidly evolving taxonomic framework driven by advances in phylogenomic. Moreover, the diversity of budding yeasts in coffee fermentations remains underexplored using high-resolution approaches such as metagenomics. To address this gap, we applied a shotgun metagenomic strategy and reconstructed metagenome-assembled genomes (MAGs) from multiple coffee fermentation samples and, using a robust phylogenomic framework based on 832 conserved single-copy genes. We confidently classified 22 yeast MAGs within the subphylum Saccharomycotina. These included well-known taxa such as Pichia kluyveri, Hanseniaspora spp., Torulaspora delbrueckii, and members of the Kurtzmaniella clade. Most MAGs were placed in strongly supported monophyletic groups (ultrafast bootstrap = 100), with short intra-clade branch lengths indicative of intraspecific variation. Pichia kluyveri emerged as the most abundant and widespread species, detected in all analyzed metagenomes, followed by Hanseniaspora spp. Our results underscore the power of high-resolution phylogenomic for classifying yeast MAGs and highlight the ecological importance of Pichia, Hanseniaspora, Torulaspora, and Kurtzmaniella in spontaneous coffee fermentations.}, }
@article {pmid41712638, year = {2026}, author = {Zhao, XD and Wang, YQ and Zhang, S and Li, JQ and Cai, YJ and Shu, X and Chen, Z and Zhang, SY}, title = {Spatially resolved denitrification coupled with methane and arsenite oxidation at the millimeter-scale straw-soil interface.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {8}, pages = {e2521285123}, pmid = {41712638}, issn = {1091-6490}, support = {52270198//National Natural Science Foundation of China/ ; 42477116//National Natural Science Foundation of China/ ; JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, mesh = {*Methane/metabolism ; Oxidation-Reduction ; *Denitrification ; *Arsenites/metabolism ; *Soil Microbiology ; *Soil/chemistry ; Nitrogen Fixation ; Nitrogen/metabolism ; }, abstract = {Straw return reshapes the biogeochemical processes in paddy soils by driving microbial transformation of key elements. Despite growing awareness of these individual processes, the integration of these processes under millimeter-scale spatiotemporal heterogeneity remains unclear. Combining high-resolution geochemical profiling with multiomics, we revealed that straw addition altered the depth-dependent dynamics of arsenic, carbon, and nitrogen, establishing a sophisticated three-layer microbial stratification. We identified 1) an 18 mm organic matter (OM)-rich layer extending from the straw layer, which serves as a methanogenic epicenter co-occurring with active nitrogen fixation microbes; 2) an overlying layer dominated by aerobic methane oxidation and denitrification microbes; and 3) a deeper substraw layer dominated by anaerobic arsenite oxidation and denitrification microbes. Significantly positively correlated abundances of transcribed mcrA with nifH genes and pmoA or aioA/arxA with denitrification genes were identified. Corroboratively, intensified co-occurrence patterns of mcrA with nifH, pmoA with denitrification, and aioA/arxA with denitrification genes were observed in the OM-rich, upper, and lower layers, respectively. Moreover, the co-occurred mcrA-nifH and aioA-nirS/arxA-narG genes in different metagenome-assembled genomes presented 80.6 to 260.8- and 1.55 to 6.85-fold greater transcriptional activity in the OM-rich and lower layers than in the other layers, respectively. Our results demonstrated that straw incorporation established a dynamic soil redox zone, restructuring millimeter-scale microbial networks and promoting potentially coupled denitrification with arsenite or methane oxidation, as well as methanogenesis with nitrogen fixation. These findings provide a mechanistic basis for optimizing subsurface straw placement and nitrate application to enhance nutrient cycling and mitigate environmental risks.}, }
@article {pmid41713061, year = {2026}, author = {Cokro, A and Albert Ng, TC and Hill, ED and Lee, C and Chandra Segeran, US and Arumugam, K and Williams, RBH and Wuertz, S}, title = {Microbial community biomarkers can forecast methane production in full-scale anaerobic digesters.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128828}, doi = {10.1016/j.jenvman.2026.128828}, pmid = {41713061}, issn = {1095-8630}, mesh = {*Methane ; Anaerobiosis ; Sewage/microbiology ; *Bioreactors/microbiology ; Biomarkers ; Wastewater ; }, abstract = {Methane production from wastewater sludge via anaerobic digestion is a complex process and a disturbance in any one of the microbial stages can lead to eventual failure. Hence, it is desirable to detect disturbances as soon as possible. Although machine learning has been used to predict methane production from a variety of different substrates, there are no studies using metagenomic or -transcriptomic microbial community data as predictor variables. We used random forest analysis on a combination of physicochemical and microbial predictors to forecast methane production from three full-scale sludge digesters representing replicates of one another in a wastewater treatment plant in Singapore. Digesters were sampled for 25 weeks, and 42 physicochemical variables were measured along with shotgun metagenome and total RNA transcriptome sequencing. Models built using samples from a single digester yielded reactor-specific predictors, largely due to the limited sample size per reactor and the influence of rarer taxa. When data from the three digesters were combined, the best predictors included both substrate-related physicochemical parameters, such as chemical oxygen demand, and microbial taxa. Simulation using learning curves indicated that 150 to 200 samples instead of the 75 used would have yielded the most accurate methane prediction. The selection of many unidentified operational taxonomic units as microbial predictors suggests the existence of important yet unknown microorganisms in anaerobic digestion. The prediction model supports onsite digester surveillance by identifying digester-specific predictors through sufficient sampling, after which only those predictors need to be measured for subsequent monitoring.}, }
@article {pmid41713162, year = {2026}, author = {Liu, X and Cai, H and Zhao, L and Ke, D and Xu, X and Li, J and Yu, J and Shen, Y and Zhu, L and Jin, Y and Zhang, M and Liu, S and Du, J and Zheng, J and Dong, R}, title = {Microplastic-associated gut microbial profile and antibiotic resistance in preschool children: a multicentre cross-sectional study in China.}, journal = {EBioMedicine}, volume = {125}, number = {}, pages = {106177}, pmid = {41713162}, issn = {2352-3964}, mesh = {Humans ; China/epidemiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Cross-Sectional Studies ; Child, Preschool ; Female ; Male ; *Microplastics/adverse effects ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification ; }, abstract = {BACKGROUND: Microplastics (MPs) are ubiquitous in ecosystems and present in the human body, causing a worldwide environmental issue. However, the extent of human exposure to MPs remains largely unknown. Although mice exposed to MPs exhibit gut microbiota dysbiosis, the impact of MPs on the human intestinal microbiota remains unclear. Furthermore, MPs can carry and spread antibiotic resistance genes (ARGs). However, their potential influence on ARG abundance is underexplored.
METHODS: A multicentre cross-sectional study was conducted in Xiamen, Shanghai, and Nanjing in China from October 2022 to March 2023. A total of 335 couples of faecal samples were collected and analysed for MPs using Py-GC/MS and gut microbiota using 16S rRNA and metagenomic sequencing.
FINDINGS: Eight types of MPs were detected in 335 faecal samples, with a median concentration of 212.1 μg/g dw. MP exposure may be associated with the composition of the host gut microbiota. Microbial function analysis indicated the significant enrichment of 62 pathways primarily related to the metabolic pathways of macronutrients, vitamins, and bioactive substances. Total plastic concentration was significantly related to the relative abundance of species and ARGs, however this could not be attributed to specific plastic polymers after adjusting for covariates.
INTERPRETATION: This study provides baseline data on the gap in understanding of preschoolers' MP exposure, supporting the hypothesis that MP exposure might disrupt gut bacterial constitution and functions. This raises concerns regarding the potential adverse effects on the human gut when exposed to MPs, particularly drug resistance risks in younger populations.
FUNDING: Project of Shanghai Municipal Financial Professional foundation (Food Safety Risk Assessment) (grant number: RA-2023-10), National Natural Science Foundation of China (grant number: 2023YFF1104800), and Key Disciplines in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025) (grant number: GWVI-11.1-42).}, }
@article {pmid41713270, year = {2026}, author = {Jiao, X and Ji, W and Zhang, X and Zhang, S and Dolfing, J and Yang, K and Xie, B and Zhang, Y and Feng, J and Wu, D}, title = {Microcystins 'steer' antibiotic resistome dynamics by synergetic metabolism and horizontal gene transfer in a megacity's water supply catchment microbiota.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141525}, doi = {10.1016/j.jhazmat.2026.141525}, pmid = {41713270}, issn = {1873-3336}, mesh = {*Gene Transfer, Horizontal ; *Microcystins/metabolism ; *Microbiota ; China ; *Microcystis/genetics/metabolism/growth & development ; *Drug Resistance, Microbial/genetics ; Water Supply ; Water Microbiology ; Drinking Water/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.}, }
@article {pmid41713418, year = {2026}, author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD}, title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.}, journal = {Cell}, volume = {189}, number = {6}, pages = {1854-1873.e17}, doi = {10.1016/j.cell.2026.01.007}, pmid = {41713418}, issn = {1097-4172}, mesh = {*Probiotics ; Humans ; Infant ; *Genome, Bacterial/genetics ; *Bifidobacterium longum/genetics/classification ; Phylogeny ; *Bifidobacterium longum subspecies infantis/genetics/classification ; Genomics ; Gastrointestinal Microbiome/genetics ; Infant, Newborn ; Milk, Human/microbiology ; }, abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.}, }
@article {pmid41713744, year = {2026}, author = {Lemée, P and Le Roux, A and Feurer, C and Houée, P and Le Grandois, P and Hirchaud, E and Soumet, C and Bridier, A}, title = {Longitudinal Analysis of Surface-Associated Bacterial Ecology and Resistome Dynamics in a Pig Slaughterhouse.}, journal = {Journal of food protection}, volume = {89}, number = {4}, pages = {100724}, doi = {10.1016/j.jfp.2026.100724}, pmid = {41713744}, issn = {1944-9097}, mesh = {Animals ; *Abattoirs ; Swine ; *Bacteria/drug effects/genetics/isolation & purification/classification ; *Drug Resistance, Bacterial ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Food Microbiology ; RNA, Ribosomal, 16S ; Phylogeny ; }, abstract = {Slaughterhouses constitute key stages for the transmission of bacterial pathogens and antimicrobial resistance throughout the meat production chain, with significant implications for food safety. This study investigated the bacterial communities and resistome profiles of surface-associated microbes in a pig slaughterhouse sampled at two-year intervals in 2017 and 2019. Thirty-five strains of Salmonella enterica serovar Typhimurium and its monophasic variant, major pathogenic serovars of the sector, were collected through the slaughtering line in this time frame, and they displayed multidrug resistance profiles characteristic of the pig sector. Whole-genome analysis revealed no clear phylogenetic clustering by site or sampling date. Both 16S rRNA metabarcoding and shotgun metagenomics underlined site-specific bacterial communities dominated by the Moraxellaceae family and with a relatively stable composition across the sampling period. The upstream of the slaughtering line (dehairing stage) was characterized by aminoglycoside and tetracycline resistance genes, predominantly associated with Acinetobacter, Escherichia, and Clostridium, alongside oxidative stress genes carried by Streptococcus. At the downstream section of the slaughtering process, the red offal platform exhibited increased diversity and abundance of antibiotic and biocide resistance determinants. These included β-lactam and carbapenem resistance genes as well as efflux pump-associated elements (adeJ), mainly linked to Acinetobacter, which was consistently enriched, suggesting its potential role as a reservoir for resistance genes. Overall, these findings provide insights into the composition, stability, and functional potential of bacterial communities in slaughterhouse environments and their possible role in shaping pathogen and resistance gene dynamics along the food production chain.}, }
@article {pmid41713817, year = {2026}, author = {Zhao, Q and Cao, Y and Zhang, Z and Yang, Y and Wang, L and Xu, M and Mao, Y and Zhang, X and Zeng, M and Yang, P and Chen, Q and Yan, H and Yang, G}, title = {Xiao-Chaihu-Tang preserves intestinal barrier and ameliorates irinotecan-evoked delayed diarrhea by anchoring endogenous tryptophol to modulate inflammation and oxidation dependent on AhR-UGT1A1-microbiota axis.}, journal = {Journal of ethnopharmacology}, volume = {363}, number = {}, pages = {121380}, doi = {10.1016/j.jep.2026.121380}, pmid = {41713817}, issn = {1872-7573}, mesh = {Animals ; *Irinotecan/toxicity ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Male ; *Diarrhea/chemically induced/drug therapy/prevention & control/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Rats ; Rats, Sprague-Dawley ; Glucuronosyltransferase/metabolism ; *Indoles/metabolism ; Intestinal Mucosa/drug effects/metabolism ; Inflammation/drug therapy ; Oxidation-Reduction ; Fecal Microbiota Transplantation ; }, abstract = {Xiao-Chaihu-Tang (XCHT), a well-known traditional formula, is commonly used to treat various types of diarrhea. It also exhibits promising efficacy against chemotherapy irinotecan (CPT-11)-induced delayed diarrhea (DD). However, its underlying mechanisms, specifically concerning endogenous metabolites, key pathways, and functional gut bacteria at the species level, remain unclear, severely restricting its clinical application.
AIM OF THE STUDY: This study aimed to elucidate the biomarkers, pathways, and functional bacteria involved in XCHT's alleviating CPT-11-evoked DD using multi-omics approaches, antagonists, and fecal microbiota transplantation (FMT).
MATERIALS AND METHODS: First, the ingredients of XCHT and absorbed compounds in rat plasma were identified using liquid chromatography-mass spectrometry (LC-MS). Next, the therapeutic effects of XCHT were assessed by monitoring perianal status, body weight, disease activity index, food and water intake, and histopathological changes in the colon (hematoxylin and eosin, alcian blue-periodic acid-schiff staining). The underlying mechanisms were studied using metabolomics and network pharmacology, which highlighted the role of endogenous biomarkers and associated pathways. Tryptophol was identified as a key correlate, and its efficacy was further validated in rat and Caco-2 models using antagonists of potential targets (AhR and UGT1A1). The levels of inflammatory cytokines, and oxidative stress markers, intestinal barrier proteins, and mucins were detected by enzyme-linked immunosorbent assay (ELISA), Western blotting, and immunofluorescence. Furthermore, functional gut bacteria were identified using metagenomic sequencing and validated using FMT, while gut leakage was detected using fluorescence in situ hybridization (FISH). Finally, the interactions between tryptophol with targets of AhR and UGT1A1 were examined using molecular docking, molecular dynamics, and surface plasmon resonance.
RESULTS: LC-MS analysis identified 43 phytochemicals in XCHT and 17 compounds absorbed in plasma. XCHT, similar to tryptophol, attenuated DD by improving perianal status, disease activity index, and colon pathology, while increasing body weight, food intake, and water intake. Metabolomics analysis revealed 33 potential endogenous biomarkers, including PGB3, LysoPA, and so on. Integrated with network pharmacology, the results indicated that the therapeutic effect of XCHT involved the regulation of tryptophan metabolism, arachidonic acid metabolism, inflammation, and oxidative stress. Tryptophol, which exhibited a strong correlation with efficacy indices, reduced inflammation and oxidation in vivo/vitro, and enhanced intestinal barrier protein and mucin expression in an AhR-UGT1A1-dependent manner. Furthermore, metagenomic sequencing and FISH demonstrated that both XCHT and tryptophol normalized the abundance of 10 gut bacterial species (for example, Lactobacillaceae bacterium, Massiliimalia timonensis, and Limosilactobacillus reuteri) and inhibited bacterial invasion. Molecular interaction studies confirmed the strong binding between tryptophol with AhR and UGT1A1.
CONCLUSION: This study demonstrates that XCHT preserves intestinal barrier integrity in rats and alleviates CPT-11-induced DD. This protective effect is mediated by modulating inflammation and oxidative stress via the tryptophol- AhR-UGT1A1-microbiota axis, providing a novel paradigm for mechanistic studies on toxicity reduction in clinical chemotherapy drugs.}, }
@article {pmid41714186, year = {2026}, author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W}, title = {Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41714186}, issn = {1751-7370}, support = {//Cluster of Excellence "Microbiomes drive Planetary Health" of the Austrian Science Fund (FWF)/ ; RS-2025000518246//Korean government (Ministry of Science and ICT)/ ; DE-SC0025455//US Department of Energy Early Career Research Program/ ; 42477318//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; U22A20590//National Natural Science Foundation of China/ ; }, mesh = {*Nitrification ; *Soil Microbiology ; *Archaea/metabolism/virology/genetics ; *Bacteria/metabolism/genetics/classification ; *Hot Temperature ; Metagenomics ; *Viruses/genetics/classification ; Ecosystem ; Climate Change ; Soil/chemistry ; }, abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle; yet, its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.}, }
@article {pmid41714776, year = {2026}, author = {Balázs, B and Boros, Á and Pankovics, P and Mátics, R and Urbán, P and Herczeg, R and Knowles, NJ and Reuter, G}, title = {Genetic characterization of two novel picornaviruses from birds, white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41714776}, issn = {2045-2322}, mesh = {Animals ; *Picornaviridae/genetics/classification/isolation & purification ; Hungary ; Genome, Viral ; Phylogeny ; *Eagles/virology ; *Picornaviridae Infections/veterinary/virology ; *Bird Diseases/virology ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; Viral Proteins/genetics ; }, abstract = {In this study, two novel picornaviruses (eagle/WE6/HUN/2014, PV454551-PV454552 and avocet/PA12/HUN/2018, PV454553) were detected in white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary, and characterized by next generation sequencing, RT-PCR and Sanger sequencing methods. The complete polyprotein coding genomes were 6,573 and 6,567 nt long and had the genome organization 5'UTR[IRES-III]-[VP4-VP2-VP3-VP1-2A-2B-2C[hel]-3A-3B[VPg]-3C[pro]-3D[pol]]-3'UTR-poly(A)n. The P1 and the 3C[pro] proteins of the eagle/WE6/HUN/2014 showed 47.9% and 62.4% aa sequence identities to the corresponding proteins of the picornavirus (MT138036) from a little egret metagenome, respectively. The 2C[hel]/3D[pol] had 44.1%/41% aa identity to the corresponding proteins of bat-origin picornaviruses (OR867633 and KX420952). The P1 protein of the avocet/PA12/HUN/2018 had 53% aa sequence identity to the P1 protein of crane70contig328 (OQ423840) from red-crowned crane metagenome; the 2C[hel], 3C[pro] proteins had 52.6%, 52.3% aa sequence identity to the corresponding proteins of picornavirus (MT138035) from bird metagenome and 3D[pol] had 43.2% aa identity to the 3D[pol] of the picornavirus (MT138036) from a little egret metagenome, respectively. The 3'UTR of avocet/PA12/HUN/2018 contained two repetitive nt sequence motifs (the 17-nt-long Motif-1 at five times forming a secondary RNA structure and the 9-nt-long Motif-2 at two times). The eagle/WE6/HUN/2014 and avocet/PA12/HUN/2019 represent the founding members of two potential novel bird-origin picornavirus species and even genera in the subfamily Heptrevirinae (family Picornaviridae).}, }
@article {pmid41714781, year = {2026}, author = {Su, JW and Elsheikha, HM and Guo, L and Liu, R and Shang, KM and Yu, HL and Ma, H and Ni, HB and Chen, BN and Zhang, XX and Yang, X}, title = {Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41714781}, issn = {2399-3642}, support = {2022KJ169//Department of Education of Shandong Province (Department of Education, Shandong Province)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Interspersed Repetitive Sequences ; *Metagenomics ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; *Goats/microbiology ; Anti-Bacterial Agents/pharmacology ; China ; *Bacteria/genetics/pathogenicity/drug effects ; Metagenome ; }, abstract = {The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here, we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including Capra hircus (79.85%) and Ovis aries (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli represents a major host for both. Correlation analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection mechanisms. Although MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying MGEs within incomplete assemblies, 19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically critical genes such as tetX and van variants. These findings expand understanding of the Caprinae gut resistome and highlight its potential role in cross-host AMR transmission, and underscore the need for targeted AMR surveillance in this reservoir.}, }
@article {pmid41714786, year = {2026}, author = {Paládi, P and Benmazouz, I and Tóth, M and Kövér, L and Lengyel, S}, title = {Spatial and temporal dynamics in the use of urban habitats by Hooded Crows.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41714786}, issn = {2045-2322}, abstract = {UNLABELLED: Understanding the habitat use of animals in cities is relevant for urban planning, human-wildlife conflict management and urban biodiversity conservation. We studied the habitat use of Hooded Crows, a nuisance bird in much of Europe, in 16 different neighborhoods (sections) of a recently crow-colonized city in E Hungary. In the breeding season, when crows defend territories, crow numbers increased with nesting site availability and the number of trashbins but were unaffected by habitat type or area of the section. However, colonization probability was negatively influenced by the number of trashbins and restaurants, was high in parks, sports complexes, and quieter residential areas, and was low in residential areas busy with traffic. Outside the breeding season, when crows move around in groups, crow numbers increased with time in the section with the highest number of trashbins, decreased in residential areas and was stable in parks and sports complexes. Our results suggest that while crows are attracted by the foraging opportunities offered by anthropogenic food sources, they avoid nesting in such areas, likely due to high human disturbance. This implies that residential areas with fewer food sources will attract fewer crows, potentially reducing human-crow conflicts. Our study also suggests that improved waste management, such as closed-top trashbins in public places or covered enclosures in zoos, may further reduce the availability of anthropogenic food sources to crows and that targeted crow control is best scheduled for the breeding season and in residential areas.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40561-z.}, }
@article {pmid41714980, year = {2026}, author = {Ceylani, T and Teker, HT and Önlü, H and Ünver, T and Allahverdi, H and Şahin, E and Atalan, E}, title = {Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41714980}, issn = {1471-2164}, support = {FOA-2024-3587//Inönü University Scientific Research Projects Coordination Unit (BAP)/ ; }, abstract = {BACKGROUND: The developmental phase is a pivotal biological period for the maturation of the gut microbiota and the establishment of lifelong metabolic health. During these period, dietary patterns that induce dysbiosis, such as the high-fat, low-fiber “cafeteria diet,” disrupt the production of key metabolites in the gut-metabolite axis, including short chain fatty acids (SCFAs) and indole-3-propionic acid (IPA). This study employs a multi-omics approach to examine the impact of cafeteria diet exposure during the developmental period (days 21–56) in 21-day-old male Wistar rats on microbiota composition, SCFA, and IPA levels, and to assess the extent to which concurrent probiotic administration can mitigate these disruptions.
RESULTS: The cafeteria diet led to a marked reduction in alpha diversity indices (Shannon p = 0.021; Simpson p = 0.034) and altered the Firmicutes/Bacteroidetes ratio (p = 0.015). Beta diversity analysis indicated a distinct separation between groups (PERMANOVA p = 0.002). Metabolite analysis revealed significant reductions in acetic acid (p = 0.004), isobutyric acid (p = 0.094), butyric acid (p = 0.0014), valeric acid (p = 0.0001), heptanoic acid (p = 0.0125), and IPA (p = 0.002), whereas probiotic administration largely restored these levels. At the species level, cafeteria diet markedly increased Segatella copri, while probiotic intervention partially restored beneficial taxa such as Faecalibacterium prausnitzii and butyrate-producing genera (Anaerostipes hadrus, Intestinimonas butyriciproducens, Blautia wexlerae, and Flintibacter sp. KGMB00164), as evidenced primarily by shotgun metagenomics. Correlation analysis further revealed strong positive associations between butyrate and F. prausnitzii (ρ = 0.65, p = 0.003) and between IPA and B. longum (ρ = 0.68, p = 0.002). Collectively, these results highlight the protective role of probiotic intervention against diet-induced dysbiosis by reinforcing microbiota metabolite interactions.
CONCLUSIONS: By integrating metagenomic and metabolomic analyses, this multi-omics study demonstrates that exposure to a high-fat cafeteria diet during the developmental period disrupts microbiota composition and metabolite production, whereas concurrent probiotic administration largely prevent these effects, serving a protective role in the gut-metabolite axis. The study underscores the potential of early-life probiotic intervention, supports SCFA and IPA production, as a critical strategy to optimize microbiota-metabolite interactions and promote long-term gut and systemic health.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12650-w.}, }
@article {pmid41715099, year = {2026}, author = {Fan, W and Tan, T and Yang, C and Cao, Y and Jin, C and Liu, X and Shang, K and Wang, J and Xu, J and Li, Y}, title = {Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.}, journal = {Respiratory research}, volume = {27}, number = {1}, pages = {}, pmid = {41715099}, issn = {1465-993X}, support = {82102252//National Natural Science Foundation of China/ ; 82272245//National Natural Science Foundation of China/ ; 202440093, 2024ZZ1022//Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Despite advances in therapeutic strategies, acute respiratory distress syndrome (ARDS) mortality remains high. Growing evidence links respiratory microbiome composition to ARDS outcomes. This investigation sought to elucidate how colonizing bacteria and their metabolites influence ARDS pathogenesis.
METHODS: Bronchoalveolar lavage fluid (BALF) from patients with pulmonary infections was analyzed by metagenomic next-generation sequencing (mNGS) to identify characteristic bacteria. Bacterial culture supernatants were analyzed by untargeted metabolomics (LC-MS) to identify metabolites. A murine ARDS model was established through intratracheal LPS instillation. Single-cell sequencing datasets from the GEO database were analyzed to reveal differential cell populations and functional alterations in murine ARDS. Potential molecular mechanisms were explored through molecular docking, RNA-seq analysis, Western boltting, and targeted gene knockdown in murine and cellular model.
RESULTS: R. mucilaginosa demonstrated enrichment in patients without ARDS (nARDS). The bacterial culture supernatant conferred substantial protection in murine models, whereas viable bacteria showed minimal efficacy. LC-MS analysis identified indole-3-acetaldehyde (IAAld) as the predominant metabolite in the supernatant. Single-cell sequencing suggested that resident alveolar macrophages (RAMs) were pivotal cells in murine ARDS model. IAAld enhanced RAMs phagocytosis, facilitating neutrophil and LPS clearance. Mechanistic studies revealed that IAAld likely activated PXR signaling, promoted NRF2 nuclear translocation, and upregulated the phagocytosis-related gene CD36. Targeted PXR knockdown eliminated these protective effects.
CONCLUSION: The respiratory commensal R. mucilaginosa synthesizes IAAld, which—independent of bacterial colonization per se—ameliorates ARDS through PXR/NRF2/CD36 axis activation, thereby enhancing macrophage phagocytic function. These findings suggest that therapeutic targeting of microbial metabolites represents a novel ARDS treatment paradigm.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-026-03551-3.}, }
@article {pmid41715166, year = {2026}, author = {Zhang, J and Xu, L and Ge, X and Zi, X and Chen, S and Liu, C and Wang, K and Zhou, J and Dou, T and Wong, JWC and Lin, Q and Kang, X and Cao, Z}, title = {Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41715166}, issn = {2049-2618}, support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 202401AU070079//Yunnan Fundamental Research Projects/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; 202301BD070001-136//Key Project of Yunnan Province Agricultural Joint Special Project/ ; 202305AC160040//Yunnan Province Young and Middle-aged Academic and Technical Leader Reserve Talent Project/ ; }, mesh = {Animals ; China ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; *Genetic Variation ; *Bacteria/genetics/classification/isolation & purification ; Gene Transfer, Horizontal ; Metagenome ; Polymorphism, Single Nucleotide ; Bacteriophages/genetics/classification ; }, abstract = {BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized.
RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses.
CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.}, }
@article {pmid41715225, year = {2026}, author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M}, title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41715225}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Sheep/microbiology/physiology/blood ; *Temperament/physiology ; *Vocalization, Animal/physiology ; Rumen/microbiology ; *Metabolome ; Female ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; gamma-Aminobutyric Acid/metabolism ; }, abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.
METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.
RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.
CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.}, }
@article {pmid41715233, year = {2026}, author = {Choi, Y and Zhou, M and Oba, M and Romero-Pérez, A and Beauchemin, KA and Duval, S and Kindermann, M and Guan, LL}, title = {Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {72}, pmid = {41715233}, issn = {2049-2618}, support = {Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; }, mesh = {Metagenome ; *Rumen/enzymology/microbiology ; Animals ; *Cattle/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Fatty Acids, Volatile/biosynthesis ; *Methane/biosynthesis ; Hydrogen/metabolism ; Metabolic Networks and Pathways/drug effects ; }, abstract = {BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.
RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.}, }
@article {pmid41715245, year = {2026}, author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {22}, pmid = {41715245}, issn = {2524-4671}, abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia.
RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals.
CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00504-x.}, }
@article {pmid41715924, year = {2026}, author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K}, title = {Novel light-driven schizorhodopsins from Antarctic Minisyncoccota (Patescibacteria) and cyanobacteria.}, journal = {Biophysical journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bpj.2026.02.022}, pmid = {41715924}, issn = {1542-0086}, abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared with archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.}, }
@article {pmid41716172, year = {2025}, author = {Nazerke, K and Ruslan, A and Saule, D and Aida, D and Svetlana, V}, title = {Advances and emerging technologies in the diagnosis of viral infections in pigs: Progress, challenges, and One Health perspectives.}, journal = {Veterinary world}, volume = {18}, number = {12}, pages = {3788-3805}, pmid = {41716172}, issn = {0972-8988}, abstract = {Viral infections continue to pose major challenges to pig health, farm productivity, and global food security. Early and accurate diagnosis is the cornerstone of disease prevention, surveillance, and control in swine populations. In recent years, remarkable progress has been achieved in molecular, serological, and digital diagnostic technologies, enabling more rapid, sensitive, and field-adaptable detection of important porcine viruses such as African swine fever virus, porcine reproductive and respiratory syndrome virus, and classical swine fever virus. This review summarizes current and emerging diagnostic approaches, highlighting polymerase chain reaction (PCR) and its advanced forms, quantitative PCR and digital PCR, as the gold standards for laboratory confirmation. The advent of next-generation sequencing and metagenomics has revolutionized pathogen discovery and genomic surveillance, providing comprehensive insights into viral evolution and transboundary transmission. Isothermal amplification techniques such as loop-mediated isothermal amplification and recombinase polymerase amplification have shown strong potential for on-farm diagnosis due to their simplicity, rapidity, and minimal equipment requirements. Innovations such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated-based assays, biosensors, lab-on-a-chip platforms, and point-of-care testing devices are bridging the gap between laboratory precision and field application, allowing rapid decision-making during outbreaks. The integration of artificial intelligence, machine learning, and geographic information systems has further enhanced diagnostic interpretation, real-time data sharing, and early outbreak prediction under the One Health framework. Despite these advances, challenges remain in ensuring assay standardization, affordability, and equitable access in resource-limited regions. Continued international collaboration, data sharing, and policy harmonization under the guidance of the Food and Agriculture Organization, the World Organization for Animal Health, and the World Health Organization are essential for the global control of swine viral diseases. Ultimately, combining molecular innovation with digital adaptability offers the most promising path toward resilient, cost-effective, and sustainable diagnostic systems for safeguarding animal and public health.}, }
@article {pmid41716262, year = {2026}, author = {Qiao, YC and Jiang, XX and Zan, JP and Chen, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG}, title = {Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691984}, pmid = {41716262}, issn = {1664-302X}, abstract = {BACKGROUND AND AIMS: Mulching is a widely used agricultural management practice with profound effects on soil properties and crop productivity. However, its impact on soil microbial community structure and function remains insufficiently understood. This study aimed to investigate how different mulching treatments influence the composition, functional potential, and interaction networks of soil microbial communities in a chieh-qua-legume rotation system.
METHODS: Metagenomic sequencing was employed to analyze soil samples subjected to four mulching treatments (biodegradable mulch, non-degradable silver mulch, non-degradable black mulch, and straw mulch) as well as a no-mulch control (CK).
RESULTS: Mulching treatments significantly altered soil microbial diversity and community structure, with straw and biodegradable mulches supporting higher diversity than the control. Biodegradable mulch was strongly correlated with changes in soil pH and enriched denitrifying bacteria such as Thauera and Comamonadaceae, while reducing the abundance of genes related to energy metabolism and carbon fixation. These findings suggest that organic carbon from mulch degradation may enhance denitrification, potentially leading to nitrogen loss. Co-occurrence network analysis revealed that biodegradable mulch promoted more complex and connected microbial networks, whereas plastic mulches resulted in simpler structures. Additionally, all mulching treatments significantly reduced the abundance of the autotrophic ammonia-oxidizing archaeon Thaumarchaeota, likely due to reduced soil oxygen under mulch.
CONCLUSION: This study provides new insights into how different mulching practices modulate soil microbial communities and their ecological functions. The results underscore the importance of tailoring mulching strategies to maintain soil health and fertility. Specifically, nitrogen supplementation is recommended when using biodegradable mulch in chieh-qua cultivation systems.}, }
@article {pmid41716274, year = {2026}, author = {Name, PE and Tibiri, EB and Tiendrébéogo, F and Sawadogo, S and Djigma, F and Traoré, L and Eni, AO and Pita, JS}, title = {Unraveling the intra-species genomic diversity of sweetpotato-infecting CRESS-DNA and RNA viruses in Burkina Faso using Oxford Nanopore sequencing.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1722370}, pmid = {41716274}, issn = {1664-302X}, abstract = {Sweetpotato is a key crop for global food security, particularly in Burkina Faso, where its productivity is increasingly threatened by viral diseases, especially those caused by CRESS-DNA viruses. However, the diversity of these viruses in Burkina Faso remains poorly characterized due to limitations of conventional diagnostic approaches. In this study, nanopore sequencing was used to investigate the diversity of CRESS-DNA viruses infecting sweetpotato in Burkina Faso. Ninety-eight symptomatic dried leaf samples from a previously established biobank were selected and analyzed. Total DNA was extracted, enriched using rolling circle amplification (RCA), and sequenced using the MinION Mk1C platform. In parallel, RNA viruses were also investigated using nanopore sequencing. RCA successfully amplified 53 of the 98 samples, from which 28 complete and 25 partial CRESS-DNA virus genomes were recovered. Sequence analyses revealed high genomic diversity, with sweet potato leaf curl virus (SPLCV) being the most prevalent. Sweet potato symptomless virus 1 (SPSMV-1) was detected for the first time in Burkina Faso in a co-infection with SPLCV. Additionally, 52 deltasatellite genomes (50 complete, 2 partial) were identified in association with SPLCV, displaying approximately 86% nucleotide identity with known sequences, suggesting the presence of genetically distinct putative deltasatellites. RNA virome analysis revealed frequent co-infections involving sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus, with SPFMV commonly co-occurring with SPLCV. Four complete SPFMV genomes were recovered and clustered within phylogroup B, forming a distinct subclade. Overall, this study highlights the remarkable diversity of viruses infecting sweetpotato in Burkina Faso and reports, for the first time, the presence of SPSMV-1 and sweepovirus-associated deltasatellites in the country. These findings underscore the importance of ongoing molecular surveillance to support effective viral disease management strategies and food security.}, }
@article {pmid41716833, year = {2026}, author = {Xie, F and Li, J and Liu, P and Xu, L and Wang, Y and Qiu, Q and Mao, S}, title = {Genome-resolved metagenomics reveals gastrointestinal microbiome adaptations in sheep responding to fiber- and starch-rich diets.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {24}, number = {}, pages = {233-245}, pmid = {41716833}, issn = {2405-6383}, abstract = {The gastrointestinal tract of ruminants hosts a specialized microbial ecosystem that has evolved to efficiently digest fiber. However, modern intensive farming practices, which often involve reduced dietary fiber and increased grain supplementation, are linked to metabolic disorders in ruminants. Despite this, the understanding of the taxonomic and functional adaptations of the gastrointestinal microbiome to dietary changes remains limited, largely due to the challenges in obtaining high-resolution characterization of microbial communities. This study employed genome-resolved metagenomics to examine how a starch-rich (SR) grain-based diet compares to a fiber-rich (FR) hay-based diet in shaping the composition and function of the gastrointestinal microbiome in the rumen, jejunum, and cecum of Hu sheep. A total of 10 sheep (approximately 180 d old, with a body weight of 25.6 ± 0.41 kg) were allocated to the 2 dietary groups (SR and FR groups) for a 28-d experimental period, and metagenomic sequencing was performed on digesta samples from different gastrointestinal regions. Using a representative microbial gene catalog (RGMGC) and 10,373 metagenome-assembled genomes from previous studies,microbial composition, strain-level diversity, and carbohydrate-active enzyme profiles at higher taxonomic and functional resolution were analyzed. The results showed that the transition from the FR diet to the SR diet significantly altered the fermentation patterns and the structure and function of the sheep gastrointestinal microbiota. Community analysis revealed microbial taxa such as Prevotella spp., Alistipes spp., RC9 spp., CAG-110 spp., and Akkermansia spp. with significantly altered abundances (P < 0.05), primarily associated with the reduced fiber content in the SR diet. Moreover, the gastrointestinal microbiome exhibited strain-level changes in carbohydrate degradation, leading to reduced metabolic functions necessary for fiber processing. Comparative genomics at the single-genome level pinpointed Prevotella as a core genus with strains showing significant functional differences, notably in the capacity to degrade plant polysaccharides. Overall, these findings provide new insights into microbial regulation of gastrointestinal health and offer valuable enzyme gene resources in ruminants.}, }
@article {pmid41716871, year = {2026}, author = {Rosenqvist, T and Cleary, M}, title = {Detecting "invisible" Phytophthora lineages in publicly available sequencing data.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag019}, pmid = {41716871}, issn = {2730-6151}, abstract = {Our understanding of microbial eukaryotic diversity is limited by biases induced by cultivation and DNA-amplification. Microbial lineages which are challenging or impossible to culture and develop universal metabarcoding primers for can be considered "invisible." These "invisible" microbes can however be detected in genomic and metagenomic sequencing datasets. This study introduces a new pipeline for targeted assembly of internal transcribed spacer (ITS) sequences from genomes and metagenomes (https://github.com/tage-ro/denim), which provides advantages in sensitivity and precision over comparable marker-gene assembly software. It further shows how publicly sequencing datasets can be screened for the genus Phytophthora, which includes economically and ecologically devastating plant pathogens. Analysis of 104 sequencing datasets resulted in 733 full ITS sequences, 1626 ITS1 sequences and 2191 ITS2 sequences associated with a variety of eukaryotic lineages. Phytophthora ITS sequences associated with known species in clades 1, 2, 4, 6, 7 and 8 were assembled, along with sequences only distantly related to known taxa. In addition, it provided potential indications of new pathogen-host interactions, with potential impacts on agriculture and human health. This study presents a new approach towards discovering and detecting "invisible" microbes, thus expanding our understanding of microbial eukaryotic diversity. Moreover, it allows detection and monitoring of new host-microbe interactions, and characterizing the geographic distribution of cultured and uncultured microorganisms.}, }
@article {pmid41716893, year = {2026}, author = {Cao, Y and Huang, J and Wu, W and Xu, Z and Wang, C and Wu, X and Zhan, C and Xing, J and Liu, J and Zhu, M and Ma, S}, title = {Clinical Utility and Therapeutic Strategy Value of Metagenomic Next-Generation Sequencing in Pulmonary Infection Among Cancer Patients.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {568562}, pmid = {41716893}, issn = {1178-6973}, abstract = {INTRODUCTION: Cancer patients, particularly those with lung cancer, are highly susceptible to pulmonary infections due to both the disease itself and the immunosuppressive effects of treatments such as chemotherapy and immunotherapy. The objective of this study was to analyze pathogenic distribution characteristics of pulmonary infections in cancer patients and evaluated the guidance of metagenomic next-generation sequencing (mNGS) on clinical administration.
METHODS: This retrospective study included 66 samples from cancer patients. Pathogens in patient specimens, encompassing peripheral blood, bronchoalveolar lavage fluid (BALF), sputum, and other samples, were identified using both mNGS and culture methods.
RESULTS: Compared to culture methods, mNGS demonstrated a sensitivity of 95.5% across all samples. In terms of overall detections, Human gammaherpesvirus 4 was identified as the most frequently detected pathogen in cancer patients, while Escherichia coli and Candida albicans were ranked as the most common bacterial and fungal pathogens, respectively. During the perioperative period, non-surgical short-term treatment, non-surgical long-term treatment, and long-term treatment groups, Escherichia coli and Achromobacter xylosoxidans were all identified. Moreover, the treatment strategies for patients were timely adjusted based on the mNGS results, resulting in a significant improvement in clinical symptoms for 59.3% (16 out of 27) of the cancer patients.
CONCLUSION: mNGS is an advanced approach for pathogen detection in cancer patients, with commendable diagnostic performance demonstrated. The results of mNGS contribute to the rapid modification of clinical medication, which may improve the survival rate of cancer patients.}, }
@article {pmid41717089, year = {2025}, author = {Shi, S and Qi, J and Peng, W and Su, X and Chen, P and Xu, S and Li, S and Ma, L and Wang, W and Jiang, K and Liu, Z and Li, W and Xiong, H and Wang, Y}, title = {Convergent gut microbiome adaptation and pervasive antibiotic resistome in Qinghai-Tibet Plateau passerines.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1733974}, pmid = {41717089}, issn = {1664-302X}, abstract = {INTRODUCTION: The Qinghai-Tibet Plateau, an extreme high-altitude ecosystem, presents a unique model for studying host-microbe-environment coevolution under environmental stress. However, the role of resident wildlife, particularly non-migratory passerines, as reservoirs and vectors for cross-boundary antibiotic resistance gene (ARG) dissemination remains poorly understood.
METHODS: Here, through metagenomic analysis of two endemic passerines (Pseudopodoces humilis and Pyrgilauda ruficollis) and their habitats.
RESULTS: We reveal convergent adaptations in their gut microbiomes, dominated by Actinomycetota, Pseudomonadota and Bacillota. Functional enrichment in carbohydrate metabolism and genetic information processing underpins host energy optimization in extreme high-altitude environments. Critically, these birds constitute a major reservoir of ARGs, harboring 153 antibiotic resistance ontologies (AROs) with nearly universal resistance to clinical antibiotic classes. The core resistome-comprising glycopeptide (van clusters), fluoroquinolone, and tetracycline resistance genes-reflects anthropogenic contamination amplified by environmental persistence. Environmental transmission pathways were unequivocally demonstrated via 47 AROs shared between avian hosts and proximal matrices (soil/grass), coupled with livestock-derived antibiotic influx through excreta, establishing the plateau as a hotspot for resistance gene flux. Strikingly, "low-abundance-high-resistance" taxa (Pseudomonadota, Actinomycetota, and Bacillota; ≤30% abundance but >80% ARG contribution) drive resistome plasticity, potentially facilitated by horizontal gene transfer.
DISCUSSION: Our findings redefine resident passerines as sentinels of ecosystem health and bridges for cross-boundary antimicrobial resistance (AMR) spread. Mitigating global AMR thus necessitates interdisciplinary strategies targeting environmental reservoirs (e.g., regulating livestock antibiotic use) and monitoring avian-mediated gene flow.}, }
@article {pmid41717629, year = {2026}, author = {Wang, X and Yang, Y and Li, Y and Zhu, Z and Khashaba, R and Yue, Q}, title = {Multi-omics reveals microbial community characteristics and flavonoid biotransformation mechanisms during mung bean sour fermentation.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101342}, pmid = {41717629}, issn = {2665-9271}, abstract = {Fermented foods are gaining popularity for their health benefits, and fermented mung bean products are recognized for their nutritional value. To investigate microbial community succession and abundance dynamics of bioactive compounds like flavonoids in fermented mung bean sour (MBS), parallel metagenomic and metabolomic analyses were performed. Metagenomic profiling identified Lactiplantibacillus, Lactococcus, Bifidobacterium, and Acetobacter as dominant genera. Functional gene analysis demonstrated a significant increase in the relative abundance of flavonoid degradation pathways, which exhibited strong positive correlations (r > 0.8, p < 0.05) with the dominant genera. Metabolomic analysis revealed a significant decrease in flavonoids, including vitexin and orientin. Moreover, increased activities of β-glucosidase and α-rhamnosidase were identified as key factors promoting the biotransformation of flavonoids into bioactive metabolites such as apigenin, naringenin, and quercetin. This study provides a foundation for further understanding the microbial conversion and utilization of flavonoid compounds in mung beans.}, }
@article {pmid41718052, year = {2026}, author = {La Via, L and Ferlito, S and Di Modica, MS and Marino, A and Nunnari, G and Cacopardo, B and Lechien, JR and Lentini, M and Lavalle, S and Botto, GC and Buscema, P and Gruppuso, L and Maniaci, A}, title = {The Global Impact of Sepsis: Epidemiology, Recognition, Management, and Health System Challenges.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {7}, number = {1}, pages = {}, pmid = {41718052}, issn = {2673-3986}, abstract = {BACKGROUND: Sepsis constitutes a major healthcare burden worldwide, with an estimated 48.9 million incident cases and 11.0 million deaths in 2017, accounting for nearly one-fifth of all global deaths. Even with advances in definitions and guidelines, significant inequalities persist in awareness, early treatment, and health system readiness.
METHODS: We performed a structured narrative review of epidemiology studies, clinical case definitions, diagnostic approaches, stewardship interventions, and health system reports. Both electronic sources (PubMed, Web of Science, Embase, Scopus) and grey literature (World Health Organization [WHO], National Institute for Health and Care Excellence [NICE], Society Critical Care [SSC]) were explored. Evidence incorporated themes were organized across recognition, diagnostics, antimicrobial therapy, organ support, guidelines, and health system determinants.
RESULTS: Measurement tools, including quick Sequential Organ Failure Assessment (qSOFA) and Sequential Organ Failure Assessment (SOFA), exhibited suboptimal sensitivity and utility in varied clinical environments. Biomarkers (procalcitonin, presepsin, CD64) and rapid molecular diagnostics, including metagenomic next-generation sequencing (mNGS) and AI-based devices, enhance detection but are limited by cost and infrastructure constraints. Each hour of delay in antibiotic therapy is associated with a 6-10% increased risk of mortality, underscoring the importance of stewardship, including the incorporation of empiric regimens with rapid de-escalation. Health system bottlenecks-human resources, funding, infrastructure-continue to be a significant determinant of outcomes, especially in low- and middle-income countries.
CONCLUSIONS: Attaining the 2030 WHO targets for sepsis involves precision diagnostics, adaptable guidelines, stewardship frameworks, and resilient health systems. Fair application and resource allocation are crucial to lower the incidence and mortality worldwide.}, }
@article {pmid41718326, year = {2026}, author = {Hernández-Cruz, E and Gómez-Godínez, LJ and Ruvalcaba-Gómez, JM and Arteaga-Garibay, RI}, title = {Optimized Method for Efficient DNA Extraction from Agricultural Soils.}, journal = {Methods and protocols}, volume = {9}, number = {1}, pages = {}, pmid = {41718326}, issn = {2409-9279}, abstract = {Soil harbors the highest concentration of microorganisms in ecosystems, and their molecular characterization through high-throughput sequencing is essential for metagenomic studies. However, obtaining high-quality, high-concentration DNA is limited by physicochemical properties (pH, heavy metals, humic acids) and adsorption to clay minerals. Although standardized commercial protocols exist, they present variable limitations depending on soil type. This study developed and validated the National Center for Genetic Resources-Microorganism Collection (CNRG-CM) method, which incorporates innovative pre-washing steps using phosphate-buffered saline (PBS) and sodium phosphate to effectively remove inhibitory humic acids and metal ions, combined with cetyltrimethylammonium bromide (CTAB)/chloroform extraction to achieve high-molecular-weight metagenomic DNA isolation. The CNRG-CM method was applied to three diverse soil types with variable physicochemical properties, recovering DNA concentrations ranging from 1000 to 1300 ng/μL ith a yield of 30 to 48 µg/g[-1], significantly exceeding those obtained with a standard commercial kit with maximum DNA concentrations of 360 ng/μL and a yield of 43 µg/g[-1]. The CNRG-CM protocol is established as an effective and adaptable alternative for metagenomic DNA extraction across diverse agricultural and ecological contexts. It enables subsequent metagenomic studies of soil microbial communities.}, }
@article {pmid41718551, year = {2026}, author = {Gröger, L and Rishik, S and Ludwig, N and Beganovic, A and Koch, M and Rheinheimer, S and Hart, M and König, P and Trampert, T and Paul, P and Boese, A and Lehr, CM and Becker, SL and Fuhrmann, G and Keller, A and Meese, E}, title = {Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2630482}, pmid = {41718551}, issn = {1949-0984}, mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; MicroRNAs/metabolism/genetics ; Caco-2 Cells ; *RNA, Bacterial/metabolism/genetics ; *Epithelial Cells/microbiology/metabolism ; *Gastrointestinal Microbiome ; }, abstract = {While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.}, }
@article {pmid41719127, year = {2026}, author = {Wang, S and Su, LY and Lan, D and Pan, H and Xiong, M and Yao, M and Deng, Y and Fan, Z and Cao, Y and Zhou, H}, title = {Adenosine signaling driven by the gut microbiota underlies chronic alcohol-induced anesthetic resistance.}, journal = {Cell reports}, volume = {45}, number = {3}, pages = {117015}, doi = {10.1016/j.celrep.2026.117015}, pmid = {41719127}, issn = {2211-1247}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Adenosine/metabolism ; *Signal Transduction/drug effects ; Mice ; Humans ; *Ethanol/pharmacology ; Male ; Mice, Inbred C57BL ; *Anesthetics/pharmacology ; Female ; }, abstract = {Chronic alcohol consumption increases anesthetic tolerance, yet the underlying in vivo mechanisms remain unclear. Here, we demonstrate that long-term alcohol exposure reduces anesthetic efficacy in both humans and mice, prolonging induction and shortening maintenance. Fecal microbiota transplantation from alcohol-exposed donors recapitulated this phenotype in naive mice, indicating a causal role of gut microbiome alterations. Metagenomic and metabolomic analyses identified elevated adenosine as a key microbiota-derived metabolite. Adenosine supplementation decreased anesthetic sensitivity, likely via downregulation of gamma-aminobutyric acid (GABA) receptors. Our findings reveal a gut microbiota-adenosine pathway mediating alcohol-induced anesthetic resistance.}, }
@article {pmid41719150, year = {2026}, author = {Ni, Y and Wang, Y}, title = {ICTV Virus Taxonomy Profile: Nipumfusiviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {2}, pages = {}, doi = {10.1099/jgv.0.002226}, pmid = {41719150}, issn = {1465-2099}, mesh = {Genome, Viral ; *DNA Viruses/classification/genetics/ultrastructure/isolation & purification ; Phylogeny ; Virion/ultrastructure/genetics ; *Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure ; Capsid Proteins/genetics/chemistry ; }, abstract = {The family Nipumfusiviridae includes DNA viruses with hosts deduced to be marine ammonia-oxidizing archaea, specifically those in the archaeal family Nitrosopumilaceae. Virus genomes have been discovered through metagenomics of samples from inlets, coastal areas, intertidal zones, epipelagic and oceanic waters, and soil. Viruses have neither been isolated nor enriched through experiments. The family Nipumfusiviridae includes several genera. The virions of nipumfusiviruses are predicted to have spindle-shaped morphology based on the analysis of the deduced structural models of the major capsid protein. Limited information can be provided about translation and replication from the genome. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Nipumfusiviridae, which is available at ictv.global/report/nipumfusiviridae.}, }
@article {pmid41719263, year = {2026}, author = {Huang, G and Gallagher, TL and Tsongalis, GJ and Lefferts, JA}, title = {Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0341560}, pmid = {41719263}, issn = {1932-6203}, mesh = {Humans ; *DNA, Fungal/genetics/analysis ; *DNA, Bacterial/genetics/analysis ; *Multiplex Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; *Fungi/genetics ; DNA, Ribosomal/genetics ; Bacteria/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Molecular methods in clinical and research applications frequently encounter complex mixtures of human and microbial DNA, sometimes alongside environmental or reagent contaminants. In metagenomic studies, the presence of host contamination poses a significant challenge, reducing the assay sensitivity of microbial detection and characterization. Different host-depletion and microbial enrichment platforms have been developed to reduce or eliminate host DNA in samples predominantly composed of human DNA. To establish an effective method to assess the efficacy of host DNA depletion or microbial enrichment platforms, this study aimed to develop a multiplex, broad-range 16S/18S ribosomal DNA droplet digital PCR (rDNA ddPCR) assay capable of simultaneously quantifying bacterial and fungal DNA, along with a human housekeeping gene, RPP30 (Ribonuclease P/MRP Subunit P30). Genomic DNA from key representatives of Gram-positive bacteria, Gram-negative bacteria, and fungi was tested in broad-range 16S/18S rDNA duplex (16S/RPP30 or 18S/RPP30) and triplex (16S/18S/RPP30) ddPCR assays to determine optimal assay conditions, specificity, and sensitivity. This assay demonstrated high sensitivity, specificity, and reproducibility, with detection limits of approximately 3 copies/µL for the 16S target (0.5 pg Staphylococcus aureus gDNA) and 1-2 copies/µL for the 18S target (16 fg of Candida albicans gDNA) in both duplex and triplex formats. Within a defined range, a linear relationship was observed between microbial DNA input and 16S/18S rDNA copy number by ddPCR. Furthermore, different commercial ddPCR master mixes had contrasting effects on the amplitudes of positive 16S/18S droplet clusters. As a proof of concept for the assay's utility in metagenomic studies, we demonstrated that one extraction kit achieved more efficient depletion of human DNA and better enrichment of microbial DNA. In summary, we developed a multiplex, broad-range 16S/18S ddPCR assay with high sensitivity and specificity, which holds promise as a QA/QC (Quality Assurance/Quality Control) platform in metagenomic studies and other research settings.}, }
@article {pmid41719397, year = {2026}, author = {Cheng, G and Jiang, X and Zhu, L and Chen, X and Liu, R and Zhu, L and Hu, X and Zhang, S and Tan, W and Lin, D and Zhang, L and Wu, C and Li, M}, title = {Intratumoral Parvimonas micra promotes esophageal squamous cell carcinoma via p-cresol-induced Treg differentiation.}, journal = {Science advances}, volume = {12}, number = {8}, pages = {eady1644}, pmid = {41719397}, issn = {2375-2548}, mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/microbiology/pathology/immunology/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Esophageal Neoplasms/microbiology/pathology/immunology/metabolism ; Tumor Microenvironment/immunology ; *Cresols/metabolism ; *Cell Differentiation/drug effects ; Animals ; Mice ; Female ; *Bacillota ; Male ; Prognosis ; Cell Line, Tumor ; Reactive Oxygen Species/metabolism ; }, abstract = {Intratumoral microbiota has emerged as a notable factor influencing cancer initiation and progression. However, its composition and functional impact in esophageal squamous cell carcinoma (ESCC) remain largely unexplored. Here, we performed metagenomic sequencing on 119 paired tumor-normal tissues from patients with ESCC and single-cell RNA sequencing on 45 samples to investigate microbe-host interactions. We identified Parvimonas micra (P. micra), an anaerobic oral-derived bacterium, as significantly enriched in tumor tissues and associated with poor prognosis. Moreover, the abundance of P. micra correlated with increased regulatory T cell (Treg cell) infiltration in the ESCC tumor microenvironment. Through cellular and animal experiments, we demonstrate that P. micra promotes tumor growth by secreting p-cresol, a metabolite of amino acid fermentation, which elevates reactive oxygen species levels and induces FOXP3[+] Treg differentiation, thereby fostering immunosuppression and tumor growth. Our study establishes a mechanistic link between intratumoral microbiota and the immune microenvironment, highlighting the microbial contribution to ESCC progression and prognosis.}, }
@article {pmid41719533, year = {2026}, author = {Ippolito, I and Hug, L}, title = {Antimicrobial resistance gene diversity, prevalence, and mobility within four landfills.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-15}, doi = {10.1139/cjm-2025-0226}, pmid = {41719533}, issn = {1480-3275}, mesh = {*Waste Disposal Facilities ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Genetic Variation ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; Metagenomics ; }, abstract = {Antibiotics in landfills create selection pressures on the microorganisms present, selecting for antibiotic resistance genes (ARGs) and antibiotic resistant organisms (ARO). The aim of this study was to assess whether landfills are hot-spots of antimicrobial resistance and whether landfills may contribute to global ARO diversity through ARG lateral gene transfer. Genome resolved metagenomic sequencing combined with sequence-search-based and deep learning tools were used to determine ARG diversity and prevalence from four active municipal landfills and their adjacent ground or surface water systems. Comparison to pristine and anthropogenic environments highlighted that landfill microbial communities contain distinct ARG signatures, including a broader diversity of ARGs. Plasmids made up 4.1%-8.4% of assembled scaffolds and carried 5.4%-12.0% of the identified ARGs in assembled data, depending on the sample type. Enriched ARG resistance mechanisms on mobile elements included multidrug resistance and antibiotic inactivation. The results indicate that landfills house a high diversity of antimicrobial resistance mechanisms and drug classes, with a moderate fraction encoded on mobile elements. Landfills are thus likely mixing grounds for ARG transfer and evolution of novel or augmented ARO lineages.}, }
@article {pmid41719987, year = {2026}, author = {Dang, X and Xu, S}, title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119906}, doi = {10.1016/j.ecoenv.2026.119906}, pmid = {41719987}, issn = {1090-2414}, mesh = {Animals ; Male ; Mice ; Hippocampus/drug effects ; *Behavior, Animal/drug effects ; Molecular Docking Simulation ; Diabetes Mellitus, Experimental ; *Alkanesulfonic Acids/toxicity ; Salmonella enterica ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; Molecular Dynamics Simulation ; Colon/microbiology ; Fluorobenzenes ; }, abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.}, }
@article {pmid41720032, year = {2026}, author = {Kong, X and He, Y and Guo, J and Chen, Y and An, D}, title = {Chain-length-associated response patterns of chlorinated paraffins on activated sludge systems driven by microbial community response.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141542}, doi = {10.1016/j.jhazmat.2026.141542}, pmid = {41720032}, issn = {1873-3336}, mesh = {*Sewage/microbiology/chemistry ; *Water Pollutants, Chemical/chemistry/toxicity ; *Microbiota/drug effects ; *Paraffin/chemistry/toxicity ; Bioreactors/microbiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bacteria/genetics/drug effects/metabolism ; *Hydrocarbons, Chlorinated/chemistry/toxicity ; }, abstract = {Chlorinated paraffins (CPs) are emerging contaminants detected in wastewater treatment plants, yet their impacts on activated sludge systems remain poorly understood. In this study, parallel sequencing batch reactors were employed to comprehensively evaluate the effects of short-chain (SCCP), medium-chain (MCCP), and long-chain (LCCP) CPs on pollutant removal performance, sludge properties, and microbial ecological responses. Under the tested nominal loading, the C24-LCCP standard led to a clear reduction in nitrogen removal efficiency, whereas MCCP and SCCP maintained stable or even enhanced phosphorus removal performance. CP exposure generally increased oxidative stress and cytotoxicity, while SCCP and MCCP further stimulated extracellular polymeric substances secretion, consistent with an enhanced floc/cell-interface protective phenotype. Metagenomic analysis revealed that SCCP and MCCP enriched genera (Acinetobacter, Dechloromonas, Zoogloea) associated with phosphorus removal and increased the abundance of key nitrogen transformation genes, whereas the C24-LCCP standard exhibited comparatively weaker shifts in functional gene profiles. Metatranscriptomic profiling indicated treatment-associated differences in transcriptional responses under the tested nominal loading, with SCCP showing the largest DEG set (>30,000 genes) in this dataset. Integrated metagenomic and metatranscriptomic analyses revealed a coordinated stress‑response program under SCCP, characterized by activation of efflux pumps, DNA repair, redox regulation, environmental stress responses, and biofilm-associated functions, together with elevated energy metabolism and ABC transporter signals. These molecular and community-level patterns aligned with the observed variations in treatment performance and sludge properties, providing convergent evidence for a chain-length-associated response framework. These findings provide comparative molecular and phenotypic evidence that may inform future risk assessment and hypothesis-driven mitigation studies on CP impacts in biological wastewater treatment systems.}, }
@article {pmid41720310, year = {2026}, author = {Zhao, W and Chen, P}, title = {Resilient biological nitrogen removal from surfactant-rich wastewater: construction of an indigenous community, quantitative tolerance assessment, and multi-level fault tolerance mechanisms.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134251}, doi = {10.1016/j.biortech.2026.134251}, pmid = {41720310}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Wastewater/chemistry/microbiology ; *Surface-Active Agents/chemistry ; Denitrification ; *Water Purification/methods ; Biodegradation, Environmental ; Nitrification ; Sewage/microbiology ; Water Pollutants, Chemical/isolation & purification ; Alkanesulfonic Acids ; }, abstract = {Linear alkylbenzene sulfonates (LAS) severely inhibit biological nitrogen removal. In this study, an indigenous microbial community (ICM) with heterotrophic nitrification-aerobic denitrification (HN-AD) capability was developed through long-term directed acclimatization. The ICM exhibited markedly enhanced resistance to LAS over a concentration range of 0-300 mg/L, maintaining nitrogen transformation rates more than twofold higher than those of conventional activated sludge. By integrating Haldane kinetic modeling with species sensitivity distribution analysis, we demonstrated that the ICM increased the 5% hazardous concentration (HC5) by 78%, thereby substantially expanding its ecological tolerance. Metagenomics and qPCR linked ICM resilience to multi-level responses; quorum sensing regulation, EPS-mediated sequestration, and enhanced redox homeostasis reinforced HN-AD performance. Dominant genera Pseudomonas and Aeromonas coupled detoxification with nitrogen removal. These findings demonstrate the ICM's transition from passive survival to active nitrogen removal reinforcement, offering quantitative benchmarks for resilient surfactant-rich wastewater treatment.}, }
@article {pmid41720311, year = {2026}, author = {Liu, C and Ji, M and Wu, W and Shi, Y and Treu, L and Wang, W and Campanaro, S}, title = {Self-sufficient fermentation paradigm for cassava stillage valorization into C6 carboxylic acids: regulatory mechanisms and novel microbe identification.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134236}, doi = {10.1016/j.biortech.2026.134236}, pmid = {41720311}, issn = {1873-2976}, mesh = {*Fermentation ; *Manihot/metabolism/chemistry ; *Carboxylic Acids/metabolism ; Hydrogen-Ion Concentration ; *Clostridium/metabolism/genetics ; Lactic Acid/metabolism ; }, abstract = {Cassava stillage (CS), a carbohydrate-rich byproduct of bioethanol production, holds significant untapped potential as a renewable resource. Upcycling this problematic wastewater offers great promise for addressing both environmental challenges and the demand for sustainable biochemicals. Here, this study proposed a self-sufficient biotechnological paradigm that directly valorizes CS into medium-chain carboxylic acids (MCCAs, e.g., caproic acid) by integrating lactic acid/butyric acid-type fermentation with microbial chain elongation (CE) by two phase fermentation regulatory. Lactic acid and butyric acid were regulated as dominant products with optimal ratio around 2 from CS degradation, and then chain elongated into caproic acid with optimal pH of 6. pH was found to play a crucial role in controlling product distribution in both phases of fermentation and shaping the microbiome. Meanwhile, chain elongation resilience was also found operational pH-dependent. Metagenomic analysis identified the bacterium Clostridium sp. BUCT163 as a putative lactic acid-driven chain elongating microbe. Whole-genome comparison between Clostridium sp. BUCT163 and Clostridium kluyveri species indicated that the genes encoding lactic acid conversion are not widespread among C. kluyveri populations. The combination of metagenomic-binning and comparative genomic analysis Clostridium sp. BUCT163 was distinguished as the novel potential lactic acid/ethanol-driven chain elongating microbe which successfully provided valuable data sets to link bacterial identities with chain elongating microbes. These findings provide foundation for the resource recovery process from CS in a self-sufficient anaerobic fermentation paradigm and the microbial management of chain elongating systems.}, }
@article {pmid41720808, year = {2026}, author = {Jin, Y and An, HJ and Zheng, TT and Li, JJ and Gao, JM and Zhong, XL and Li, BH and Liu, YY and Zhuang, XJ and Chen, JH and Rao, JH}, title = {Adenosine from high-fat-diet-tolerant monkey-derived Limsolactobacillus reuteri MacFasB02 modulates cholesterol metabolism to alleviate hyperlipidemia and inflammation.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00765-z}, pmid = {41720808}, issn = {2396-8370}, support = {82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 2024GDASZH-2024010101//GDAS' Project of Science and Technology Development/ ; }, abstract = {Hyperlipidemia is a leading global health challenge, limited by the safety liabilities of current pharmacotherapies. Here, we isolated a novel Limosilactobacillus reuteri strain, MacFasB02, from fecal samples of cynomolgus monkeys tolerant to chronic high-fat diet (HFD). This study aimed to systematically evaluate its probiotic properties and therapeutic potential against hyperlipidemia. In vitro, MacFasB02 exhibited robust growth, acid production, and tolerance to acidic and bile environments. In HFD-fed mice, 13-week MacFasB02 administration reduced weight gain, serum triglycerides, low-density lipoprotein cholesterol and total cholesterol, while ameliorating hepatic steatosis and inflammation, as well as restoring intestinal barrier integrity by enhanced villus architecture, goblet cell function, and tight junction proteins expression. Metagenomic analysis revealed gut microbiota remodeling. Transcriptomic profiling coupled with in vivo validation demonstrated upregulation of Apoa1 and Pltp in cholesterol metabolism. Untargeted metabolomics integrated with whole-genome sequencing and supernatant metabolite profiling identified adenosine as a key MacFasB02-derived metabolite in purine metabolism. Consistently, In vitro experiments showed that adenosine reduced lipid accumulation and inflammation in hepatocytes by regulating Apoa1 and Pltp to modulate cholesterol metabolism. Collectively, MacFasB02 exerts dual lipid-lowering and anti-inflammatory effects probably via adenosine-mediated modulation of cholesterol metabolism, promising potential as a live biopharmaceutical agent for hyperlipidemia.}, }
@article {pmid41720887, year = {2026}, author = {Clarenne, A and Suarez, LV and Muggeo, A and Meurice, J and Lecomte-Thenot, Q and Perotin, JM and Bessaci-Kabouya, K and Mulette, P and Abely, M and Gouriou, S and Dury, S and Deslée, G and Héry-Arnaud, G and Guillard, T}, title = {Assessing anaerobe detection in routine sputum analyses from cystic fibrosis patients.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41720887}, issn = {2045-2322}, support = {RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//University Hospital of Reims/ ; }, mesh = {*Cystic Fibrosis/microbiology ; *Sputum/microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Bacteria, Anaerobic/isolation & purification/genetics/classification ; Male ; Female ; Adult ; Young Adult ; Middle Aged ; Adolescent ; }, abstract = {Pulmonary involvement in cystic fibrosis (CF) includes bronchiectasis and chronic airway infection, with nearly half of the airway bacteria being anaerobes. Some anaerobic species, such as Porphyromonas catoniae, have been identified as predictive biomarkers for Pseudomonas aeruginosa colonization, with P. catoniae decreasing as the disease progresses. Although 16S rRNA metagenomics offers a comprehensive view of airway anaerobes, it is not routinely performed in clinical microbiology laboratories. This study aimed to evaluate the ability of routine sputum culture to identify strict anaerobes in people with CF (pwCF) compared to 16S rRNA sequencing, and to assess the impact of sample transport conditions. Sputum from 48 pwCF was analyzed by anaerobic culture and 16S rRNA sequencing. Strict anaerobes were detected in 95.8% of patients by culture and 100% by 16S rRNA sequencing. Culture identified 23 strict anaerobic species (mean 2.6 per sample), while 16S rRNA sequencing revealed nearly 100 species (mean 43 per sample). Importantly, culture isolated key genera such as Veillonella and Prevotella, core members of the CF airway anaerobiome. Transport conditions (aerobic vs. anaerobic) did not affect anaerobe detection. These new findings support changes in the processing of CF sputum in the everyday practice of clinical microbiology laboratories and promote the characterization of the culturable anaerobic airway microbiota.}, }
@article {pmid41721729, year = {2026}, author = {Wang, H and Zhao, Z and Lin, L and Dong, A and Deng, Y and Zhou, J and Ju, F}, title = {Candidatus Dermatophostum as a novel genus of polyphosphate-accumulating organisms for high-strength wastewater treatment.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41721729}, issn = {1751-7370}, support = {WU2024MY003//Westlake University-Muyuan Joint Research Institute/ ; 42477517//National Natural Science Foundation of China/ ; 42207546//National Natural Science Foundation of China/ ; }, mesh = {*Wastewater/microbiology ; Phylogeny ; *Polyphosphates/metabolism ; *Bacteroidetes/metabolism/genetics/classification/isolation & purification ; Water Purification/methods ; Metagenome ; Bioreactors/microbiology ; Phosphorus/metabolism ; Genome, Bacterial ; }, abstract = {Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named here as Candidatus Dermatophostum, which shows specific preference for high-phosphorus environments. Its representative species, Ca. Dermatophostum ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Integrative meta-omics combining genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis, and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across wastewater treatment plants worldwide, underscoring both its diverse metabolic capabilities and potential engineering implications for mitigating nitrous oxide (N2O) emissions for EBPR system. Finally, we propose a ppk1-based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.}, }
@article {pmid41721873, year = {2026}, author = {Sankar, SA and Girijan, SK and Shambhugowda, YB and Busala, SKK and Narayanane, S}, title = {Decoding the biotic networks and functional potential of seamount sediments in the Arabian sea.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41721873}, issn = {1573-4978}, mesh = {*Geologic Sediments/microbiology ; Metagenomics/methods ; Biodiversity ; Nitrogen/metabolism ; Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Fungi/genetics ; Microbiota/genetics ; Bacteria/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited.
METHODS AND RESULTS: A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes.
CONCLUSIONS: The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.}, }
@article {pmid41722379, year = {2026}, author = {Steinberger, Y and Doniger, T and Marchi, E and Eshel, G and Bocchi, S and Zapperi, S and La Porta, CAM}, title = {Fungal community structure and network connectivity as indicators of soil health under long-term land use.}, journal = {The Science of the total environment}, volume = {1020}, number = {}, pages = {181545}, doi = {10.1016/j.scitotenv.2026.181545}, pmid = {41722379}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Fungi/classification/physiology ; *Agriculture/methods ; *Environmental Monitoring/methods ; Israel ; Soil/chemistry ; *Mycobiome ; Biodiversity ; Seasons ; }, abstract = {Agriculture practices induce profound changes in soil biological properties and soil functioning. However, we still lack an understanding of how soil fungal biodiversity responds to various practices. Metagenomic tools were used to investigate soil fungal communities and inferred ecological functions based on functional guild classification in response to the effect of climate region and land management. This study assessed how seasonal timing and long-term land management affect soil fungal communities, with the aim of exploring their potential as candidate indicators of soil biological status. We collected soil samples across two regions of Israel (Mediterranean north and semi-arid south), three land-use types-orchard (OR), field crops (FC), and non-cultivated control (CO)-and two seasons-autumn and spring. Abiotic parameters varied significantly by season, region, and depth, underscoring the importance of considering sampling time in soil assessment. Fungal community composition showed marked differences between land uses, suggesting sensitivity to long-term management. CO and OR soils consistently exhibited higher fungal diversity and network connectivity, while FC soils had lower richness and unique taxa. A stable core community of 10 genera was found across treatments. Functional guilds were dominated by saprotrophs, though specific taxa and guild contributions varied by management type and season. Overall, our results emphasize the importance of sampling timing and land-use history in shaping fungal communities and support the potential of fungal-based indicators for assessing soil status across agricultural systems.}, }
@article {pmid41722567, year = {2026}, author = {Thurimella, K and Wu, E and Li, C and Graham, DB and Owens, RM and Plichta, DR and Sokol, CL and Xavier, RJ and Bacallado, S}, title = {Identifying microbial protease allergens through protein language model-guided homology.}, journal = {Cell systems}, volume = {17}, number = {3}, pages = {101510}, pmid = {41722567}, issn = {2405-4720}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AI151163/AI/NIAID NIH HHS/United States ; }, mesh = {*Allergens/immunology/genetics/chemistry ; Humans ; *Serine Proteases/immunology ; Animals ; Deep Learning ; Hypersensitivity/immunology ; *Peptide Hydrolases/immunology ; }, abstract = {Emerging research links the gut, skin, and oral microbiomes to allergies, with serine proteases (SPs) identified as potential allergens. This study leverages deep learning and pre-trained protein language models (pLMs) to uncover allergenic SPs in metagenomic data. First, we develop a model to identify the catalytic serine residue in serine hydrolases, demonstrating how pLMs capture structural information. Next, we create a deep learning framework to detect candidate SP allergens across gene catalogs, using the conserved catalytic triad to identify homologs in gut and oral sites despite low sequence identity. Our model predicts a putative SP allergen resembling V8 protease, a known trigger for protease-activated receptor 1. It also identifies a cysteine protease similar to Der f 1 from dust mites. Immunization with these proteases induced allergic responses, validating their allergenic potential experimentally. This approach uncovers candidate allergens beyond traditional methods, offering new targets for allergy research. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid41722709, year = {2026}, author = {Arhin, SG and Esposito, G and Cesaro, A}, title = {Single-stage microbial conversion of fish waste into linear and branched medium-chain fatty acids.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134253}, doi = {10.1016/j.biortech.2026.134253}, pmid = {41722709}, issn = {1873-2976}, mesh = {Fermentation ; Animals ; *Fatty Acids/biosynthesis/metabolism ; *Fishes ; Saccharomyces cerevisiae/metabolism ; *Waste Products/analysis ; Anaerobiosis ; Hydrogen-Ion Concentration ; }, abstract = {Anaerobic fermentation of biowaste into medium‑chain fatty acids (MCFAs) offers a scalable route for resource recovery within a circular bioeconomy framework, yet production from protein‑rich substrates such as fish waste remains underexplored. This study investigated the valorization of fish waste into MCFAs via mono- and co-fermentation in a single-stage chain elongation process. By leveraging endogenous electron donors and protein ammonification, the system maintained favorable pH conditions and sustained MCFA synthesis without external chemical inputs. Mono-fermentation favored isocaproate (4-methylvaleric acid) production, reaching a peak yield of 166.9 ± 11.6 mg COD/g VS (5.8 ± 0.4 g COD/L). Co-fermentation with carbohydrate-rich food waste in equal proportions shifted selectivity toward n-caproate (214.5 ± 18.8 mg COD/g VS) and n-heptanoate (145.8 ± 27.7 mg COD/g VS), achieving a maximum total MCFA yield of 366.3 ± 53.1 mg COD/g VS (12.8 ± 1.9 g COD/L). Bioaugmentation with Saccharomyces cerevisiae triggered solventogenesis and excessive ethanol oxidation (EEO) possibly due to elevated ammonium concentrations. Although sodium 2-bromoethanesulfonate (BES) addition transiently suppressed EEO, EEO resumed as H2 production declined, suggesting that promoting lactate-driven chain elongation via co‑fermentation is a more robust strategy under ammonia stress. Metagenomic analysis revealed that isocaproate formation during mono‑fermentation was associated with Stickland‑type amino‑acid fermentation, with Sporanaerobacter acetigenes as a potential key contributor. In contrast, co‑fermentation enriched genes associated with lactate metabolism, acetyl‑CoA generation, and linear MCFA synthesis, primarily linked to Clostridia and Betaproteobacteria. These results reveal tunable routes to straight‑ and branched‑chain MCFAs from protein‑rich waste, supporting green approaches to platform chemical generation.}, }
@article {pmid41722974, year = {2026}, author = {Ji, M and Gong, J and Liu, Z and Liu, X and Wang, X and Ao, C and Tan, J}, title = {Multi-omics investigation of microbial community dynamics and metabolic regulation in mulberry wine fermentation under temperature and acid stress.}, journal = {Food microbiology}, volume = {137}, number = {}, pages = {105022}, doi = {10.1016/j.fm.2025.105022}, pmid = {41722974}, issn = {1095-9998}, mesh = {Fermentation ; *Wine/microbiology/analysis ; *Morus/microbiology/metabolism ; Saccharomyces cerevisiae/metabolism/genetics ; *Microbiota ; Temperature ; Hydrogen-Ion Concentration ; Ethanol/metabolism ; Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; *Acids/metabolism ; Lactobacillus/metabolism/genetics ; Stress, Physiological ; Multiomics ; }, abstract = {This study employed an integrated approach of metagenomics and metabolomics to investigate microbial community dynamics during mulberry wine fermentation under varying temperatures (17-29 °C) and pH levels (3.0-4.5). Twenty treatment combinations, spanning 27 days, captured the temporal dynamics of microbial communities and metabolic activity. Environmental stress significantly shaped community assembly, with Saccharomyces cerevisiae acting as the dominant fermentation organism and Lactobacillus spp. associated with organic acids. Core population analysis revealed specialized functions in ethanol production, acid resistance, and flavor biosynthesis. An optimal fermentation efficiency of 82 % and an ethanol content of 9.1 % vol. were achieved with the response surface method, resulting in optimal fermentation conditions of 23 ± 1 °C with a pH of 3.5 ± 0.1. Multi-omics correlation network analysis revealed coordinated associations among gene expression, enzymatic activities, and metabolite profiles, including coordinated expression patterns of flavor compound biosynthesis pathways. This research provides evidence-based optimization strategies for industrial mulberry wine production, enhancing understanding of stress-responsive microbial adaptation mechanisms.}, }
@article {pmid41723054, year = {2026}, author = {Prideaux, L and Goire, N and Crook, S and Dreyer, L and Sherry, N and Mahony, AA}, title = {A case of Helicobacter cinaedi meningitis confirmed via metagenomics sequencing.}, journal = {Pathology}, volume = {58}, number = {3}, pages = {377-379}, doi = {10.1016/j.pathol.2025.10.011}, pmid = {41723054}, issn = {1465-3931}, }
@article {pmid41723172, year = {2026}, author = {Honda, T and Yu, S and Mai, D and Baumgart, L and Chan, EM and Babnigg, G and Yoshikuni, Y}, title = {CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69903-1}, pmid = {41723172}, issn = {2041-1723}, support = {DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {Plant roots release a wide array of metabolites into the rhizosphere, shaping microbial communities and their functions. While metagenomics has expanded our understanding of these communities, little is known about the physiology of their members in host environments. Transcriptome analysis via RNA sequencing is a common approach to learning more, but its use has been challenging because of low bacterial biomass and interference from plant RNA. To overcome this, we developed a randomly-barcoded promoter-library insertion sequencing (RB-PI-seq) combined with chassis-independent recombinase-assisted genome engineering (CRAGE). Using Pseudomonas simiae WCS417 as a model rhizobacterium, this method enabled targeted amplification of barcoded transcripts, bypassing plant RNA interference and allowing measurement of thousands of promoter activities during Arabidopsis root colonization. Our analysis revealed temporally resolved transcriptional regulation, including those associated with cell growth, chemotaxis, plant immune suppression, biofilm formation, and stress responses, reflecting the coordinated physiological adaptation to the root environment. Additionally, we discovered that transcriptional activation of xanthine dehydrogenase and a lysozyme inhibitor is crucial for evading plant immune systems. This framework is scalable to other bacterial species and provides new opportunities for understanding rhizobacterial gene regulation in native environments.}, }
@article {pmid41723316, year = {2026}, author = {Moreno, IJ and Bogdanov, A and Palenik, B}, title = {Common capacity for far-red light photosynthesis in a canyon thermophilic freshwater system.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {41723316}, issn = {1433-4909}, abstract = {UNLABELLED: Photosynthetic life is based on absorbing sunlight and turning it into biologically usable energy. In many cases however, canopy-like structures and cavern-like habitats in terrestrial environments can limit the intensity and alter the spectra of light. One acclimation to use filtered light in the near infrared range, typically between 700 and 800 nm is named far-red light photoacclimation or FaRLiP as in recent studies of cyanobacteria. Here we report the common capacity for FaRLiP in the dominant cyanobacterial genera in a canyon hot spring microbial mat ecosystem. We identified FaRLiP in the genomes of cyanobacterial isolates and the metagenomes of mat samples. We show using absorption spectroscopy and HPLC that under far red-light specific isolates show an increase in far red-light absorption and the presence of Chl f. Springs in narrow canyons are a microniche where FaRLiP seems highly ecologically advantageous.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00792-026-01422-9.}, }
@article {pmid41723359, year = {2026}, author = {Wang, L and Xu, J and He, P and Hong, W and Jin, Y and Zeng, J and Liu, L and Liu, L}, title = {Refractory peritoneal dialysis-associated peritonitis caused by Mycobacterium tuberculosis identified by mNGS: a case report.}, journal = {BMC nephrology}, volume = {27}, number = {1}, pages = {}, pmid = {41723359}, issn = {1471-2369}, support = {0038481190612016//Zhuhai High-Level Talent Team Fund/ ; }, mesh = {Humans ; Female ; Adult ; *Peritoneal Dialysis/adverse effects ; *Mycobacterium tuberculosis/isolation & purification ; *Kidney Failure, Chronic/therapy/complications ; *Peritonitis, Tuberculous/diagnosis/etiology/drug therapy/microbiology ; Antitubercular Agents/therapeutic use ; *Peritonitis/microbiology/diagnosis/etiology ; Lupus Erythematosus, Systemic/complications/therapy ; }, abstract = {BACKGROUND: Peritoneal dialysis-associated peritonitis (PDAP) is a common complication in patients undergoing peritoneal dialysis (PD) and may lead to technique failure or poor prognosis. Tuberculosis-related peritonitis in this setting is rare and difficult to diagnose because of nonspecific clinical manifestations and frequently negative conventional microbiological tests. Reporting such cases may help improve awareness and diagnostic strategies.
CASE PRESENTATION: We report the case of a 34-year-old woman with systemic lupus erythematosus and end-stage renal disease who was receiving maintenance peritoneal dialysis. She presented with fever, abdominal pain, and diarrhea. Repeated conventional bacterial and fungal cultures of peritoneal dialysis effluent and blood were negative, and empirical antibiotic therapy failed to achieve sustained clinical improvement. Metagenomic next-generation sequencing of the peritoneal dialysis effluent detected Mycobacterium tuberculosis, providing supportive diagnostic information. Based on the combined clinical presentation, molecular findings, and immunological testing, anti-tuberculosis therapy was initiated. The patient's symptoms gradually resolved, and peritoneal dialysis was temporarily suspended for 11 days before being successfully resumed. No recurrence of peritonitis was observed during a 6-month follow-up period.
CONCLUSIONS: This case highlights the diagnostic challenges of tuberculosis-related peritonitis in patients undergoing peritoneal dialysis. Metagenomic next-generation sequencing may serve as a useful adjunctive diagnostic tool in selected patients with persistent symptoms and repeatedly negative conventional cultures, facilitating earlier diagnosis and appropriate management.}, }
@article {pmid41723514, year = {2026}, author = {Şapcı, AOB and Mirarab, S}, title = {krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {41723514}, issn = {1474-760X}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; ASC150046//Advanced Cyberinfrastructure Coordination Ecosystem/ ; 1R35GM142725/NH/NIH HHS/United States ; #2138259//National Science Foundation/ ; 1R35GM142725/NH/NIH HHS/United States ; 1R35GM142725/NH/NIH HHS/United States ; }, mesh = {*Phylogeny ; Metagenomics/methods ; Likelihood Functions ; Algorithms ; *Software ; }, abstract = {Comparing each sequencing read in a sample to a reference database is a fundamental step in wide-ranging applications. Results of these comparisons can enable phylogenetic characterization. However, phylogenetic placement is currently only possible at scale for marker genes, a small fraction of the genome. We introduce krepp, an alignment-free k-mer-based method that enables placing reads from anywhere on the genome on an ultra-large reference phylogeny (e.g., 123,853 leaves). We show that krepp is scalable and computes accurate distances that approximate those using alignments, leading to accurate placements. These precise phylogenetic identifications improve our ability to compare and characterize metagenomic samples.}, }
@article {pmid41723970, year = {2026}, author = {Wang, L and Wang, J and Zhu, Q and Zhang, Q and Qian, J}, title = {Rapid diagnosis of a mixed pulmonary infection with Rhizopus microsporus, Aspergillus fumigatus, Pneumocystis jirovecii, and Cytomegalovirus in a Lymphoma patient using metagenomic next-generation sequencing: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {2}, pages = {117320}, doi = {10.1016/j.diagmicrobio.2026.117320}, pmid = {41723970}, issn = {1879-0070}, mesh = {Humans ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Aspergillus fumigatus/genetics/isolation & purification ; Pneumocystis carinii/genetics/isolation & purification ; *Coinfection/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Metagenomics/methods ; Cytomegalovirus Infections/diagnosis ; Cytomegalovirus/genetics/isolation & purification ; COVID-19/diagnosis ; Immunocompromised Host ; SARS-CoV-2/genetics/isolation & purification ; Rhizopus/genetics/isolation & purification ; }, abstract = {Immunocompromised patients are at high risk for life-threatening polymicrobial infections, often challenging to diagnose conventionally. We report a 60-year-old male with relapsed angioimmunoblastic T-cell lymphoma, fever, and pancytopenia post-chemotherapy. Chest CT showed scattered inflammation. Bronchoalveolar lavage fluid (BALF) culture grew only Klebsiella aerogenes, but fluorescent staining revealed aseptate hyphae. Metagenomic next-generation sequencing (mNGS) of BALF identified concurrent infections with Rhizopus microsporus, Aspergillus fumigatus, Pneumocystis jirovecii, cytomegalovirus, and SARS-CoV-2 within 48 hours. Targeted therapy with isavuconazole, sulfamethoxazole-trimethoprim, and ganciclovir was promptly initiated. Despite therapy, the patient deteriorated due to profound immunodeficiency and was discharged palliatively. This case highlights mNGS as a rapid diagnostic tool for mixed infections, though clinical correlation remains essential.}, }
@article {pmid41724049, year = {2026}, author = {Wang, D and Xin, J and Lai, C and Sun, N and Yang, Y and He, Y and Duan, L and Luo, J and He, Y and Zhang, Y and Zhang, Y and Wang, H and Zeng, D and Bai, Y and Ni, X}, title = {High fluoride exposure disrupts gut microbiota and induces intestinal barrier damage via RhoA/ROCK-mediated cytoskeletal remodeling.}, journal = {Ecotoxicology and environmental safety}, volume = {312}, number = {}, pages = {119898}, doi = {10.1016/j.ecoenv.2026.119898}, pmid = {41724049}, issn = {1090-2414}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; rho-Associated Kinases/metabolism ; Mice ; Cytoskeleton/drug effects ; rhoA GTP-Binding Protein/metabolism ; *Fluorides/toxicity ; Male ; Intestinal Mucosa/drug effects ; Signal Transduction/drug effects ; Intestines/drug effects ; Permeability ; Mice, Inbred C57BL ; }, abstract = {Fluoride pollution-whether of geological or anthropogenic origin-disrupts gut microbiota-host homeostasis and compromises the intestinal barrier. We established an acute high-fluoride mouse model via intragastric NaF, integrating metagenomics, metabolomics, and molecular biological techniques to clarify the underlying mechanism of enhanced intestinal permeability caused by fluoride exposure in vivo. Mechanistically, high fluoride exposure activates the RhoA/ROCK signaling pathway, increases the level of phosphorylated myosin light chain (p-MLC), induces filamentous actin (F-actin) rearrangement, and disrupts the apical junctional complex (AJC)-characterized by downregulated expression or abnormal localization of AJC-related proteins (ZO-1, Claudin-1, β-catenin, Occludin). It also alters the morphology of intestinal epithelial cells, ultimately increasing ileal permeability. At the microbiota level, high fluoride disrupted the ileal microbiota; specifically, at the species level, Bifidobacterium sp. SO1 and Schaalia turicensis were identified as the key species with high specificity and high occupancy under fluoride exposure. Lactobacillus and Akkermansia were abnormally enriched in the intestines of mice exposed to fluoride. Metabolomic analysis revealed that high fluoride exposure enriched multiple pathways including linoleic acid metabolism and sphingolipid metabolism, altering the levels of 11 cytoskeleton-related metabolites. Correlation analysis confirmed that Bifidobacterium sp. SO1 and Schaalia turicensis were strongly correlated with damage phenotypes, pathway molecules, and metabolites, indicating that these two strains are closely associated with cytoskeleton changes and increased intestinal permeability under high fluoride exposure. Collectively, our findings reveal that gut microbiota drive fluoride-induced intestinal barrier dysfunction through the "microbiota-RhoA/ROCK-cytoskeleton" axis, highlighting a novel host-microbe interaction mechanism underlying environmental toxin-mediated gut injury.}, }
@article {pmid41724250, year = {2026}, author = {Li, Y and Kang, L and Qin, X and Fei, R and Lu, A and Qishuang, H}, title = {Dual mechanism of electrochemical regulation to reduce soil Nitrous Oxide emissions-microbial recruitment and electron transfer pathway optimization.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134255}, doi = {10.1016/j.biortech.2026.134255}, pmid = {41724250}, issn = {1873-2976}, mesh = {*Nitrous Oxide/metabolism ; *Soil/chemistry ; *Soil Microbiology ; Electron Transport ; Oxidation-Reduction ; Fertilizers ; Denitrification ; Nitrogen/metabolism ; Microbiota ; *Electrochemical Techniques/methods ; Urea ; }, abstract = {Greenhouse gas emissions from agricultural nitrogen cycling, primarily Nitrous Oxide (N2O), are intrinsically linked to fertilizer dynamics. Conventional mitigation strategies emphasize synthetic fertilizer reduction, yet suffer from inefficiency and lack of sustainability. This study introduces an electrochemical regulation approach and, through comparative analysis of two fertilizers (ammonium sulfate vs. urea), elucidates dual mechanisms (redox modulation and microbial community engineering). Key findings: (1) 500 mV electrostimulation enriched nitrate-reducing microbiota, reducing N2O by 11.9 ± 5.9% (sulfate) and 14.2 ± 4.4% (urea) via enhanced denitrification; (2) Electrode interventions accelerated N2O-to-N2 conversion (15.8 ± 1.4% and 14.9 ± 8.9%) by optimizing redox fluxes and boosting electroautotrophic Pseudomonas spp. activity; (3) Urea exhibited delayed electroresponsiveness (6-10 h lag) due to slower amide nitrogen hydrolysis kinetics compared to sulfate; (4) Metagenomics confirmed upregulation of nitrogen metabolic genes (norC: 2.9×, nirD: 2.7×, narI: 2.6 ×) and restructured microbial networks. This study elucidates a fundamental electro-microbial mechanism that reconfigures nitrogen-transforming networks, providing a novel paradigm for managing soil biogeochemical cycles.}, }
@article {pmid41724273, year = {2026}, author = {Yang, X and Chen, H and Wu, T and Ji, ZY and Wang, ZW and Liu, ZL and Yang, JK and Zhao, Y and Zhou, M and Wang, XB}, title = {Neobavaisoflavone, a functional metabolite derived from valnemulin, ameliorates DSS-induced ulcerative colitis through activation of the AMPK signaling pathway.}, journal = {Biochemical pharmacology}, volume = {248}, number = {}, pages = {117841}, doi = {10.1016/j.bcp.2026.117841}, pmid = {41724273}, issn = {1873-2968}, abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease (IBD), is characterized by sustained mucosal inflammation, disrupted epithelial barrier function, microbial dysbiosis, and impaired intestinal homeostasis. If chronic uncontrolled inflammation persists, it may lead to the development of colorectal cancer or other severe clinical complications. Emerging evidence suggests that cellular senescence promotes inflammatory cascades, aggravating UC symptoms and implicating a pathophysiological link to disease progression. Our previous studies have demonstrated that the anti-senescence compound Valnemulin (VAL) can mitigate colonic senescence and alleviate UC symptoms. In this study, subsequent integrative metagenomic and metabolomic analyses revealed that VAL's pharmacological mechanism involves restructuring the gut microbial community composition, enhancing the colonization abundance of beneficial bacteria, and thereby promoting the production of their key metabolites, which collectively contribute to UC remission. In vitro and in vivo studies demonstrated that VAL's anti-senescence effects are mediated by Neobavaisoflavone (NBIF), a functional metabolite produced by beneficial gut bacteria. NBIF effectively activates the AMP-activated protein kinase (AMPK) pathway, significantly reducing the expression levels of senescence marker proteins p16, p53, and p21. Consequently, this mechanism ameliorates the senescent phenotype in intestinal epithelial cells and contributes to the overall improvement of colonic tissue senescence in UC pathology. Concomitantly, NBIF also reduces levels of pro-inflammatory cytokines IL-1β, TNF-α, and IL-6, thereby attenuating DSS-induced pathological damage in UC. This study not only proposes a novel anti-senescence strategy for UC treatment but also elucidates the pivotal role of the gut microbiota-metabolite-AMPK axis in regulating intestinal inflammation.}, }
@article {pmid41724378, year = {2026}, author = {Lin, YT and Graells, T and Sayols-Baixeras, S and Dekkers, KF and Schillemans, T and Baldanzi, G and Wuopio, J and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J}, title = {Association between the gut microbiota and estimated glomerular filtration rate in two Swedish population-based cohorts.}, journal = {Kidney international}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.kint.2026.01.021}, pmid = {41724378}, issn = {1523-1755}, abstract = {INTRODUCTION: Evidence for gut-kidney interactions in early kidney disease is limited, particularly in community-dwelling adults with largely preserved kidney function. Here, we quantified links between gut microbiota and estimated glomerular filtration rate (eGFR) in two population-based Swedish cohorts.
METHODS: Deep shotgun metagenomics profiled fecal samples from 9788 adults in the Swedish CArdioPulmonary BioImage Study (SCAPIS) discovery cohort (mean age 58 ± 4 years; 52% women) and 2080 adults in the Malmö Offspring Study (MOS) replication cohort (mean age 40 ± 14 years; 52% women). Linear regression related the relative abundance of 494 metagenome-assembled species to the creatinine-based eGFR (by CKD-EPI equation), adjusting for demographics, albuminuria, cardiovascular risk factors and technical variables. Species passing false discovery rate under 0.05 in SCAPIS were tested in MOS for significant concordant direction. Functional enrichment linked eGFR-associated species to gut metabolic modules and plasma metabolites; partial Spearman correlations were used to assessed metabolite/species/eGFR relationships.
RESULTS: The alpha diversity showed a modest inverse association with eGFR across both cohorts. We identified 44 bacterial species consistently associated with eGFR in both cohorts, collectively explaining 7% of its variance. Enrichment analysis highlighted histidine and carnitine metabolism among the top three pathways involved. Their key products, trimethylamine N-oxide and imidazole propionate, were inversely related to eGFR, and a metabolite panel accounted for 51% of eGFR variation, underscoring metabolite-mediated microbial effects. Sensitivity analyses upheld these findings.
CONCLUSIONS: Gut microbial diversity and 44 reproducible species are independently linked to kidney function in community-dwelling adults. Enrichment of histidine and carnitine pathways and their circulating metabolites implicates microbial metabolism as a contributor to eGFR variability, suggesting tractable targets for early kidney protection.}, }
@article {pmid41724403, year = {2026}, author = {Zhang, Y and Liu, Y and Zhang, S and Li, Y and Zhao, L and Wang, Z and Wang, Q and Zhang, N and Bachert, C and Bröker, BM and Wang, X and Zhang, L and Lan, F}, title = {Staphylococcal superantigen-specific IgE reveals functional superantigen production beyond Staphylococcus aureus in CRSwNP.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2026.02.013}, pmid = {41724403}, issn = {1097-6825}, abstract = {BACKGROUND: Staphylococcal superantigen-specific IgE (SAg-IgE) correlates with disease severity in patients with type 2 (T2) chronic rhinosinusitis with nasal polyps (CRSwNP). Although Staphylococcus aureus is recognized as a primary source of SAgs, SAg-IgE is detected even in patients with culture-negative S aureus.
OBJECTIVE: We sought to identify the source of SAgs in SAg-IgE-positive patients with T2 CRSwNP with culture-negative S aureus.
METHODS: Metagenomic sequencing was conducted in patients with T2 CRSwNP with repeatedly negative S aureus cultures, stratified by SAg-IgE status. We screened clinical isolates for SAg genes and evaluated SAg functionality by measuring SAg-specific T-cell receptor repertoire expansion and T2 inflammatory responses in an ex vivo infection model.
RESULTS: The SAg-IgE-positive group showed significantly higher abundances of S epidermidis, S aureus, Lysinibacillus xylanilyticus, and S capitis compared with the SAg-IgE-negative group. Interestingly, in all participants in whom S aureus was detected, S capitis was also present, albeit at low abundance. Redundancy analysis demonstrated clustering of the Staphylococcus genus, SAg-IgE, and IL-5, supporting a potential link between the Staphylococcus genus and SAg-driven immune responses. Notably, a clinical S capitis isolate carried SEA (staphylococcal enterotoxin A) and SEC genes and secreted functional SAgs, which triggered the clonal expansion of SEA/SEC-specific T-cell receptors and exacerbated the T2 inflammatory response via IL-33 induction.
CONCLUSIONS: Metagenomic sequencing reveals that S capitis, beyond S aureus, produces functional SAg to drive T2 response in SAg-IgE-positive patients with CRSwNP when conventional cultures fail to detect S aureus. Independent of culturable bacterial load, tissue SAg-IgE positivity reliably indicates bacterial colonization and SAg exposure in CRSwNP.}, }
@article {pmid41724632, year = {2026}, author = {You, TY and Lee, NY and Tsai, WC and Lo, CL and Chen, PT and Chen, SY and Jan, HE and Ko, WC}, title = {Etiological identification of Orientia tsutsugamushi by metagenomic next-generation sequencing in an adult with septic shock in Taiwan.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2026.02.002}, pmid = {41724632}, issn = {1995-9133}, }
@article {pmid41724800, year = {2026}, author = {Bhuyan, B and Chutia, B and Singh, LS}, title = {Emerging strategies for heavy metal removal in soils: plant-microbe interactions and omics perspectives.}, journal = {Archives of microbiology}, volume = {208}, number = {5}, pages = {}, pmid = {41724800}, issn = {1432-072X}, mesh = {*Metals, Heavy/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Plants/microbiology/metabolism ; *Soil Microbiology ; Soil/chemistry ; Metabolomics ; Bacteria/metabolism/genetics ; Proteomics ; }, abstract = {Rapid industrial expansion, intensive agricultural practices, and widespread petroleum extraction have led to the significant buildup of heavy metals (HMs) in soils and related ecosystems, posing serious environmental and public health risks. Hence, this review highlights the major sources, ecological impacts, and toxicity of HMs in the environment. However, physical and chemical remediation methods can reduce HMs concentrations, but issues such as high operational costs, prolonged treatment durations, and poor sustainability limit their suitability for large-scale application. Thus, bioremediation methods, especially those that utilize plants and microbes, have gained increasing attention as eco-friendly and cost-effective options. Plant-microbe-based interactions play an important role, as they act synergistically to facilitate metal uptake, stabilization, transformation, and detoxification of HMs in contaminated soils. Though, it is important to understand the plant-microbe interactions, especially since most current research is about how plants and microbes can work together to clean up contaminants in their natural environments. However, achieving higher remediation performance under stress conditions depends on the selection of plant and microbial species. Therefore, this review explores the mechanisms of plant-microbe interactions along with omics technologies employed to analyze samples for understanding this interaction in HMs-contaminated soils at the metagenomics, metatranscriptomics, proteomics, and metabolomics levels in enhancing the effectiveness of remediation. This review article also highlights key factors affecting remediation efficiency and discusses limitations, challenges, and future prospects of plant-microbe interactions in HMs-contaminated soils.}, }
@article {pmid41724868, year = {2026}, author = {Aciole Barbosa, D and de Maria, YNLF and Menegidio, FB and de Oliveira, RC and Jabes, DL and Nunes, LR}, title = {Dysbiosis of the enteric DNA virome correlates with the development of cachexia in a murine Lewis lung carcinoma (LLC) model.}, journal = {Archives of virology}, volume = {171}, number = {3}, pages = {}, pmid = {41724868}, issn = {1432-8798}, mesh = {Animals ; *Cachexia/virology/etiology/microbiology ; *Dysbiosis/virology ; *Virome ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Disease Models, Animal ; *Carcinoma, Lewis Lung/complications/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Male ; }, abstract = {Cachexia, a multifaceted wasting syndrome, profoundly impacts quality of life and survival rates in cancer patients. Gut inflammation is identified as a key player among the contributing factors for its development. Consequently, numerous studies have sought to characterize changes in gut microbiota of cachectic individuals, given the well-established roles of the gut microbiota in controlling and/or triggering both local and systemic inflammation in their hosts. Most of these investigations have applied mouse models of tumor-induced cachexia to show correlations between alterations in bacterial and fungal abundance in the digestive tract and the onset of cancer cachexia (CC). However, the role of viral dysbiosis in CC development remains unexplored. The present study aims to address this gap by characterizing the gut virome during the progression of murine cancer cachexia. Although our approach was limited to DNA viruses, our findings reveal that cachectic animals with Lewis lung carcinoma exhibited a subtle yet statistically significant modulation in composition (R[2] = 0.17622; p = 0.05). A linear discriminant analysis effect size (LEfSe) analysis revealed that the dysbiosis observed in the gut virome of CC animals was mostly characterized by a significant enrichment in giant viruses of the family Phycodnaviridae (LDA score, 4.2582; p-value, 0.004; pwrapp, 0.9984) and significantly decreased populations of bacteriophages of the families Microviridae (LDA score, 4.3458; p-value, 0.0127; pwrapp, 0.9065) and Inoviridae (LDA score, 3.3028; p-value, 0.0017; pwrapp, 0.9992). This cachexia-associated viral dysbiosis shares similarities with virome alterations documented in other conditions linked to gut inflammation, including, ulcerative colitis, Crohn's disease, and Clostridioides difficile infection. These new insights suggest the potential contributions of viral communities to the pathophysiology of CC and other inflammation-driven diseases.}, }
@article {pmid41724983, year = {2026}, author = {Yang, K and Li, J and Li, L and Fu, L and Liu, W and Jia, Z and Wang, Z and Wei, Z and Zhang, F}, title = {Soil antibiotic resistome in farmland exhibits higher diversity and horizontal transfer potential than adjacent pastureland in agro-pastoral ecotone.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41724983}, issn = {2524-6372}, support = {CCPTZX2024QN03//National Center of Pratacultural Technology Innovation Special fund for innovation platform construction/ ; 42407171//National Natural Science Foundation of China/ ; 2025T180072, GZB20240311//China Postdoctoral Science Foundation/ ; }, abstract = {BACKGROUND: Soil antibiotic resistant genes (ARGs) and mobile genetic elements (MGEs) are associated with agricultural land-use differences. However, assessing the soil antibiotic resistome differences between farmland and pastureland is often limited due to geographically unbalanced sample collection. Leveraging a typical agro-pastoral ecotone in northern China as the study model, we compared the soil microbiome and resistome between 15 adjacent farmland and pastureland pairs using metagenomic sequencing.
RESULTS: Results showed that farmland soils harbored higher soil ARG diversity (+ 2.75%), MGE diversity (+ 1.62%) and multidrug resistance-related gene abundance (+ 19.5%) than pastureland. Among them, genes conferring multidrug resistances were dominant in farmland, mainly carried by Pseudomonadota. While, vancomycin-resistant ARGs were dominant in pastureland, mainly carried by Actinomycetota. Metagenome-assembled genomes revealed that sul2 conferring sulfonamide resistance was shared by both Pseudomonadota and Acidobacteriota in farmland together with insertion sequence ISVsa3. Structural equation model analysis integrating with soil geography, pedology and microbiome data showed microbial community and soil properties were identified as major driving factors shaping soil antibiotic resistome diversity in both land-use contexts. MGE diversity showed a clear positive effect on ARG diversity in farmland soils but a minor effect in pastureland.
CONCLUSIONS: Together, this study elucidates the shared and distinguished soil antibiotic resistome pattern between farmland and pastureland, extending our understanding of driving factors in agricultural soil ARG contamination.}, }
@article {pmid41725012, year = {2026}, author = {Ramírez, AL and Páez, L and Vega, L and Aya, V and Hernández, C and Luna, N and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Metagenomic analysis of the human gut virome reveals functional signatures and viral stability across hospitalized and non-hospitalized diarrheal and non-diarrheal individuals.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41725012}, issn = {1757-4749}, abstract = {BACKGROUND: The human gut virome is a fundamental yet understudied component of the intestinal microbiome. However, its taxonomic composition and functional potential in Latin American populations remain poorly understood, particularly under clinical stressors such as hospitalization and diarrhea conditions often linked to microbial dysbiosis.
METHODS: We conducted a hybrid metagenomic analysis of the human gut virome from 37 fecal samples: 10 from patients admitted to intensive care units (ICU), 13 from hospitalized patients outside the ICU (Non-ICU), and 14 from non-diarrheic individuals, including taxonomic and functional profiling of viruses and detection of viral auxiliary metabolic genes (vAMGs).
RESULTS: We identified 494 high-quality viral vOTUs, from which 37,619 ORFs were predicted. Taxonomically, Caudoviricetes and Intestiviridae were consistently present across all groups, supporting their role as part of a conserved core virome. Functionally, we identified 309 putative vAMGs spanning 90 functional categories, primarily related to metabolism and environmental information processing. Non-diarrheic individuals harbored a higher number and diversity of vAMGs compared to hospitalized groups (Kruskal-Wallis, p < 0.01), whereas ICU and Non-ICU patients showed reduced and more variable functional profiles. Beta diversity analysis revealed that diarrhea status, rather than hospitalization per se, was associated with modest but significant shifts in functional composition (PERMANOVA, R² = 0.047, p = 0.025), driven by quantitative changes in shared AMGs rather than the presence of unique functions. Notably, resistance-related vAMGs, including bacitracin transporters and Zinc D-Ala-D-Ala carboxypeptidase, were detected across samples, highlighting the potential of phages as mobile reservoirs of antibiotic resistance.
CONCLUSION: Together, our findings indicate that hospitalization and diarrhea do not markedly alter the taxonomic structure of the gut virome but are associated with modest shifts in viral functional potential. The maintenance of a stable viral community alongside variable AMG repertoires suggests that phages may modulate host-microbiome interactions primarily through functional fine-tuning rather than large-scale community restructuring. Our study provides evidence for the ecological resilience of the human gut virome and underscores the need to integrate viral communities into resistome research.}, }
@article {pmid41725015, year = {2026}, author = {Wang, R and Wang, Z and Liao, W and Wang, T and Su, Y}, title = {Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41725015}, issn = {2049-2618}, support = {31872670//National Natural Science Foundation of China/ ; 2021A1515010911//Guangdong Basic and Applied Basic Research Foundation/ ; 202206010107//Science and Technology Projects in Guangzhou/ ; JCYJ20210324141000001//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; }, mesh = {*Rhizosphere ; *Mikania/microbiology/growth & development/metabolism ; *Soil Microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; *Introduced Species ; Glutamate-Ammonia Ligase/metabolism/genetics ; Metagenomics ; Soil/chemistry ; Allelopathy ; Nitrogen Fixation ; Metabolomics ; Glutamate Dehydrogenase/metabolism/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification/enzymology ; Nitrate Reductase/genetics/metabolism ; }, abstract = {BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses.
RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation.
CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.}, }
@article {pmid41725821, year = {2026}, author = {Wang, C and Zhang, C and Shah, AM and Wang, Z and Qiu, S and Xu, Z and Xue, B and Wang, L and Hu, R and Zou, H and Jiang, Y and Xiao, J and Peng, Q}, title = {The optimal dietary crude protein level improves goat production performance by enhancing the body's antioxidant function and energy metabolism.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1734810}, pmid = {41725821}, issn = {1664-302X}, abstract = {The current research was conducted to evaluate the impact of various crude protein (CP) concentrations in diets on growth performance, nutrient digestibility, nitrogen deposition, rumen fermentation, microbial community, and serum metabolomics in growing goats. Fifty healthy 4-month-old Chuannan black goats (Capra hircus) with similar body weight (13.75 ± 0.27 kg) were randomly distributed into 5 groups. Goats were fed diets with five different levels of CP: 8.12% (T8), 10.15% (T10), 12.17% (T12), 14.13% (T14), and 16.18% (T16), respectively. The total duration of the trial was 70 d, including a 14-day adaptation period. The average daily gain and feed conversion ratio displayed a quadratic upsurge and reduce respectively, with the rise of CP content in the diet. The group T14 exhibited the highest average daily gain and demonstrated the best feed conversion efficiency. A linearly (p < 0.05) increase of the digestibility of dry matter, neutral detergent fiber, and acid detergent fiber was observed, whereas a quadratic effect (p < 0.001) on nitrogen intake, fecal nitrogen, and urinary nitrogen was obtained with the increase of dietary CP. Moreover, dietary CP levels had a quadratic effect on the concentration of ruminal ammonia nitrogen (p = 0.021), rumen microbial protein (p = 0.042), total volatile fatty acid (p = 0.012), acetate (p = 0.040), isobutyrate (p = 0.024), and isovalerate (p < 0.001). Microbial metagenomics results showed that the relative abundance of Burkholderia and Bacillus increased (p < 0.05), while the relative abundance of Pseudomonas and Salmonella decreased (p < 0.05) when comparing group T14 to group T8. Metabolomic results showed that differently expressed metabolites were found to enrich the proline, glutathione and arginine metabolism, and citric acid cycle metabolic pathway. The concentration of serum genistein was positively correlated (p < 0.05, r = 0.665) with the abundance of Bacillus and negatively correlated (p < 0.05, r = -0.734) with the abundance of Pseudomonas. It is concluded that a dietary CP level of 14% enhances the antioxidant function and energy metabolism of the goats by altering the composition of rumen microorganisms, thereby improving production performance.}, }
@article {pmid41726216, year = {2026}, author = {Gui, J and Long, C and Fu, Y and He, H and Li, J and Wang, F}, title = {Performance Evaluation of Targeted Nanopore Sequencing in Non-Tuberculous Mycobacteria Identification: A Comparative Study in Shenzhen, China.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {572430}, pmid = {41726216}, issn = {1178-6973}, abstract = {OBJECTIVE: This study aims to analyze the performance differences between targeted nanopore sequencing, Sanger sequencing, and metagenomic sequencing in comparatively identifying non-tuberculous mycobacteria (NTM) species. Additionally, it explores the clinical application potential of targeted nanopore sequencing for identifying NTM clinical isolates in the Shenzhen region.
METHODS: This retrospective study collected a total of 50 suspected NTM isolates from drug-resistant tuberculosis surveillance across 10 districts in Shenzhen, China, between December 2024 and June 2025. The species of the NTM isolates were initially identified using fluorescence PCR probe melting curve analysis. Genomic DNA was extracted from all 50 isolates, and species identification was performed using targeted nanopore sequencing (tNS), metagenomic sequencing (mNGS), and Sanger sequencing. The Jaccard similarity index, Kappa coefficient for classification consistency, and F1 score for model performance were calculated to evaluate the concordance among the three sequencing methods and assess the detection performance of targeted nanopore sequencing in NTM species identification.
RESULTS: The most frequently detected NTM species by tNS, mNGS, and Sanger sequencing were M.abscessus and M.fortuitum, while M. tuberculosis was predominantly identified through mNGS results. Among the 50 suspected NTM samples, 18 (36%) showed complete concordance between tNS, mNGS, and Sanger sequencing, with the highest agreement observed between mNGS and tNS (28 samples, 56%). The final species identification reference results for the 50 samples were confirmed through a comprehensive evaluation using the Jaccard similarity coefficient, precision, and recall. Based on reference results, the F1 scores for tNS, mNGS, and Sanger sequencing were 0.927, 0.896, and 0.543, respectively. The tNS exhibited the highest concordance with the reference results, outperforming the other two methods.
CONCLUSION: tNS represents a preferred auxiliary methodology for clinical identification of NTM isolates in Shenzhen, China, with identification results optimally validated through integration with mNGS findings. This study provides strong support for the application of tNS technology for NTM species identification.}, }
@article {pmid41726388, year = {2025}, author = {Donbraye, E and McLeod, L and Carson, CN and Chai, Z and Lacoste, SR and Herman, EK and McCarthy, EL and Hill, JE and Erickson, NEN and Pollock, C and Links, MG and Otto, SJG and Gow, S and Stothard, P and Campbell, JR and Waldner, CL}, title = {Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1704412}, pmid = {41726388}, issn = {2297-1769}, abstract = {INTRODUCTION: Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal swabs to describe sequencing data from BRD associated viruses. Changes in virus composition were identified between arrival to a feedlot and 14 days on feed (DOF). These data were also assessed for the simultaneous characterization of bacteria and antimicrobial resistance genes (ARGs).
METHODS: Nasal swabs were obtained from fall-placed calves (FPC) and yearlings (YRL) from western Canadian commercial feedlots. Evidence of respiratory viruses were identified by sampling 380 animals during processing on arrival to the feedlot and again after 14 DOF using Nanopore metagenomic sequencing.
RESULTS: Twenty-one distinct viruses from 12 viral families were identified, with multiple viruses detected in most samples. In FPC arrival samples, the most common BRD associated viruses were bovine rhinitis B virus (BRBV; 46%), bovine coronavirus (BCoV; 32%), influenza D virus (IDV; 17%), bovine respiratory syncytial virus (BRSV; 8.5%), and bovine parainfluenza virus 3 (BPIV-3; 4.2%). The prevalences of bovine herpesvirus type 1 (BoHV-1; 2.7%), BPIV-3 (12%), BRSV (26%), and IDV (51%) were higher in 14 DOF samples compared to arrival samples (p < 0.05). Bovine viral diarrhea virus 1 (BVDV-1) and 2 (BVDV-2) were rarely detected at either time. The most prevalent viruses detected in YRL arrival samples were BRBV (42%), BRSV (39%), BPIV-3 (20%), IDV (16%), BCoV (12%), and BVDV-2 (7.5%). The prevalences of BRSV (60%), BPIV-3 (39%), and BVDV-2 (17%) were higher in 14 DOF samples than arrival samples (p < 0.05). BRSV (OR 7.0, 1.7-29) and BPIV-3 (OR 5.7, 1.5-21) were more likely to be detected in arrival samples from YRL than FPC (p = 0.01). In 14 DOF samples, BPIV-3 (OR 4.9, 1.3-19, p = 0.02) and BVDV-2 (OR 13, 2.0-83, p = 0.01) were identified more frequently in YRL than FPC. These data allowed the identification of respiratory bacteria and 33 ARGs in parallel with assessment of the viral components. The most prevalent bacteria detected in FPC at arrival were Mannheimia haemolytica (35%), Histophilus somni (35%) and Pasteurella multocida (23%). Detection of M. haemolytica increased at 14 DOF (p = 0.02), while P. multocida detection decreased (p = 0.03). At both arrival and 14 DOF in YRL, M. haemolytica was the most prevalent bacterium, followed by P. multocida and H. somni with no significant differences between arrival and 14 DOF samples. ARGs were detected more frequently in the 14 DOF samples than at arrival for both FPC (p = 0.03) and YRL (p = 0.01). The most commonly detected ARGs were associated with resistance to lincosamides and aminoglycosides; however, ARGs associated with other antimicrobials used in cattle including tetracyclines were also identified.
DISCUSSION: Changes in the prevalence of BRD associated viruses early in the feeding period reflect transmission and the potential risk of developing the disease. Frequent detection of BCoV, BRSV, and BPIV-3 in newly arrived feedlot cattle suggests the need for improved vaccination before shipping or limitations in existing commercial vaccine preparations.}, }
@article {pmid41726584, year = {2026}, author = {Xie, G and Zhou, Q and Liao, J and Zheng, Y and Wang, W and Shen, K}, title = {The ketogenic diet alters microbiome-metabolome profiles to improve West syndrome therapy.}, journal = {Pediatric investigation}, volume = {10}, number = {1}, pages = {10-24}, pmid = {41726584}, issn = {2574-2272}, abstract = {IMPORTANCE: The ketogenic diet (KD) is effective in managing epilepsy, particularly West syndrome (WS); however, the role of gut microbiome (GM) and metabolome in its efficacy remains unclear. Understanding these mechanisms could optimize the KD for WS treatment.
OBJECTIVE: To identify microbiome-metabolome signatures associated with KD efficacy in WS by analyzing changes in GM composition and metabolic pathways.
METHODS: Fecal samples were collected from WS patients (n = 16) and healthy children (n = 24). Metagenome and metabolome analyses were performed to assess GM composition and metabolic profiles.
RESULTS: WS patients showed GM imbalances compared to healthy children. Disease status contributed sufficiently to the GM. The abundance of Bacteroides, Parabacteroides, and Faecalibacterium was lower in WS (3.30% vs. 39.86%, P-adj = 0.140; 0.14% vs. 0.73%, P-adj = 0.023; 0.04% vs. 1.35%, P-adj = 0.018), whereas Bifidobacterium and Escherichia were higher (6.08% vs. 2.23%, P-adj = 0.140; 7.57% vs. 0.15%, P-adj < 0.001). After KD, Parabacteroides (particularly P. distasonis) and Bacteroides (particularly B. fragilis) increased (0.14% vs. 0.35%, P-adj = 0.034; 3.30% vs. 21.18%, P-adj = 0.380); Bifidobacterium (particularly B. breve) and Escherichia (particularly E. coli) decreased from 6.08% and 7.57% to 1.24% and 2.52%, respectively. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that ATP-binding cassette (ABC) transporters, fatty acid biosynthesis, tyrosine metabolism, and other pathways were significantly altered in patients with WS, and these alterations were reversed following ketogenic diet (KD) consumption. The KD also altered intestinal metabolites. Integrative analysis of microbial features, gene functions, and metabolites revealed that Bacteroides species and P. distasonis were significantly associated with ABC transporters, alanine aspartate and glutamate metabolism, and negatively correlated with 3-sulfinoalanine, suggesting potential regulatory roles in metabolic pathways.
INTERPRETATION: KD induces significant shifts in GM composition and metabolic pathways, which may contribute to its therapeutic efficacy in WS. The restoration of Bacteroides and Parabacteroides dominance, alongside alterations in gene functions and neurotransmitter-related metabolites, suggests a potential mechanism for the antiepileptic effects of KD.}, }
@article {pmid41726864, year = {2026}, author = {Vaziri, GJ and Pritchard, JC and Howard, JI and Stamm, GE and O'Connor, DH and Newman, CM and Aliota, MT and Dzikwi-Emennaa, A}, title = {Metagenomic surveillance of undiagnosed febrile illness in Nigeria does not reveal the etiological agent for most patients.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.07.704564}, pmid = {41726864}, issn = {2692-8205}, abstract = {Molecular and microscopy-based diagnostic capacity is often insufficient or unavailable in places where infectious disease burdens are highest, such as in West Africa. Rapid diagnostic testing (RDT) can provide quick and affordable diagnoses of common infections but is an imperfect solution due to limitations around detecting and dealing with false negative and false positive results. An alternative to RDT is unbiased metagenomic sequencing for pathogen surveillance. Here, we present data from unbiased metagenomic sequencing used to identify causes of undiagnosed febrile illness in Jos, Plateau State, Nigeria. Proof of concept for this approach has been demonstrated by several groups who have identified epidemic and endemic viral diseases like Lassa fever, yellow fever, and Chikungunya. Here, we show that unbiased deep sequencing and metagenomic analysis can be used to identify RNA viruses in clinical samples. We sequenced RNA from sera of patients (n = 343), many of whom were acutely febrile (76 %) in a survey of clinics in Jos. We detected five human-infecting viruses in 39 (11 %) specimens. Among these were hepatitis B virus, human pegivirus, and several anelloviruses. While most of the viruses identified are unlikely to cause clinical symptoms in the patients we sampled, their presence demonstrates the validity of our approach. Additionally, our sequencing data allowed us to identify genetic material from potentially pathogenic bacteria, another possible etiological agent of febrile illness.}, }
@article {pmid41726920, year = {2026}, author = {Jensen, JSL and Maharjan, S and Münch, PC and Shen, J and Bowcutt, B and Sumner, JT and Morgan, XC and Thompson, KN and Nguyen, LH and Franzosa, EA and Huttenhower, C}, title = {Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726920}, issn = {2692-8205}, support = {T32 AI049928/AI/NIAID NIH HHS/United States ; }, abstract = {Viruses are crucial components of microbial communities, both phage that infect bacterial community members as well as pathogenic and other eukaryotic viruses. However, they remain unobserved by most current technologies, due to combinations of experimental and analytical factors. To address the latter, we developed the BAQLaVa algorithm for high-resolution profiling of >120,000 viral species (viral genome bins, VGBs) via reference-based metagenome (MGX) or metatranscriptome (MTX) alignment to complementary nucleotide markers and proteome sets. In comprehensive benchmarking, BAQLaVa substantially outperformed alternatives, achieving species-level recall and precision regularly over 90%. We applied BAQLaVa to MGX and MTX samples from the HMP2 IBDMDB cohort to identify previously undescribed viral perturbations in inflammatory bowel diseases. Most notably, virome diversity was reduced in tandem with bacterial diversity during inflammation, in contrast to previous findings based on a narrower range of viral detection. A subset of viruses were enriched during IBD, associated with carriage of abortive infection anti-defense systems such as AbiL and PD-λ-2, as well as genes involved in the regulation of lysogeny. Leveraging the corresponding viral profiles, we also inferred phage-host relationships using scalable co-occurrence and covariation signals, even in the absence of host references or genome annotations. By enabling high sensitivity and specificity viral profiling from metagenomes or metatranscriptomes, BAQLaVa provides a scalable framework for virome epidemiology and systematic analysis of virus-host interactions.}, }
@article {pmid41726932, year = {2026}, author = {Montes, A and Klopmanbaerselman, D and Lee, B and Quiñones, B and Shim, H}, title = {Temporal dynamics of microbiome communities within urban compost piles undergoing the heat process.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726932}, issn = {2692-8205}, abstract = {Urban composting supports soil health but also intersects with food safety, where compost is produced near farms and communities. Here, we profiled temporal microbiome dynamics across a 6-week heat compost cycle from the urban compost piles using paired physicochemical panels and long-read metagenomics. Nutrient composition and pH shifted with compost age, coinciding with stage-structured microbial succession, including temperature-linked turnover of compost communities from mesophilic to thermotolerant taxa. Bacterial profiles included the presence of antimicrobial resistance genes and foodborne-associated genera early in the cycle, with reduced representation during the thermophilic phase. Analysis of previously unclassified long reads reveals an extensive repertoire of putative bacteriophages, including several complete genomes and candidates linked to foodborne bacteria, and their abundance is coupled to the host abundance. Together, these results support thermophilic composting as a key mitigation step for microbiological hazards in urban-adjacent systems and identify compost piles as a promising reservoir for discovering candidate lytic phages for downstream isolation and host-range testing.}, }
@article {pmid41726958, year = {2026}, author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726958}, issn = {2692-8205}, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, }
@article {pmid41727025, year = {2026}, author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YP}, title = {Alamandine/MrgD Pathway Modulates Gut-Bone Marrow Axis in Aging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41727025}, issn = {2692-8205}, abstract = {Aging is associated with colon epithelial barrier integrity and upregulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in aging via modulating gut-BM axis. Mice of age 2-3 (Young) or 22-24 months (Old) were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated by using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Fecal microbiome was analyzed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Cecal or serum bacterial metabolites were analyzed. The pro-myelopoietic potential of cecal supernatants (CS) was tested in the Young-BM cells. MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in aging was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels that were antagonized by the NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the aging microbiome and decreased Bacillota/Bacteroidota. Ala decreased the CD80[+] and increased CX3CR[+] cells in the Old colons. Old-CS induced myelopoiesis in vitro in BM cells with higher number of monocytes and pro-inflammatory macrophages which was not observed in the CS derived from Ala-treated Old mice. Ala is a promising pharmacological agent for reversing the leaky gut of aging by restoring homeostasis in the gut-BM axis.}, }
@article {pmid41728114, year = {2026}, author = {Jiang, YL and Dong, SZ and Xu, YB and Fan, JL and Zhang, YM and Huang, SS}, title = {Metagenomic next-generation sequencing for diagnosis of immune checkpoint inhibitor-associated pneumonitis: a retrospective comparative clinical performance study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1730022}, pmid = {41728114}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; *Pneumonia/diagnosis/chemically induced/microbiology/etiology ; Sensitivity and Specificity ; Neoplasms/drug therapy ; Aged, 80 and over ; Immunotherapy/adverse effects ; }, abstract = {OBJECTIVE: To evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in distinguishing immune checkpoint inhibitor-related pneumonitis (CIP) from infectious pneumonia in cancer patients undergoing immunotherapy.
METHODS: A retrospective tertiary hospital cohort included 34 cancer patients (Feb 2022-Jan 2024) with prior ICI exposure, new/worsening respiratory symptoms, imaging infiltrates, and both mNGS and conventional microbiological testing (CMT). Final diagnoses were adjudicated by a multidisciplinary panel. We compared pathogen detection rates, sensitivity, specificity, and turnaround times (TAT) between mNGS and CMT.
RESULTS: In the infectious pneumonia group, mNGS detected pathogens in 17/18 cases (94%), whereas CMT detected only 6/18 (33%). In the CIP group, mNGS was negative in 14/16 cases (88%), compared with 11/16 negatives by CMT (69%). Using the adjudicated diagnosis as the reference, mNGS showed sensitivity 88%, and specificity 94%. In contrast, CMT's sensitivity was 69%, and specificity 33%. The median TAT for mNGS was 24 hours (IQR 22-31 h), versus 121.5 hours (IQR 80.5-156 h) for CMT (P < 0.001).
CONCLUSION: mNGS outperforms CMT in both diagnostic accuracy and timeliness for distinguishing CIP from infectious pneumonia among immunotherapy recipients. Incorporation of mNGS into the diagnostic workflow for suspected CIP may improve etiological discrimination and enable timely, individualized treatment. Further large-scale prospective studies are required to confirm these findings.}, }
@article {pmid41728322, year = {2026}, author = {Kim, DD and Worby, CJ and Wharton, H and Miklos, A and Chieng, B and Njenga, SM and Earl, AM and Pickering, AJ}, title = {Metagenomic strain tracking reveals patterns of bacterial spread and the impact of water chlorination.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41728322}, abstract = {Bacterial infections are a major cause of morbidity and mortality among children under five in low- and middle-income countries (LMICs). Children in LMICs are exposed to and colonized by a range of pathogenic bacteria, yet patterns of bacterial exchange between humans are not well known, in part because culturing and sequencing single bacterial isolates is labor-intensive. Here, we apply a machine learning strain tracking approach to metagenomic data from 511 stool samples from children and mothers across urban and rural Kenyan communities to characterize bacterial dissemination and assess if community-wide water chlorination disrupts transmission. We identified distinct strain-sharing dynamics across species; potentially pathogenic taxa (e.g., Escherichia, Enterococcus, Campylobacter) exhibited distance-dependent dissemination driven by young children, while commensal taxa (e.g., Bifidobacterium, Bacteroides) showed patterns consistent with dietary exposure. Drinking water chlorination reduced community-level strain-sharing in rural communities. Our study provides the first strain-level insights into multi-species bacterial transmission dynamics in LMIC communities, identifying distinct dissemination pathways for facultative versus mostly anaerobic bacteria. Moreover, our findings highlight the utility of metagenomic strain tracking to uncover how community spread can be disrupted.}, }
@article {pmid41728963, year = {2026}, author = {Enuh, BM and Myers, KS and Ackman, P and Weiland, T and Beach, N and Young, M and Donohue, TJ and Noguera, DR}, title = {Metagenomes and metagenome-assembled genomes from a nutrient removal plant at Los Angeles County Sanitation Districts (LACSD) that transitioned from high to low dissolved oxygen.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0149425}, pmid = {41728963}, issn = {2576-098X}, abstract = {Operating biological nutrient removal (BNR) wastewater treatment plants with low dissolved oxygen (DO) conditions can reduce energy costs. We report on five metagenomes and 492 metagenome-assembled genomes (MAGs) obtained from samples collected at the Pomona water reclamation plant before and after a DO reduction from 3.5 to 0.7 mg/L.}, }
@article {pmid41728976, year = {2026}, author = {La, N and Rattanapitoon, NK and Thanchonnang, C and Rattanapitoon, SK}, title = {Beyond a viral succession timeline: a phase-transition framework and re-analysis highlight hidden instability in the proposed "phage clock".}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0230725}, pmid = {41728976}, issn = {1098-5336}, }
@article {pmid41728996, year = {2026}, author = {Li, Z and Zhang, H and Wei, T and He, L and Wang, Y}, title = {Anoxia-adapted cyanobacteria in a marine blue hole.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0257625}, pmid = {41728996}, issn = {1098-5336}, support = {42376149//National Natural Science Foundation of China/ ; KCXFZ20240903093905008//Science and Technology Major Project (Sustainable Development Special Project) of Shenzhen/ ; }, mesh = {*Cyanobacteria/genetics/physiology/classification/metabolism ; *Seawater/microbiology ; Phylogeny ; China ; Oxygen/metabolism ; Metagenome ; Anaerobiosis ; Symbiosis ; Genome, Bacterial ; Adaptation, Physiological ; }, abstract = {Vertical transmission of marine particles brings ocean surface cyanobacteria into the deep ocean, where heterotrophic cyanobacterial lineages probably evolve to adapt to new environments even in oxygen-depleted zones. At present, active cyanobacteria have rarely been reported in dark and anoxic water columns in the deep sea. In this study, we recovered three metagenome-assembled genomes of cyanobacteria from the Yongle blue hole located in the South China Sea, two of which were actively transcribed in a dark, anoxic environment at 250 m depth, through integrated metagenomic and metatranscriptomic analyses of water samples from 21 stratified depths collected using in situ microbial fixation and filtration. These anoxia-adapted cyanobacteria were phylogenetically approximate to the sponge cyanobacterial symbionts, while the genomic features showed similarities with both free-living and sponge symbiotic counterparts. They exhibit genomic features shared with symbiotic lineages, including loss of substrate utilization, biosynthesis pathways, DNA repair, and circadian regulation. Conversely, they retain selected metabolic characteristics of free-living lineages, including phenylalanine biosynthesis and phosphoserine metabolism. Additionally, the discovery of taurine transport proteins in the genomes suggests the potential for organic sulfur uptake from the environment. Altogether, these findings reveal a distinct genomic configuration in cyanobacteria inhabiting a permanently dark and anoxic marine system, characterized by the retention of oxygen-dependent metabolic potential alongside sustained transcriptional suppression under in situ conditions. This study provides new insights into the ecological persistence and evolutionary adaptation of cyanobacteria under long-term oxygen limitation.IMPORTANCEWe report metabolically active cyanobacteria thriving in darkness and oxygen deprivation at 250 m depth in the ocean. Genomics results show these microbes share evolutionary roots with sponge cyanobacterial symbionts but developed unique adaptations for anoxic and sulfidic environments. Strikingly, they retain photosynthesis genes as genomic remnants (with no detected transcription) while losing genes critical for environmental stress responses, including DNA repair, osmotic regulation, and circadian control, suggesting a potential evolutionary connection to symbiotic relatives. Crucially, they maintain metabolic autonomy via phenylalanine biosynthesis and light-independent serine biosynthesis, exhibiting traits absent in most symbionts. This demonstrates how cyanobacteria adapt to anoxic environments through targeted genome reduction, revealing novel survival strategies in oxygen-depleted oceans and providing a research case for microbial resilience during marine deoxygenation.}, }
@article {pmid41729067, year = {2026}, author = {Liu, Y and Zhang, T and Liu, J and Dong, X}, title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {8}, pages = {6824-6839}, doi = {10.1021/acs.jafc.5c14510}, pmid = {41729067}, issn = {1520-5118}, mesh = {*Proanthocyanidins/metabolism/chemistry ; *Caffeic Acids/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; *Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics ; Probiotics/metabolism ; Humans ; *Polymers/metabolism/chemistry ; Feces/microbiology ; *Lactobacillaceae/metabolism/genetics/isolation & purification ; Animals ; }, abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.}, }
@article {pmid41729089, year = {2026}, author = {Liu, J and Zheng, X and Jia, C and Sun, Z and Zhou, W and Zhang, J and Chen, Y and Zhou, Z and Tian, Y and Xiao, G and Du, L and Fan, C and Sun, L and Yue, M}, title = {Zoonotic Bordetella bronchiseptica infection at the swine-human interface: unveiling the evolutionary path from an animal to a human pathogen.}, journal = {Emerging microbes & infections}, volume = {15}, number = {1}, pages = {2637286}, pmid = {41729089}, issn = {2222-1751}, mesh = {*Bordetella bronchiseptica/genetics/pathogenicity/isolation & purification/physiology ; Animals ; Swine ; Humans ; *Bordetella Infections/microbiology/veterinary/transmission/epidemiology ; Plasmids/genetics ; *Swine Diseases/microbiology/transmission/epidemiology ; Virulence/genetics ; *Bacterial Zoonoses/microbiology/transmission/epidemiology ; *Zoonoses/microbiology/transmission ; Genome, Bacterial ; Evolution, Molecular ; }, abstract = {Bordetella bronchiseptica, long regarded as a veterinary pathogen, is now emerging as a zoonotic threat to humans, particularly in immunocompromised individuals. We report a sentinel event involving a synchronized B. bronchiseptica outbreak in swine and their human caretaker, providing a unique opportunity to examine cross-species transmission and adaptation at the genomic level. Comparative genomics revealed that the human-adapted isolate (RL57) and its swine progenitor (XX35) share an identical chromosome, with XX35 harbouring an extra conjugative plasmid. Remarkably, RL57 did not simply lose this plasmid; instead, the entire plasmid was integrated into the chromosome via site-specific recombination. This integration allowed permanent retention of plasmid-encoded virulence and fitness genes, after which the plasmid was discarded to eliminate its replicative burden - a "capture-and-discard" mechanism of evolution. Following plasmid loss, the RL57 strain exhibited hypervirulence, faster growth, enhanced thermotolerance, and increased biofilm formation, indicating successful adaptation to the human host. Plasmid loss paradoxically rewired bacterial metabolism: sulfur assimilation and sulfonate utilization pathways were upregulated to fuel host adaptation. Strikingly, despite a collapse in transcription of specific metabolic modules, translational compensation maintained high protein levels, driving robust biofilm formation and thermal tolerance. These findings reveal a previously unrecognized evolutionary strategy in which plasmid integration followed by subsequent plasmid loss amplifies pathogenicity and host adaptability. Finally, we propose a One Health surveillance triad - metagenomic tracking of plasmid-chromosome dynamics, recombination hotspot screening, and metabolic shift monitoring - to proactively identify and mitigate such zoonotic events.}, }
@article {pmid41729207, year = {2026}, author = {Gouda, MNR and Subramanian, S}, title = {Functional Genomics and Enzymatic Diversity of Gut Bacteria in Apis mellifera: A Multi-Approach Study from India.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41729207}, issn = {1432-0991}, mesh = {Bees/microbiology ; Animals ; India ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/enzymology/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Phylogeny ; Genomics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The gut microbiota of the western honey bee Apis mellifera plays a vital role in host nutrition, digestion, immunity, and overall colony health. Although the functional and enzymatic capabilities of bee-associated microbes are increasingly recognized, studies integrating culture-dependent screening with metagenomic functional profiling remain scarce. This study characterizes the gut bacterial communities of forager and hive bees from the Indian subcontinent using cultivation, 16S rRNA gene sequencing, enzyme assays, and metagenomic analysis. A total of 165 isolates were obtained, yielding 85 unique strains deposited in GenBank. Metagenomic assembly generated 7.78 million non-redundant genes, including 11,050 KEGG-annotated and 2.43 million CAZy-annotated genes. Forager bees showed pronounced enrichment of carbohydrate-processing pathways such as glycolysis/gluconeogenesis (22.9%), galactose metabolism (4.42%), starch and sucrose metabolism, and ABC transporters (9.80%), consistent with their nectar- and pollen-rich diet. Culture-based biochemical assays revealed substantial enzymatic diversity among isolates belonging to Bacillus, Enterobacter, Serratia, Cedecea, Clostridium, Lysinibacillus, and Aneurinibacillus. High invertase activities were recorded in Xanthomonas sp. HAmf44 (2.509 U/mg), Clostridium argentinense HAmf20 (2.470 U/mg), Lysinibacillus fusiformis HAmh15 (2.509 U/mg), and Bacillus paralicheniformis HAmh05 (2.333 U/mg). Strong lipolytic activities were observed in Cedecea davisae HAmf19 (6.062 U/mg), Pseudomonas aeruginosa HAmh21 (5.927 U/mg), and Enterobacter cloacae HAmf26 (3.349 U/mg). Significant variation among isolates (p = 0.001) underscored the functional diversity of the gut microbiota. Integrating KEGG orthologs with species abundance revealed that dominant taxa-including Gilliamella, Snodgrassella, Lactobacillus, and Bifidobacterium-drive key metabolic pathways. Overall, this study provides the first combined enzymatic and metagenomic assessment of A. mellifera gut microbiota from India and identifies high-performing strains with probiotic potential to enhance honey bee nutrition and colony productivity.}, }
@article {pmid41729287, year = {2026}, author = {Lima, NSM and Gomes-Pepe, ES and Kock, FVC and Colnago, LA and da Costa Aguiar Alves, PL and de Macedo Lemos, EG}, title = {Efficiency of Imazapic Degradation: an Assessment of LacMeta Treatments Utilizing Whole Cell.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41729287}, issn = {1432-0991}, abstract = {UNLABELLED: The extensive use of herbicides such as imazapic, from the imidazolinone class, raises environmental concerns due to its persistence and toxicity in ecosystems and subsequent crops. Enzymatic bioremediation emerges as a sustainable alternative for the mitigation of these contaminants. This study investigated the potential of the metagenomic laccase, LacMeta, expressed in Escherichia coli BL21 (DE3), to degrade imazapic using a whole-cell approach. LacMeta expression was optimized with CuSO4, which proved to be four times more effective than IPTG. The E. coli + LacMeta cells demonstrated high tolerance to the herbicide, maintaining cell viability even at high doses (350 g/ha). Notably, the enzymatic activity of LacMeta was not inhibited by imazapic; on the contrary, it was stimulated, reaching a specific activity nearly three times higher in the presence of the herbicide compared to the control. Degradation was confirmed by UV-Visible spectroscopy, which showed the disappearance of imazapic’s characteristic peaks (200–280 nm) over 15 days. [1]H-NMR and FTIR analyses corroborated the degradation, indicating structural changes in the herbicide molecule, particularly in the aromatic ring region (signals at 8.25 and 8.50 ppm). Phytotoxicity assays with lettuce seeds (Lactuca sativa) confirmed that treatment with the LacMeta-containing supernatant cell free significantly reduced the toxicity of imazapic in the soil. The results demonstrate that LacMeta has high potential for the bioremediation of imazapic, and the whole-cell approach represents a promising and cost-effective strategy for the decontamination of environments impacted by this herbicide.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00284-026-04760-1.}, }
@article {pmid41730403, year = {2026}, author = {Liu, W and Zhang, Z and Wu, W and Yan, X and Huang, Y and Feng, H and Mou, Q and Wan, J and Yan, M and Tang, H and Liang, J and Zhang, Y and Peng, C and Pan, X}, title = {Ligilactobacillus murinus confers a dual benefit: Counteracting crotonis fructus-induced intestinal toxicity and synergizing with its processed form against ulcerative colitis.}, journal = {Journal of ethnopharmacology}, volume = {363}, number = {}, pages = {121420}, doi = {10.1016/j.jep.2026.121420}, pmid = {41730403}, issn = {1872-7573}, mesh = {Animals ; *Colitis, Ulcerative/chemically induced/microbiology/drug therapy/pathology ; Caenorhabditis elegans ; Gastrointestinal Microbiome/drug effects ; *Croton/chemistry/toxicity ; Mice ; *Probiotics/pharmacology/administration & dosage/therapeutic use ; Male ; Disease Models, Animal ; Dextran Sulfate ; *Lactobacillus ; Mice, Inbred C57BL ; *Plant Extracts/toxicity ; }, abstract = {Ulcerative colitis (UC) poses a major clinical challenge. Classical Chinese medical texts record the use of Crotonis Fructus (CF), the seeds of Croton tiglium L., for treating conditions like "chronic dysentery" presenting symptoms similar to UC. However, the clinical application of both raw and processed CF is limited due to intestinal toxicity.
AIM OF THE STUDY: This study investigates the role of gut microbiota in mitigating the intestinal toxicity induced by CF and in enhancing the anti-UC efficacy of its processed form.
METHODS: Metagenomic analysis investigated CF-induced intestinal toxicity. The benefits of probiotics combined with CF or processed CF cream were evaluated in Caenorhabditis elegans (C. elegans) and a dextran sulfate sodium (DSS)-induced mouse model. Their combined effect was further assessed in DSS-exposed C. elegans, with qRT-PCR measuring intestinal barrier integrity.
RESULTS: Metagenomic analysis revealed that CF-induced intestinal toxicity was associated with gut microbiota dysbiosis characterized by a pronounced reduction in Ligilactobacillus murinus (L. murinus). Supplementation with L. murinus alleviated CF-induced damage in C. elegans. In DSS-induced UC mice, both L. murinus and processed CF cream ameliorated colitis and suppressed TNF-α, IL-6, and IL-1β. When co-administered in DSS-exposed C. elegans, two agents acted synergistically, leading to greater restoration of intestinal barrier integrity and more pronounced upregulation of barrier-function genes.
CONCLUSION: This study demonstrates that L. murinus plays a dual role: it mitigates CF-induced intestinal toxicity and acts synergistically with processed CF cream to enhance UC treatment, providing a microbiome-based strategy for safer clinical application.}, }
@article {pmid41730992, year = {2026}, author = {Escalante, C and Reyes, AM and Zhao, C and Balkcom, KS and Jacobson, AL and Strayer-Scherer, A and Martin, KM and Koebernick, J and Huseth, A and Kozieł, E and Small, I and Greene, JK and Otulak-Kozieł, K and Mulvaney, MJ and Price, PP and Briseño, RIA and Bag, S and Conner, K}, title = {Metatranscriptomics analysis reveals the cotton virome in the southern United States.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41730992}, issn = {2045-2322}, mesh = {*Gossypium/virology/genetics ; *Virome/genetics ; *Plant Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; Plant Diseases/virology ; *Transcriptome ; United States ; Metagenomics ; Gene Expression Profiling ; }, abstract = {High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.}, }
@article {pmid41731364, year = {2026}, author = {Liu, Y and Sun, H and Tan, X and Li, K and He, Z and Hu, S}, title = {Ultra-deep metagenomic sequencing enables reconstruction of diverse, high quality microbial genomes from human urine samples.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04826-x}, pmid = {41731364}, issn = {1471-2180}, support = {2021YFF0703805//National Key Research and Development Program of China/ ; }, }
@article {pmid41731377, year = {2026}, author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M}, title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04837-8}, pmid = {41731377}, issn = {1471-2180}, }
@article {pmid41731555, year = {2026}, author = {Yasuda, S and Palomo, A and Smets, BF and Terada, A}, title = {Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41731555}, issn = {2049-2618}, mesh = {*Ammonia/metabolism ; *Nitrites/metabolism ; *Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Oxidation-Reduction ; *Microbiota/genetics ; Metagenome ; Nitrification ; Phylogeny ; Water Pollutants, Chemical/metabolism ; Waste Disposal Facilities ; }, abstract = {BACKGROUND: In the late stages of landfill operation, leachate becomes brackish and contains high concentrations of ammonia with limited organic carbon. At leachate treatment facilities, it is typically subjected to nitrification followed by denitrification, with methanol supplied as an external electron donor. This unique environment may harbor novel microorganisms, including nitrifiers. Although a variety of microorganisms are involved in nitrification, their substrate specificity and salinity tolerance remain insufficiently understood. In this study, a genome-centric metagenome analysis was conducted on the microbiome from a leachate treatment facility at a closed landfill.
RESULTS: A total of 68 metagenome-assembled genomes (MAGs) were reconstructed, including 64 putative novel species. Among these, two Nitrospira MAGs were recovered: a novel complete ammonia-oxidizing bacterium (comammox), Nitrospira LAS72 (88.72% completeness, 2.10% contamination), and canonical nitrite-oxidizing Nitrospira LAS18 (99.98% completeness, 2.29% contamination). Comparative genomic analysis with 260 publicly available Nitrospira genomes revealed that LAS18 represents a new sub-lineage within lineage VII of the Nitrospira genus. Two ammonia-oxidizing archaea (AOA), Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, were also identified, while canonical ammonia-oxidizing bacteria were not detected. Given the brackish conditions (1.23% salinity) and the methanol-fed operation of the treatment facility, the genomic potential for osmotic stress adaptation and methanol metabolism was investigated. Comammox Nitrospira LAS72 harbors biosynthetic pathways for several compatible solutes (osmoprotectants), including glycine betaine, proline, trehalose, and L-glutamate. Moreover, comammox Nitrospira LAS72 possesses genetic potential for oxidizing formaldehyde, suggesting that it may exploit these methanol-derived intermediates as energy sources. These features indicate that LAS72 may withstand osmotic fluctuations through the production of various osmoprotectants and thrive under the unique conditions of a methanol-fed environment.
CONCLUSIONS: The discovery of novel comammox Nitrospira and canonical Nitrospira forming a new sub-lineage within lineage VII of the Nitrospira genus in an ammonia-rich brackish environment provides the first genomic evidence for evolutionary adaptation among nitrifiers to saline, methanol-fed environments. These findings enhance our understanding of the ecological and evolutionary dynamics shaping nitrifier communities in complex treatment ecosystems. Video Abstract.}, }
@article {pmid41731616, year = {2026}, author = {Fan, S and Lu, J and Cui, H and Ding, W and Li, S and Sun, J and Li, YX and Zhang, W}, title = {Unlocking the unexplored AMPSphere in marine rare species.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02326-0}, pmid = {41731616}, issn = {2049-2618}, abstract = {BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action.
RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (< 0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems.
CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.}, }
@article {pmid41732151, year = {2026}, author = {Liu, X and Han, H and Zhang, X and Kong, F and Dai, D and Hao, Y and Wang, W and Li, S}, title = {Potassium carbonate improves milk quality by enhancing rumen metabolism in Holstein cows.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {24}, number = {}, pages = {534-548}, pmid = {41732151}, issn = {2405-6383}, abstract = {Mid-lactation is a key stage in dairy production characterized by high milk yields and metabolic stress in cows. Dietary potassium carbonate may enhance milk quality, but its response mechanisms, particularly the link between rumen microbiome changes and production performance, remain poorly understood. To address this knowledge gap, a total of 60 multiparous Holstein cows (parity = 2.47 ± 1.06, body weight = 601 ± 25 kg, and days in milk = 127.83 ± 31.91) were divided into four groups (n = 15 cows per group) using a randomized complete block design and fed the corresponding diets for 84 days. The feed treatments were as follows: a control group (CON, basal diet), a low dose group (LD, basal diet + 250 g/d K2CO3·1.5H2O per head), a medium dose group (MD, basal diet + 500 g/d K2CO3·1.5H2O per head), and a high dose group (HD, basal diet + 750 g/d K2CO3·1.5H2O per head). The results showed that potassium carbonate supplementation significantly influenced rumen fermentation patterns, particularly by increasing acetate (P = 0.008) and isovalerate concentrations (P < 0.001). Milk fat (P = 0.004) and protein percentage (P = 0.006) exhibited the most pronounced effects in the MD group. The rumen microbiota and metabolome revealed significant alterations in microbial community structure and function. Notably, the results indicated that in the MD group, there was an increase in the abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) genes associated with crucial metabolic pathways: amino acid biosynthesis, long-chain fatty acid biosynthesis and fatty acid elongation pathways. These findings suggest that dietary supplementation with 500 g/d of potassium carbonate optimizes milk composition by modulating the rumen microbiota and associated metabolic pathways, supporting the potential for targeted nutritional strategies in dairy management.}, }
@article {pmid41732362, year = {2026}, author = {Tanja, Z and Maja, R}, title = {Gut microbiomes of wild and domesticated mammals and birds in Slovenia, Europe: 16S rRNA sequencing data.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112564}, pmid = {41732362}, issn = {2352-3409}, abstract = {From a One Health perspective, the gut microbiota of animals acts as a major driver of microbial exchange between animals and the environment. Animals continuously release gut microbes into their surroundings, shaping environmental and human microbial communities and potentially dispersing pathogens. Characterizing gut microbiota across diverse animal hosts is therefore critical for understanding the patterns of microbial spread through ecosystems and their impact on animal, human and environmental health. Here, we introduce a large, taxonomically diverse dataset of fecal microbiomes from 715 individual animals representing over 50 mammalian and avian species. We collected samples from both wild and domestic animals with an emphasis on capturing microbial diversity across a wide range of taxa and ecological contexts. The samples were subjected to 16S rRNA gene sequencing, targeting the V3-V4 hypervariable region. Bioinformatic analysis was performed using Usearch to generate zero-radius operational taxonomic units (ZOTUs). This dataset was generated primarily for the development of microbial source tracking (MST) assays used for identifying the sources of fecal pollution in contaminated water. However, it provides a valuable resource for broader microbiome research. It enables comparative studies across host species, trophic guilds, and environmental contexts such as domestication.}, }
@article {pmid41732369, year = {2026}, author = {Fu, R and Li, J and Wang, M and Xiao, D and Li, F and Zhu, X}, title = {Microscopic-scale gut microbiota dataset of Kunming mice revealed by 16S rRNA gene high-throughput sequencing.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112572}, pmid = {41732369}, issn = {2352-3409}, abstract = {Gut microbiota profoundly influence host physiology, yet most studies rely on bulk-scale intestinal samples, overlooking microbial heterogeneity at the micro-scale. Here, we present a dataset generated from 378 colonic micro-scale grains (20-40 µm) and 20 bulk samples collected from four Kunming mice. Using Illumina NovaSeq 6000 sequencing of the 16S rRNA V4 region, we obtained over 8.0 million raw reads, processed into 1506 amplicon sequence variants (ASVs) spanning 19 phyla and 203 genera. Firmicutes and Bacteroidetes were the dominant phyla across scales, while marked differences were observed in ASV richness (p < 0.001, Wilcoxon test) and network complexity (number of edges, p = 0.03, Wilcoxon test) between bulk samples and micro-scale grains. The dataset, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1249752, provides a high-resolution view of gut microbial spatial organization at the sub-100 µm scale. These data advance current understanding of microbial assembly processes, interspecies interactions, and scale-dependent community structure, thereby serving as a valuable resource for microbiome ecology and future mechanistic studies.}, }
@article {pmid41732520, year = {2026}, author = {Aguilar Ticona, JP and Amorim Santos, L and Meng, X and Nery, N and Fofana, MO and de Moraes, L and Morais Strobel, I and Vitoriano, R and Silveira Cucco, M and Andrade Belitardo, EMM and Thakku, G and Cruz, JS and Detweiler, AM and Neff, N and Tato, CM and Reis, MG and Costa, F and Cummings, DAT and Ko, AI and Khouri, R}, title = {Metagenomic surveillance reveals off-season circulation of respiratory viruses during the COVID-19 pandemic in Salvador, Brazil.}, journal = {New microbes and new infections}, volume = {70}, number = {}, pages = {101717}, pmid = {41732520}, issn = {2052-2975}, abstract = {BACKGROUND: Evidence from multiple countries suggests that the COVID-19 pandemic disrupted the transmission of other respiratory viruses. We characterized respiratory virus transmission during the pandemic in Salvador, Brazil, a tropical region in the Southern Hemisphere.
METHODS: From November 2021 to October 2022, we conducted biweekly household visits in an urban informal settlement to screen individuals with respiratory symptoms. Symptomatic individuals and their contacts were interviewed, and nasal swabs collected. Virus identification was performed using multiplex RT-qPCR, followed by metagenomic analysis in a subset of symptomatic participants with negative RT-qPCR results.
RESULTS: We screened 3174 residents from 1174 households, identifying 669 symptomatic episodes and detecting 219 respiratory viruses. including coinfections, SARS-CoV-2 was the most common with 118 cases (54%), followed by Influenza A with 39 (18%), Rhinovirus with 22 (10%), Human Parainfluenza Virus with 15 (7%), Respiratory Syncytial Virus with 13 (6%), and seasonal Human Coronaviruses with 12 (5%). Co-infections were observed, with combinations involving SARS-CoV-2, Influenza A, and Respiratory Syncytial Virus being the most common. Peaks of Influenza, HPIV, and RSV occurred in late 2021 during low Delta circulation, while Omicron BA.1 emerged in January 2022. Influenza and RSV showed low transmission during Brazil's winter months, and seasonal coronaviruses reappeared two years after the pandemic onset.
CONCLUSION: Multiplex RT-qPCR and metagenomic analysis allowed rapid detection and sequencing. An off-season influenza peak was identified, possibly due to relaxed hygiene measures or accumulated susceptibility after SARS-CoV-2 interventions. The household secondary attack rate for influenza was lower than for Omicron BA.1, possibly reflecting lower transmissibility or pre-existing immunity.}, }
@article {pmid41732893, year = {2026}, author = {Zheng, Y and Li, Y and Song, C and Chai, Z and Fu, J and Dang, C and Ju, F and Wang, B and Niu, J and Zheng, M}, title = {Functional Dominance and Competitive Strategy of Comammox Bacteria among Ammonia Oxidizers in Urban Secondary Effluent-Constructed Wetlands.}, journal = {Environmental science & technology}, volume = {60}, number = {9}, pages = {7194-7207}, doi = {10.1021/acs.est.5c10262}, pmid = {41732893}, issn = {1520-5851}, mesh = {*Wetlands ; *Ammonia/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism ; Nitrification ; Wastewater ; }, abstract = {Amid growing concerns over water pollution, the secondary effluent from wastewater treatment plants poses significant threats to aquatic ecosystems with limited self-purification capacity. Secondary effluent-constructed wetlands (SECWs) offer a sustainable solution for advanced nitrogen removal from this low-ammonia effluent, yet the functional role of comammox bacteria remains largely unexplored in such habitats. This study investigated the abundance, activity, kinetics, and ecological adaptations of comammox in typical SECWs. Quantitative PCR and amplicon sequencing revealed that comammox Nitrospira ubiquitously presented across all samples, even numerically dominated over ammonia-oxidizing bacteria/archaea (AOB/AOA). Consistent results from double-inhibition assays and DNA-stable isotope probing microcosm experiments indicated that comammox actively participated in nitrification, contributing 2.03-3.89 times those of canonical nitrifiers. Substrate kinetic and metagenomic analyses identified the Nitrospira nitrosa cluster as the sole active comammox population in SECWs, which exhibited relatively lower ammonia affinity (Km(app) = 0.055 ± 0.007 mg N/L) than other comammox species and distinct genomic adaptations to SECW-specific stressors, potentially explaining its dominance. Compared to AOB, comammox combines high substrate affinity with environmental resilience, aligning with K-strategist traits that enable it to outperform r-strategist AOB in SECWs. Overall, it is within this niche differentiation among comammox species and nitrifiers that the N. nitrosa cluster numerically and functionally dominated the nitrification process in SECWs, positioning comammox Nitrospira as pivotal biocatalysts for advanced nitrogen removal in engineered ecosystems.}, }
@article {pmid41733350, year = {2026}, author = {Bian, K and Busch, A and Norton, J and Bott, C and Gonzalez, R and Curtis, K and Tolofari, D and Khunjar, W and Graham, KE and Pinto, AJ}, title = {Quantitative metagenomics using a portable protocol.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0217925}, pmid = {41733350}, issn = {1098-5336}, support = {5100//Water Research Foundation/ ; DE-EE0009270//U.S. Department of Energy/ ; }, mesh = {*Metagenomics/methods/instrumentation ; *Nanopore Sequencing/methods ; Wastewater/microbiology ; Sequence Analysis, DNA/methods ; *Bacteria/genetics/classification/isolation & purification ; Water Microbiology ; }, abstract = {A field-deployable DNA sequencing approach for quantitative microbial community profiling can enable rapid responses for a range of applications in the water sector-from process control to wastewater surveillance. Current quantitative approaches require complex instrumentation and have long turnaround times for DNA recovery and absolute quantitation. In this study, we report a field-deployable rapid detection and rapid absolute quantitation (rD+rQ) workflow that leverages real-time Nanopore sequencing for quantitative metagenomics. This workflow integrates a high-molecular-weight DNA recovery protocol for diverse environmental matrices of relevance to the water sector, and multiplexed Nanopore sequencing with barcoded spike-in-based calibration (BSINC). BSINC using multispecies genomic spike-in controls exhibits significantly higher calibration accuracy compared to conventional approaches that utilize either a single DNA fragment or single organism spike-in controls. Dynamic detection and quantitation limits were established based on the coverage fraction of sequenced genomes and the coefficient of variation of genome copy numbers across replicates to enhance the accuracy and precision of microbial quantitation. The rD+rQ workflow achieves species-level identification and absolute quantitative results comparable to digital PCR in environmental samples. This portable laboratory and easy-to-use rD+rQ workflow should facilitate rapid decision-making for the water industry.IMPORTANCERapid and real-time monitoring of microbial communities is critical for a vast array of applications in environmental microbiology and biotechnology. While recent developments in portable sequencing technologies and associated workflows make onsite analysis possible, these approaches do not provide quantitative data on microbial concentrations. In this study, we present a sample and data processing workflow that enables nontargeted and quantitative microbial community profiling and demonstrate its validity on complex environmental samples. This approach for acquiring quantitative data can drive rapid decision-making from bioprocess control to wastewater-based epidemiology.}, }
@article {pmid41734043, year = {2026}, author = {Thakur, M and Dolker, S and Wangmo, LK and Sharma, LK and Acharya, S and Mohapatra, P}, title = {Illumina-Based Metagenomic Insights into the Gut Microbiome of Amblyomma helvolum (Koch, 1844) Parasitizing Xenochrophis trianguligerus from Great Nicobar Island, India.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {26}, number = {4}, pages = {233-240}, doi = {10.1177/15303667261423035}, pmid = {41734043}, issn = {1557-7759}, mesh = {Animals ; India ; *Gastrointestinal Microbiome ; *Amblyomma/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics ; *Snakes/parasitology ; *Tick Infestations/veterinary/parasitology/epidemiology ; }, abstract = {During a faunal survey in Great Nicobar Island, we collected four Amblyomma helvolum ticks infesting the snake Xenochrophis trianguligerus and processed for gut-metagenomic analysis using Illumina paired-end sequencing. A total of 8.7 million high-quality reads were generated, revealing that the gut microbiome was dominated by Bacteria (∼99.9%), primarily represented by Proteobacteria (∼95.7%), followed by minor fractions of Firmicutes, Actinobacteria, and Bacteroidetes. The predominant bacterial families were Alcaligenaceae, Bradyrhizobiaceae, Boseaceae, and Rickettsiaceae, with Achromobacter xylosoxidans emerging as the most abundant species (∼30% of total reads). Species-level analyses revealed a complex microbial community dominated by Achromobacter, Brevibacillus, Stutzerimonas, and Aeromicrobium. Several putative opportunistic pathogens were detected, including Myroides sp., Sphingobacterium sp., Stutzerimonas stutzeri, Cutibacterium acnes, Mycobacterium abscessus, Staphylococcus hominis, Achromobacter xylosoxidans, and Pseudomonas otitidis. This study represents the first metagenomic characterization of A. helvolum from India and provides baseline data on reptile-tick-associated microbial diversity from Great Nicobar Island. The findings underscore the importance of molecular surveillance in remote ecosystems and highlight the potential of reptile ticks as reservoirs of opportunistic and zoonotic bacteria.}, }
@article {pmid41734489, year = {2026}, author = {Sabatino, R and Gini, C and Borgomaneiro, G and Sbaffi, T and Corno, G and Sun, K and Zhang, XH and Di Cesare, A}, title = {Sinking particles as repository of antimicrobial resistome diversity in the Sansha Yongle Blue Hole.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181585}, doi = {10.1016/j.scitotenv.2026.181585}, pmid = {41734489}, issn = {1879-1026}, mesh = {China ; Bacteria/genetics ; *Seawater/microbiology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; *Environmental Monitoring ; *Water Microbiology ; *Drug Resistance, Microbial/genetics ; }, abstract = {The aquatic environment plays a central role in the selection and spread of antimicrobial resistance genes (ARGs). Using metagenomic approaches, several studies have provided a comprehensive view of the antimicrobial resistome across different aquatic ecosystems. However, unique aquatic systems, such as oceanic blue holes, remain largely unexplored. Free-living and particle-associated samples from the Sansha Yongle Blue Hole (South China Sea) were analyzed by shotgun metagenomics to characterize the antimicrobial resistome and the potential mobility of detected ARGs. The diversity of the antimicrobial resistome significantly decreased with increasing water depth. This trend was driven by the free-living bacterial community, whereas it remained stable in particle-associated communities. Additionally, the latter showed a higher frequency of co-occurring ARGs and mobile genetic elements on the same contigs, with a frequent plasmid localization of these genes. Overall, particle-associated bacteria proved essential for sustaining antimicrobial resistome diversity. Furthermore, these findings suggest that horizontal transfer of ARG may be more frequent within particle-associated communities along the water column of the blue holes, potentially contributing to the persistence of resistances in deep marine waters.}, }
@article {pmid41734506, year = {2026}, author = {Liu, X and Ding, J and Ji, B and Pastore, C and di Bitonto, L and Li, A}, title = {Synergistic effects of zero-valent iron-activated carbon on microalgal-bacterial granular sludge under antibiotic stress: Pollutant transformation and antibiotic resistance gene risk.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141581}, doi = {10.1016/j.jhazmat.2026.141581}, pmid = {41734506}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Iron/chemistry ; *Microalgae/metabolism ; *Anti-Bacterial Agents/toxicity ; *Water Pollutants, Chemical/metabolism/toxicity/chemistry ; *Drug Resistance, Microbial/genetics ; *Sulfamethoxazole/chemistry/metabolism/toxicity ; *Charcoal/chemistry ; Bacteria/genetics/drug effects ; Molecular Docking Simulation ; Genes, Bacterial ; Bioreactors ; }, abstract = {Microalgal-bacterial granular sludge (MBGS) technology remains insufficiently understood regarding the strategies and mechanisms for mitigating antibiotics and antibiotic resistance genes (ARGs). In this study, a non-aerated MBGS system coupled with zero-valent iron-activated carbon (ZVI-AC) was established to evaluate sulfamethoxazole (SMX) removal, effluent toxicity, ARGs control and to elucidate the underlying multi-scale mechanisms using molecular docking and metagenomic analyses. The results showed that, under SMX stress, the introduction of ZVI-AC maintained average COD removal above 94.0 % and increased the SMX degradation rate constant by 69.2 %. The "micro-electrolysis-like" effect generated by ZVI-AC increased sludge electron transport activity by 55.0 %, promoted MBGS stability (average granule size of 872.7 μm) and reduced effluent suspended solids to ≤ 10.0 mg/L, thereby significantly enhancing the structural stability and operational robustness of the MBGS system. For the transformation and toxicity reduction of SMX, molecular docking showed that the enzyme CYP102 interacted with SMX with a binding energy of -8.6 kcal/mol, indicating its significant role in accelerating SMX degradation and removing highly toxic metabolites TP163 and TP246, effectively reducing overall biological toxicity. In addition, metagenomic sequencing and qPCR analyses showed that the potential ARGs-host bacteria (g_Leptolyngbya) was significantly reduced, and that key ARGs (intI1 and sul1) were also significantly reduced, indicating a decreased risk of horizontal ARGs transfer. Specifically, ZVI-AC enhances SMX removal through micro-electrolysis-like and CYP450 enrichment as well as reducing ARGs via host bacteria suppression. Overall, this study provides new insight into how ZVI-AC enhances MBGS systems.}, }
@article {pmid41734642, year = {2026}, author = {Zhao, W and Liu, Y and Yu, G and Xia, S and Wang, S and Li, Y and Zhong, S and Zou, D}, title = {Microelectric field-enhanced air-lift A/O process: Mechanisms for advanced nutrient removal in low C/N rural domestic sewage.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129036}, doi = {10.1016/j.jenvman.2026.129036}, pmid = {41734642}, issn = {1095-8630}, mesh = {*Sewage/chemistry ; Nitrogen ; Phosphorus ; Carbon ; *Waste Disposal, Fluid/methods ; }, abstract = {The predominant challenge in treating rural domestic sewage (RDS) stems from its low carbon/nitrogen ratio (C/N), which fundamentally restricts the direct applicability of conventional municipal sewage treatment processes. To address this challenge, this study developed an innovative microelectric field-enhanced air-lift A/O process. The results demonstrated that this process achieved average removal efficiencies of 78.91% for total nitrogen (TN) and 93.80% for total phosphorus (TP), representing a significant improvement over conventional process. Mechanistic investigations revealed that the enhanced nitrogen removal primarily originated from the microelectric field-driven efficient reduction of NO3[-]-N in the anoxic zone, while phosphorus elimination resulted from synergistic interactions among chemical (sweep-flocculation by iron oxides/ions), physical, and biological processes. Microelectric field can stimulate microorganisms to produce more extracellular polymeric substances (EPS) and increase the ratio of protein (PN) and polysaccharide (PS). Metagenomic-based taxonomic comparison illustrated significant enrichment of nitrifying and denitrifying bacteria in the microelectric field-enhanced system, especially promoting the growth of autotrophic denitrifying bacteria, thereby providing an alternative electron source for nitrogen removal. Furthermore, the increased abundance of nitrogen/phosphorus metabolism-related functional genes and key enzymes provided molecular-level evidence for the enhanced metabolic pathways. Through parameter optimization, the optimal operating conditions were determined as follows: hydraulic retention time (HRT) of 12 h, internal recirculation ratio of 150-170%, and voltage of 1 V. This study demonstrated that microelectric field-enhanced technology offered an efficient and feasible strategy for addressing the challenges of nitrogen and phosphorus removal in RDS with low C/N.}, }
@article {pmid41734917, year = {2026}, author = {van der Sande, MAB and Valia, D and Tigoi, C and Stoesser, N and Stamm, L and Marten, A and Riems, B and Musyimi, R and Sibidou, Y and Schurch, AC and Tiendrebeogo, EW and Mwaringa, S and Kohns Vasconcelos, M and Ingelbeen, B and Tinto, H and Bielicki, JA and Cooper, BS and Berkley, JA and van Kleef, E}, title = {ALARUM: Active One Health surveillance in LMICs to monitor and predict Antimicrobial Resistance Using Metagenomics - a cross-sectional study protocol.}, journal = {BMJ open}, volume = {16}, number = {2}, pages = {e107465}, pmid = {41734917}, issn = {2044-6055}, mesh = {Humans ; *Metagenomics/methods ; *One Health ; Cross-Sectional Studies ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Kenya/epidemiology ; Burkina Faso/epidemiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Research Design ; }, abstract = {BACKGROUND: In rural sub-Saharan Africa (sSA), the burden of antimicrobial resistance (AMR) remains high. As AMR continues to rise, there is a strong need for practical, implementable surveillance to monitor and mitigate risks, as well as inform timely, evidence-based clinical decision-making. Emerging evidence points to possible community-level drivers, such as transmission between human, animal and environmental reservoirs as contributing factors, yet microbiological surveillance or opportunities for wastewater-based surveillance are often limited and insufficient in these settings. Therefore, alternative sustainable and affordable approaches are needed. We intend to build on the demonstrated potential of metagenomic profiling of pooled faecal material, which accurately predicted population-level AMR prevalence in invasive Enterobacterales infections.
METHODS AND ANALYSIS: We aim to validate this metagenomic pooled approach on additional populations, and to evaluate whether AMR patterns could be similarly predicted from surveillance of community One Health reservoirs. We will assemble existing data from hospital-based microbiology diagnostic laboratories in rural Burkina Faso and Kenya, and determine to what extent community-level metagenomic data, and/or faecal material of patients on hospital admission, can predict AMR in clinical isolates. We will perform community-level surveys in eight clusters per country, randomly selecting 15 households per cluster. We will systematically sample suspected environmental AMR exposure sites in and around households (soil, drinking water, latrines, chicken faeces) and collect data on community-level antibiotic use, hygiene practices, contact with domestic animals and sanitary facilities. Samples and data will be collected twice: during the dry and during the rainy season.In addition to evaluating the accuracy of predicting resistance in clinical isolates, we will quantify community-level exposure risks. We will conduct metagenomic profiling on pooled DNA extracts from human stool samples (hospital and community-level) and from household environments. Bayesian statistical models will quantify relationships between AMR gene abundance in the environment and in human stool, and invasive bacteria identified among clinical patients, accounting for geography and seasonality. A cost-utility analysis will determine under what circumstances the use of pooled metagenomic data to inform empirical antibiotic policies would represent an efficient use of resources.
ETHICS AND DISSEMINATION: The proposed surveillance protocol is developed in partnership with local communities and local and international researchers and has received ethical approval in Kenya and Burkina Faso. It will assess whether intermittent, pooled-sample metagenomics provides a viable, low-cost and practical approach for population-level AMR surveillance in settings that-like many in rural sSA-lack systematic microbiological diagnostics and where sewage systems for wastewater-based surveillance are absent. By providing an alternative to routine microbiological-based surveillance where this proves challenging to implement, this approach may help improve treatment outcomes, contribute to equity and public health. Findings will be disseminated through peer-reviewed publications and academic conferences and will contribute to the recently proposed WHO AMR surveillance strategy, which combines survey-based approaches with routine AMR surveillance.}, }
@article {pmid41735391, year = {2026}, author = {Kovács, ÁB and Wehmann, E and Bekő, K and Grózner, D and Bali, K and Kreizinger, Z and Sawicka, A and Bányai, K and Gyuranecz, M}, title = {Genome-wide association study of Mycoplasma anserisalpingitidis strains for antibiotic susceptibility.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41735391}, issn = {2045-2322}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genome-Wide Association Study ; Microbial Sensitivity Tests ; *Mycoplasma/genetics/drug effects ; Animals ; *Drug Resistance, Bacterial/genetics ; *Mycoplasma Infections/microbiology/veterinary/drug therapy ; Genome, Bacterial ; }, abstract = {Mycoplasma anserisalpingitidis is a facultative pathogenic bacterium affecting waterfowl, predominantly geese and sporadically ducks. Understanding the molecular basis of antimicrobial resistance mechanisms is crucial in the preservation of antibiotic efficiency. This study aimed to elucidate the genetic background of antibiotic susceptibility profiles of 110 M. anserisalpingitidis strains against nine antimicrobial agents. Significant associations between k-mers and five (tylvalosin, tilmicosin, enrofloxacin, lincomycin, spectinomycin) of the nine antimicrobial agents were identified by pyseer. Significant associations were found in multiple coding sequences that encode various members of efflux pumps, epigenetic regulation and topoisomerases among many other groups of functions. Certain k-mers associated with genes found putative prophage-like sequences suggest potential horizontal gene transfer events that could facilitate the acquisition of novel resistance mechanisms. Based on our findings, the genetic background of antimicrobial resistance of M. anserisalpingitidis is composed of multiple factors. Our results not only correlated with the majority of known antibiotic resistance mechanisms (e.g. drug target modification, efflux pumps, methyltransferases) but also showed potentially novel genes that could play a significant role in antimicrobial resistance. The results may serve to expedite the diagnosis of M. anserisalpingitidis antibiotic susceptibility profiles and support the fight against the spreading of resistance.}, }
@article {pmid41735773, year = {2026}, author = {Liu, H and Zhang, Z and Xu, Y and Wen, J}, title = {Soybean roots recruit plant-beneficial Pseudomonas via secreting 3,4-dihydroxybenzaldehyde.}, journal = {Plant physiology}, volume = {200}, number = {3}, pages = {}, doi = {10.1093/plphys/kiag075}, pmid = {41735773}, issn = {1532-2548}, support = {32071637//National Natural Science Foundation of China/ ; }, mesh = {*Pseudomonas/physiology/metabolism ; *Glycine max/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Benzaldehydes/metabolism ; Rhizosphere ; Phytophthora/physiology ; Plant Diseases/microbiology ; Disease Resistance ; Soil Microbiology ; }, abstract = {Rhizosphere microbiota mediate plant defense against soil-borne diseases, yet the mechanisms by which resistant soybean cultivars assemble protective microbiomes remain poorly understood. Using metagenomics, metabolomics, in vitro assays, and genetic approaches, we compared near-isogenic lines (Williams82, resistant; Williams, susceptible) to dissect plant-metabolite-microbe interactions mediating Phytophthora root rot resistance. Transplanting rhizosphere soil from the resistant cultivar to susceptible plants significantly reduced Phytophthora root rot severity, correlating with Pseudomonas enrichment and accumulation of the key rhizosphere metabolite 3,4-dihydroxybenzaldehyde. We isolated a core beneficial strain, Pseudomonas parafulva ZY6, from the resistant rhizosphere. In vitro, 3,4-dihydroxybenzaldehyde treatment promoted ZY6's biofilm formation, motility, and growth, while inhibiting Phytophthora sojae at higher concentrations. Knockout and overexpression of GmTL29 via hairy root transformation altered rhizosphere levels of 3,4-dihydroxybenzaldehyde, which in turn modulated the colonization of ZY6, the abundance of P. sojae, and the relative abundance of beneficial taxa such as Pseudomonas. Exogenous 3,4-dihydroxybenzaldehyde (0.1 μmol g-1 soil) significantly reduced Phytophthora root rot disease index, increased rhizosphere bacterial diversity, and enriched Bacillus and Pseudomonas. Our study demonstrates that resistant soybeans shape a disease-suppressive rhizosphere, in which 3,4-dihydroxybenzaldehyde contributes as a prebiotic by selectively enriching beneficial microbes. These findings offer a metabolite-based strategy to engineer rhizosphere communities for sustainable soil-borne disease management.}, }
@article {pmid41735826, year = {2026}, author = {Qian, Q and Li, N and Cha, S and Zheng, S and Li, W and Yin, G and Sun, M and Ye, P and Hu, M and Shi, R and Zhang, Y and Shen, W}, title = {Identification and functional characterization of Pseudomonas fluorescens as a novel intratumoral bacterium in colorectal cancer.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04827-w}, pmid = {41735826}, issn = {1471-2180}, support = {82303959//The National Natural Science Foundation of China/ ; 81302162//National Natural Science Foundation of China Youth Foundation/ ; SSPW2022-KF06//Open Project of Zhenjiang Traditional Chinese Medicine Spleen and Stomach Disease Clinical Medicine Research Center/ ; GSP-ZXY20//Zhongda Hospital Affiliated to Southeast University, Jiangsu Province High-Level Hospital Construction Funds/ ; }, }
@article {pmid41735848, year = {2026}, author = {Van Uffelen, A and Gobbo, A and Fraiture, MA and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K}, title = {Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12668-0}, pmid = {41735848}, issn = {1471-2164}, }
@article {pmid41736108, year = {2026}, author = {Bruni, A and Garofalo, E and Russo, A and Pelaia, C and Longhini, F and Bona, E and Aquila, I and Navalesi, P and Boscolo, A and , }, title = {Characterization of lung microbiota in pneumonia: a pilot study in ICU and non-ICU patients.}, journal = {Journal of anesthesia, analgesia and critical care}, volume = {6}, number = {1}, pages = {}, pmid = {41736108}, issn = {2731-3786}, abstract = {OBJECTIVE: To identify potential differences in lung microbiota according to clinical severity, age, and gender in pneumonia patients compared to controls.
DESIGN: Pilot study.
SETTING: Single center (Azienda Ospedaliera Universitaria Dulbecco, Catanzaro, Italy).
PATIENTS: Thirty-three individuals-11 ICU patients requiring invasive mechanical ventilation, 11 non-ICU patients, and 11 cadaver controls without lung disease.
INTERVENTIONS: Bronchoalveolar lavage sample collection and analysis via microbiological cultures and metagenomic sequencing.
MEASUREMENTS AND MAIN RESULTS: Bacteroidota and Verrucomicrobiota phyla were more abundant in older (≥65 years) ICU and non-ICU patients versus controls. Massilia timonae showed a significantly lower relative abundance at the group level in cases compared to controls, potentially increasing infection susceptibility. Higher microbiota diversity was observed in older patients.
CONCLUSIONS: Alterations in lung microbiota composition were observed in pneumonia patients, with differences that appeared more evident in older patients. Microbiota phenotyping may offer novel insights into pneumonia pathophysiology and pulmonary dysbiosis.}, }
@article {pmid41736367, year = {2026}, author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS}, title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {2}, pages = {e2511012}, doi = {10.71150/jm.2511012}, pmid = {41736367}, issn = {1976-3794}, support = {//Incheon St. Mary's Hospital/ ; //Catholic University of Korea/ ; //National Research Foundation of Korea/ ; 2023R1A2C1007759//Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; }, mesh = {Humans ; *Basal Cell Carcinoma/microbiology ; Pilot Projects ; *Skin/microbiology ; *Microbiota/genetics ; *Skin Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Middle Aged ; Female ; Republic of Korea ; Aged ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Aged, 80 and over ; Skin Microbiome ; }, abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.}, }
@article {pmid41736423, year = {2026}, author = {Dongqi, LI and Tongxing, W and Zixuan, W and Yihui, Y and Jie, LI and Jiaojiao, GU and Cuiru, LI and Aili, W and Lingling, S and Yongjie, M and Zeyu, Z and Yunlong, H and Huailin, G}, title = {Improving glucose tolerance in obese rats: the role of Jinlida granules () in gut microbiota modulation.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {46}, number = {1}, pages = {62-72}, pmid = {41736423}, issn = {2589-451X}, support = {2017YFC700500//National Key Research and Development Program 'Modernization Research of Traditional Chinese Medicine': Cardiovascular Event Chain (Metabolic Syndrome, Atherosclerosis, Myocardial Infarction, Arrhythmia, Heart Failure)/ ; 223777155D//Key R&D Program of Hebei: Traditional Chinese Medicine Innovation Project: Clinical Research on the Treatment of Diabetes Foot with Collateral Drugs and the Mechanism of Its Influence on Collateral Vessel Reconstruction/ ; 2023179//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Jinlida Granules in Treating Intestinal Dysfunction of diabetes and Its Effect on Short Chain Fatty Acids/ ; 2018200//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Tongluo Therapy for Diabetes Foot and Its Influence on Microcirculation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Rats ; *Obesity/drug therapy/microbiology/metabolism/genetics ; Male ; *Drugs, Chinese Herbal/administration & dosage ; Humans ; Glucose Tolerance Test ; Diet, High-Fat/adverse effects ; Zonula Occludens-1 Protein/metabolism/genetics ; Claudin-1/metabolism/genetics ; Blood Glucose/metabolism ; }, abstract = {OBJECTIVE: To investigate the effects of Jinlida granules (, JLD) on body weight, glucose tolerance, intestinal inflammation and barrier function in high-fat diet (HFD)-induced obese rats and explore the regulation of the gut microbiota as a potential treatment mechanism.
METHODS: Sprague-Dawley rats were divided into control, HFD, low-dose JLD (L-JLD), high-dose JLD (H-JLD), and sitagliptin groups. The rats, with the exception of those in the control group, were fed a HFD to establish an obesity model while simultaneously receiving 0.5% carboxymethyl cellulose, L-JLD, H-JLD or sitagliptin for 25 weeks. We assessed body weight, conducted oral glucose tolerance tests, and analysed faecal samples using metagenomic sequencing. Haematoxylin-eosin (HE), Masson and immunohistochemical (IHC) staining were employed to evaluate histological changes in the colon tissue. Immunofluorescence (IF) staining was used to measure the expression levels of Zonula occludens-1 (ZO-1) and Claudin-1 in colon tissue. The colon tissue was also subjected to transcriptomic evaluation.
RESULTS: JLD treatment significantly reduced body weight and enhanced glucose tolerance in obese rats. It alleviated colonic tissue damage, decreased collagen deposition, inhibited macrophage infiltration, and increased the expression of the tight junction proteins ZO-1 and Claudin-1. Metagenomic analysis revealed JLD-induced shifts in the gut microbiota composition (increasing the abundance of Turicibacter, Faecalibaculum, Coriobacteriaceae and Lactobacillus reuteri), enriching beneficial bacteria and metabolic pathways (increasing the biosynthesis of various secondary metabolites, ascorbate and aldarate metabolism, oxidative phosphorylation, C5-branched dibasic acid metabolism and beta-alanine metabolism). Transcriptomic analysis revealed downregulation of inflammatory and immune pathways (inhibition of the tumour necrosis factor signalling pathway, advanced glycation end products-receptor for advanced glycation end products signalling pathway, toll-like receptor signalling pathway, and interleukin-17 signalling pathway), suggesting a comprehensive modulatory effect of JLD on intestinal health and metabolic function.
CONCLUSIONS: JLD granules effectively improve glucose tolerance and ameliorate obesity-related intestinal dysfunctions in HFD-induced obese rats. These benefits are likely mediated through the modulation of the gut microbiota, the suppression of intestinal inflammation, the enhancement of barrier function, and the attenuation of proinflammatory pathways. Our findings offer novel insights into the therapeutic potential of JLD, emphasizing its role in integrating gut microbiota management into the treatment of metabolic disorders.}, }
@article {pmid41736479, year = {2026}, author = {Kong, S and Ning, Z and Chen, Z and Zhang, M}, title = {Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of 1,2,3-Trichloropropane in Groundwater by a Non-Dehalogenimonas Consortium.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {98}, number = {3}, pages = {e70318}, doi = {10.1002/wer.70318}, pmid = {41736479}, issn = {1554-7531}, support = {252S7601D//Hebei Province Science and Technology Support Program/ ; 242S4201Z//Hebei Province Science and Technology Support Program/ ; }, mesh = {*Groundwater/chemistry/microbiology ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Propane/analogs & derivatives/metabolism ; *Microbial Consortia ; }, abstract = {1,2,3-Trichloropropane (TCP), a highly mobile chemical byproduct, has severely exacerbated groundwater environment deterioration. Due to the lack of effective natural attenuation pathways, TCP typically exhibits a fate of persistent retention within aquifers. To address this challenge, instead of relying on limited specific strains, this study focused on exploring broad-spectrum co-metabolic substrates to enhance the degradation efficiency of a non-Dehalogenimonas synergistic consortium optimized through long-term directed domestication. Results indicated that the average degradation rate of the domesticated consortium increased to 19.06 μmol L[-1] d[-1], achieving complete removal within 3.5 days, thereby effectively altering the environmental persistence of TCP. Microbial community and metagenomic analyses revealed that this transformation process was driven by a synergistic alliance comprising Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides, realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination". Crucially, the consortium demonstrated exceptional broad-spectrum adaptability to various co-metabolic substrates, where sodium acetate and lactate significantly enhanced the degradation efficiency. This study confirms that utilizing suitable co-metabolic substrates can effectively activate the non-Dehalogenimonas consortium to regulate the migration and fate of pollutants in complex groundwater environments, offering an efficient bioremediation strategy to arrest groundwater contamination.}, }
@article {pmid41736790, year = {2026}, author = {Yu, S and Niu, H and Zhang, Y and Yu, L and Zhang, Q and Liu, X and Sang, Y and Wang, R and Zhang, M}, title = {Characterization of gut microbiota in patients with diabetic kidney disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1713005}, pmid = {41736790}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Diabetic Nephropathies/microbiology ; Feces/microbiology ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; }, abstract = {INTRODUCTION: Diabetic kidney disease (DKD) is a major complication of diabetes mellitus (DM). Although dysbiosis of the gut microbiota in DKD has been reported, the specific microbial species associated with disease progression from DM to DKD remain insufficiently defined.
METHODS: We conducted shotgun metagenomic sequencing on fecal samples from 55 healthy participants, 47 patients with DM, and 38 patients with DKD. Gut microbiota diversity, composition, and functional pathways were compared across groups; correlations with glycemic and renal indices were evaluated.
RESULTS: Overall alpha-diversity showed no significantly difference between DKD and healthy controls; however, the simpson's index was higher in DKD than in DM (p < 0.05). There was a difference in beta-diversity between DKD and the healthy control (p = 0.002), but no significant difference was observed between the DKD and DM group. Bacteria significantly enriched in DM/DKD include Mediterraneibacter, Enterocloster, Shigella, Limosilactobacillus, and Thomasclavelia, which showed positive correlations with glycemic indicators (HbA1c, fasting blood glucose) and renal indicators (BUN, UACR). In contrast, health-enriched bacteria, Phocaeicola, Faecalibacterium, Lachnospira, Agathobacter, Odoribacter, and Paraprevotella were negatively correlated with these parameters. Functional analysis revealed that compared to the DM group, the DKD group enriched pathways related to aromatic amino acid biosynthesis (phenylalanine, tyrosine, tryptophan), biofilm formation, and lipopolysaccharide biosynthesis. Gut microbial shifts along the DM-DKD correlates with adverse glycemic and renal phenotypes, as well as functional characteristics associated with inflammation and barrier injury. These findings suggest that microbially driven metabolic and structural pathways represent potential targets for mitigating the progression of DKD.
CONCLUSION: This study elucidates the distinct characteristics of the gut microbiota in DKD patients and highlights potential microbial markers involved in the progression from DM to DKD.}, }
@article {pmid41736795, year = {2026}, author = {Pan, H and Wu, L and Sheng, S}, title = {Metagenomic profiling of the gut microbiome to predict orthopedic healing responses in postmenopausal women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771312}, pmid = {41736795}, issn = {2235-2988}, mesh = {Humans ; Female ; *Postmenopause ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; *Wound Healing ; }, abstract = {INTRODUCTION: Recovery following orthopedic procedures in postmenopausal women is often prolonged and more complex due to age-related physiological changes, including reduced bone mineral density, altered hormonal profiles, impaired immune regulation, and delayed tissue regeneration. Conventional recovery assessment methods such as radiographic imaging, range-of-motion evaluation, and functional mobility tests provide valuable clinical information but offer limited insight into the underlying biological processes that influence healing. Emerging evidence indicates that the gut microbiome plays a critical role in regulating inflammation, immune homeostasis, and tissue repair, highlighting its potential as a predictive biomarker for post-surgical recovery outcomes. This study investigated the association between gut microbiome dynamics and recovery following orthopedic surgery in postmenopausal women.
METHODS: Stool samples were collected from preoperative (baseline) and 6 weeks postoperative time points. Microbial profiling was performed using 16S rRNA gene sequencing on the Illumina MiSeq platform, and data processing and taxonomic analysis were conducted using QIIME2. Microbial diversity was evaluated through alpha diversity metrics to assess community richness and beta diversity to characterize compositional differences over time. Clinical recovery was assessed using radiographic imaging, the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and the Timed Up and Go (TUG) functional mobility test. To evaluate the predictive potential of the gut microbiome, a random forest machine learning model was trained using microbial abundance data and correlated with clinical recovery outcomes.
RESULTS: The results revealed significant temporal shifts in gut microbial composition during the recovery period. Bacterial diversity varied across time points, with Firmicutes and Bacteroidetes identified as the dominant phyla. Increased abundance of these taxa was strongly associated with improved functional outcomes and faster recovery. In contrast, elevated levels of Proteobacteria and Escherichia were linked to delayed healing and poorer clinical performance. The predictive model achieved an accuracy of 85%, demonstrating the robustness of gut microbiome signatures as indicators of postoperative recovery.
DISCUSSION: Overall, this study highlights the significant influence of gut microbiome composition on orthopedic recovery in postmenopausal women. Identification of microbial biomarkers associated with favorable healing outcomes provides a foundation for developing microbiome-guided, personalized therapeutic strategies to enhance postoperative recovery and improve long-term musculoskeletal health.}, }
@article {pmid41736799, year = {2026}, author = {Zhao, Q and Wang, D and Lin, H and Zhou, T and Zhang, J and Shang, J and Cai, D and Sun, Y and Hu, Z and Zhang, J}, title = {Unraveling the activity of phage-carrying antibiotic resistance genes in constructed wetlands.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1764958}, pmid = {41736799}, issn = {2235-2988}, mesh = {*Wetlands ; *Bacteriophages/genetics ; *Bacteria/genetics/drug effects/virology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Gene Expression Profiling ; }, abstract = {Antimicrobial resistance (AMR) is a global public health challenge, and risk assessments based solely on gene abundance often underestimate the immediacy of resistance dissemination. This study presented a carrier-centric framework integrating metagenomic and metatranscriptomic profiling with deep learning-based identification of mobile genetic elements, applied to a full-scale constructed wetland (CW). CW overall reduced ARG burdens, with genomic abundance in plants, sediments, and water decreasing by 98.5%, 80.9%, and 88.8%, respectively. However, transcriptional activity showed an opposite trend, with sediments exhibiting the highest ARG expression, highlighting their pivotal role in the persistence and dissemination of resistance. In sediments, phage-mediated expression increased sharply from 4.0% to 92.5%, exceeding plasmid-associated levels by ~276-fold, revealing a low-abundance but high-activity residual risk pattern. Furthermore, 16 of the 310 recovered nonredundant MAGs were identified as phage hosts, 11 of which were potentially pathogenic, antibiotic-resistant bacteria (PARB) and were more active in sediments than in water or plants. These findings indicate that transduction within high-density, biofilm-associated niches constitutes a key terminal risk source. In addition, sediment acts as a high-risk reservoir where redox and ionic gradients, together with residual lomefloxacin and other antibiotics, enhance phage infectious activity and the accumulation of ARGs. Through cross-compartment transmission along the sediment-water interface, these phage-associated and PARB populations continuously seed the overlying water. It is recommended that ARG risk assessment shift from static abundance to an activity-aware, carrier- and host-resolved approach, prioritizing sediment-targeted transcript monitoring and phage transduction early warning to support risk mitigation in CW.}, }
@article {pmid41736897, year = {2025}, author = {Badillo-Pazmay, GV and Fortunato, C and Cianfruglia, L and Novazzi, F and Spezia, PG and Rosa, L and Limongi, D and Prezioso, C and D'Argenio, V and Scudiero, O and Bevilacqua, L and Malavolta, M and Russo, P and Maggi, F and Balietti, M and Giacconi, R}, title = {The gut and circulating virome: emerging players in aging and longevity.}, journal = {Frontiers in aging}, volume = {6}, number = {}, pages = {1731621}, pmid = {41736897}, issn = {2673-6217}, abstract = {A growing body of evidence indicates that the human virome, comprising both the gut and circulating viral communities, plays a critical role in shaping host physiology across the lifespan. In the context of aging, this complex viral ecosystem is increasingly recognized as a key modulator of immune function, inflammation, and metabolic balance, with direct implications for healthspan and longevity. While much attention has traditionally focused on bacterial components of the microbiota, recent advances in metagenomics have uncovered age-related shifts in the composition and function of the virome, including expansion of specific bacteriophage families, reactivation of latent viruses, and the persistence of commensal viral pathobionts. These changes are tightly linked to immunosenescence, chronic inflammation, and neurodegeneration, hallmarks of unhealthy aging. Notably, centenarians appear to harbor a unique virome signature marked by increased viral diversity, enhanced lytic activity, and the enrichment of phage-encoded metabolic functions, suggesting a potential protective role in extreme longevity. Despite these insights, significant challenges remain in virome profiling, including technical biases, database limitations, and the vast proportion of taxonomically unassigned sequences known as "viral dark matter". This review highlights emerging data on the aging virome, underscores its relevance within the Geroscience framework, and discusses current barriers and future directions for translating virome research into clinical aging studies.}, }
@article {pmid41736978, year = {2026}, author = {Ling, Y and Yang, DX and Xia, YN and Bao, CP and Zhang, F and Xu, XJ and Sun, BH}, title = {Effects of Age, Sex, and Social Network on Antibiotic Resistance Genes in the Gut Microbiome of Tibetan Macaques (Macaca thibetana).}, journal = {Ecology and evolution}, volume = {16}, number = {2}, pages = {e73137}, pmid = {41736978}, issn = {2045-7758}, abstract = {The transmission and dissemination of antibiotic resistance genes (ARGs) have increasingly drawn global attention. However, our knowledge of the antibiotic resistance gene pool in wild primates' gut microbiomes and its influencing factors remains limited. In this study, we focus on a social group of Tibetan macaques (Macaca thibetana) in Huangshan, utilizing behavioral and metagenomic data to investigate the effects of host sex, age, and social network on the ARG profiles of the gut microbiome. Our results demonstrate a high diversity of ARGs in the gut microbiota of Tibetan macaques, with multidrug, glycopeptide, and peptide resistance genes being the most prevalent. Although host age, sex, and social networks did not significantly affect the overall diversity of ARGs, these factors were significantly correlated with the relative abundance of several highly abundant ARG types, including gryB, rpoB, macB, novA, efrA, patB, Staphylococcus aureus mupA conferring mupirocin resistance, RanA, and cdeA. Further analysis revealed extensive interactions between gut bacteria and ARGs, with age emerging as a potentially key factor in this covariation process. These findings provide new insights into the formation and transmission mechanisms of antibiotic resistance in the gut microbiome of wildlife, particularly in social primates.}, }
@article {pmid41737133, year = {2025}, author = {Wu, R and Zu, W and Wei, L and Wu, R and Su, S and A, R and A, T and E, N and Li, H and Hu, R and Li, L}, title = {Metagenomics and metabolomics integrated to explore the protective mechanisms of Mongolian medicine Zadi-5 in myocardial ischemic model rats.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1677322}, pmid = {41737133}, issn = {1664-302X}, abstract = {BACKGROUND: Myocardial ischemia (MI) is a pathological state of abnormal energy metabolism caused by insufficient blood and oxygen supply to the coronary arteries. The "gut-heart axis" theory plays an important role in myocardial ischemia occurrence, mechanism, prevention, and cure. Traditional Mongolian medicine posits that "internal diseases originate from gastrointestinal dysfunction," linking the intestine, a key component of the digestive system, to physiological and pathological changes in the heart. Furthermore, the traditional Mongolian clinical treatment of cardiovascular diseases includes guidelines for digestive system function corresponding to the modern concept of the gut-heart axis. Accordingly, Zadi-5, a traditional Mongolian medicine, has been used for over 200 years to prevent and treat cardiovascular diseases. However, the mechanism by which the gut microbiota and metabolism are regulated to protect an ischemic heart is unclear.
AIM: This study aimed to investigate the potential mechanism by which Zadi-5, through its interaction with the gut microbiota and metabolic pathways, alleviates myocardial ischemic injury induced by a high-fat diet and isoproterenol (ISO).
METHODS: Sprague-Dawley rats were divided into control, model, Zadi-5 high-dose, and Zadi-5 low-dose groups. All groups, except the control group, were fed a high-fat diet for 4 weeks. Subsequently, all animals received subcutaneous injections of 4 mg/kg ISO daily for 3 days to induce a myocardial infarction (MI) rat model. The pharmacological effects of Zadi-5 on MI were assessed using electrocardiography (ECG), hematoxylin-eosin (HE) staining of myocardial tissue, and serum levels of cardiac troponin T (cTn-T), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C). Furthermore, fecal metagenomics and serum untargeted metabolomics were performed to investigate the protective mechanisms of Zadi-5 against MI. Finally, MetOrigin was used to analyze the correlation between key metabolic pathways and the gut microbiota to elucidate the mechanism by which Zadi-5 protects against myocardial ischemia.
RESULTS: First, the MI rat model was successfully established by ISO, and Zadi-5 significantly preserved MI injury, according to ECG recording, index of TC, TG, LDL-C, cTn-T, LDH, CK-MB, and histopathology results. Second, Zadi-5 regulates gut microbiota diversity and abundance, as well as glutamine and glutamate metabolism. The mechanism is related to the gut microbiota phyla Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteroidetes, and classes Gammaproteobacteria, Betaproteobacteria, Bacteroidia, Actinomycetes, Clostridia, and Bacilli. Zadi-5 also regulates L-glutamic acid, L-glutamine, ornithine, and oxaceprol metabolisms.
CONCLUSION: Zadi-5 exerts cardioprotective effects in MI rats by improving dysbiosis of the gut microbiota and regulating the glutamate-glutamine metabolism pathway. This may represent only one of the complicated protective mechanisms of Zadi-5 against MI. The cardioprotective mechanisms of Zadi-5 will be explored at the molecular and cellular levels.}, }
@article {pmid41737867, year = {2026}, author = {Niu, X and Yu, Q and Cao, L and Shen, W and Tian, J}, title = {Challenges in Diagnosis and Treatment of HIV-Negative Host Pulmonary Talaromyces marneffei in Non-Endemic Areas: A Case Report with a History of Pulmonary Tuberculosis.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {582375}, pmid = {41737867}, issn = {1178-6973}, abstract = {Talaromyces marneffei is an important opportunistic fungal pathogen closely related to acquired immunodeficiency syndrome (AIDS), and its infection is relatively rare in human immunodeficiency virus (HIV)-negative populations. Although HIV-related immunosuppression remains the main risk factor, the history of treated tuberculosis and subsequent structural lung damage may constitute an underrecognized predisposing condition in non-epidemic areas, especially in elderly patients. This report described a 69-year-old HIV-negative male pulmonary infection case from a non-endemic area of T. marneffei, with a history of treated pulmonary tuberculosis and residual fibrotic lesions on imaging. The patient complained of chest tightness and cough for one month and fever (temperature 38.0-38.5°C) for a week upon admission. The chest computed tomography (CT) scan observed patchy consolidation and multiple cavities in the upper lobes of both lungs, accompanied by pulmonary texture disorder and pleural adhesions and thickening. The imaging findings were difficult to distinguish from active pulmonary tuberculosis. The diagnosis of T. marneffei infection was confirmed through sputum culture, bronchoscopy sampling culture, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), and metagenomics next-generation sequencing (mNGS). After diagnosis, the patient was given oral voriconazole 200 mg every 12 hours, resulting in gastrointestinal intolerance. Subsequently, the dosage was adjusted to 100 mg every 12 hours, and the gastrointestinal symptoms improved significantly. The patient was eventually discharged but subsequently lost to follow-up. The case emphasizes that among HIV-negative individuals in non-epidemic areas of T. marneffei, for patients with unexplained pneumonia, especially those who have a history of tuberculosis and other potential immunological impairments, the differential diagnosis approach should be broadened and modern diagnostic techniques should be actively applied. It also highlights the importance of addressing drug tolerance issues and implementing long-term follow-up management in clinical treatment.}, }
@article {pmid41737956, year = {2026}, author = {Zhang, B and Wang, X and Qi, X and Zhang, L and Pei, N and Tao, Z and Liu, J}, title = {Bacterial co-detection is associated with higher multidrug-resistant Pseudomonas aeruginosa risk: insights from the MIMIC-IV database and metagenomic analysis.}, journal = {JAC-antimicrobial resistance}, volume = {8}, number = {1}, pages = {dlag023}, pmid = {41737956}, issn = {2632-1823}, abstract = {BACKGROUND: Pseudomonas aeruginosa (PA) poses a significant clinical challenge due to its high antibiotic resistance. While microbial communities aid in spreading antibiotic resistance genes (ARGs), their role in the emergence of multidrug-resistant Pseudomonas aeruginosa (MDR-PA) is unclear. This study examines the impact of bacterial interactions on MDR-PA prevalence and underlying mechanisms.
METHODS: This retrospective cohort study analysed 2965 PA-positive culture patients from the Medical Information Mart for Intensive Care IV (MIMIC-IV version 3.1) database, stratified by bacterial co-detection with PA. Propensity score matching (PSM) and logistic regression were used. Metagenomic sequencing was performed on deep endotracheal secretions from 19 PA ventilator-associated pneumonia (VAP) patients, constructing an ARGs dissemination network within the lower respiratory tract (LRT) microbiota. Comparative analysis of LRT microbiota and ARGs profiles was conducted between PA-VAP survivors and non-survivors.
RESULTS: Patients with bacterial co-detection with PA had a significantly higher MDR-PA prevalence and mortality than those with PA-only detection. Logistic regression identified bacterial co-detection as an independent risk factor for MDR-PA (adjusted OR 2.14; 95% CI 1.64-2.83, P < 0.001) and subsequent mortality (adjusted OR 1.67; 95% CI 1.30-2.14, P < 0.001). Metagenomic analysis of 19 PA-VAP cases suggested that horizontal gene transfer (HGT) may facilitate inter-species dissemination of ARGs (e.g. eptB, smeE, ANT(4')-Ia) between PA and other co-colonizing LRT microbiota. Distinct ARG profiles were observed between PA-VAP survivors and non-survivors.
CONCLUSION: Our findings indicate that bacterial co-detection with PA elevates the risk of MDR-PA and worsens clinical outcomes, potentially driven by HGT-mediated ARG exchange within the host microbiota.}, }
@article {pmid41738431, year = {2026}, author = {Khade, K and Dadachanji, R and Bhonde, G and Patil, A and Bhor, VM and Mukherjee, S}, title = {Gut microbiota dysbiosis in Indian women with PCOS may be linked to metabolic and hormonal dysregulation.}, journal = {Future microbiology}, volume = {21}, number = {2}, pages = {153-165}, pmid = {41738431}, issn = {1746-0921}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Polycystic Ovary Syndrome/microbiology/metabolism ; *Dysbiosis/microbiology/metabolism ; Adult ; India ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Fatty Acids, Volatile/metabolism/analysis ; Feces/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Protein Precursors ; Hyperandrogenism/microbiology/metabolism ; Sex Hormone-Binding Globulin/metabolism ; Haptoglobins ; }, abstract = {AIM: Polycystic ovary syndrome (PCOS) is a common gynecological and cardiometabolic disorder in reproductive-aged women. Recently gut microbiota alterations have been identified as key contributors to PCOS pathophysiology, but it remains understudied in Indian population.
METHODS: 16S rRNA gene amplicon sequencing using Illumina-MiSeq platform was conducted in 57 PCOS and 30 control women. Diversity indices were assessed and significantly altered taxa were identified by differential abundance tests (Wilcoxon-rank-sum test, ANCOMBC2 and LEfSe) in total and hyperandrogenism-based PCOS subgroups. We quantified levels of short-chain fatty acids (SCFAs) and gut barrier integrity marker, zonulin and LPS by HPLC and ELISA respectively.
RESULTS: Our study showed significantly altered beta diversity between PCOS and control groups, driven by hyperandrogenism. PCOS women demonstrate enrichment of Ligilactobacillus species, not previously reported to our knowledge, along with Collinsella species and markedly reduced SCFA-producing taxa, Oscillospiraceae. Additionally, levels of zonulin and fecal butyric acid, a potent SCFA, were significantly altered in PCOS women. Significantly altered taxa correlated with gonadotropin and SHBG levels and were involved in important metabolic pathways in total and PCOS subgroups.
CONCLUSION: Our study offers new insights into the mapping of gut microbiota in PCOS women from western India and implicates hyperandrogenism in driving dysbiosis.}, }
@article {pmid41738442, year = {2026}, author = {Ma, X and Johnson, KB and Li, C}, title = {Copepod Grazing and Prokaryotic Decomposition Amplify the Effect of Diatom-Dinoflagellate Regime Change on Biological Carbon Pump Efficiency.}, journal = {Environmental science & technology}, volume = {60}, number = {9}, pages = {7092-7110}, doi = {10.1021/acs.est.5c11967}, pmid = {41738442}, issn = {1520-5851}, mesh = {*Diatoms ; *Copepoda ; Animals ; *Dinoflagellida ; Phytoplankton ; Carbon ; }, abstract = {Copepod fecal pellets (FPs) are an important but highly variable component of the global Biological Carbon Pump (BCP). This study decoupled and quantified how copepod grazing and prokaryotic activities affect BCP efficiency under different phytoplankton dietary regimes. With a diet of diatoms, copepod FP production rates double, FP sinking rates triple, and FP decomposition rates are significantly lower relative to those with dinoflagellate diets. When dinoflagellates are the primary producers, inefficient grazing and enhanced prokaryotic activity synergistically decrease the efficiency of FP exports to the deep ocean. This finding confirms previous observations. Opportunistic particle-attached (PA) prokaryotes are crucial for FP decomposition. Metagenomic analyses revealed that CAZymes and lysosomal enzyme abundances highly correlated with FP decomposition rates, representing important bioindicators of FP decomposition. These functional enzymes targeting phytoplankton- and copepod-intestine-derived macromolecules from the PA prokaryotic communities were key to FP decomposition. Genomic properties of the Planctomycetota revealed that strong motile ability, detoxification systems, and macromolecule degradation enzymes enabled the success of these opportunistic PA prokaryotes. Elevated temperatures amplified FP decomposition rates by enhancing enzyme abundances and especially accelerated the decomposition of FPs composed of dinoflagellates. This reduced BCP efficiency, as rapidly recycled organic materials remain in surface waters. Our findings highlight the synergistic biological activities amplifying the effects of phytoplankton composition changes on BCP efficiency. This underscores the importance of considering grazing regimes in combination with microbial dynamics in assessing ocean carbon cycling.}, }
@article {pmid41738467, year = {2026}, author = {Goldsworthy, A and Olsen, M and Shiratuddin, MF and McKirdy, S and Alghafri, R and Senok, A and Alfalasi, H and Wong, KW and Tajouri, L}, title = {A Pilot Metagenomic Study Demonstrating Virtual Reality Head Mounted Displays Utilized in Medical Education Are Reservoirs of Viable Pathogenic Microbes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70255}, pmid = {41738467}, issn = {2045-8827}, support = {//Australian Government Research Training Program Scholarship/ ; }, mesh = {Pilot Projects ; Metagenomics ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Humans ; *Virtual Reality ; *Education, Medical ; }, abstract = {Virtual reality (VR) devices are increasingly being utilized within operating theaters and intensive care units where appropriate sanitation is vital to ensure that patients do not unnecessarily acquire hospital-associated infections. The morphology of VR devices in conjunction with the variety of materials and internal components provides challenges to their repurposing. This study aimed to evaluate the microorganisms remaining on VR headsets following sanitation by laboratory staff in a medical education anatomy teaching facility. The external components and internal facial interface were swabbed and separately cultured on four AGAR plates (Horse Blood, Nutrient, bile Esculin, and Mannitol Salt). Colonies were counted, sampled, pooled and subsequently processed for shotgun metagenomic sequencing. A higher number of colonies were present on surfaces closest to the eyes and facial interface compared to the external components. Metagenomic analysis identified 27 pathogenic bacteria including 4 "ESKAPE" pathogens (Enterobacter sp., Staphylococcus aureus, Klebsiella spp. and, Escherichia coli) and numerous organisms associated with ocular infections. A broad range of antimicrobial resistance genes were identified conveying resistance to Methicillin, Aminoglycosides, Macrolides, Tetracyclines, and Polymixins. Further research is required to ensure that current sanitization practices of VR head mounted displays are appropriate within high-risk hospital settings.}, }
@article {pmid41738753, year = {2026}, author = {Brothwell, JA and Toh, E and Xing, Y and Dong, Q and Xu, LH and Giacani, L and Beiras, CG and Mitjà, O and Gao, X and Spinola, SM}, title = {The etiology of exudative cutaneous ulcers in a yaws-endemic community prior to receipt of antimicrobials is similar to that found in communities after mass treatment with azithromycin.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0091925}, doi = {10.1128/msphere.00919-25}, pmid = {41738753}, issn = {2379-5042}, abstract = {Mass drug administration (MDA) of azithromycin (AZ) and case finding and treatment of children with cutaneous ulcers (CUs) have been trialed as strategies to eliminate yaws. Metagenomic sequencing of CU swabs obtained from children 3 to 4 years after the initiation of a yaws elimination campaign on Lihir Island showed enrichment for Treponema pallidum subsp. pertenue (TPE), Haemophilus ducreyi (HD), Streptococcus pyogenes (SP), and several anaerobic bacteria. Whether these results were influenced by AZ pressure or are generalizable to other populations is unknown. Here, we performed quantitative PCR (qPCR) for TPE, HD, and SP DNAs and metagenomic sequencing on 260 CU specimens collected from children on New Britain Island, whose inhabitants had not received MDA of AZ. Based on qPCR results, specimens were classified as containing no pathogens, a single pathogen, or multiple pathogens. 31.9% of the specimens contained SP, 28.1% HD, and 25.4% TPE DNAs; mixed infections with two or three pathogen DNAs occurred in 16.5% of cases. No pathogen DNA was detected in 31.5% of the specimens, which were defined as idiopathic ulcers (IUs). In most categories, the same pathogen(s) used to classify the ulcers by qPCR were the most abundant taxa present in the specimens. In IU, the most abundant taxon was Arcanobacterium haemolyticum; however, its relative abundance was similar across all groups, suggesting that this organism may adapt to the CU environment rather than represent a cause of IU. These data indicate that TPE, HD, and SP are the primary causes of CU in this untreated population.IMPORTANCECutaneous ulcers (CUs) affect ~100,000 children annually in tropical regions. After mass drug administration (MDA) of azithromycin (AZ) failed to eradicate yaws, the World Health Organization proposed an integrated disease management strategy to control CU, which emphasizes identifying the causative pathogens in each population. This is critical because organisms associated with CU vary geographically, with Treponema pallidum subsp. pertenue (TPE), Haemophilus ducreyi (HD), Streptococcus pyogenes (SP), and Leishmania spp. predominating in different countries. We previously found that TPE, HD, and SP DNAs were enriched in CU specimens from children on Lihir Island in Papua New Guinea (PNG), a population heavily exposed to AZ. Here, we show that these three organisms were also the major pathogens in CU specimens from children on New Britain Island in PNG, whose population had not received MDA of AZ, suggesting that our previous findings are generalizable within PNG and not a consequence of AZ exposure.}, }
@article {pmid41738755, year = {2026}, author = {Ren, X-Y and Ji, J-H and Hu, L and Bao, P and Xie, B-B and Li, S and Musat, N and Musat, F and Chen, S-C}, title = {In situ interrogation of microorganisms mediating hydrocarbon degradation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0259125}, pmid = {41738755}, issn = {1098-5336}, support = {226-2025-00166//Fundamental Research Funds for the Central Universities/ ; 42507165//National Natural Science Foundation of China/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; ZR2025MS514//Shandong Provincial Natural Science Foundation/ ; NNF22OC0071609//the Novo Nordisk Foundation through the Young Investigator Award ReFuel/ ; }, mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics/classification ; *Archaea/metabolism/genetics/classification ; Metagenomics ; Phylogeny ; }, abstract = {Microbially mediated hydrocarbon biodegradation is a cornerstone of natural attenuation and engineered bioremediation, yet the in situ mechanisms and key microbial players remain incompletely resolved due to the historical reliance on cultivation-based approaches. Recent advances in cultivation-independent tools, particularly metagenomics, stable isotope probing (SIP), and single-cell techniques, now enable more effective identification of active microbial populations, their functional genes, and metabolic networks directly mediating hydrocarbon degradation in situ. These studies have unveiled a far greater phylogenetic and functional diversity than previously recognized, including the unexpected co-existence of alkane-oxidizing archaea and bacteria in similar environments. The underlying microbial actors exploit distinctive enzymes to initialize hydrocarbon oxidation under oxic and anoxic conditions and achieve complete degradation through complex ecological networks that involve cooperative and/or competitive interactions with other community members such as viruses. These findings offer better insights into the functioning of the microorganisms that control the fate of hydrocarbons in situ and, as a final outcome, help tailor bioremediation strategies for better performance.}, }
@article {pmid41738843, year = {2026}, author = {Feng, T and Wu, Y and Xu, Y and Chen, WH}, title = {A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag016}, pmid = {41738843}, issn = {2047-217X}, abstract = {BACKGROUND: The ruminant gastrointestinal tract (GIT) serves as a natural microbial reservoir in which vitamin-synthesizing microbes play key integrated roles in digestion, nutrient absorption, and metabolic balance; however, studies systematically elucidating their functional characteristics and ecological roles remain limited due to the lack of a large-scale reference genome catalog for ruminant gastrointestinal vitamin-synthesizing microbes. Here, based on 2,325 metagenomic samples from 8 ruminant hosts, we comprehensively reconstructed and analyzed the ruminant GIT microbiome and the distribution patterns of vitamin-synthesizing microbes.
RESULTS: We reconstructed a unified ruminant gastrointestinal microbiome catalog (CRMC) with 39,696 MAGs, achieving the highest mapping rate (∼83.45%) among 2,325 metagenomic datasets, surpassing GTDB, RGMGC, and other catalogs. Across the 8 ruminant hosts, we identified a total of 17,349 vitamin-synthesizing microbes spanning 9 biosynthetic pathways (thiamine, riboflavin, niacin, pantothenate, pyridoxine, biotin, folate, cobalamin, and menaquinone). These microbes exhibited unified pathway selection patterns consistent with those in the human gut microbiome. Furthermore, within the major vitamin-synthesizing pathways commonly selected across ruminants, vitamin-synthesizing microbes displayed concentrated co-selection of specific functional gene nodes, revealing that despite taxonomic differences among gastrointestinal vitamin-synthesizing communities, they share highly convergent pathway preferences and common node-level selection patterns.
CONCLUSIONS: Together, by reconstructing the ruminant GIT microbiome reference genome catalog (CRMC), we elucidated the core microbial taxa and their functional features across ruminants, as well as the pathway preferences and distribution patterns of vitamin-synthesizing microbes. These findings provide an effective reference for advancing ruminant GIT microbiome research, offering gene co-selection insights for microbial synthetic biology design, and guiding microbiome-based interventions in ruminant systems.}, }
@article {pmid41740284, year = {2026}, author = {Wang, D and Huang, N and Hou, X and Chen, L and Jiang, Y and Liu, S and Zhu, S}, title = {Inorganic nitrogen in inflowing water governs dissolved organic matter transformation regulated by sediments in recipient basin.}, journal = {Water research}, volume = {296}, number = {}, pages = {125603}, doi = {10.1016/j.watres.2026.125603}, pmid = {41740284}, issn = {1879-2448}, mesh = {*Nitrogen ; *Geologic Sediments/chemistry ; Lakes ; China ; }, abstract = {Frequent Water Diversion Project significantly regulates the biogeochemical processes and water quality of surface systems, yet it remains poorly understood how recipient basin sediments respond to the inflowing water for mediating the dynamic transformation of dissolved organic matter (DOM). This study systematically conducted a long-term incubation experiment to simulate the interactions of recipient sediments of Dongping Lake, China, with the inflowing waters from different sources. Results showed the significant divergence and heterogenization in aromaticity and molecular weight of DOM in the overlying layer after a 75 day-incubation, during which sunlight irradiation and inorganic nitrogen levels were key in driving the biogeochemical transformation. Metagenomic analyses confirmed that inorganic nitrogen concentrations in the inflowing water governed microbial community succession, with Proteobacteria and Cyanobacteria sensibly responding to nitrogen level fluctuations. Further, nitrate and ammonia nitrogen influenced dissimilatory nitrate reduction activity and exerted positive feedback on the refractory carboxylic-rich alicyclic molecules (CRAM) metabolisms, thereby controlling the aromatization or humification processes of DOM. Specially, compositional characteristics of DOM were primarily determined by the abundance and activity of key functional genes, including narG, narZ, nxrA, narH, narY, nxrB, narI, and narV. This study provides new insights into the significant role of the Water Diversion Project in determining the dissolved organic carbon pool of inflowing water in recipient basins, enhancing biogeochemical understanding of its water quality responses.}, }
@article {pmid41740290, year = {2026}, author = {Gong, Q and Zeng, W and Hao, X and Yuan, Z and Wen, J and Wang, X and Peng, Y}, title = {Mixotrophic partial denitrification coupled with anammox achieves robust nitrogen removal under organic-rich conditions: Insights into metabolic adaptations of sulfur-oxidizing and anammox bacteria.}, journal = {Water research}, volume = {296}, number = {}, pages = {125599}, doi = {10.1016/j.watres.2026.125599}, pmid = {41740290}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrogen/metabolism ; *Sulfur/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism ; Wastewater ; Waste Disposal, Fluid/methods ; Ammonia/metabolism ; Bioreactors/microbiology ; }, abstract = {Sulfur-driven partial denitrification coupled with anammox (SPDA) process is a promising sustainable nitrogen removal pathway. However, its microbial adaptability and metabolic mechanism under long-term organic-rich conditions remain poorly understood. In this study, a single-stage mixotrophic partial denitrification-anammox (MPDA) system, driven by both thiosulfate and organic carbon from real domestic wastewater, was established and operated for 292 days. The system demonstrated excellent and robust performance, achieving average ammonia and total nitrogen removal efficiencies of 93.3% and 90.9%, respectively, despite fluctuating organic loading rates (0.35-0.45 kg COD/m[3]/d). [15]N isotopic tracing revealed that the PDA processes driven by thiosulfate and organic carbon contributed 51.3% and 27.7% of nitrogen removal, respectively. DNA-SIP experiments identified key facultative mixotrophic sulfur-oxidizing bacteria (SOB) (e.g., Thiobacillus and norank_f_Hydrogenophilaceae) as primary contributors to nitrite supply. Notably, the core anammox bacteria, Candidatus Brocadia, exhibited a positive correlation with organic load and was actively labeled by organic [13]C-carbon, suggesting previously overlooked organoautotrophic activity. Metagenomic analysis revealed that Thiobacillaceae employed the Calvin cycle for carbon fixation and possessed a complete pentose phosphate pathway, while Brocadiaceae utilized the Wood-Ljungdahl pathway alongside a near-complete TCA cycle and robust glycogen metabolism to support their mixotrophic capabilities. This study provides novel insights into the metabolic plasticity and synergistic interactions between SOB and anammox bacteria, demonstrating the feasibility and mechanism of the MPDA process for efficient nitrogen removal in organic-laden wastewater.}, }
@article {pmid41740355, year = {2026}, author = {Lee, J and Hong, S and Choi, J and Song, H and Han, JH and Suh, YD and Yeon, SC and Cho, S}, title = {Whole-genome shotgun metagenomics reveals environmental perturbations in the gut microbiome and resistome of wild raccoon dogs rescued at a wildlife center.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181588}, doi = {10.1016/j.scitotenv.2026.181588}, pmid = {41740355}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Raccoon Dogs/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Raccoon dogs are potential vectors for the transmission of zoonotic pathogens and antimicrobial resistance, with their gut microbiome carrying genetic determinants of virulence and resistance. However, previous studies have primarily relied on traditional culture-based approaches, limiting our understanding of the entire dynamics and genetic potential of the gut microbiome in raccoon dogs. In this study, we employed both culture-dependent approach and whole-genome shotgun sequencing in raccoon dogs undergoing rehabilitation for eight weeks. We integratively assessed how rehabilitation-related environmental shifts influence the gut microbiome and resistome. Rehabilitation induced shifts in gut microbiome composition. Notably, within-group diversity decreased at week eight, indicating increased compositional similarity. Throughout rehabilitation, a total of 18 genera (e.g., Paeniclostridium, Psychrobacter) significantly increased, and 40 genera (e.g., Intestinimonas, Erysipelatoclostridium) decreased in abundance. Rehabilitation also induced shifts in the gut resistome, with reduced within-group diversity at weeks four and eight, indicating increased compositional similarity over time. Overall, 253 antimicrobial resistance genes (ARGs) present at week 0 disappeared, whereas 273 ARGs were acquired during rehabilitation. Additionally, the abundance of 15 ARGs significantly decreased and that of 33 increased, with beta-lactamases being the most common among the latter. Culture-dependent methods revealed a marked increase in bacteria resistant to third-generation cephalosporins, monobactams, and sulfonamides. Changes in microbiome composition during rehabilitation indirectly influenced the resistome and virulome through mobile genetic elements. Our findings suggest that rehabilitation-induced perturbations in the gut microbiome and resistome of raccoon dogs are likely driven by environmental shifts such as diet and habitat. These changes may affect their post-release fitness and raise concerns owing to the potential dissemination of zoonotic pathogens and antimicrobial resistance.}, }
@article {pmid41740416, year = {2026}, author = {Fan, Z and Wu, J and Li, R and Li, H and Xu, Y}, title = {Co-application of organic fertilizer and biochar ameliorates the triple composite pollution of microplastics, antibiotic resistance genes, and heavy metals in soil.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141520}, doi = {10.1016/j.jhazmat.2026.141520}, pmid = {41740416}, issn = {1873-3336}, mesh = {*Fertilizers ; *Charcoal/chemistry ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil Microbiology ; *Microplastics/analysis ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Environmental Pollution/prevention & control ; }, abstract = {Intensive facility agriculture is increasingly threatened by the co-occurrence of heavy metals (HMs), micro-/nano plastics (MNPs), and antibiotic resistance genes (ARGs), yet effective strategies for mitigating ternary composite pollution remain limited. Here, a five-year field trail was conducted to evaluate the imparts of different fertilization regimes on the occurrence, interaction, and mitigation of composite pollution in facility agricultural soils, with a particular attention on the co-application of biochar and organic fertilizer. The results showed that conventional fertilization exacerbated the accumulation and synergistic risks of HMs, MNPs, and ARGs, whereas its co-applied with biochar significantly reduced individual pollutant loads and lowered the comprehensive ternary pollution index by 28.0-62.2 %. Variance partitioning and structural equation modeling revealed that microbial community structure played a dominant role in regulating composite pollution, exceeding the contribution of soil physicochemical properties. The biochar-organic fertilizer amendment reshaped microbial community assembly by narrowing ecological niche breadth, enhancing community stability, which primarily drove a targeted enrichment of functional taxa (e.g. Nitrospira, Sphingopyxis, Hydrogenophaga, and Steroidobacter) involved in microplastic degradation and heavy metal immobilization, concurrently suppressing ARGs host populations. Metagenomic analyses indicated a dual-level regulation of microbial carbon metabolism. The treatment enhanced fermentation-driven, energy-efficient carbon conversion pathways in functional microbes responsible for plastic degradation and metal immobilization, while concurrently inhibiting carbon fixation-dependent metabolic functions in ARG-associated hosts, thereby reducing their ecological competitiveness. Overall, this study highlights carbon resource-driven microbial metabolic differentiation as a central mechanism for the synergistic mitigation of complex soil pollution and provides a practical fertilization strategy for sustainable pollution control in protected agricultural systems.}, }
@article {pmid41740635, year = {2026}, author = {Hsu, CY and Almajidi, YQ and Abohassan, M and Gafarov, R and Basunduwah, TS and Hjazi, A and Arora, V and Nayak, PP and Shukla, SK and Jayabalan, K}, title = {Pharmacomicrobiomics in blood cancers: How the gut microbiome and its metabolites shape drug efficacy and toxicity.}, journal = {Critical reviews in oncology/hematology}, volume = {221}, number = {}, pages = {105229}, doi = {10.1016/j.critrevonc.2026.105229}, pmid = {41740635}, issn = {1879-0461}, abstract = {Clinical management of hematologic cancers is frequently complicated by marked, unpredictable inter-patient variation in both therapeutic benefit and adverse effects. Beyond host genetics, accumulating mechanistic and translational data implicate the gut microbiota and its small-molecule metabolome as active modifiers of drug chemistry, host immune tone, and clinical outcomes. In this review we synthesize three recurring, actionable findings: (1) discrete microbial enzymes, most prominently bacterial β-glucuronidases, repeatedly re-activate hepatic drug-glucuronides in the gut and amplify local gastrointestinal toxicity (e.g., irinotecan and mycophenolate), a pathway successfully targeted in preclinical and translational studies. (2) loss of anaerobic short-chain fatty acid production, especially butyrate, is a recurrent, causal mediator of mucosal injury and aggravated graft-versus-host disease after allogeneic hematopoietic cell transplantation. (3) reduced gut microbial diversity and the depletion of key functional taxa predict worse transplant outcomes (including mortality), arguing that baseline ecosystem state is a prognostic biomarker that merits routine consideration in trial design. Building on these syntheses, we propose a compact clinical framework for hematology trials and practice: (A) baseline ecosystem phenotyping (shotgun metagenome + targeted metabolite panel including butyrate and measured bacterial β-glucuronidase activity), (B) risk-stratified interventions (enzyme-targeted inhibitors, defined consortia, or metabolite replacement for high-risk patients), and (C) embedded holo-omic endpoints to confirm on-target biochemical modulation and link molecular change to clinical benefit. Together, these elements move Pharmacomicrobiomics beyond descriptive cataloging toward mechanistic stratification and testable interventions that can reduce unexplained variability in drug response and toxicity for patients with leukemia, lymphoma and myeloma.}, }
@article {pmid41740877, year = {2026}, author = {Orth, HM and Meierkord, D and Holtfreter, MC and Luedde, T and Schmidt-Chanasit, J and Feldt, T}, title = {Zika virus infection in a German traveller to the Maldives, August 2025.}, journal = {Travel medicine and infectious disease}, volume = {70}, number = {}, pages = {102960}, doi = {10.1016/j.tmaid.2026.102960}, pmid = {41740877}, issn = {1873-0442}, mesh = {Humans ; *Zika Virus Infection/diagnosis/virology ; *Zika Virus/genetics/isolation & purification/classification ; *Travel ; Phylogeny ; Germany ; Indian Ocean Islands ; Adult ; RNA, Viral ; Female ; Male ; Travel-Related Illness ; Maldives ; }, abstract = {BACKGROUND: Zika virus (ZIKV) is a neurotropic flavivirus associated with generally mild disease but the risk of congenital abnormalities when contracted during pregnancy. Reports from the Maldives are rare.
METHODS: We describe a ZIKV infection in a traveller returning from the Maldives in August 2025, including clinical findings and molecular diagnostics with metagenomic sequencing and phylogenetic analysis.
RESULTS: ZIKV ribonucleic acid was detected by reverse transcription polymerase chain reaction, and sequencing identified the ZIKV Asian lineage. However, the limited sequence length precluded precise phylogenetic placement.
CONCLUSION: This case underlines the ongoing risk of ZIKV transmission in areas where compatible arthropod vectors are present. Since there is no systematic surveillance in the Maldives, the detection of ZIKV infections in returning travellers is becoming increasingly important for assessing the epidemiological situation.}, }
@article {pmid41741009, year = {2026}, author = {Li, S and Yan, Q and Tong, J and Li, Y and Bai, L and Peng, Q}, title = {Distinct Defence Mechanisms of Allelopathic Rice Against Quinclorac-Susceptible and -Resistant Barnyardgrass: Involvement of Specific Metabolites and Rhizosheath Microbiota.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.70611}, pmid = {41741009}, issn = {1467-7652}, support = {U22A20461,32372564//National Natural Science Foundation of China/ ; }, abstract = {Allelopathic rice is increasingly recognised as a promising strategy for sustainable weed management. Resistance to the herbicide quinclorac is widespread in barnyardgrass, but it remains unclear whether allelopathic rice exerts the same defence against herbicide-susceptible and -resistant barnyardgrass. We conducted integrated transcriptomic, metabolomic, and metagenomic analyses to investigate the responses of allelopathic rice to quinclorac-susceptible (S) and -resistant barnyardgrass (R) lines. Distinct chemical strategies were identified in allelopathic rice: Terpenoids (e.g., carnosic acid, phytocassane B, and ipomeatetrahydrofuran) mainly suppressed S, while amino acids (e.g., pipecolic acid, L-glutamate, and L-histidine) were key against R. Correspondingly, terpenoid biosynthesis and nitrogen metabolism were the most enriched pathways under S and R stress, respectively. Additionally, terpenoid accumulation correlated positively with salicylic acid (SA) and jasmonic acid (JA) concentrations in roots under S. Both terpenoids and amino acids formed the stable ecological networks with rhizosheath microbiota. Functional metagenomic analysis further showed that ABC transporter and quorum sensing pathways were upregulated under S, whereas nitrogen fixation predominated under R. Notably, amino acids formed a nitrogen-related ecological network with nitrogen-metabolising microbiota, contributing to improved plant-available soil nitrogen and total nitrogen content in rice plants. Bioassays showed that exogenous pipecolic acid (≥ 40 μM) and L-histidine (80 μM) inhibited barnyardgrass seedling growth without affecting allelopathic and non-allelopathic rice. These findings demonstrate that allelopathic rice employs divergent chemical-microbial defence strategies against S and R barnyardgrass, highlight the dual role of amino acids, and provide a basis for precision weed management, particularly for herbicide-resistant weeds in paddy fields.}, }
@article {pmid41741460, year = {2026}, author = {Lin, Y and Kouraki, A and Cheetham, NJ and Louca, P and Bowyer, RC and Pope, R and Asnicar, F and Zhang, X and Visconti, A and Falchi, M and Spector, TD and Segata, N and Valdes, AM and Menni, C}, title = {Gut microbiome composition and function reflect socioeconomic deprivation.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41741460}, issn = {2055-5008}, support = {MR/W026813/1 and MR/Y010175/1//UKRI/MRC grants/ ; }, abstract = {Socioeconomic status (SES) correlates with adverse health outcomes, but the underlying biological mechanisms remain unclear. We examined how area-level deprivation (Townsend Deprivation Index) influences gut microbiome composition and function and whether the gut microbiome mediates the effects of deprivation on metabolic and mental health. A total of 1390 females from TwinsUK with shotgun metagenomes were included in this study. We found that higher Townsend deprivation was associated with reduced alpha diversity (Beta [95% CI] = -1.60 [-3.00, -0.21]) and distinct microbial composition shifts (PERMANOVA P = 0.001). Twelve species and 22 functional pathways were linked to deprivation, distinguishing between deprivation groups (AUC = 0.725-0.744), with altered energy metabolism in deprived individuals. Townsend deprivation was associated with anxiety (OR [95%CI] = 1.09 [1.01, 1.18]) and diabetes (OR [95% CI] = 1.16 [1.03, 1.30]). Importantly, Intestinimonas massiliensis and Lawsonibacter sp_NSJ_51 partially mediate the effect of anxiety. Lawsonibacter sp_NSJ_51 also mediated the deprivation-diabetes association. These findings suggest that socioeconomic deprivation influences microbiome composition and function, mediating disparities in metabolic and mental health.}, }
@article {pmid41741786, year = {2026}, author = {Flinn, H and Marshall, A and Holcomb, M and Burke, M and Kara, G and Cruz-Pineda, L and Soriano, S and Treangen, TJ and Villapol, S}, title = {Antibiotic-induced gut microbiome remodeling reduces neuroinflammation in traumatic brain injury.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09737-1}, pmid = {41741786}, issn = {2399-3642}, support = {R56AG080920//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; EF-2126387//NSF | BIO | Division of Emerging Frontiers (EF)/ ; }, abstract = {Traumatic brain injury induces neuroinflammation and gut microbiome dysbiosis, yet the effects of short-term antibiotic treatment on these processes remain poorly understood. To address this, male mice received controlled brain injuries followed by a brief course of oral antibiotics. Antibiotic treatment reduced bacterial abundance in feces and altered microbial diversity, with more pronounced shifts after two injuries. Despite this disruption, antibiotic-treated mice exhibited smaller lesion volumes, reduced cell death, attenuated microglial and macrophage activation, lower pro-inflammatory cytokine levels, and decreased astrogliosis and peripheral immune cell infiltration compared with vehicle-treated mice after two injuries. In the gut, increasing injury severity was associated with villus shortening and loss of mucus-producing cells, and antibiotic treatment further modified these injury-related changes. Circulating levels of short-chain fatty acids and associated microbial metabolic functions were reduced by antibiotic exposure. In contrast, germ-free mice showed increased lesion volumes and exacerbated gliosis following brain injury. Long-read metagenomic sequencing identified Parasutterella excrementihominis and Lactobacillus johnsonii as taxa that persisted despite antibiotic treatment. Collectively, these results suggest that antibiotics can reduce brain damage after injury through mechanisms not explained by short-chain fatty acids, while also highlighting potential drawbacks of altering the gut microbiome.}, }
@article {pmid41742303, year = {2026}, author = {Palma, DE and Schapheer, C and Gaete, A and Aravena, P and Albarrán-Cuitiño, C and Aguado-Norese, C and González, M and Cambiazo, V}, title = {The root system of Pappostipa frigida as a hotspot of active bacterial communities in the Andean steppe of the Atacama desert.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00867-x}, pmid = {41742303}, issn = {2524-6372}, support = {FONDECYT 1241424//ANID/ ; FONDECYT 1211893//ANID/ ; }, abstract = {BACKGROUND: In arid ecosystems, soil microorganisms experience prolonged drought and nutrient limitation, resulting in widespread dormancy and a decoupling between microbial presence and activity. The rhizosphere is a resource-rich microenvironment where plants, inputs may alleviate these constraints and regulate microbial metabolic states. However, it remains unclear whether root system effects in extreme environments reflect taxonomic turnover or the activation of dormant soil bacteria. Here, we investigated whether the rhizosphere-surrounding soil (RSS) of Pappostipa frigida, a dominant perennial grass of the Andean steppe of the Atacama Desert, reshapes soil bacterial communities primarily by promoting the activation of dormant taxa rather than by recruiting distinct bacterial populations, and how this process influences microbial diversity, activity, and functional potential.
RESULTS: We employed a combination of soil physicochemical analyses, RNA/DNA metabarcoding, shotgun metagenomic sequencing and culture-based assays to compare bulk soil (BS) and RSS bacterial communities. The active bacterial community in the RSS exhibited significantly higher diversity and Shannon index than those in BS, whereas total (DNA-based) communities showed no significant differences between soil compartments. Taxonomic structure was primarily shaped by soil compartment rather than nucleic acid type, and active bacteria in the RSS showed a stronger correlation with total bacterial populations than those in the BS. Notably, 65% of putatively dormant bacterial taxa in BS were detected as active in RSS, and 75% were recoverable in culture. Additionally, 24% were members of PGP bacterial families. Functionally, the bacterial communities of the BS were enriched in sporulation genes, whereas active bacterial communities in the RSS showed higher abundances of genes associated with osmotic stress tolerance, siderophore synthesis, and resuscitation-promoting factors.
CONCLUSIONS: Our results indicate that the root system of Pappostipa frigida functions as a localized hotspot of microbial activity in an extreme arid environment by promoting the activation of dormant members of the soil microbial seed bank rather than by recruiting distinct taxa. By integrating microbial activity, functional traits, and culturability, this study highlights the central role of plant-associated microenvironments in regulating microbial life-history strategies in drylands and provides a mechanistic framework for understanding plant-microbe interactions under chronic environmental stress.}, }
@article {pmid41742321, year = {2026}, author = {Mazzoni, C and Ochana, BL and Orlanski-Meyer, E and Ya'acov, AB and Focht, G and Harpenas, E and Shmorak, S and Ledder, O and Lev-Tzion, R and Shemer, R and Shteyer, E and Dor, Y and Yassour, M}, title = {Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02344-6}, pmid = {41742321}, issn = {2049-2618}, abstract = {BACKGROUND: Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized as a non-invasive way to profile the gut microbiome, and both clinical practice and research on inflammatory bowel diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, excessive immune cell recruitment and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics.
METHODS: We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of pediatric IBD patients and controls (Pediatric cohort, N = 134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large complementary external cohort including adult IBD patients and controls (Adult cohort, N = 689 adults, the Netherlands), not only to compare microbial patterns across the age spectrum, but also to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomic sequencing.
RESULTS: We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage, and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD cohorts.
CONCLUSIONS: The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients. Video Abstract.}, }
@article {pmid41742329, year = {2026}, author = {Cai, G and Wu, Y and Chen, Z and Yang, X and Jiang, X and Wang, Q and Cai, R and Wang, H}, title = {Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41742329}, issn = {2049-2618}, support = {42476092//National Natural Science Foundation of China/ ; 42476122//National Natural Science Foundation of China/ ; 2025A1515010891//Guangdong Provincial Department of Science and Technology/ ; 2022B1515020017//Guangdong Provincial Department of Science and Technology/ ; }, mesh = {*Polysaccharides/metabolism ; *Flavobacteriaceae/genetics/metabolism/classification/isolation & purification ; Phylogeny ; *Seaweed/microbiology ; Diatoms/microbiology ; Glycoside Hydrolases/genetics ; Dinoflagellida/microbiology ; }, abstract = {BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear.
RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles.
CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.}, }
@article {pmid41742841, year = {2026}, author = {Wang, Y and Wu, H and Qu, M and Zhang, C and Xu, Z and Pei, Y and Zhao, C and Wang, J and Ma, S and Lyu, N and Xu, X and Bi, Y and Zhu, B and Gao, GF}, title = {A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e74581}, doi = {10.1002/advs.74581}, pmid = {41742841}, issn = {2198-3844}, support = {2023YFC2307101//National Key Research and Development Program of China/ ; 235200810058//Project for Young Scientists of the Joint Funds of Science and Technology Research and Development Plan of Henan Province, China/ ; 30501278//Young TopNotch Talents Foundation of Henan Agricultural University/ ; }, abstract = {Migratory birds play an important role in the spread of antimicrobial resistance (AMR); however, gaps in surveillance data from vital regions along migratory flyways across China limit the detection of emergent threats. Here, we assembled 340 metagenomes from 52 bird species covering 11 provincial administrative districts in China, presenting a specialized migratory microbial genome and gene catalog to archive the genomic and functional diversity of gut microbiomes in wild birds. This comprehensive migratory bird microbial genome and gene (MBGG) catalog includes 5823 metagenome-assembled genomes (MAGs), 13 072 plasmid sequences, and 44 974 viral genomes, which represent 1709 candidate species spanning 36 phyla. The catalog also contains over 20 million non-redundant protein-encoding genes, the use of which is confirmed by the mining of 15 678 secondary metabolite biosynthetic gene clusters, 1814 known antibiotic resistance genes, and 7219 virulence factors. The number of clinically critical ARGs identified in Grus japonensis was the highest, followed by Cygnus cygnus and Sibirionetta formosa, which indicated that these species are hotspot species of clinically critical AMR dissemination. Moreover, we mapped the profile of bacterial zoonotic/opportunistic pathogens carried by wild birds and evaluated their associations with publicly available genomes. Finally, the precise migratory movements for 10 bird species using a global positioning system tracking system help to assess the movement of microorganisms and AMR risk. Collectively, this valuable resource provides the basis for the integration and unification of global wild bird microbiomes, timely sharing, and assessing the uncertainty of migratory microbiomes in the future.}, }
@article {pmid41743088, year = {2026}, author = {Li, Q and Liu, S and Wang, J and Yu, L and Sun, S}, title = {Case Report: A rare case of ANCA-positive Q fever endocarditis-associated glomerulonephritis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1701814}, pmid = {41743088}, issn = {2296-858X}, abstract = {BACKGROUND: Q fever is a zoonotic disease caused by Coxiella burnetii and is endemic worldwide. Q fever endocarditis is commonly found in adults and is rarely seen in children. Infectious endocarditis can also lead to renal damage. Here, we present a case of Q fever endocarditis-associated glomerulonephritis in a Chinese boy with positive Antiproteinase 3 antibody (PR3)-antineutrophil cytoplasmic antibody (ANCA).
CASE PRESENTATION: A 12-year-old Chinese boy presented with intermittent fever and hematuria for 2 months. He was diagnosed with Tetralogy of Fallot at birth and underwent multiple cardiac surgeries between 1 and 4 years of age. The examinations showed positive serum mycoplasma antibody and increased serum Epstein-Barr virus (EBV) DNA. However, antibiotic and antiviral treatment was not effective. PR3-ANCA antibody was positive (109.8-158.8CU), while anti-myeloperoxidase (MPO) antibody, anti-glomerular basement membrane (GBM) antibody, antinuclear antibodies (ANA), and double-stranded DNA (dsDNA) were negative. Chest CT showed bronchitis. Ophthalmic examination and ENT examinations revealed no abnormalities. Coxiella burnetii was found positive by metagenomics next generation sequencing (mNGS) and immunofluorescence assay (IFA) in the detection of pathogenic microorganisms causing bloodstream infections. Prominent vegetation was present on the pulmonary valve, as demonstrated by cardiac ultrasound. Secondary hyperplastic glomerulonephritis was considered by renal biopsy. Therefore, the final diagnosis was Q fever endocarditis-associated glomerulonephritis. Doxycycline was given to the boy orally and daily, and no fever occurred again. Sixteen months later, hematuria disappeared and PR3-ANCA remainded positive.
CONCLUSIONS: Q fever endocarditis should be considered for children presenting with chronic fever, hematuria and positive ANCAs, especially those with a history of congenital heart disease or cardiac operation. It is very helpful for the diagnosis to undergo these examinations, including mNGS, cardiac ultrasound and renal biopsy.}, }
@article {pmid41743122, year = {2026}, author = {Shen, S and Ning, M and Li, M and Qian, S and Ye, X and Zhuang, Q and Wu, S and Wan, X and Dong, Z}, title = {Sevelamer inhibits the formation of cholesterol gallstones by modulating bile acid metabolism.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1737631}, pmid = {41743122}, issn = {1663-9812}, abstract = {BACKGROUND: The purpose of this study was to investigate the effect and mechanism of Sevelamer hydrochloride (Sev) on cholesterol gallstone formation via the intestinal Fxr-Fgf15 signaling pathway in a mouse model.
METHODS: A cholesterol gallstone mouse model was established. Mice were divided into groups treated with Sev, Fxr agonist, or controls. The incidence and severity of gallstones, along with liver/body weight ratio, were recorded. Total cholesterol (TC) and total bile acid (TBA) levels were measured. Biliary cholesterol supersaturation index (CSI) was calculated. Serum ALT and AST levels were quantified by ELISA. The expression of Fxr-Fgf15 pathway-related molecules and bile acid transporters were detected by RT-PCR and Western blot. Targeted bile acid metabolomics characterized ileal bile acid profiles, while metagenomics assessed gut microbiota alteration.
RESULTS: Sev treatment reduced hepatic lipid deposition, lowered biliary CSI, attenuated gallbladder wall thickening, improved liver function, and decreased TC levels. Mechanistically, Sev inhibited the intestinal Fxr-Fgf15 pathway, promoting hepatic bile acid synthesis and altering ileal bile acid composition. Fxr agonist reversed these effects, increasing Fgf15/Shp expression, suppressing bile acid synthesis, elevating CSI, and partially restoring gallstone susceptibility. Sev reshaped gut microbiota diversity, reducing Blautia and enriching Bacteroidales and Roseburia at genus level. Concurrently, Sev modulated the ileal bile acid pool, decreasing Fxr-activating bile acids and increasing Fxr-antagonizing bile acids. Microbiota-bile acid correlation analysis highlighted significant associations between specific taxa and bile acid profiles.
CONCLUSION: Sev might prevent cholesterol gallstone formation by inhibiting the intestinal Fxr-Fgf15 pathway, promoting hepatic bile acid synthesis, reducing biliary cholesterol supersaturation, and restoring gut microbiota balance.}, }
@article {pmid41743140, year = {2026}, author = {Su, S and Pan, J and Wu, H and Ouyang, S and Chen, L and Zeng, Y and Deng, N}, title = {Tree species diversity promotes soil microbial carbon fixation gene abundance via nutrient-mediated interactions in subtropical forests.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751295}, pmid = {41743140}, issn = {1664-302X}, abstract = {Soil microbial carbon (C) fixation represents a vital yet uncertain component of forest carbon cycling, and its underlying mechanisms especially depth-specific responses remain unclear. To address this, we integrated metagenomics and machine learning to examine these relationships along a tree species richness gradient (1-8 species), analyzing both topsoil (0-10 cm) and subsoil (10-20 cm). Results revealed distinct vertical stratification in soil properties and microbial carbon fixation strategies. Microbial carbon fixation gene abundance was primarily driven by soil organic carbon (SOC) and nitrate nitrogen (NO3[-]-N), exhibiting a nonlinear threshold at ~85 g kg[-1] SOC. The promoting effect of SOC peaked at moderate richness (3-5 species) but declined at higher richness. Depth-resolved analysis revealed that the Calvin cycle gene rbcL responded mainly to richness in topsoil, whereas rTCA cycle genes (korA, korC) were more sensitive in subsoil These findings demonstrate that tree diversity enhances microbial carbon fixation through nutrient-mediated mechanisms, but these effects are nonlinear, context-dependent, and depth-specific. Incorporating such complexity is essential for accurately predicting forest carbon sequestration.}, }
@article {pmid41743204, year = {2026}, author = {Xu, K and Guan, P and Du, W and Zeng, H and Chen, M and Lv, Z and Liu, Y and Shao, M and Qu, B}, title = {Warming outweighs nitrogen deposition in shaping rhizosphere microbial structure involved in carbon, nitrogen, and phosphorus cycling in Ambrosia trifida.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1686326}, pmid = {41743204}, issn = {1664-462X}, abstract = {INTRODUCTION: Ambrosia trifida, a harmful invasive plant, poses significant ecological and economic threats and is expected to spread further under future warming and nitrogen deposition scenarios. According to plant-soil feedback and enhanced mutualist hypothesis, invasive plants may gain a competitive edge by recruiting specific microorganisms. However, little is known about the composition and functional potential of its rhizosphere microbiome.
METHODS: In this study, we combined metagenomics with widely targeted metabolomics to investigate the interactions between root exudates and soil microbial communities under experimental warming and nitrogen deposition.
RESULTS AND DISCUSSION: The results showed that warming and nitrogen addition together promoted biomass accumulation. And their combination enhanced soil nutrient content. Warming increased the abundance of functional genes involved in carbon fixation (e.g., acs, acsA, PCCA, MUT), whereas nitrogen addition suppressed nitrification and denitrification genes. Warming also enhanced the abundance of genes related to inorganic phosphate solubilization (ppk, ppx), phosphorus mineralization (phnPP, phnF, glpQ), and phosphorus transport (pstBC, ugpABCE). Functionally, warming increased the relative abundance of beneficial taxa such as Sphingomicrobium, Massilia, and Nocardioides, while reducing Pseudomonas, Trinickia, and Rhizomicrobium. Nitrogen deposition had a comparatively weaker effect on the functional microbial community. Correlation analysis between metabolites and functional genes suggested that alkaloids, organic acids, and phenolic compounds may be key drivers of microbial functional shifts. Overall, our findings demonstrate that warming has a greater influence than nitrogen deposition on shaping the rhizosphere soil microbial community and enhancing nutrient cycling functions, potentially increasing the risk of A. trifida invasion under future climate change.}, }
@article {pmid41743327, year = {2026}, author = {Lee, SC and Tee, MZ and Shen, Z and Er, YX and Neelam, R and Cadwell, K and Segre, JA and Lim, YAL and Loke, P}, title = {Functional divergence of the gut microbiome associated with lifestyle and helminth infection in Indigenous Peninsular Malaysian.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41743327}, issn = {2693-5015}, abstract = {Gut microbiome catalogs from Indigenous Southeast Asian populations remain underrepresented. Here, we integrated metagenomic and metatranscriptomic data from Indigenous Orang Asli (OA) in Peninsular Malaysia and urban residents of Kuala Lumpur (KL), together with immune profiling, to investigate gut microbial activity and functions associated with lifestyle and helminth infection. Prevotella showed significantly higher transcriptional activity in OA, whereas Bacteroides was more active in KL, corresponding to distinct immune signatures. Microbial genome-wide association studies (mGWAS) revealed Prevotella copri_A variants were linked to lifestyle and host immunity, while Blautia strain variation was associated with helminth infection. Malaysian metagenome-assembled genomes (MAGs) uncovered 307 novel species, predominantly within Clostridia. Among these, the novel HGM13006 species were enriched with genes for starch and sucrose metabolism, and the novel Ruminococcus_D species in flagellar assembly and chemotaxis. Together, these findings provide function-level insights into gut microbiome variation associated with lifestyle and helminth infection in an indigenous population.}, }
@article {pmid41743798, year = {2026}, author = {Wang, X and Ma, T and He, W and Shan, T and Zhang, G and Peng, F and Chen, L and Ma, J and Ding, C and Niu, P and Chen, T}, title = {Disrupted Tryptophan Metabolism Mediates Manganese-Induced Neurogenesis and Neuroinflammatory Impairments: Rescue by Exogenous Melatonin.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {2}, pages = {275-290}, pmid = {41743798}, issn = {2833-8278}, abstract = {Manganese (Mn) is a common environmental pollutant, and excessive exposure can lead to motor dysfunction resembling Parkinson's disease. Increasing evidence suggests that Mn impairs endogenous neurogenesis and hinders neural repair. This study aims to investigate the effects of both acute and long-term Mn exposure on neurogenesis and to elucidate the underlying mechanisms. By establishing acute (7 and 14 days) and long-term (2 and 4 months) Mn exposure mouse models, we assessed neurogenesis under different exposure conditions. The mRNA sequencing, untargeted metabolomics, and metagenomics were employed to uncover the molecular pathways involved in Mn-induced neurogenesis impairment. The results revealed that early stage Mn exposure, including acute and 2 months exposure, transiently promoted neurogenesis. However, prolonged Mn accumulation in the brain led to suppressed neurogenesis, accompanied by neuroinflammation and oxidative stress, which contributed to a vicious cycle of neural damage. Multiomics analyses identified dysregulation of the tryptophan metabolic pathway as a key mechanism, with a marked reduction in melatonin levels following Mn exposure. Notably, exogenous melatonin supplementation effectively rescued Mn-induced impairments in neurogenesis, neuronal integrity, and neuroinflammation. These findings provide new insights into Mn neurotoxicity and highlight melatonin as a potential therapeutic agent for Mn-related neural damage.}, }
@article {pmid41743802, year = {2026}, author = {Wei, H and Xu, Y and Jin, B and Zhao, X and Yang, X and Guan, Q and Gao, B and Zhang, Z and Sun, H and Ye, Y and Ikeda, A and Xia, Y}, title = {Population-Level Amplicon and Metagenomic Analyses Uncover Distinct Effects of Landscape-Level Pesticides on the Maternal Gut Microbiome.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {2}, pages = {246-258}, pmid = {41743802}, issn = {2833-8278}, abstract = {The environment dominates over host genetics in shaping the gut microbiome, which plays a pivotal role in modulating human health. Experimental evidence supports the notion that exposure to pesticides could perturb the gut microbiome, and the toxicant-induced dysbiosis may affect host homeostasis. However, the field of human studies, especially in early life, is still in its infancy. We aimed to evaluate the effects of landscape pesticide exposure on the maternal gut microbiome. Here, we assessed the blood levels of a broad array of pesticides in 405 pregnant women. Gut microbial compositions and functional profiles were assessed by using both 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. Microbial alpha diversity indices were regressed on host and environmental factors using linear models. Differences in overall microbial compositions were evaluated by using univariable permutational multivariate analyses of variance (PERMANOVA) with Bray-Curtis dissimilarities. All pesticides, as well as other host and environmental factors, were correlated to the gut microbiome at the phylum, genus, species, and pathway levels employing the multivariable regression models adjusted for the potential covariates, respectively. The joint effects of the mixture of pesticide exposure on the gut microbiome were investigated using quantile g-computation. Microbial ecological networks were constructed via Spearman correlations to explore species co-occurrence patterns related to pesticide exposure. Significant associations were observed between exposure to various pesticides individually or as a mixture and maternal gut microbiome features. Specific taxa and pathways were enriched or depleted in response to varying pesticide concentrations, indicating the potential exposure-response relationships. Notably, mirex exposure showed a positive correlation with both the relative abundance of Blautia_wexlerae and the sucrose biosynthesis II pathway. Microbial co-occurrence network analyses revealed marked shifts in species interactions associated with increasing levels of pesticide exposure. Mediation analyses further identified a greater number of microbial taxa, particularly Blautia_wexlerae, as significant mediators linking pesticide exposure to alterations in microbial functional pathways. Our large-scale amplicon and metagenomic analyses unraveled the extensive impacts of landscape-level pesticides on the maternal gut microbiome. Further observational and experimental research is warranted to validate our findings as well as to elucidate whether and how these microbial changes affect maternal and offspring health.}, }
@article {pmid41743993, year = {2026}, author = {Li, G and Puumala, E and Zhang, Z and Rajapakse, NS and Ristagno, EH and Wolf, MJ and Rodning, AA and Simner, PJ and Gaensbauer, JT and Patel, R}, title = {Cerebrospinal Fluid Metagenomic Next-Generation Sequencing in Pediatric Central Nervous System Infection: Clinical Experience and Diagnostic Stewardship Strategies.}, journal = {Open forum infectious diseases}, volume = {13}, number = {2}, pages = {ofag054}, pmid = {41743993}, issn = {2328-8957}, abstract = {BACKGROUND: Identification of the microorganisms causing infection in children with central nervous system infection is important. Conventional cerebrospinal fluid (CSF) tests may provide limited pathogen detection. CSF metagenomic next-generation sequencing (mNGS) may provide broader pathogen detection in a single assay.
METHODS: Results of CSF mNGS testing performed at Mayo Clinic on patients and nonpatients between January 2024 and June 2025 were retrospectively analyzed. The subcohort of children treated at Mayo Clinic was analyzed to assess test performance as compared with conventional CSF diagnostics and potential clinical impact.
RESULTS: In total 134 patients (138 CSF mNGS tests) from 22 US states and 2 international sites were included. Overall positivity was 16% with viruses representing most (59%) detections. In the Mayo Clinic subcohort (n = 15), test positivity was 27%: organisms included single detections of Streptococcus mitis group and HIV type 1, as well as 2 detections of Epstein-Barr virus, all confirmed by conventional tests. Positive results were associated with CSF pleocytosis (P = .026). Higher yield was observed in participants whose care was overseen by pediatric infectious diseases (PID) specialists (P = .026) and when a specimen hold strategy was applied (P = .033). Most results (87%) did not alter antimicrobial therapy, with 2 negative results contributing to antimicrobial de-escalation.
CONCLUSIONS: CSF mNGS demonstrated higher diagnostic yield in patients whose specimens showed CSF pleocytosis and in those who had PID consultation. Diagnostic stewardship strategies were applied, including specimen hold approaches and PID consultation.}, }
@article {pmid41744501, year = {2026}, author = {Whitham, JM and Goller, CC}, title = {Improving knowledge of metagenome-assembled genomes (MAGs) through bioinformatics and article annotation.}, journal = {Journal of microbiology & biology education}, volume = {}, number = {}, pages = {e0022625}, doi = {10.1128/jmbe.00226-25}, pmid = {41744501}, issn = {1935-7877}, support = {R25 GM130528/GM/NIGMS NIH HHS/United States ; }, abstract = {DNA from microbial communities can be sequenced and assembled to gain insight into the microbes that may be present in unique environments. Powerful computational tools, combined with more accessible sequencing technologies, have enabled metagenome-assembled genome (MAG) analysis in course-based settings. However, the computational methods and assumptions surrounding the creation of MAGs, as well as their application in understanding microbes in biomes, are often complex and intimidating to new users. The metagenomics course we designed enrolls undergraduate and graduate students in a half-semester lab experience. We hypothesized that collaborative annotation of specific bioinformatics research articles, paired with student application of tools using guided case studies on the powerful KBase bioinformatics web platform, would enhance learning of key MAG concepts. Student learning outcomes on conceptual quizzes, as well as learner perceptions of the assignment and confidence in using KBase and other bioinformatics tools, were analyzed. Assessments and surveys of student perceptions were collected over several semesters using consistent assignments, readings, and KBase narratives. Learning gains were identified for specific MAG analysis concepts and data interpretation. Nevertheless, misconceptions continue, and confidence in bioinformatics approaches varies. Additional exploration of qualitative data may suggest concepts to reinforce and resources to support learners. Combining KBase, collaborative annotation of primary literature, guided case studies, and aligned assessments effectively promotes students' conceptual and mechanistic understanding of MAGs and the assumptions underlying their creation and use.}, }
@article {pmid41744504, year = {2026}, author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T}, title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0137325}, pmid = {41744504}, issn = {2379-5077}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Metabolomics/methods ; Metagenomics/methods ; *Intestine, Small/microbiology ; Bacteria/classification/genetics/metabolism ; Male ; Female ; *Ileum/microbiology ; }, abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.
IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.}, }
@article {pmid41745076, year = {2026}, author = {Murmu, M and Singh, R and Gaikwad, R and Banodkar, A and Barage, S and Sudhakara, P and Santhosh Kumar, AW}, title = {Comparative Analysis of Oral Microbiome in Indian Type 2 Diabetes Mellitus (T2DM) and Periodontitis Cohorts.}, journal = {Diseases (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {41745076}, issn = {2079-9721}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) and periodontitis are highly prevalent immune-inflammatory diseases that interact bidirectionally. However, how early-onset T2DM, periodontitis, and adverse lifestyle behaviors collectively remodel the gingival plaque microbiome at the ecological network level remains poorly understood in Indian populations.
METHODS: A cross-sectional 16S rRNA gene (V3-V4) sequencing study was conducted on supragingival and subgingival plaque from 60 adults (30-40 years) recruited in Mumbai. Participants were categorized as healthy (H, n = 10), periodontitis (P, n = 10), T2DM (n = 20), and T2DM with periodontitis (T2DM_P, n = 20). Comprehensive demographic, anthropometric, metabolic, periodontal, dietary, lifestyle, and oral hygiene data were collected. Sequence data were processed using QIIME2-DADA2, followed by diversity, differential abundance, and genus-level co-occurrence network analyses (Spearman |r| ≥ 0.6, FDR < 0.05; core prevalence ≥ 70%).
RESULTS: α-diversity showed no marked depletion across groups, whereas Bray-Curtis β-diversity revealed significant global separation, with maximal dissimilarity between H and T2DM_P. Healthy individuals with favorable lifestyle behaviors harbored scaffold-forming taxa such as Corynebacterium matruchotii, Lautropia mirabilis, and Capnocytophaga spp. In contrast, P and T2DM_P groups showed enrichment of proteolytic, inflammation-adapted genera including Porphyromonas, Tannerella, Treponema, Fretibacterium, Peptostreptococcus, and Selenomonas. Network analysis revealed a shift from commensal-rich modular networks to densely connected, keystone-centered disease modules.
CONCLUSION: Early-onset T2DM and periodontitis, particularly under adverse lifestyle behaviors, reorganize plaque microbial composition and interaction architecture rather than depleting diversity, highlighting plaque-based keystone taxa and networks as targets for microbiome-informed risk stratification and integrated medical-dental-lifestyle interventions.}, }
@article {pmid41745125, year = {2026}, author = {Gori Savellini, G and Alessandri, G and Beligni, G and Badano, D and Fanciulli, PP and Frati, F and Cusi, MG}, title = {Metagenomic sequencing discloses the virome composition of mosquitoes and sandflies from Central-Southern Tuscany, Italy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0186725}, doi = {10.1128/spectrum.01867-25}, pmid = {41745125}, issn = {2165-0497}, abstract = {Mosquitoes and sandfly species are well-known vectors of viral pathogens of public health concern. However, the diversity and ecology of viruses within mosquitoes, including those responsible for clinical and sub-clinical infections in humans, remain poorly understood. In this study, we investigated the presence of phleboviruses and flaviviruses in Aedes albopictus and Culex pipiens mosquitoes, as well as Phlebotominae species, collected from the Siena and Grosseto districts (Tuscany, Italy) during the 2022-2024 summer season. Furthermore, A. albopictus and C. pipiens larvae were reared under laboratory conditions, and adults were collected for further virological analysis. Molecular investigations (reverse-transcription polymerase chain reaction [RT-PCR]) detected phleboviruses and/or flaviviruses in several batches of both field-collected and laboratory-reared flies. Notably, the highest incidence and co-circulation of both viral genera were observed in samples from the 2024 season. Furthermore, metagenomic analysis was performed on only 42 out of 67 RT-PCR-positive pools of mosquitoes and sandflies. This approach aimed to identify wild-type or recombinant viruses and assess the virome of autochthonous arthropods, contributing to knowledge on viral ecology in southern Tuscany and potential threats to humans. The resulting data revealed a wide viral community shared among mosquitoes, spanning over 30 taxonomic virus families, albeit no potential human pathogen virus was identified. Furthermore, our findings confirmed the mosquito specificity of certain endogenous arthropod viruses and provided evidence of their potential transovarial transmission in some cases. The present study provides a comprehensive analysis of the mosquitoes and sandflies virome, contributing to viral surveillance efforts and underscoring the need for enhanced monitoring of arthropod-borne pathogens.IMPORTANCEIn this study, we analyzed the co-circulating phleboviruses and flaviviruses, providing foundational data on the diversity, composition, and transmission of insect-specific and vector-borne viruses in Central-Southern Tuscany, an area increasingly exposed to arbovirus threats due to climate change and globalization. This is the first comprehensive metagenomic study to characterize the virome of Aedes albopictus, Culex pipiens, and Phlebotomine spp. in this region. Furthermore, we identified for the first time Punique virus (PUNV) in Italy, a phlebovirus with potential (though not yet confirmed) human pathogenicity.}, }
@article {pmid41745296, year = {2026}, author = {Wang, Y and Insuk, C and Olson, C and Xu, J}, title = {Metagenomic and Genomic Analyses Reveal Prevalent Spread and Evolution of the Bat White-Nose Pathogen Pseudogymnoascus destructans in Western Canada.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745296}, issn = {2309-608X}, support = {2000803492//Environment and Climate Change Canada/ ; }, abstract = {Bats play a crucial role in the ecosystem. However, North American bat populations have experienced a dramatic decline since 2006 due to white-nose syndrome, a disease caused by Pseudogymnoascus destructans (Pd). This fungus can invade and damage the skin on bat wings and muzzles during hibernation. Since 2021, Pd has been reported at selected sites in western Canada, the region with the highest bat diversity in Canada, eliciting urgent calls for action among diverse stakeholders. Here we analyze nine metagenomes of bat guanos and wing swabs and the genomes of five Pd strains from western Canada to investigate the distribution and diversity of Pd in this region. Pd was found in all nine metagenomic samples and the metagenome sequences enabled us to identify the associated bat species. Divergence time estimates of Pd based on whole-genome sequences suggest that Pd likely entered Alberta two to five years before its first official report. Furthermore, we found evidence of abundant gene copy number variations in this species. Together, our metagenomic and genomic analyses indicate that Pd is more prevalent than currently recognized and is evolving and diversifying. Continued surveillance with more comprehensive methods is needed to accurately track its spread and facilitate timely management of white-nose syndrome in North America.}, }
@article {pmid41745484, year = {2026}, author = {Serna-García, R and Lanzoni, Y and García-Depraect, O and Muñoz, R and Cantera, S}, title = {Harnessing Biogas into High-Value Chemicals: The Role of Algal-Methanotrophic Co-Cultures.}, journal = {Marine drugs}, volume = {24}, number = {2}, pages = {}, pmid = {41745484}, issn = {1660-3397}, support = {CIAPOS/2022/70//Generalitat Valenciana, Conselleria de Educación, Universidades y Empleo/ ; PID2022-139110OA-I00//Spanish Ministry of Science and Innovation/ ; UIC393, UIC 379//Regional Government of Castilla y León/ ; }, abstract = {The conversion of biogas into high-value chemicals for pharmaceutical, cosmetic, and nutraceutical markets offers an attractive alternative to conventional fossil-based production routes, enabling circular value chains with significant socio-economic impact. This study evaluated the valorization of biogas into osmolyte and carotenoid compounds with market prices ranging from 1000 to 7000 $·kg[-1]. Specifically, an algal-methanotrophic co-culture operated under saline conditions, preventing external microbial contamination and stimulating osmolytes and carotenoids, was assessed for its capacity to simultaneously remove methane (CH4) and carbon dioxide (CO2), with efficiencies of 92 and 89%, respectively. while producing ectoine, hydroxyectoine, lutein, β-carotene, and astaxanthin. Shotgun metagenomic analyses identified the key microorganisms driving the process, predominantly alkaliphilic and halophilic green algae (Chlorella, Dunaliella) and cyanobacteria (Leptolyngbya), and halotolerant methanotrophs (Methylotuvimicrobium) and methylotrophs (Methylophaga). Metagenomics further revealed the presence of key metabolisms related to C1 utilization and biosynthetic genes associated with carotenoid and osmolyte production, confirming the metabolic potential of the consortium to convert biogas-derived carbon directly into high-value compounds. Overall, these results demonstrate the feasibility of an efficient, biologically driven bio-platform capable of transforming greenhouse gas-rich waste streams into economically relevant bioactive molecules, contributing to global priorities in sustainable biomass-to-biochemical innovation.}, }
@article {pmid41745624, year = {2026}, author = {Liu, Y and Diao, M and Hao, Y and Liu, Z and Ma, H and Zou, Y and Ma, L and Wang, L and Zhi, W and Yu, Q}, title = {Acute High-Intensity Noise Exposure Induces Cognitive Impairment and Arachidonic Acid Metabolism-Related Molecular Alterations in Rats: A Multi-Omics Study.}, journal = {Metabolites}, volume = {16}, number = {2}, pages = {}, pmid = {41745624}, issn = {2218-1989}, abstract = {Background: Acute high-intensity noise exposure represents a critical environmental stressor; however, its impact on brain function and the underlying mechanisms remain incompletely understood. This study aimed to investigate the effects of acute high-intensity noise exposure on cognitive function in rats, utilizing multi-omics analysis to explore potential mechanisms. Methods: Rats were exposed to acute noise at 120 dB, and brain function was evaluated using the novel object recognition (NOR) test, recordings of electroencephalographic activity, and histopathological examination. Longitudinal serum metabolomics and fecal metagenomics were performed on samples collected at 0 h, 7, 14, and 28 days post-exposure. Quantitative profiling of oxylipins and proteomics were conducted at a critical time point, followed by integrative multi-omics network analysis. Results: Acute high-intensity noise exposure significantly reduced the recognition index in the NOR test, increased theta-band power, and induced hippocampal neuronal damage. Multi-omics analyses revealed time-dependent alterations in gut microbiota and metabolic profiles, identifying day 7 as the critical response window, with arachidonic acid (AA)-derived metabolites consistently downregulated across omics layers. Integrated analysis revealed a coordinated microbiota-oxylipins-proteins network, highlighting key AA-derived oxylipins (e.g., 8-HETE, 12-HETE) that correlated with specific gut microbiota and proteins involved in lipid metabolism and inflammation. Conclusions: Acute high-intensity noise exposure induces cognitive impairment and systemic molecular disturbances. AA-centered lipid metabolism acts as a key hub linking gut microbiota dysbiosis with inflammatory and metabolic protein alterations, providing multi-omics evidence for coordinated microbiota-lipid-protein dysregulation underlying noise-induced neurobiological dysfunction.}, }
@article {pmid41745919, year = {2026}, author = {Elmagzoub, WA and Weidmann, M and Elnaiem, MHE and Dennig, A and Waller, U and Bernhard, A and Junhold, J and Abd El Wahed, A and Truyen, U and Ceruti, A}, title = {Microbiome as a Tool to Monitor Aquarium Systems.}, journal = {Veterinary sciences}, volume = {13}, number = {2}, pages = {}, pmid = {41745919}, issn = {2306-7381}, abstract = {The bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses to external influences. Over one year (October 2021-October 2022), water and swab samples were collected from one seawater tank and six filtration systems at regular intervals. Bacterial cultivation included total bacterial counts. Metagenomic analysis was performed on samples corresponding to environmental events using Oxford Nanopore sequencing. Taxonomical analysis at the phylum and genus levels used EPI2ME software. Diversity analyses and statistical tests were performed using R. Total bacterial counts increased steadily after inoculation and stabilized by the end of the collection period. Diversity analysis revealed significant differences within and between freshwater and saltwater tanks. Each aquarium exhibited a distinct bacterial community with frequent compositional changes. Despite environmental conditions and maintenance interventions and resulting disturbances that affected the microbiome, the overall nitrifying capacity remained unaffected. Nitrifying taxa emerged as potential indicators for environmental effects. Combined with investigations of ecological function, next-generation sequencing could facilitate the development of aquarium management protocols, ultimately improving fish welfare.}, }
@article {pmid41746166, year = {2026}, author = {Joshi, B and Zulk, JJ and Serchejian, C and Hameed, ZA and Larson, AB and Terwilliger, AL and Kumar, D and Mysorekar, IU and Britton, RA and Maresso, AW and Patras, KA}, title = {Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0054325}, doi = {10.1128/iai.00543-25}, pmid = {41746166}, issn = {1098-5522}, abstract = {Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs, including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, ΦHP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage demonstrated replication and lytic activity in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage-resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed the interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal ΦHP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed in uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable prevention strategy for UTI.}, }
@article {pmid41746975, year = {2026}, author = {Wang, G and Liu, L and Zhang, H and Mao, P and Lu, S and Zhang, X and Li, X and Song, C}, title = {Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0343817}, pmid = {41746975}, issn = {1932-6203}, mesh = {Humans ; *Tacrolimus/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Liver Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Immunosuppressive Agents/therapeutic use/pharmacology ; Adult ; Feces/microbiology ; Aged ; Dysbiosis ; Transplant Recipients ; Tandem Mass Spectrometry ; Metabolome/drug effects ; }, abstract = {BACKGROUND: Liver transplantation (LT) is an effective treatment for patients with end-stage liver disease. In recent years, more and more evidence has supported the association between gut microbiota dysbiosis and the pathogenesis and progression of liver diseases.
METHODS: The study included 36 patients who received tacrolimus treatment after liver transplantation. Patients were stratified into subgroups according to three key variables: tacrolimus treatment duration, whole-blood tacrolimus concentration, and tacrolimus concentration-to-dose (C/D) ratio. Fecal samples and whole-blood specimens were collected from all participants. The Illumina HiSeq X platform was used to detect the gut metagenome, analyzing the composition and characteristics of the gut microbiota. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology was employed to detect metabolites of the gut microbiota, revealing their metabolic profiles.
RESULTS: As the duration of tacrolimus use increased, the diversity of the gut microbiota also increased, and the abundance of Escherichia coli_D and Bacteroides stercoris rose. Additionally, the abundance of Brunovirus and Uetakevirus tended to decrease. The abundance of gene functions related to chemical carcinogenesis and bacterial invasion of epithelial cells significantly decreased. In the gut microbiota metabolites, 16 substances like Astragaloside A and Acetyl-L-carnitine significantly increased, while 108 substances like Capsaicin and TLK significantly decreased. Within a certain range, as the concentration of tacrolimus in whole blood increased, the diversity of the gut microbiota increased. The abundance of Phocaeicola and Klebsiella increased, and the abundance of Peduovirus among viruses also rose. However, excessively high concentrations may lead to a decrease in the diversity of the gut microbiota and a decrease in the abundance of Phocaeicola. With respect to the C/D ratio, increased ratios were linked to significantly higher levels of 57 fecal metabolites (e.g., PC 34:2, 5-Methyl-2'-deoxycytidine), whereas 13 metabolites (e.g., FAHFA 2:0/16:0) showed substantial declines.
CONCLUSIONS: Tacrolimus treatment is associated with distinct alterations in gut microbiota and metabolites among LT recipients. These findings provide a preliminary framework for future investigations aimed at optimizing immunosuppressive regimens, although their clinical translational potential requires validation in larger-scale, prospective cohort studies.}, }
@article {pmid41747414, year = {2026}, author = {Zhang, Q and Bao, C and Wang, K and Liu, L and Huang, H and Cai, S and Lu, H and Zheng, S and Luo, J and Kong, J}, title = {The impact of bronchiectasis on the lung microbiota of community-acquired pneumonia patients: An mNGS-based study.}, journal = {Computational biology and chemistry}, volume = {123}, number = {}, pages = {108948}, doi = {10.1016/j.compbiolchem.2026.108948}, pmid = {41747414}, issn = {1476-928X}, abstract = {BACKGROUND: Changes in lung microbiota are associated with bronchiectasis and its clinical parameters. However, it is unclear whether distinct microbiota patterns reflect the characteristic lung status in bronchiectasis.
OBJECTIVE: This study aimed to identify key microbiota associated with community-acquired pneumonia (CAP) complicated with bronchiectasis and explore its relationship with clinical features.
METHODS: A single-center retrospective study enrolled 59 CAP patients who underwent bronchoscopy. Bronchoalveolar lavage samples were analyzed using metagenomic next-generation sequencing. The top 10 bacterial species and α- and β-diversity indices were compared between patients with and without bronchiectasis. Linear discriminant analysis was used to identify distinctive microbes. Spearman was used to analyze the correlation between the distinctive microbes and clinical characteristics.
RESULTS: The CAP with bronchiectasis group was dominated by Pseudomonas, while Prevotella dominated the non-bronchiectasis group. The bronchiectasis group had significantly lower α-diversity and distinct β-diversity compared to the non-bronchiectasis group. Stutzerimonas was identified as a key microbe in the bronchiectasis group, positively correlated with lymphocyte percentage and count, and negatively correlated with neutrophil percentage. Pseudomonas aeruginosa and Nocardia pneumoniae were key species in the bronchiectasis group.
CONCLUSION: The composition and diversity of lung microbiota in patients with CAP combined with bronchiectasis are significantly different. The genus Stutzerimonas can serve as a key marker to distinguish bronchiectasis from non-bronchiectasis patients to reflect the characteristic lung microbiota status. This study provides a potential basis for disease stratification and personalized management.}, }
@article {pmid41747516, year = {2026}, author = {Hu, X and Yu, K and Chai, B and Tang, Q and Gao, X and Wang, J and Yan, Z and Li, Y and Zhang, L and Wang, C and Lei, X and Chen, B and He, L}, title = {Polyethylene microplastics specifically drive the dissemination of ARGs: Mechanisms involving microbial community restructuring and horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181587}, doi = {10.1016/j.scitotenv.2026.181587}, pmid = {41747516}, issn = {1879-1026}, mesh = {*Microplastics/toxicity ; *Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity/analysis ; *Polyethylene ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Lakes/microbiology ; }, abstract = {As emerging contaminants, the impact of microplastics (MPs) on antibiotic resistance genes (ARGs), virulence factors (VFs), and host microbial communities in lakes remains unclear. To address this, we conducted a 28-day incubation experiment using water from Yiquan Lake, employing metagenomic sequencing to investigate the effects of different types of microplastics-polyethylene (PE), polystyrene (PS), polypropylene (PP), and a mixture (Mix), each at a concentration of 1 item/L-compared to a raw water control (RAW). Results showed significant enrichment of Proteobacteria and Bacteroidetes in PE and Mix groups. Genera such as Agrobacterium and Microbacterium increased in PE and PS groups, serving as major hosts of ARGs and VFs. Network analysis revealed positive correlations between Agrobacterium, Escherichia, and ARGs, suggesting horizontal gene transfer may facilitate the spread of resistance and virulence. Two-factor PS formed highly connected yet competitive networks, whereas Mix constructed modular and stable networks. Single-factor PE enhanced microbial connectivity but reduced ARGs connectivity, while Mix increased the modularity of both microbes and ARGs. PE elevated the abundance of ARGs, VFs, and mobile genetic elements, with multidrug resistance and efflux pumps as dominant mechanisms. Additionally, PE downregulated quorum sensing transporter genes while upregulating regulatory factors, significantly promoting RND efflux systems (AcrAB-TolC) to maintain resistome homeostasis. This study highlights the distinct environmental effects of different MPs, underscoring the need to prioritize PE-related risks in aquatic ecosystems. Improved management of plastic waste in and around lakes is recommended to mitigate MP-mediated ARG dissemination and preserve freshwater ecosystem services.}, }
@article {pmid41747669, year = {2026}, author = {Lin, C and Li, J and Zhao, A and Jiang, Y and Chen, F and Chen, L and Xu, J and Zhang, W and Huang, M and Ma, D and Xu, Q and Wang, C}, title = {Effect of electric field on lactic acid and ethanol production from food waste anaerobic fermentation.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {170}, number = {}, pages = {109248}, doi = {10.1016/j.bioelechem.2026.109248}, pmid = {41747669}, issn = {1878-562X}, mesh = {*Ethanol/metabolism ; *Fermentation ; *Lactic Acid/biosynthesis/metabolism ; Anaerobiosis ; *Electricity ; Temperature ; *Waste Products ; *Food ; Food Loss and Waste ; }, abstract = {Electro-fermentation (EF) enhances product yields from food waste (FW). This study investigated the coupled effects of temperature (40 or 55 °C) and electric field (0.2-1.4 V) on ethanol and lactic acid production via anaerobic fermentation (AF). Results showed that a 1.4 V field at 40 °C (G23) boosted ethanol yield by 37.1%, while a 0.2 V field at 55 °C (G3) increased lactic acid yield by 60.3%. Notably, 0.2 V at 40 °C (G14) simultaneously enhanced both products. EF accelerated hydrolysis of polysaccharides and proteins, and modulated microbial communities, enriching key functional genera (Bacillus at 55 °C; Lactobacillus/Weissella at 40 °C). Metagenomic analysis revealed upregulated genes for ethanol dehydrogenase, lactate dehydrogenase, and NADH dehydrogenase under respective optimal conditions. This work demonstrates that tailored EF conditions can steer metabolic pathways, offering an efficient strategy for dual-bioproduct recovery from FW.}, }
@article {pmid41747681, year = {2026}, author = {Chen, Z and Wang, X and Xu, Y and Chen, S}, title = {Molecular mechanisms underlying the mitigation of nitrous oxide emissions by hyperthermophilic composting fertilizer.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129067}, doi = {10.1016/j.jenvman.2026.129067}, pmid = {41747681}, issn = {1095-8630}, mesh = {*Nitrous Oxide ; *Fertilizers ; *Composting ; Soil/chemistry ; Soil Microbiology ; Bacteria ; Greenhouse Gases ; }, abstract = {Nitrous oxide (N2O) emissions associated with fertilized agricultural soils are a major source of greenhouse gases. While hyperthermophilic composting reduces N2O emissions, how its products affect the niche distribution of nitrogen (N) cycling microorganisms and regulate N2O source-sink mechanisms remains unclear, limiting its application in soil ecosystems and further technology development. To address this, we established a pot-based experiment with different organic fertilizer treatments: no fertilization (NF), hyperthermophilic composting fertilization (HTCF), and thermophilic composting fertilization (TCF). Using gas chromatography combined with metagenomic sequencing and binning approaches, we investigated the effects of HTCF on soil N2O emissions and the associated microbial mechanisms. The results showed that organic fertilization significantly altered soil properties, influencing bacterial community succession and N2O emissions. Compared to TCF (9.57 g), HTCF (14 g) increased pakchoi biomass by 47.02%. Meanwhile, HTCF (2835 mg m[-2]) reduced N2O emissions by 47.15% compared to TCF (5364 mg m[-2]). HTCF decreased the abundance of N2O-producing genes, including norB and nirK, thereby contributing to lower N2O emissions. HTCF altered microbial community structure, resulting in a greater relative abundance of obligate N2O-reducing bacteria carrying the nosZ gene, which could contribute to reduced N2O emissions. HTCF significantly enriched microorganisms such as Nostoc, Rhizobium, Mesorhizobium, and Piscinibacter, maintaining a stable soil environment and promoting the smooth progress of N fixation and nitrification. These findings elucidate microbial mechanisms underlying HTCF-induced N2O mitigation and provide a scientific basis for integrated fertilization strategies to reduce greenhouse gas emissions.}, }
@article {pmid41747689, year = {2026}, author = {Zhang, F and Zhou, T and Feng, Y and Chen, Y and Zhao, Q and Han, Q and Liu, J and Zhang, D and Jiang, H and Zhang, H}, title = {Metagenomic insights into the impacts of Vulcanococcus proliferation on microbial communities in a coastal bay.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107939}, doi = {10.1016/j.marenvres.2026.107939}, pmid = {41747689}, issn = {1879-0291}, mesh = {Metagenomics ; Seawater/microbiology ; Bays/microbiology ; *Metagenome ; *Microbiota ; *Enterococcaceae/genetics/physiology ; }, abstract = {Cyanobacterial blooms pose a major ecological challenge globally, with their outbreaks exerting profound effects on aquatic ecosystems. Vulcanococcus, a recently described cyanobacterial genus previously thought to be restricted to freshwater habitats, was documented in this study proliferation in seawater for the first time. Here, we reconstructed prokaryotic metagenome-assembled genomes (MAGs), including Vulcanococcus and the associated bacteria, enabling the assessment of their metabolic potential and influence of proliferation of Vulcanococcus on marine ecosystems. The proliferation of Vulcanococcus significantly altered the prokaryotic community compositions in the water, leading to a marked decline in the stability of prokaryotic co-occurrence networks. Comparative genomic analysis revealed that Vulcanococcus MAGs clustered within the freshwater Vulcanococcus clade, suggesting a possible freshwater origin. The high-quality Vulcanococcus MAG possess a complete set of urea transporter genes as well as urease genes, highlighting its potential for efficient urea utilization. The genome of Vulcanococcus encodes critical genes involved in vitamin B1 biosynthesis and is capable for de novo vitamin B12 synthesis, implying that proliferation of Vulcanococcus may serve as an important source of B vitamins for phytoplankton. Furthermore, Vulcanococcus exhibited significant correlations with eukaryotic phytoplankton, including diatoms and dinoflagellates, suggesting that Vulcanococcus may enhance B-vitamin availability for phytoplankton. Overall, these findings provide novel insights into the ecological roles and metabolic versatility of Vulcanococcus in marine environments, underscoring its potential impact on microbial community dynamics and nutrient cycling.}, }
@article {pmid41747700, year = {2026}, author = {Zhang, H and Du, Y and Guan, E and Xu, X and Zhang, P and Gao, L}, title = {Microbial mechanisms of protein degradation and nicotine removal during aerobic composting of tobacco waste as the sole nitrogen source.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141461}, doi = {10.1016/j.jhazmat.2026.141461}, pmid = {41747700}, issn = {1873-3336}, mesh = {*Composting ; *Nicotiana/metabolism ; *Nicotine/metabolism ; *Nitrogen/metabolism ; Plant Leaves/metabolism ; Biodegradation, Environmental ; Aerobiosis ; Cattle ; Animals ; Microbiota ; Fermentation ; *Plant Proteins/metabolism ; Manure ; Peptide Hydrolases/metabolism ; Bacteria/metabolism ; }, abstract = {The massive accumulation of tobacco waste poses threats to environment safety and human health due to its high nicotine content. While aerobic composting represents an effective strategy for managing waste biomass, its application to fresh discarded tobacco leaves remains unreported. This study pioneered the use of tobacco leaves in aerobic composting and investigated the microbial mechanisms driving substrate transformation. Waste tobacco leaves are rich in protein and can be used as the sole nitrogen source of composting. The microbiota was characterized by a higher abundance of Bacillota and Pseudomonadota, but a lower abundance of Actinomycetota, compared with that during cattle manure composting as a control. The degradation of proteins in tobacco leaves was primarily mediated by proteases (e.g., families S8, S9, M42) secreted by Bacillota. Notably, a greater abundance of S8 family proteases was induced, of which two exhibiting larger substrate cavity volumes. Nicotine content decreased rapidly during initial fermentation, achieving a removal rate exceeding 97 % and meeting European Union safety standards. This degradation was primarily driven by the pyrrolidine pathway via Stutzerimonas stutzeri and Pseudomonas sp. Seed germination and pot experiments demonstrated the superior growth promoting effects of fermented tobacco leaves over cattle manure product. These findings elucidate the microbial mechanisms of tobacco waste fermentation and provide a theoretical basis for screening efficient nicotine-degrading strains and developing value-added fermentation products.}, }
@article {pmid41747725, year = {2026}, author = {Chen, K and Liu, Y and Rong, J and Dai, N and Xu, C and Li, H and Zhong, L and Wang, B and Ji, Z and Xie, S and Xu, Y and Yang, F and Wang, J and Li, D and Gu, Y and Zhou, X and Li, Y and Chen, M and Chen, Y and Li, W and Tang, Z and Cai, J and Xu, J and Xia, S and Zhan, Q and Zhou, Z}, title = {Strain-level genetic heterogeneity and colonization dynamics drive microbiome therapeutic efficacy.}, journal = {Cell host & microbe}, volume = {34}, number = {3}, pages = {393-405.e5}, doi = {10.1016/j.chom.2026.02.002}, pmid = {41747725}, issn = {1934-6069}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Genetic Heterogeneity ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology ; *Lung Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Metagenome ; Female ; Bacteria/classification/genetics ; Male ; Phylogeny ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise, yet its efficacy in non-small-cell lung cancer (NSCLC) remains unclear. We demonstrate that FMT improves anti-PD-1 efficacy and progression-free survival in a single-arm trial of advanced PD-L1-negative NSCLC. Analyzing over 2,000 metagenomes from diverse disease cohorts and healthy controls via a high-resolution strain-tracking framework, we reveal that phylogenetically distinct strains within identical species exert opposing therapeutic effects, resolving prior inconsistencies. We identify conserved ecological principles where engraftment relies on species-intrinsic metabolic and immune evasion traits. Crucially, successful colonization by specific beneficial strain variants correlates with positive clinical outcomes. Finally, we identify 38 priority species with robust engraftment potential and significant heterogeneity as candidates for precision therapeutics. These findings establish a strain-function-efficacy paradigm, elucidating the mechanistic basis of variable outcomes and guiding next-generation microbiome drug development.}, }
@article {pmid41747730, year = {2026}, author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C}, title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.01.021}, pmid = {41747730}, issn = {1097-4172}, abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.}, }
@article {pmid41747902, year = {2026}, author = {Corso, D and Melita, M and Massaccesi, N and Quero, GM and Basili, M and Di Cesare, A and Sabatino, R and Sbaffi, T and Fazi, S and Rakaj, A and Luna, GM and Amalfitano, S}, title = {Constructed wetlands for aquaculture wastewater treatment: Insights on the structural and functional shifts of the aquatic microbial community.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134278}, doi = {10.1016/j.biortech.2026.134278}, pmid = {41747902}, issn = {1873-2976}, mesh = {*Wetlands ; *Aquaculture ; *Wastewater/microbiology ; *Water Purification/methods ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens, such as members of the genera Francisella and Campylobacter, and acted as a buffer system in ARG dissemination, with sediments serving as reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.}, }
@article {pmid41747903, year = {2026}, author = {Li, LX and Yang, TT and Yuan, Y and Han, YL and Zhao, Q and Wang, WH and Sun, Y and Cao, XX and Jiang, XL and Li, T and Wang, X}, title = {Rapid enrichment of ternary carbon-fixing microbial consortia from anaerobic sludge via pressurized pre-autotrophic strategy for scalable microbial electrosynthesis.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134276}, doi = {10.1016/j.biortech.2026.134276}, pmid = {41747903}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Microbial Consortia/physiology ; Anaerobiosis ; Acetates/metabolism ; *Autotrophic Processes ; *Carbon Cycle ; *Bioelectric Energy Sources/microbiology ; Pressure ; Electrodes ; Carbon/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {As a promising platform for microbially catalyzed carbon capture, microbial electrosynthesis (MES) is constrained by inoculation strategies that limit carbon fixation efficiency and scalability. Mixed-culture inocula outperform pure cultures in functional redundancy and ecological resilience in large systems, but slow acclimation and erratic community composition yield inconsistent performance. Here, this study presents a pressurized pre-autotrophic (PA) strategy that rapidly enriches carbon-fixing microorganisms (CFMs) from anaerobic sludge, in comparison with direct autotrophic (DA) and electrode reversal (ER) strategies. PA increased CFM abundance to 51%, 3.5-fold higher than in DA-MES and ER-MES (both 15%). Acetate production in PA-MES reached 14.47 g·m[-2]·d[-1]. In addition to enhanced acetate productivity, PA-MES exhibited superior electrochemical performance, achieving the highest Faradaic efficiency for acetate and energy efficiency among the tested systems, together with the lowest energy consumption per unit acetate. Metagenomic analysis revealed a PA-defined core community with coordinated activation of the Wood-Ljungdahl, rTCA, and methanogenic pathways, providing redundant routes for stable CO2 fixation. By transforming mixed-culture inocula into a functionally cohesive carbon-fixing community, the PA strategy enables rapid startup and sustained carbon fixation, offering a practical framework for scalable MES.}, }
@article {pmid41747907, year = {2026}, author = {Wang, Z and Hong, Y}, title = {Atmospheric and room-temperature plasma mutagenesis of microalgae for efficient swine wastewater treatment and bioresource recovery.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134287}, doi = {10.1016/j.biortech.2026.134287}, pmid = {41747907}, issn = {1873-2976}, mesh = {*Wastewater/chemistry/microbiology ; Animals ; *Microalgae/genetics/metabolism ; *Mutagenesis ; Swine ; Nitrogen/isolation & purification ; *Water Purification/methods ; *Temperature ; *Chlorella/genetics/metabolism ; Phosphorus ; *Plasma Gases/pharmacology ; }, abstract = {In response to the serious harm of swine wastewater (SW) and the drawbacks of existing treatment technologies, this study innovatively applies atmospheric and room-temperature plasma (ARTP) mutagenesis, followed by a four-round screening process strategy (solid actual SW (ASW) medium, growth in liquid ASW, comprehensive performance in the sterilized ASW (S-ASW), final evaluation in the unsterilized ASW (US-ASW)) to cultivate high-performance mutant microalgae for the efficient treatment of ASW without complex and expensive pretreatment or other strengthening methods. Chlorella sorokiniana HWY30-4 was eventually selected for its good adaptability and ASW treatment performance. The removal efficiencies of Chlorella sorokiniana HWY30-4 to total nitrogen (TN), NH4[+]-N, and total phosphorus (TP) for US-ASW were 60.31%, 80.07%, and 94.12%, respectively. In addition, HWY30-4 accumulated abundant high-value substances (0.06 g/L polysaccharides, 0.13 g/L proteins, and 0.23 g/L lipids) while treating US-ASW. Metagenomics revealed that the performance enhancement mechanisms mainly involve the enhanced critical metabolic pathways, alongside beneficial microbial synergies. This study offers an efficient and viable route for simultaneous ASW treatment and bioresource recovery, underscoring the potential of ARTP-based strain improvement in strengthening the microalgal performance for environmental governance.}, }
@article {pmid41748019, year = {2026}, author = {Piccinno, G and Asnicar, F}, title = {Advanced computational analysis in metagenomic studies to support precision medicine.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.02.018}, pmid = {41748019}, issn = {1469-0691}, abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a nondiseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.
OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.
SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.
CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multicohort data analysis, integration, and validation methods.
IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.}, }
@article {pmid41748043, year = {2026}, author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG}, title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.}, journal = {Experimental gerontology}, volume = {216}, number = {}, pages = {113079}, doi = {10.1016/j.exger.2026.113079}, pmid = {41748043}, issn = {1873-6815}, mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Middle Aged ; Male ; *Bed Rest/adverse effects ; Female ; *Frailty/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Feces/microbiology ; Aging/physiology ; RNA, Ribosomal, 16S/genetics ; Exercise ; }, abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.}, }
@article {pmid41748159, year = {2026}, author = {Liu, W and Lu, Y and Ng, SC and Chan, FK and Sung, JJ and Yu, J}, title = {Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337280}, pmid = {41748159}, issn = {1468-3288}, abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to autism spectrum disorder (ASD) in children. However, the role of bacterial genomic structural variations (SVs) in ASD remains largely unexplored.
OBJECTIVE: We aimed to identify bacterial SVs associated with ASD and explore their mechanistic role and clinical application.
DESIGN: We collected faecal metagenomes from 452 children (261 ASD, 191 neurotypical) across an in-house and seven public datasets. Using linear mixed-effects modelling, we identified ASD-associated SVs and compositional shifts and validated candidate SVs in humanised gut microbiome mice.
RESULTS: We identified 100 bacterial SVs significantly associated with ASD (p<0.05). These SVs were enriched in genes involved in critical biological processes, including ion and amino acid metabolism and bacterial growth regulation in ASD. In particular, we found important SVs in Bacteroides uniformis related to thiamine and iron metabolism. Moreover, SVs in Ruminococcus torques were associated with the MazF (endoribonuclease toxin) and MazE (antitoxin) system, a key regulator of pathobiont proliferation. Validation in humanised mouse models confirmed significant correlations between these SV signatures and ASD-like behaviours, such as reduced social interaction and increased repetitive behaviours. Both phylogeographically conserved and regionally restricted SVs showed strong associations with ASD. A diagnostic model combining nine SVs and three bacterial species achieved an area under the receiver operating characteristic curve of 81.1%, outperforming models based solely on variable SVs (79.1%), deletion SVs (75.2%) or bacterial species abundance alone (72.3%).
CONCLUSION: Our findings suggest the significant role of bacterial genomic SVs in ASD and highlight their potential as diagnostic biomarkers.}, }
@article {pmid41748627, year = {2026}, author = {Huang, Z and Petersen, JM}, title = {Recovery of metagenome-assembled genomes from Spartina alterniflora root microbiome in Fujian Province, China.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06914-z}, pmid = {41748627}, issn = {2052-4463}, support = {2025J01967//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, abstract = {The saltmarsh cordgrass Spartina alterniflora proliferates along the coast of China. Like all plants, S. alterniflora hosts a specific microbiome that plays crucial roles in sustaining plant growth and health. Till now, very few studies have investigated the root microbiome of S. alterniflora in China, where it is considered an invasive pest. Here, ~350 Gbp metagenomes of S. alterniflora were generated from 8 sampling sites in South Fujian Province, China. 798 bacterial metagenome-assembled genomes (MAGs) and 7 archaeal MAGs were obtained, which were de-replicated into 205 and 3 representative genomes at a 95% ANI cutoff. The recovered bacterial MAGs mainly belonged to Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Campylobacterota. Sedimenticolaceae were prevalent at all sampling sites, accounting for 4-30% of the corresponding MAGs. These genomic datasets provide a new resource for investigating S. alterniflora root microbiomes, particularly valuable considering current efforts to eradicate this species in China.}, }
@article {pmid41749104, year = {2026}, author = {Baz, L}, title = {Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12700-3}, pmid = {41749104}, issn = {1471-2164}, }
@article {pmid41749291, year = {2026}, author = {Haro-Moreno, JM and Díaz-Arinero, E and Aldeguer-Riquelme, B and Rubio-Portillo, E}, title = {Effects of marine heatwaves on the dynamics of marine coastal microbial communities.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00861-3}, pmid = {41749291}, issn = {2524-6372}, support = {CIGE/2022/21//Generalitat Valenciana/ ; }, abstract = {BACKGROUND: Climate change is projected to intensify and prolong marine heatwaves, characterized by abnormally high sea surface temperatures. These events can profoundly alter ecosystem composition and functioning, sometimes triggering mass mortality events. The Mediterranean Sea, due to its semi-enclosed nature, is particularly susceptible to warming, with future climate scenarios predicting a temperature increase of up to 3.8 °C and at least one persistent heatwave annually by 2100. Despite this vulnerability, the effects of marine heatwaves on seawater microbial and viral communities remain poorly understood.
RESULTS: Using microcosm experiments, we examined microbial and viral dynamics under control conditions (20 °C) and two simulated marine heatwaves (MHWs) (23 °C and 25 °C). By the end of the experiment, microbial assemblages in all three conditions were dominated by metagenome-assembled genomes (MAGs) that were not detected in the initial natural sample, indicating the competitive success of rare biosphere taxa over initially abundant species. Virulence factors and antibiotic resistance genes increased in relative abundance throughout the incubation, but such increase was amplified under warming conditions. Temperature also shaped viral strategies, with heatwaves showing a higher percentage of integrated lysogenic viruses compared to control samples. This trend was consistent with observations from natural samples, where lysogenic viruses peaked during warmer months.
CONCLUSIONS: The shift toward lysogeny observed under elevated temperatures may enhance horizontal gene transfer, accelerating the spread of virulence and antibiotic resistance genes. In fact, we observed an increased abundance of these genes in samples under heat stress. These processes could weaken ecosystem resilience, disrupt microbial-driven biogeochemical cycles, and amplify risks to marine and human health. Our study underscores the need to integrate microbial and viral responses into predictions of ocean functioning in a rapidly warming world.}, }
@article {pmid41749685, year = {2026}, author = {Zhu, Y and Tang, Y and Qi, X and Zhu, X}, title = {Transformer Models, Graph Networks, and Generative AI in Gut Microbiome Research: A Narrative Review.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {41749685}, issn = {2306-5354}, support = {Grant No. LCMYZHYX-KFKT202303//Open Project of the Sichuan Provincial Key Laboratory for Clinical Immunology and Translational Medicine/ ; Grant No. 2022JC03//Scientific Research Foundation of Chengdu Women's and Children's Central Hospital/ ; }, abstract = {BACKGROUND: The rapid advancement in artificial intelligence (AI) has fundamentally reshaped gut microbiome research by enabling high-resolution analysis of complex, high-dimensional microbial communities and their functional interactions with the human host.
OBJECTIVE: This narrative review aims to synthesize recent methodological advances in AI-driven gut microbiome research and to evaluate their translational relevance for therapeutic optimization, personalized nutrition, and precision medicine.
METHODS: A narrative literature review was conducted using PubMed, Google Scholar, Web of Science, and IEEE Xplore, focusing on peer-reviewed studies published between approximately 2015 and early 2025. Representative articles were selected based on relevance to AI methodologies applied to gut microbiome analysis, including machine learning, deep learning, transformer-based models, graph neural networks, generative AI, and multi-omics integration frameworks. Additional seminal studies were identified through manual screening of reference lists.
RESULTS: The reviewed literature demonstrates that AI enables robust identification of diagnostic microbial signatures, prediction of individual responses to microbiome-targeted therapies, and design of personalized nutritional and pharmacological interventions using in silico simulations and digital twin models. AI-driven multi-omics integration-encompassing metagenomics, metatranscriptomics, metabolomics, proteomics, and clinical data-has improved functional interpretation of host-microbiome interactions and enhanced predictive performance across diverse disease contexts. For example, AI-guided personalized nutrition models have achieved AUC exceeding 0.8 for predicting postprandial glycemic responses, while community-scale metabolic modeling frameworks have accurately forecast individualized short-chain fatty acid production.
CONCLUSIONS: Despite substantial progress, key challenges remain, including data heterogeneity, limited model interpretability, population bias, and barriers to clinical deployment. Future research should prioritize standardized data pipelines, explainable and privacy-preserving AI frameworks, and broader population representation. Collectively, these advances position AI as a cornerstone technology for translating gut microbiome data into actionable insights for diagnostics, therapeutics, and precision nutrition.}, }
@article {pmid41750438, year = {2026}, author = {Suzhaeva, L and Egorova, S and Polev, D and Saitova, A and Starkova, D}, title = {Fluoroquinolone Resistance Patterns in Multidrug-Resistant Escherichia coli from the Gut Microbiota of Young Children.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41750438}, issn = {2079-6382}, abstract = {Background/Objectives: The high prevalence of fluoroquinolone-resistant E. coli in healthy children represents a significant public-health risk, facilitating the spread of antimicrobial resistance and increasing the potential for difficult-to-treat extraintestinal infections with severe clinical outcomes. This study aimed to investigate the prevalence of fluoroquinolone resistance in multidrug-resistant E. coli isolated from presumptively healthy children in St. Petersburg, Russia, with a particular focus on fluoroquinolone resistance determinants. Methods: Phenotypic AST was performed on 307 E. coli isolates from fecal pediatric samples, comprising 230 isolates from 2012 to 2013 and 77 isolates from 2021 to 2022. A subset (n = 47) of MDR isolates underwent whole-genome sequencing. Results: The frequency of MDR E. coli strains rose significantly from 15.7% to 32.5% over the study period. The most significant increases in resistance among E. coli strains were to third-generation cephalosporins (CTX, CTZ) and fluoroquinolones (CIP), rising fourfold over a decade. Based on phenotypic resistance profiles of MDR E. coli to quinolones, the highest resistance rates were observed for MFX (80.9%) followed by NAL (74.5%), LVX (44.7%) and CIP (40.4%). Genotypic analysis revealed distinct pathways: low-level NAL resistance required only an S83 mutation in gyrA, whereas low-level MFX resistance was predominantly conferred by a plasmid-borne qnr gene. In contrast, resistance to CIP and LVX involved at least three QRDR mutations: S83L and D87N/Y in gyrA, and S80I in parC. Notably, our study showed the predominance of the ST131 and ST38 clones in E. coli isolated from pediatric samples. Conclusions: Our findings suggest that the efficacy of moxifloxacin for empirical treatment of infections caused by MDR E. coli might be severely compromised. Overall, the current study highlights that the pediatric gut microbiota serves as a reservoir for resistant E. coli with the expansion of multidrug-resistant clones independently of direct antibiotic selection pressure.}, }
@article {pmid41750446, year = {2026}, author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A}, title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41750446}, issn = {2079-6382}, support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.}, }
@article {pmid41750451, year = {2026}, author = {Agga, GE and Loughrin, J}, title = {Evaluation of Anaerobic Digestion Amended with Micro-Aeration and/or Sound Treatment on the Resistome and Virulence Factor Gene Profiles in Poultry Litter.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41750451}, issn = {2079-6382}, support = {5040-12630-007-000-D//U.S. Department of Agriculture, Agricultural Research Service/ ; }, abstract = {Background: Commercial broiler farms produce a large amount of litter that must be removed. Anaerobic digestion (AD) is animal manure management technology with the added benefit of producing reusable energy. Our team previously showed that the micro-aeration and sound treatment of animal manure during AD increase biogas production. However, their influence on antimicrobial resistance genes (ARGs) and bacterial virulence factor genes (VFGs) is unknown. Therefore, the objective of this study was to evaluate the effect of AD on the resistome and VFGs in poultry litter (PL) and see if the effect is modified by micro-aeration and/or sound treatments. Methods: A field experiment was conducted in four anaerobic digesters that consisted of a control (a standard AD system with no air or sound), micro-aeration, sound, and combined micro-aeration and sound treatments. Overall, 21 samples were collected and analyzed with shotgun metagenomic sequencing. The samples included digestate samples (n = 12) from the four digesters obtained at 6 (baseline, i.e., before beginning of micro-aeration and sound treatments), 23 and 42 weeks, raw PL samples (n = 4), two disks comprised of the same wood as the bedding material, an initial digestate seed sample, and two initial week 0 mix samples. Results: Across all sequence reads (n = 3190) obtained from 21 samples, over 80% of the resistome was composed of four antimicrobial classes: macrolides-lincosamides-streptogramins, tetracyclines, aminoglycosides, and glycopeptides. While the total number of ARGs declined in the control digestor, it increased over time in micro-aerated or sound-treated digesters, and their combination greatly increased the number of ARGs detected. This is a new finding, and it clearly shows that micro-aeration, sound, and their combination treatment during the anaerobic digestion of PL enriches ARGs. In contrast, sound-treated AD by itself significantly (p = 0.035) reduced the mean total ARG abundance compared to the control. The number and abundance of ARGs detected in the initial digestate and PL were lower than those in the AD samples, indicating their enrichment during the AD process. On the other hand, although the AD samples had a lower frequency and abundance of VFGs than the PL, AD did not completely remove the VFGs, and their detection frequency increased over time. While micro-aeration increased the abundance of VFGs compared to the control, this effect was countered by its combination with sound treatment, offering a good animal manure treatment strategy to reduce bacterial VFGs. Conclusions: Although additional research may be required, it was shown that while sound treatment may enrich the occurrence of ARGs, it seems promising to reduce the abundance of ARGs and VFGs during the AD of PL. On the other hand, micro-aeration, alone or when combined with sound treatment, increases the abundance of both ARGs and VFGs. Moreover, the study showed that AD, with or without micro-aeration and sound treatment, is not effective for the complete removal of ARGs and VFGs from poultry litter. Rather, AD systems may act as a hotspot for ARGs, and post-AD treatments such as composting need to be evaluated.}, }
@article {pmid41750879, year = {2026}, author = {Samantaray, P and Saha, S}, title = {Decoding the Microbial Diversity of Indian Fermented Foods: Integrating Ethnobiology, Multi-Omics and Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, pmid = {41750879}, issn = {2304-8158}, support = {SRMAP/URG/SEED/2023-24/049//SRM University Andhra Pradesh/ ; }, abstract = {India's diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms-primarily lactic acid bacteria, yeasts, and molds-contribute functional properties that extend beyond food transformation to confer health benefits, including probiotic potential and metabolic regulation. This review integrates classical microbiological studies with modern molecular approaches such as metagenomics, metatranscriptomics, and metabolomics to elucidate the microbial diversity of Indian fermented foods. It highlights how geography, substrates, and ethnic traditions shape region-specific microbial consortia sustained through long-standing ethno-microbiological practices. Special focus is given to the glycemic modulation achieved through microbial fermentation, wherein organic acid production and resistant starch formation lower glycemic index and improve glucose metabolism. These processes, along with enhanced nutrient bioavailability, vitamin synthesis, and immunomodulation, illustrate the broader functional potential of fermentation. The review also examines interactions between food-borne microbes and the human gut microbiota, underscoring implications for personalized nutrition. Finally, it discusses modernization and commercialization strategies and outlines future directions involving multi-omics integration, indigenous starter cultures, and microbiome-based innovations to harness India's microbial heritage for improved health and sustainable food development.}, }
@article {pmid41751034, year = {2026}, author = {Wang, J and Cheng, M and Huang, F and Chen, L and Xu, W and Cai, J and Chen, Z and Zhao, Y and Zhang, X}, title = {Metagenomic-Metabolomic Integration Reveals Gut Microbiota Dynamics and Metabolic Changes in Super-Geriatric Captive Giant Pandas.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751034}, issn = {2076-2615}, support = {2025ZNSFSC0252//the Science and Technology Project of Sichuan Province/ ; }, abstract = {Age-related changes throughout the lifespan are known to influence gut microbiota composition, microbial functional potential, and host-associated metabolic processes. Understanding these age-related variations is important for elucidating their potential physiological implications at different life stages. However, information regarding the gut microbiome and metabolomic characteristics of super-geriatric captive giant pandas (Ailuropoda melanoleuca) remains limited. In this study, fecal samples were collected from adult and super-geriatric captive giant pandas and analyzed using metagenomic sequencing combined with untargeted metabolomics. The gut microbiota of super-geriatric individuals exhibited a marked decrease in Bacillota and an enrichment of Pseudomonadota compared with adult individuals. Functional profiling revealed age-associated shifts in microbial metabolic potential, with a transition from biosynthesis-dominated pathways toward pathways related to substrate degradation and energy utilization. Metabolomic analyses further revealed pronounced metabolic alterations in super-geriatric giant pandas, including elevated levels of unsaturated fatty acids and changes in bile acid-related metabolites. Alterations in gut microbiota composition, particularly the relative enrichment of Pseudomonadota-associated taxa, were associated with inflammation-related metabolic features. Collectively, these findings indicate coordinated changes in gut microbial composition and metabolic profiles during aging. Overall, this study characterizes age-associated alterations in gut microbiota structure and fecal metabolic signatures in super-geriatric captive giant pandas, providing a scientific basis for future studies on microbiota-metabolism interactions and for improving nutritional management and health monitoring strategies in aged individuals of this endangered species.}, }
@article {pmid41751100, year = {2026}, author = {Yang, L and Xu, Z and Liu, D}, title = {The Effects of Dual-Yeast Compound Preparation on the Intestinal Health and Metabolism of Lambs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751100}, issn = {2076-2615}, support = {NDYB2022-5//Inner Mongolia Agricultural University High-level/excellent Doctoral Talent Introduction Research Project/ ; BR230118//University Basic Scientific Research Business Expenses Project-Young Teachers Research Ability Enhancement Fund Project, 2023 Financial Funds/ ; 2025MS03114//Natural Science Foundation of Inner Mongolia Autonomous Region Project/ ; SYKJZD202302//Discipline Project of College of Veterinary Medicine, Inner Mongolia Agricultural University/ ; }, abstract = {Microecological preparations exert beneficial effects on the health of young ruminant animals; however, the mechanism is unclear. As a result, the present study analyzed the effects of yeast cultures on the growth properties, microbiome, and metabolism of weaned lambs. In this study, a total of 20 weaned lambs were randomly, stochastically divided into four teams: the control group (Group A) were fed a basic diet; Group B were fed with Saccharomyces cerevisiae BC strain culture (30 g/head/d); Group C were fed with Kluyveromyces marquez XR4 strain culture (30 g/head/d); Group D were fed with a composite culture of the two yeast strains (30 g/head/d). The study lasted for 40 days, with daily records of lamb feed intake and weight. Lamb feces were collected regularly for metagenomic sequencing and metabolomics analysis. The average daily weight gain and average daily yield of Group D lambs were significantly higher than those of Group A lambs (p < 0.01). The feed utilization rate in the yeast-fed groups was considerably higher than in the control group (p < 0.05), indicating that the addition of yeast crops to lamb feed might improve lamb feed performance. Bacteroides and the mTOR signaling pathway were dramatically enriched in the intestines of weaned lambs in the yeast-culture-fed groups, and their expression levels of ketones and benzoic acid compounds were significantly upregulated. These results indicated that yeast culture had excellent effects on weaned lambs in regulating immunological functioning and the intestinal environment, protecting the enteric mucosal barrier, improving digestion and nutritional absorption, and enhancing antioxidant function. In summary, adding yeast culture to weaned lamb feed can generate a positive effect on its productivity performance and gut health. These findings provide novel insights into promoting the health of young ruminants.}, }
@article {pmid41751138, year = {2026}, author = {Xu, Z and Liang, M and Li, J and Song, B and Zhang, M and Jiang, H and Chai, J and Zhao, J and Deng, F and Li, Y}, title = {16S rRNA Gene and Metagenomic Analysis Revealed an Association Between Cecal Microbiota and Pork Umami.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751138}, issn = {2076-2615}, support = {2023YFE0124400//National Key Research and Development Program of China/ ; 2023B10564001//Specific University Discipline Construction Project/ ; No. 32202715//National Natural Science Foundation of China/ ; }, abstract = {Umami is a key determinant of pork flavor, but the association between the intestinal microbial community and umami differences remains unclear. Here, we used the taste-sensing electronic tongue system to divide the Duroc × Landrace × Yorkshire pigs into high, medium and low groups. We combined 16S rRNA gene and shotgun metagenomic sequencing to study the differences in the microbial community composition and functional genes. The results showed that the microorganisms in the cecum of different groups had a similar core microbial community. The Shannon diversity analysis showed that there were no significant differences among the different groups. The Bray-Curtis distance indicated that there were differences in the bacterial communities between the high umami group and the other two groups. The LEfSe analysis and Spearman correlation analysis revealed that the uncultured species CAG-632 sp900539185 maintained a high abundance in the high umami group and was significantly correlated with umami. Metagenomic functional analysis revealed distinct functional signatures among umami groups, with enrichment of genes related to carbohydrate transport and metabolism, butanoate and other short-chain fatty acid pathways, nitrogen utilisation, cell-surface structures, adhesion and RNA metabolism in high umami groups. These research findings indicate that the differences in the delicious flavor of pork are more likely to be associated with specific microbial species and the functional characteristics of the cecal microbial community, rather than the overall situation of the entire microbial community.}, }
@article {pmid41751141, year = {2026}, author = {Xue, F and Zhang, F and Zhuang, Q and Jiang, L and Sun, M and Shang, J and Xiong, B}, title = {Metagenomic Insights into the Modulatory Effects of Thiamine Supplementation for Treating Subclinical Ketosis Dairy Cows.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751141}, issn = {2076-2615}, support = {20242BAB20311//Natural Science Foundation Project of Jiangxi Province/ ; 2024YFD1300600//Integrated Demonstration of Intelligent Feeding and Environmental Control Technologies for Cattle and Sheep/ ; }, abstract = {(1) Background: The objective of this study was to investigate the modulatory effects of thiamine on BHBA metabolism, milk yield, and the rumen microbial ecosystem. (2) Methods: A total of 24 SCK dairy cows with similar body conditions were selected and randomly allocated to SCK (SCK) or SCK with thiamine supplement (SCKT) treatment. Twelve healthy dairy cows served as the control (CON) treatment. Milk yield, milk quality, ruminal fermentability parameters, rumen and fecal microbial communities were further measured. (3) Results: Thiamine significantly decreased BHBA content, milk CFUs, and somatic cells, while significantly increasing milk yield, milk fat, acetate, and the A/P ratio (p < 0.05). Thiamine-treated cows exhibited significantly increased ruminal and fecal Proteobacteria but significantly decreased ruminal Firmicutes (p < 0.05) as well as fecal Spirochaetes and Cyanobacteria (p < 0.05), compared with SCK cows. Functional analysis showed that differential rumen bacteria exhibited high energy metabolism, nucleotide metabolism, and glycan biosynthesis and metabolism, while the metabolism of terpenoids and polyketides were the primary functional pathways of differential fecal microbiota. (4) Conclusions: Thiamine supplementation in SCK cows effectively alleviated subclinical ketosis by reducing BHBA content, enhancing ruminal fermentability, and proliferating rumen microbial communities, leading to improved milk yield in the early-lactation period.}, }
@article {pmid41752202, year = {2026}, author = {Jung, S}, title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, pmid = {41752202}, issn = {1422-0067}, support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; }, mesh = {*Colorectal Neoplasms/epidemiology/genetics/microbiology ; Humans ; *Fusobacterium nucleatum/genetics ; *Polyketides/metabolism ; *Peptides/metabolism ; *Gastrointestinal Microbiome ; Mutation ; *Bacteriocins/metabolism/genetics ; *Microbiota ; }, abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.}, }
@article {pmid41752220, year = {2026}, author = {Kareem, HA and Khan, MF}, title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, pmid = {41752220}, issn = {1422-0067}, support = {82930-NP//University College Dublin Internal Fund/ ; }, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Soil Pollutants/metabolism ; *Fluorocarbons/metabolism ; Soil Microbiology ; *Environmental Restoration and Remediation/methods ; }, abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.}, }
@article {pmid41752933, year = {2026}, author = {Mahbub, MH and Hase, R and Yamaguchi, N and Asai, Y and Harada, M and Ichimura, N and Hayakawa, Y and Inohana, Y and Umakoshi, Y and Yamaguchi, R and Kimura, R and Tsujimura, H and Matsumoto, M and Higashijima, F and Yoshimoto, T and Kimura, K and Hirano, T and Ohishi, K and Doi, K and Matsunaga, K and Tanabe, T}, title = {Gut Microbial Diversity and Community Structure Are Largely Similar Between Apparently Healthy Elderly Japanese Males and Females: A Shotgun Metagenomic Study.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, pmid = {41752933}, issn = {2075-1729}, support = {21K10397//This research was supported by a joint project funded by Yamaguchi Prefecture, Yamaguchi City, Shimadzu Corporation, Kao Corporation, and Kyodo Milk Industry Co., Ltd. It was also supported by a Grant-in-Aid for Scientific Research from the Japan Society/ ; }, abstract = {Sex differences in gut microbiota may affect health and aging, but evidence in elderly populations is limited and inconsistent. This study examined sex-specific similarities and differences in gut microbiota diversity and composition among apparently healthy elderly Japanese individuals using shotgun metagenomic sequencing. A cross-sectional study was conducted in 100 community-dwelling adults aged 75-83 years (54 males, 46 females). Fecal samples underwent metagenomic sequencing. Alpha and beta diversity were assessed across six taxonomic levels, and taxonomic differences were evaluated using non-parametric tests. No significant sex differences were observed in alpha diversity indices (Shannon, Simpson, evenness, Chao1) at any taxonomic level. Beta diversity based on Bray-Curtis dissimilarity and PCoA also showed no sex-specific clustering. However, certain taxa differed in relative abundance. Males showed higher abundances of Bacteroidota (phylum), Bacteroidia and Betaproteobacteria (class), and Bacteroidales and Burkholderiales (order) (p < 0.05). No significant differences were detected at the family, genus, or species levels. Overall, gut microbial diversity and community structure were largely similar between elderly males and females, with only modest sex-associated differences at higher taxonomic levels. These findings suggest that biological sex may have a limited influence on gut microbiota composition in advanced age and provide population-level reference data for future longitudinal and interventional studies in elderly cohorts.}, }
@article {pmid41753552, year = {2026}, author = {Shulga, EY and Islamov, BR and Sukhanov, AY and Frolov, M and Laikov, AV and Trachtmann, NV and Validov, SZ}, title = {Biotechnological Potential and Metabolic Diversity of Lignin-Degrading Bacteria from Decaying Tilia cordata Wood.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753552}, issn = {2076-2607}, support = {FMEG-2025-0028//The government assignment for the FRC Kazan Scientific Center of RAS/ ; }, abstract = {Lignin is a complex aromatic polymer that constitutes a major fraction of plant biomass and represents a valuable renewable carbon resource. Naturally decaying wood serves as an environmental reservoir of microorganisms capable of degrading lignin. In this study, we isolated and characterized sixteen bacterial strains from decaying Tilia cordata wood using an enrichment culture technique with lignin as the sole carbon source. Taxonomic identification via 16S rRNA gene sequencing revealed microbial diversity spanning the genera Bacillus, Pseudomonas, Stenotrophomonas, and several members of the Enterobacteriaceae family, including Raoultella terrigena isolates. Metagenomic sequencing of the wood substrate revealed an exceptionally rich and balanced bacterial community (Shannon index H' = 5.07), dominated by Streptomyces, Bradyrhizobium, Bacillus, and Pseudomonas, likely reflecting a specialized consortium adapted to lignin rich late-stage decay. Functional phenotyping demonstrated that all isolates possess ligninolytic potential, evidenced by peroxidase/laccase-type activity through methylene blue decolorization. Dynamic Light Scattering (DLS) and HPLC analyses showed that some isolates, such as Raoultella terrigena MGMM806, effectively depolymerized lignosulfonate into low molecular weight fragments (1.23 nm), while others accumulated intermediate metabolites or completely mineralized the substrate. Growth profiling on monolignol substrates revealed a broad spectrum of catabolic specialization in lignin monomer degradation. The results demonstrate a complex system of metabolic partitioning within a natural bacterial consortium. This collection represents a foundational genetic resource for developing engineered biocatalysts and synthetic microbial communities aimed at the efficient conversion of lignin into valuable aromatic compounds.}, }
@article {pmid41753592, year = {2026}, author = {Özdemir, K}, title = {Characterization of a Boron-Tolerant Nocardia niigatensis Isolated from Boron-Rich Soils: Physiological, Enzymatic, and Genomic Insights.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753592}, issn = {2076-2607}, support = {BAP-19-1003-003//Bandırma Onyedi Eylül University Scientific Research Projects Coordination Unit (BAP)/ ; }, abstract = {In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27-37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations.}, }
@article {pmid41753628, year = {2026}, author = {Meinen-Jochum, J and Satheesh, V and Masonbrink, RE and Rodriguez-Gallegos, J and Wright, DA and Severin, AJ and Mellata, M}, title = {Sequencing and Analysis of Chicken Segmented Filamentous Bacteria Genome Revealed Unique Avian-Specific Features.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753628}, issn = {2076-2607}, support = {20236701539078//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; }, abstract = {Segmented filamentous bacteria (SFB) are host-specific, immune-modulating microorganisms that colonize the small intestine of various vertebrate species, playing a crucial role in stimulating immune maturation during early life. Previous research on the genomes of SFB from humans, rats, and mice has revealed significant differences among SFB strains associated with various hosts, suggesting that their evolution is closely linked to their relationships with specific hosts. However, the genome of SFB from chickens has not been extensively investigated. In this study, we present the metagenomic reconstruction of an SFB genome derived from the ileum of layer Lohmann Select Leghorn (LSL) chickens. We utilized Hi-C sequencing techniques to assemble the LSL-SFB and annotate the avian SFB from both turkeys and chickens. Our reference-guided consensus assembly, followed by Hi-C scaffolding, produced a high-quality genome for LSL-SFB. Our pangenomic analysis revealed substantial conservation of core gene clusters among mammalian SFB strains, but we also identified a distinct repertoire of genes in chicken and turkey SFB. Furthermore, metabolic network analysis indicated a reduced capacity for biosynthesis, signifying an increased reliance on the host, as shown by the absence of key biosynthetic and utilization pathways. We also discovered a unique flagellin subunit (fliC-2) in chicken SFB from different genetic lines and confirmed its interaction with the chicken flagellin receptor, Toll-like receptor five. This study provides the first high-quality genome and annotation of LSL-SFB, alongside that of turkeys, offering valuable insights into the mechanisms of host specificity and adaptation. Understanding the interactions between host-specific SFB and their hosts, as well as their role in promoting immune maturation, is essential for improving intestinal health.}, }
@article {pmid41753632, year = {2026}, author = {Wang, M and Tian, W and Liu, Z and Yan, D and Li, Y and Cao, A and Wang, Q and Fang, W}, title = {Differential Selection Effects of Continuous AITC Fumigation on Soil Microbial Communities and Functions and Identification of Tolerant Strains.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753632}, issn = {2076-2607}, support = {2024YFD1701900//The National Key R&D Program of China/ ; 32572893//The National Natural Science Foundation of China/ ; CAAS-CSAL-202401//The Innovation Project of the Chinese Academy of Agricultural Sciences/ ; }, abstract = {Allyl isothiocyanate (AITC) is effective as a bio-based fumigant in controlling soil-borne diseases; however, the selective pressure it exerts on soil microecology and evolutionary dynamics remains inadequately characterized. This study systematically investigated the remodeling effects of continuous AITC fumigation on soil microbial communities, functional genes, and functional strains by integrating metagenomic analysis and pure culture techniques. Results demonstrate that AITC drives directional selection from "sensitive" to "tolerant" microorganisms. Fungal communities exhibit greater cumulative damage than bacterial communities, with the proportion of significantly suppressed fungi increasing linearly from 9.3% at baseline to 35.7%. At the genus level, sensitive groups were predominantly enriched in pathogen-associated genera, e.g., Pseudomonas and Xanthomonas, whereas tolerant groups, represented by Bacillus and Streptomyces, maintained ecological dominance under continuous stress. Functionally, AITC induced differential evolution of functional gene repertoires. Nitrogen cycle genes (e.g., amoC) exhibited high negative sensitivity, with significant downregulation by 20%, whereas the TCA core module in the carbon cycle exhibited strong robustness. Virulence assays confirmed EC50 values for tolerant beneficial bacteria (Bacillus spp.) (>40 mg·L[-1]) were significantly higher than those for pathogens (1.3-7.9 mg/L). This study established a microbial "sensitive-tolerant" response framework under AITC stress, revealing the core potential of endogenous tolerant strains for the precise ecological restoration of fumigated soils.}, }
@article {pmid41753645, year = {2026}, author = {Liu, M and Zhao, L and Li, T and Li, X and Jiang, H and Yang, P}, title = {Deciphering the Arterial and Venous Blood Bacterial DNA Profile: Pioneering Insights into Coronary Heart Disease Etiology and Progression.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753645}, issn = {2076-2607}, support = {2023YFC3503702//National Key Research and Development Program of China/ ; No. ZRJY2023-QM11//Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; }, abstract = {BACKGROUND: Coronary heart disease (CHD) is the leading cause of death and disability worldwide. The human microbiota, particularly gut bacteria, plays a role in the development of CHD. However, determining the contribution of gut bacteria translocation to systemic circulation in the progression of atherosclerosis remains challenging.
METHODS AND RESULTS: In this exploratory study, we conducted 16S rRNA-based metagenomic analysis to characterize systemic bacterial profiles in a cohort of 27 patients with CHD (9 with severe coronary artery stenosis and 18 with mild to moderate stenosis). We compared microbial diversity between arterial and venous blood and across different blood fractions. For the first time, we observed higher microbial diversity in plasma than in serum. We also identified differences in microbial richness among arterial whole blood, venous whole blood, arterial plasma, venous plasma, arterial serum, and venous serum, with 15, 22, 43, 10, 4, and 3 genera showing significant differences, respectively. Many of the detected blood taxa belonged to genera typically found in intestinal, oral, or skin microbiota, although their precise source cannot be determined from this study.
CONCLUSIONS: Our study provides preliminary evidence of distinct bacterial profiles between arterial and venous blood fractions in patients with CHD, as determined by 16S rRNA sequencing. These findings should be interpreted with caution given the small sample size and the absence of a healthy control group, and they warrant confirmation in larger, controlled studies.}, }
@article {pmid41753646, year = {2026}, author = {Bosco, G and Vaccalluzzo, A and Russo, N and Pino, A and Caggia, C and Randazzo, CL}, title = {Effect of By-Products from Pistachio Skin on Gastrointestinal Microbiota of Healthy Lambs as Sustainable Feeding Ingredient.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753646}, issn = {2076-2607}, support = {Piano Nazionale Di Ripresa E Resilienza (PNRR) - Missione 4 Componente 2, Investimento 1.4 - D.D. 1032 17/06/2022, CN00000022//European Union Next-GenerationEU/ ; }, abstract = {Pistachio skin is a by-product that is considered a promising novel feed ingredient for ruminants; however, its role in shaping the lamb gastrointestinal tract microbiota is poorly studied. The present study aimed to investigate, through a metagenomics approach, the effects of integrating pistachio skin into the diet on the faecal and ruminal microbiota of healthy lambs. Faecal samples, collected at the beginning (d0) and 58 days after the start of the dietary treatment (d58), and ruminal samples, collected after slaughter, were subjected to Illumina MiSeq analysis of the 16S rRNA gene. The results revealed that, although temporal variations were observed, the supplementation of pistachio skin did not markedly affect the overall faecal microbiota structure. Conversely, specific rumen taxa were selectively modulated by the experimental diet. In conclusion, the use of pistachio skin as a feed ingredient can be considered a suitable and sustainable dietary strategy that modulates specific rumen microbial groups, thereby preserving the stability of the gut microbiota in lambs.}, }
@article {pmid41753649, year = {2026}, author = {Feng, Y and Liu, S and Ke, H and Li, H and Zhao, H and Dang, X and Mou, C and Zhou, J and Huang, Z and Deng, Y and Li, Q}, title = {A Pseudotumorous Syndrome Associated with an As-Yet-Unidentified Eukaryotic Parasite Causing Functional Gonadal Arrest in Largefin Longbarbel Catfish (Hemibagrus macropterus).}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753649}, issn = {2076-2607}, support = {2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; }, abstract = {This study presents the first documented case of a disease syndrome in cultured largefin longbarbel catfish (Hemibagrus macropterus). The condition is characterized by massive abdominal pseudotumor formation, severe cachexia, and functional gonadal arrest. Comprehensive pathological investigation revealed that the pseudotumor was encapsulated by fibroblasts and primarily composed of host-derived, poorly differentiated hyperplastic cells, interspersed with invasive, basophilic Type III cells. These cells and associated inflammatory-fibrotic lesions were also disseminated in the gill, kidney and spleen. Systematic diagnostic approaches, including microbiology and transmission electron microscopy, found no evidence of conventional bacterial or viral pathogens. Metagenomic analysis further supported these findings and suggested a link to infection by an as-yet-unidentified eukaryotic parasite, with Microsporidia or Ichthyosporea being the primary candidates. Functional (KEGG) profiling of the pseudotumor tissue further revealed a molecular signature consistent with active cellular proliferation and metabolism. We propose that the pseudotumor acts as a metabolically active "nutrient sink," driving the systemic catabolism that underlies the severe cachexia and reproductive arrest. This work provides the first case of a eukaryotic parasite-induced pseudotumorous syndrome in fish, which represents an emerging threat to conservation aquaculture and offering novel insights into parasite-mediated host metabolic hijacking and tumor-mimicry.}, }
@article {pmid41753674, year = {2026}, author = {Ece, G and Aktaş, A and Koyuncu Özyurt, Ö and Demirbakan, H and Alışkan, HE and Sağlık, İ and Zorbozan, O and Çetin Duran, A and Uğur, AR and Öcal, D and Uzunoğlu, E and Kaya, E and Mutlu Sarıgüzel, F and Bayındır, F and Yetkin, G and Altındiş, M and Yenice Aktaş, S and Kula Atik, T}, title = {Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753674}, issn = {2076-2607}, abstract = {The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.}, }
@article {pmid41753703, year = {2026}, author = {Zhang, L and Xu, L and Zhang, Z and Liu, Z and Chen, Y}, title = {The Remediation Mechanism of Soil Atrazine Contamination by Vermicompost: A Metagenomic Perspective.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753703}, issn = {2076-2607}, support = {XDA28110201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {Atrazine persistence poses serious environmental threats. This study used metagenomics and qPCR to elucidate the remediation mechanism of vermicompost in atrazine degradation pathways. Seven treatments were established: unsterilized soil (CKn); sterilized soil amended with 45 (SsV1), 60 (SsV2), and 75 (SsV3) days of vermicompost; and unsterilized soil with the same vermicompost (SnV1, SnV2 and SnV3). Vermicompost significantly restructured soil microbial communities. SsV1 exhibited the highest Proteobacteria abundance (51.38%), while SsV3 markedly increased Bacteroidetes abundance (10.34%). Functional annotation revealed that vermicompost enriched carbohydrate metabolism-related COG units and upregulated CAZymes (e.g., CE1 and CE10 families), providing energy support for degrading microbial communities. Regarding metabolic pathways, SnV2 exhibited the highest atrazine degradation abundance (2.94%), significantly enriching Bauldia (4.84 RPKM) for dechlorination. During cyanuric acid ring-opening, SnV3 significantly enriched Pseudorhodoplanes (12.14 RPKM). During terminal mineralization, SsV2 increased Caenimonas abundance (15.25 RPKM) and introduced the exogenous genus Pseudorhodoplanes (7.78 RPKM). qPCR confirmed SnV2's trzN (day 20) and atzB (day 40) reached 9.03 × 10[4] and 6.95 × 10[7] copies/g, respectively. These findings indicate vermicompost accelerated atrazine mineralization by enriching degradative microbial communities and promoting key functional gene expression, with 60-day vermicompost demonstrating superior performance. This study provides a robust theoretical framework for remediating atrazine-contaminated soil by vermicompost.}, }
@article {pmid41753722, year = {2026}, author = {Ayilaran, E and Kilonzo-Nthenge, A}, title = {Metagenomic Insights into Antimicrobial Resistance in Small-Scale Poultry and Cattle Farms.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753722}, issn = {2076-2607}, support = {2018-68006-28103//National Institute of Food and Agriculture/ ; Grant No. 2018-68006-28103//United States Department of Agriculture/ ; }, abstract = {Antimicrobial resistance (AMR) poses a critical challenge to global health, with food animal production systems recognized as significant reservoirs of antimicrobial-resistant bacteria. This study evaluated the prevalence and distribution of antimicrobial resistance genes (ARGs) and virulence factors (VFs) across small-scale poultry and cattle farms. A total of 468 samples (soil, feces, water, and natural land soil) were collected from four farms and analyzed using shotgun metagenomics. Proteobacteria (34.91%) were the dominant phylum across environments, followed by Cyanobacteria (15.67%), Actinobacteria (14.95%), Firmicutes (10.57%), and Bacteroidetes (8.69%). Tetracycline (33.41%) and beta-lactam (30.30%) resistance genes were the most abundant, with macrolide (9.32%) and aminoglycoside (8.39%) resistance also detected. Both tetracycline and beta-lactam resistance genes were significantly enriched across sample types (p < 0.05). The detection of diverse VFs alongside ARGs highlights the pathogenic potential of bacterial communities in these production systems. Collectively, the findings reveal that small-scale animal farms are reservoirs of AMR with implications for public health through foodborne transmission. Targeted surveillance and control measures are necessary to prevent the dissemination of ARGs into the broader food chain and to safeguard both human and animal health.}, }
@article {pmid41753740, year = {2026}, author = {Machineski, GDS and Menoncin, AS and Leonardo, HCL and Colozzi Filho, A}, title = {Riparian Forest Restoration Drives the Recovery of Soil Chemistry, Microbial Community Structure, and Enzymatic Activity in the Itaipu Reservoir Protection Zone.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753740}, issn = {2076-2607}, support = {Vitorias 4500074504 Itaipu/IDR-Paraná-Fapeagro//ITAIPU Binacional Convênio/ ; }, abstract = {Riparian forests play a critical role in protecting soil and water resources and maintaining ecosystem stability. In this study, we evaluated the response of soil chemical and microbial attributes to different stages of riparian forest restoration in the protection zone of the Itaipu Reservoir (Brazil). Soil samples were collected during summer and winter from sites representing four restoration stages (initial, 3, 19, and 30 years), as well as from an adjacent agricultural field and a native forest used as reference systems. We assessed soil chemical properties, microbial biomass carbon, basal respiration, enzymatic activities, and the soil microbial community structure using 16S rRNA gene sequencing. Principal component analysis (PCA) revealed a clear restoration gradient, with older restored sites progressively converging toward the native forest condition. Soil chemical properties showed gradual recovery along the restoration trajectory, with increases in soil organic carbon, cation exchange capacity, and base saturation. In contrast, the availability of P, K, Ca, and Mg declined at early restoration stages and increased with restoration age. Microbial biomass carbon increased by approximately 60% from early restoration to native forest conditions, while metabolic quotients (qCO2) decreased, indicating greater microbial efficiency and reduced metabolic stress. Enzyme activities related to C, P, and S cycling increased by 1.5- to 3-fold with restoration age. Sequencing analyses indicated a progressive convergence of microbial community composition toward that of the native forest, driven by shifts in relative abundance and the enrichment of forest-associated taxa, such as Verrucomicrobia and Acidobacteria, at advanced restoration stages. Overall, long-term riparian forest restoration promoted substantial recovery of soil chemical fertility and microbial community structure and functioning, reinforcing the role of soil microbiota as a sensitive indicator of ecosystem resilience and restoration success.}, }
@article {pmid41753762, year = {2026}, author = {Labrín-Sotomayor, NY and Becerra-Lucio, PA and Ruiz-González, H and Peña-Ramírez, YJ}, title = {Taxonomic and Functional Diversity of Leaves and Stem Endophytes of Eight Agave Species.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753762}, issn = {2076-2607}, support = {YJPR 5103711808 2024-2025 and NYLS 5103711911 research grants//El Colegio de la Frontera Sur/ ; }, abstract = {More than 63% of Mexico's territory is classified as arid or semiarid, where plants belonging to the genus Agave have evolved. Adaptation to drylands resulted from biochemical, physiological, and anatomical properties shared with other crassulacean plants; however, microbial symbionts also play critical roles in plants' growth, health, and drought tolerance. To explore endophytic communities in Agave plants, we used a shotgun metagenomic approach. The taxonomic and functional diversity of endophytes were studied in the leaves and stem organs of Agave americana, A.angustifolia, A. fourcroydes, A. karwinskii, A. potatorum, A. tequilana, A. cupreata, and A. rodacantha. The microbial community structure did not differ significantly among species, regardless of geographic origin or local environmental conditions, whereas significant differences were observed between organs. We found 4058 genera shared among organs, of which 957 genera are exclusive to the stem and 492 to the leaves. The community analysis of stems and leaves identified bacterial genera, including Acinetobacter, Klebsiella, Escherichia, Corynebacterium, and Streptomyces. Significant differences were also observed between organs in the functional annotations. The dominant functional categories were associated with cell signaling and protein metabolism in both organs.}, }
@article {pmid41753775, year = {2026}, author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Ventosa, A and Sánchez-Porro, C}, title = {Uncovering the Prokaryotic Diversity of Hypersaline Soils of Odiel Saltmarshes Natural Area Through Metagenome-Assembled Genomes.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753775}, issn = {2076-2607}, support = {PID2020-118136GB-I00//MCIN/AEI/10.13039/501100011033/ ; PID2023-148654NB-I00//MCIN/AEI/10.13039/501100011033/ ; 2022-04801//Swedish Research Council (Vetenskapsrådet)/ ; PRE2018-083242//Spanish Ministry of Science and Innovation/ ; }, abstract = {The hypersaline soils of the Odiel Saltmarshes Natural Area in Southwest Spain harbor highly diverse microbial communities adapted to extreme conditions. However, their genomic diversity remains largely unexplored. In addition to high salinity, these soils are contaminated with heavy metals, creating a hostile environment of great interest for studying extremophilic microorganisms and their metabolic adaptations. This study aims to characterize the uncovered prokaryotic taxa as Candidatus species inhabiting the hypersaline soils of the Odiel Saltmarshes, based on their metagenomic assembled genomic sequences. The reconstructed genomes were assessed for quality based on completeness and contamination thresholds and subsequently taxonomically classified. Comparative genomic analysis of six high-quality MAGs revealed key metabolic traits related to survival under extreme salinity and heavy metal conditions. The findings provide new insights about microbial diversity of hypersaline environments and expand the catalog of known prokaryotic genomes. Detailed characterization of six novel Candidatus taxa highlights the unique adaptations of these microorganisms, enhancing our understanding of life in extreme habitats.}, }
@article {pmid41753780, year = {2026}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC}, title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753780}, issn = {2076-2607}, support = {2020-67017-30776//USDA-NIFA/ ; }, abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.}, }
@article {pmid41754080, year = {2026}, author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F}, title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, pmid = {41754080}, issn = {2072-6643}, support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Milk ; Animals ; Feces/microbiology/chemistry ; Adult ; Bacteroides ; *Body Weight ; Obesity/microbiology/diet therapy ; Middle Aged ; Streptococcus thermophilus ; }, abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.}, }
@article {pmid41754175, year = {2026}, author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H}, title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, pmid = {41754175}, issn = {2072-6643}, support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Methylamines/metabolism/blood ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Choline/administration & dosage/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism/etiology ; Mice ; *Metagenomics ; *Machine Learning ; Liver/metabolism/pathology ; Feces/microbiology ; }, abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.
METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.
RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.
CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.}, }
@article {pmid41754394, year = {2026}, author = {Rabello, E and de-Paris, F}, title = {Tuberculosis Diagnostic Methods: Clinical Applicability, Implementation Challenges, and Integrated Testing Strategies.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754394}, issn = {2076-0817}, support = {https://ror.org/010we4y38.//This research was funded by the Fundo de Incentivo à Pesquisa e Eventos (FIPE) from the Hospital de Clínicas de Porto Alegre (HCPA) - https://ror.org/010we4y38./ ; }, mesh = {Humans ; *Tuberculosis/diagnosis/microbiology ; Nucleic Acid Amplification Techniques/methods ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Tuberculosis (TB) remains one of the leading causes of death from a single infectious agent worldwide, a burden further exacerbated by HIV co-infection and the increasing prevalence of drug-resistant strains. Although a wide range of laboratory diagnostic methods are currently available, their applicability, implementation, and clinical impact vary substantially across healthcare settings with different levels of complexity and resources. This review provides a comprehensive overview of the main laboratory diagnostic methods for active and latent TB, emphasizing their clinical applicability, implementation challenges, and role within integrated diagnostic strategies. Conventional approaches, such as smear microscopy and culture, are discussed alongside modern diagnostic technologies, including automated nucleic acid amplification tests (NAATs), loop-mediated isothermal amplification (LAMP), line probe assays (LPAs), next-generation sequencing (NGS), and lateral flow assays, highlighting their strengths and limitations in distinct epidemiological and operational contexts. Unlike existing WHO guidelines and prior reviews that predominantly focus on test performance and recommendation status, this review adopts an implementation-oriented perspective, critically examining diagnostic methods in light of real-world constraints, regional disparities, and evidence gaps. Particular attention is given to limitations related to laboratory infrastructure, biosafety, workforce capacity, and sustainability, as well as to under-addressed areas such as latent TB, metagenomic approaches, and the investigation of co-pathogens. By integrating WHO guidance with contextual and operational considerations, this review aims to support rational test selection and the development of flexible, integrated diagnostic workflows tailored to local health system capacity, patient populations, and clinical scenarios, thereby strengthening the effectiveness and equity of TB diagnostic strategies.}, }
@article {pmid41754400, year = {2026}, author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M}, title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754400}, issn = {2076-0817}, mesh = {Humans ; Child, Preschool ; *Choledochal Cyst/microbiology ; Infant ; Male ; Female ; Child ; Age Factors ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Biliary Tract/microbiology ; }, abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.}, }
@article {pmid41754413, year = {2026}, author = {Kibenge, F and Kibenge, M and Vargas, D and Godoy, M}, title = {Amarilloviruses of Aquatic Animals.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754413}, issn = {2076-0817}, support = {I-11251070//FONDECYT/ ; }, mesh = {Animals ; Genome, Viral ; *Aquatic Organisms/virology ; *Flaviviridae/genetics/classification/isolation & purification ; Phylogeny ; Fishes/virology ; }, abstract = {The family Flaviviridae has been expanded to include the highly divergent flavi-like viruses into three new families, Flaviviridae, Pestiviridae, and Hepaciviridae, in the order Amarillovirales. Classical flavivirids are small, enveloped viruses with positive-sense ssRNA genomes lacking a 3' poly(A) tail and ~9.0-13.0 kb in length, with a single open reading frame (ORF) encoding structural proteins at the N-terminus and nonstructural proteins at the C-terminus. Members infect a wide range of mammals, birds, and insects, and many are host-specific and pathogenic. Although the RNA-directed RNA polymerase (RdRP) gene sequences of the flavi-like viruses group phylogenetically with those of classical flavivirids, flavi-like viruses often encode larger polyproteins and possess substantially longer genomes of up to ~40 kb, and some have a 3' poly(A) tail. Their host range extends across the whole animal kingdom and angiosperm plants. This review describes the reported flavi-like viruses of aquatic animals, providing a meaningful update on all three new families in Amarillovirales that have been discovered using metagenomics in fish, crustaceans, mollusks, and echinoderms. These amarilloviruses include pathogenic viruses of aquatic animals, such as Cyclopterus lumpus virus (CLuV) detected in moribund lumpfish, and infectious precocity virus (IPV) found in iron prawn syndrome (IPS)-affected farmed giant freshwater prawns.}, }
@article {pmid41754473, year = {2026}, author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A}, title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754473}, issn = {2076-0817}, mesh = {*Biofilms/growth & development ; Humans ; Pilot Projects ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Biodiversity ; Archaea/genetics/isolation & purification/classification ; Fungi/genetics/classification/isolation & purification ; Male ; Viruses/classification/genetics/isolation & purification ; Female ; Middle Aged ; }, abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.}, }
@article {pmid41754515, year = {2026}, author = {Zaluzhnyi, V and Verhoeven, JTP and Stenson, GB and Lang, AS and Dufour, SC and Canuti, M}, title = {Characterization of a Novel, Highly Divergent Paramyxovirus Discovered in a Bearded Seal of Subarctic Canada.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754515}, issn = {1999-4915}, support = {RGPIN 2020-04131 (S.C.D.)//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Phylogeny ; *Seals, Earless/virology ; Genome, Viral ; *Paramyxoviridae/genetics/classification/isolation & purification ; *Paramyxoviridae Infections/veterinary/virology ; Viral Proteins/genetics ; Canada ; Arctic Regions ; }, abstract = {Seals are keystone animals in the Arctic and a valuable resource for Indigenous communities, but their virome is poorly understood. Through a preliminary investigation of the virome of seven North Atlantic bearded seals (Erignathus barbatus) from northwest Newfoundland, Canada, we discovered a new member of the Paramyxoviridae, a family including important animal pathogens. The complete coding genome sequence (15,898 nt) of the novel paramyxovirus, which we named bearded seal-associated paramyxovirus 1 (BSAPV-1), encoded five core paramyxoviral proteins-nucleoprotein, matrix, fusion, hemagglutinin-neuraminidase, and polymerase-and three proteins with no identifiable homologues that may represent the phosphoprotein, a small hydrophobic protein, and a transmembrane protein. Phylogenetic analysis, including BSAPV-1 and all 153 currently known paramyxoviral species, positioned the novel virus in a long-branched clade with Wenzhou Pacific spadenose shark paramyxovirus (Skoliovirinae, Scoliodonvirus scoliodontis), its closest relative (pairwise identity of the L protein: 30.1%). According to ICTV criteria, BSAPV-1 is likely the first member of a novel paramyxoviral subfamily. As the virus was found in combined tracheal/fecal swabs of a single animal, we could not conclude whether this is a seal virus or a virus associated with seal food. This study expands our knowledge about marine paramyxoviruses, and future studies should investigate BSAPV-1 ecology, spread, and host spectrum.}, }
@article {pmid41754522, year = {2026}, author = {Atkins, H and Stegman, N and Putonti, C}, title = {Diverse Temperate Coliphages of the Urinary Tract.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754522}, issn = {1999-4915}, support = {1R15AI171873-05/NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; *Coliphages/genetics/classification/isolation & purification/ultrastructure/physiology ; *Urinary Tract Infections/microbiology/virology ; *Urinary Tract/virology/microbiology ; *Escherichia coli/virology/isolation & purification ; Host Specificity ; Genome, Viral ; Escherichia coli Infections/microbiology ; Whole Genome Sequencing ; Phylogeny ; Prophages/genetics/classification/isolation & purification ; }, abstract = {While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract.}, }
@article {pmid41754608, year = {2026}, author = {Zheng, H and Shankar, A and Osis, G and Burgin, A and Sheth, M and Kiani, KG and Duong, YT and Cowan, D and Switzer, WM}, title = {Identification of Significant Genomic Changes and Compartmentalization of Simian Foamy Virus in a Human Zoonotically Infected by a Chimpanzee (Pan troglodytes troglodytes).}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754608}, issn = {1999-4915}, mesh = {Animals ; *Pan troglodytes/virology ; *Simian foamy virus/genetics/classification/isolation & purification ; Humans ; *Genome, Viral ; Phylogeny ; *Retroviridae Infections/virology/veterinary/transmission ; *Zoonoses/virology ; Male ; Viral Load ; Genomics ; Genetic Variation ; Ape Diseases/virology ; }, abstract = {Despite increasing reports of zoonotic simian foamy virus (SFV) infections globally, knowledge of its genetic adaptation in humans and impact on viral transmission and pathogenicity remains limited. We obtained complete SFV genomes using metagenomics analysis of viral isolates from peripheral blood lymphocytes (PBLs) and throat specimens from a worker (Case 6) and source chimpanzee (B1) that bit him. We analyzed viral diversity in three genomic regions (LTR, tas, and bet) involved in replication and latency using longitudinal specimens (PBLs, throat, saliva, urine, and semen) from Case 6 over five years, and PBLs from B1 and five additional chimpanzees over three years. Proviral loads were measured using a validated qPCR assay. Phylogenetic analysis revealed nearly identical SFV genomes in Case 6 and B1. Overall, bet sequences exhibited high genetic stability across body compartments and over time, with evidence of compartmentalization in Case 6 urine and semen specimens. G→A substitutions in GG and GA motifs in bet indicated heterogeneous APOBEC-associated editing across hosts and anatomical compartments following zoonotic transmission. Case 6 had significant deletions in the LTR region that were absent in B1 and other chimpanzees. Length variation in tas, including truncated forms, was observed across longitudinal specimens from Case 6, B1, and other chimpanzees. Proviral loads were consistently low and undetectable in most Case 6 urine specimens. Together, analysis of this SFV transmission pair identifies genomic changes likely to affect viral replication and persistence, highlighting mechanisms that may limit secondary transmission and pathogenicity of SFV in humans.}, }
@article {pmid41754611, year = {2026}, author = {Anderson, M and Orf, GS and Holzmayer, V and Olivo, A and Harris, BJ and Berg, MG and Yu, G and Achari, A and Federman, S and Chiu, CY and James, L and Mampunza, S and Cloherty, GA and Rodgers, MA}, title = {Next-Generation Sequencing Reveals Continued Circulation of Rare HIV-1 Subtypes in the Democratic Republic of the Congo and Refines the Estimate of the Emergence Dates of Three Subtypes.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754611}, issn = {1999-4915}, support = {NA//Abbott/ ; }, mesh = {*HIV-1/genetics/classification/isolation & purification ; Democratic Republic of the Congo/epidemiology ; Humans ; *HIV Infections/epidemiology/virology ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; Genome, Viral ; Genetic Variation ; Male ; Female ; Whole Genome Sequencing ; Genotype ; Adult ; }, abstract = {HIV-1 diversified for decades within the Democratic Republic of the Congo (DRC) before spreading globally in the early 1980s. Thus, the DRC is home to some of the most ancestral and diverse HIV-1 strains. Recent serosurveys conducted from 2017 to 2019 in Kinshasa, DRC, indicated high prevalence of HIV-1, yet sequence data is lacking from this period. Given the history of circulating rare HIV-1 subtypes in the DRC, a viral whole-genome sequencing study was conducted to determine current diversity in the greater Kinshasa area. Next-generation sequencing (NGS) through metagenomic and target enrichment methods was conducted on 197 specimens collected from 2017 to 2019. A large array of HIV subtypes (A, B, C, D, F1, G, H, J, and K), circulating recombinant forms (CRF01_AE, CRF02_AG, CRF05_DF, CRF11_cpx, CRF13_cpx, CRF25_cpx, CRF 45_cpx, and CRF92_C2U), unique recombinant forms, and unclassifiable sequences were observed, with many branching in basal positions within, or outside of, many subtypes on phylogenetic trees. Incorporating these new sequences into Bayesian inference of phylogeny pushes back the dates of the most recent common ancestors of HIV-1 group M and the rare subtypes G, H, and J by between 3 and 7 years each. The DRC continues to harbor diverse and rare HIV-1 subtypes that could challenge diagnostic tests, treatments, and vaccines. In addition to shifting subtype emergence dates, the sequences from our study are evidence that rare strains continue to circulate and should be regularly monitored.}, }
@article {pmid41755800, year = {2026}, author = {Ding, J and Wang, M and Xu, X and Wang, D and Chen, X and Li, S and Zheng, X and Che, Y and Deng, Y and Lam, TTY and Li, L and Zhang, T}, title = {Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e08389}, doi = {10.1002/advs.202508389}, pmid = {41755800}, issn = {2198-3844}, support = {T21-705/20-N//Theme-based Research Scheme/ ; 17202522//General Research Funds/ ; COVID1903015//Health and Medical Research Fund/ ; }, abstract = {The increasing global burden of antimicrobial resistance (AMR) has been identified as a critical public health crisis, necessitating the development of robust, real-time surveillance frameworks to evaluate AMR dynamics. Sewage surveillance is emerging as a promising tool that utilizes sewage fingerprinting to provide comprehensive and unbiased information on antibiotic resistance genes (ARGs) within human populations. Here, we conducted a large-scale, year-long field surveillance of resistome in the community sewage using both short- and long-read metagenomic sequencing. We examined samples collected from 95 geographically distributed sites across Hong Kong, covering a population of 4.8 million residents, during summer and winter seasons. Our findings revealed distinct seasonal patterns through high-resolution resistome profiling. We found that the resistome structures shifted from the community sewage collected at sewer manholes to the influent of wastewater treatment plants (WWTPs), driven by taxonomic variation. Notably, community sewage exhibited a significantly higher similarity to the resistome of human feces than WWTP influent, which provides insights for selecting suitable sampling sites for epidemiological ARG surveillance. The application of long-read sequencing markedly enhanced our understanding of the phylogenetic diversity of ARG hosts and uncovered a broad spectrum of potentially mobile ARGs with varied genetic backgrounds. Furthermore, we observed multiple local ARG transmission patterns and subsequently evaluated their potential threats to public health based on the gene trees to inform future epidemiological control strategies. Overall, this work expands our current understanding of community sewage for population-level AMR monitoring and establishes a baseline for advancing sewage surveillance efforts to better combat AMR.}, }
@article {pmid41756353, year = {2026}, author = {Martins, GL and Monteiro, GGTN and Lange, M and de Freitas, AS and do Nascimento Silva Barbosa, L and van Leeuwen, J and de Carvalho Soares, JE and Hanada, RE and Gleixner, G and Tsai, SM}, title = {Land-use intensification reshapes microbial phosphorus cycling, organic matter composition, and phosphorus fractions in Amazonian soils.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag027}, pmid = {41756353}, issn = {2730-6151}, abstract = {Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. While forest-to-agriculture conversion fundamentally reshapes plant-microbe-soil interactions and P cycling, these dynamics are further modulated by the intensity of land management. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus monoculture. We investigated how microbial and low molecular weight organic compounds (LMWCs) composition interacted with soil physicochemical attributes, acid phosphatase activity, and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to mineral fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and LMWC composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus monoculture. Pseudomonadota and nutrient-rich LMWC were more abundant in the agroforest, whereas Ascomycota and nutrient-poor LMWC predominated the citrus plantation. Genes related to "P acquisition" were more abundant in forest and agroforest soils, while genes related to "P-compound synthesis" were more abundant in the citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and LMWC resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.}, }
@article {pmid41756416, year = {2026}, author = {Catchpole, R and McLean, J and St John, E and Reysenbach, AL and Krupovic, M and Terns, MP}, title = {CRISPR spacers reveal diverse and abundant Thermococcales viruses in hydrothermal vents.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41756416}, issn = {2693-5015}, abstract = {Viruses are the most pervasive biological entities on Earth and they profoundly shape host ecology and evolution. However, for many microbial lineages, knowledge of their viromes remains limited, especially for those inhabiting remote environments, including deep-sea ecosystems. Here, we leverage one of the most extensively cultivated and genomically characterized archaeal lineages, the Thermococcales, to identify novel viral genomes. By utilizing CRISPR spacers from isolates and spacer arrays reconstructed from metagenomes, we mined mobile genetic elements (MGEs) in 1,172 publicly available and newly sequenced hydrothermal vent metagenomic datasets. Comparative genomics and identification of viral hallmark proteins revealed 620 viral genomes across 19 taxonomic families, most of which were previously undescribed. Structural modeling of major capsid proteins (MCPs) revealed diverse virion morphotypes, including viruses with spindle-shaped, head-tailed, icosahedral, filamentous, ovoid and bacilliform virions, greatly expanding the previously limited Thermococcales virome. Family-level comparisons uncovered extensive flux of virus-encoded replication proteins that are evolutionarily and structurally distinct from host homologs, as well as dramatic variation in glycan-binding lectins suggestive of diverse infection strategies. Together, our results substantially broaden the Thermococcales virosphere and demonstrate the power of combining cultivated isolates with culture-independent, CRISPR-guided metagenomics to interrogate archaeal virus diversity and evolution.}, }
@article {pmid41756466, year = {2026}, author = {Brunner, A and Mahout, M and Amoros, J and Rahmoun, M and Jarry, M and Bordenstein, SR and Bordenstein, SR and Trouche, B and Reveillaud, J}, title = {Extensive mobilome dynamics in a widespread endosymbiont: long read metagenomics reveal dimeric plasmids and highly fragmented prophages in Wolbachia from Culex pipiens.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41756466}, issn = {2693-5015}, abstract = {BACKGROUND: The obligate, intracellular bacteria Wolbachia have gained increasing interest due to their selfish modifications of host arthropod reproduction, impacts on host evolution, and utility in vector control efforts to reduce arbovirus transmission. Despite their highly reduced genomes, Wolbachia harbor a rich global mobilome that includes phages and plasmids in mosquito vectors. However, these mobile genetic elements are structurally complex, and standard genome assemblies often fail to resolve their organization and their functional relationships, leaving gaps in our understanding of how they evolve, mobilize, and influence host genomes.
RESULTS: Here, we present the first near-complete genome of Wolbachia and its mobile elements from the vector Culex pipiens molestus in Montpellier (France), reconstructed from Oxford Nanopore long read sequencing of single female ovaries without prior DNA amplification. Additional short reads from individuals of the same strain were used to assess and validate candidate mutations, particularly in repetitive regions. We report the assembly of a new dimeric form of the pWCP plasmid, providing evidence that the element is a replicating molecule and functionally active. We also observed extensive fragmentation of prophage WO regions despite long read sequencing, underscoring their structural complexity. Raw long read analyses recovered multiple alternative gene syntenies within WO regions, pointing to heterogeneous prophage architectures missed by the assembly and marked diversity of WO elements in Wolbachia of Culex pipiens (wPip) group strains.
CONCLUSIONS: Taken together, our results show the high dynamism of the endosymbiont genome that is shaped by integrated and episomal active mobile elements.}, }
@article {pmid41756881, year = {2026}, author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Yardimci, GG and Merritt, JL}, title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41756881}, issn = {2692-8205}, abstract = {BACKGROUND: Inflammatory oral diseases are associated with reproducible shifts from commensal-dominated microbiota toward pathobiont-enriched communities, yet the ecological mechanisms underlying the emergence of inflammophiles remain poorly understood. This study aims to investigate if host-derived inflammatory environments act as selective pressures that restructure microbial metabolism and community organization during disease progression.
METHODS: We performed 16S rRNA gene sequencing of patient-matched pediatric dental plaque and odontogenic abscess specimens to capture microbial community transitions across an inflammatory ecological gradient. Community ecology modeling and inferred metagenomic analyses were used to identify taxa and functional programs associated with commensal and inflammophilic states.
RESULTS: Patient-matched comparisons revealed a reproducible ecological selection gradient linking inflammatory environments to expansion of metabolically specialized inflammophiles and depletion of carbohydrate-utilizing commensals. Commensal-dominated plaque communities exhibited anabolic, carbohydrate-centered metabolic capacity, whereas abscess microbiota were enriched for catabolic metabolism, amino acid fermentation, and antimicrobial resistance, consistent with adaptation to inflammation-driven nutrient landscapes and immune pressure.
CONCLUSIONS: These findings support a model in which host inflammation drives ecological restructuring of the oral microbiome toward metabolically adapted inflammophilic communities. Defining the metabolic requirements and selective pressures governing these transitions provides a framework for microbiome-directed therapeutic strategies aimed at restoring ecological stability during inflammatory dysbiosis.}, }
@article {pmid41756930, year = {2026}, author = {Yuan, L and Qin, Y and West-Roberts, J and Anantharaman, K and Wang, H and Zou, Y and Duan, Y and Camargo, AP and Koonin, EV and Chen, L}, title = {A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41756930}, issn = {2692-8205}, abstract = {Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.}, }
@article {pmid41757006, year = {2026}, author = {Tran, HN and Kirven, KJ and Davenport, ER}, title = {SCiMS: Sex Calling in Metagenomic Sequences.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757006}, issn = {2692-8205}, abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.
RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.
CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS.}, }
@article {pmid41757095, year = {2026}, author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ}, title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757095}, issn = {2692-8205}, abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus, reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.}, }
@article {pmid41757098, year = {2026}, author = {Duan, L and Baumgartner, WA and Wanyama, JW and Okyere, L and Alvarado, DA and Minhas, BF and Gaulke, CA}, title = {Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757098}, issn = {2692-8205}, abstract = {Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure.}, }
@article {pmid41757355, year = {2025}, author = {Lai, CM and Xiao, XS and Liu, LW and Li, XL and Luo, YW and Liang, YQ and Cheng, Y and Qin, Y}, title = {The impact of nanodrugs on the metagenome of tobacco rhizosphere soil.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1715400}, pmid = {41757355}, issn = {1664-302X}, abstract = {The occurrence of tobacco diseases seriously restricts the healthy development of the tobacco industry. Soil microorganisms play an important role in regulating ecosystem functions. However, the impact of nanodrugs on the rhizosphere microbial community of tobacco and its related functions is still unclear. Therefore, this study combined field experiments to evaluate the effect of nanodrugs in reducing diseases and combined metagenomic sequencing to further explore the micro-ecological mechanism of nanodrugs in stably reducing soil biological barriers. The results show that nanodrugs can significantly improve the health level of tobacco. Metagenomic sequencing found that nanodrugs treatment increased the diversity and abundance of bacterial communities and could regulate the structure of soil microbial communities. It could selectively recruit beneficial microorganisms such as Sphingomonas, Bradyrhizobium, Pseudomonas, and Nocardioides to assist tobacco in disease control. GO function analysis showed that nanodrug treatment groups had significant enrichment of energy metabolism-related functions such as electron transfer activity, ATPase activity, and redox processes. KEGG pathway analysis showed that the relative abundance of key metabolic pathways such as fatty acid metabolism, aminoacyl-tRNA biosynthesis, ribosome, and purine metabolism was significantly increased. This study found that nanodrugs may indirectly promote plant health and alleviate tobacco diseases by shaping microbial community structure, enriching beneficial bacterial communities, and activating key metabolic pathways. These findings provide a theoretical basis for the application of NMs in the regulation of agricultural micro-ecosystems.}, }
@article {pmid41757357, year = {2025}, author = {Secker, B and Nayak, A and Husain, AA and Arora, S and Nag, A and Shrivastava, SK and Singer, AC and Gomes, RL and Acheampong, E and Chidambaram, SB and Bhatnagar, T and Vetrivel, U and Kashyap, RS and Atterbury, RJ and Blanchard, AM and Monaghan, TM}, title = {Metagenomic insights into the urban-rural variation of antimicrobial resistance and pathogen reservoirs in untreated wastewater from central India.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1722229}, pmid = {41757357}, issn = {1664-302X}, abstract = {INTRODUCTION: Rapid and scalable surveillance of antimicrobial resistance (AMR) is urgently needed in resource-constrained countries where routine monitoring is limited. Wastewater-based metagenomics offers a potential solution for early detection and geographic mapping of AMR.
METHODS: We conducted a retrospective DNA shotgun metagenomic analysis of untreated wastewater collected across Nagpur, India (February-April 2021). A total of 422 grab samples were pooled into 138 composite samples from 10 urban zones and rural catchments. The bacterial microbiota and resistome were profiled, and urban-rural patterns were compared using diversity metrics and correlation analyses.
RESULTS: Across all samples, 871 bacterial genera were detected, dominated by Proteobacteria, with frequent presence of Pseudomonas, Acinetobacter, Aeromonas, Acidovorax and Bacteroides. Beta diversity revealed statistically significant but subtle urban-rural compositional shifts. Of 33 globally important pathogens examined, 13 were detected at generally low relative abundance (<1%). Vibrio cholerae appeared in one sample, while Aeromonas spp. were most prevalent. Seven pathogens occurred in ≥10% of samples, with Aeromonas, Citrobacter, and Enterobacter differing significantly between locations (p < 0.05). The resistome comprised 606 unique antimicrobial resistance genes (ARGs), dominated by drug/biocide efflux determinants, followed by macrolide-lincosamide-streptogramin B genes driven largely by 23S rRNA mutations. Carbapenemases (blaNDM, blaKPC) and colistin resistance (mcr) were detected at lower abundance. Correlation analyses linked Pseudomonas with mexEF/emhABC efflux and copBCDRS copper resistance operon, Acinetobacter with oxa and dfrA, and Aeromonas with ctx, tetA, sul1, dfrB/F, and gyrA/parC.
DISCUSSION: These findings show that wastewater metagenomics sensitively resolved clinically relevant pathogens and ARGs in an Indian urban-rural setting, capturing nuanced geographic structure. Integrating routine DNA metagenomics into One Health environmental surveillance could strengthen AMR early warning and guide interventions in resource-constrained contexts.}, }
@article {pmid41757394, year = {2026}, author = {Wang, Z and Kojima, R and Kiji, R and Fujita, K and Tachibana, R and Tsuchiya, R and Uchiyama, T and Minagawa, Y and Mizuno, T and Igarashi, K and Noji, H and Kamiya, M and Urano, Y}, title = {Low-Background Cancer Imaging with a Bioorthogonal Fluorescence Probe and Engineered Reporter Enzyme Bearing a Targeting Moiety.}, journal = {Journal of the American Chemical Society}, volume = {148}, number = {11}, pages = {11492-11502}, pmid = {41757394}, issn = {1520-5126}, mesh = {*Fluorescent Dyes/chemistry/metabolism ; Humans ; Animals ; Mice ; *Optical Imaging/methods ; *Glycoside Hydrolases/metabolism/chemistry/genetics ; *Neoplasms/diagnostic imaging ; Protein Engineering ; Cell Line, Tumor ; }, abstract = {Combinatorial use of an antibody-reporter enzyme conjugate and a fluorescence probe activated by the enzyme is a powerful strategy for fluorescence-guided cancer surgery. However, conventional probes for typical reporter enzymes lack sufficient bioorthogonality, leading to high background signals in nontarget tissues. We screened a library of HMRef (rhodol derivative)-based fluorescence probes with various sugar moieties and found that HMRef-β-d-Fucose is bioorthogonal in mammalian systems but is activated by a metagenomic glycosidase, Td2F2. Directed evolution generated a mutant with a kcat/Km of 3.3 × 10[5]/M/sec, 7.3 times higher than wild-type Td2F2 and comparable to β-galactosidase (LacZ) with its corresponding probe. Theoretical calculation suggested the E296G mutation facilitates probe access to the enzyme's active site. In a proof-of-concept study, SKOV-3 cells, which endogenously express HER2, were visualized with minimal background in the mesentery of a mouse model using HMRef-β-d-Fucose and engineered Td2F2 conjugated or fused to a HER2-binding antibody or nanobody.}, }
@article {pmid41757490, year = {2026}, author = {Wang, Y and Schleheck, D and Marinova, E and Wessels, M and Schaller, S and Anselmetti, FS and Schwalb, A and Pedersen, MW and Epp, LS}, title = {Prokaryotic assemblages recovered by sedimentary DNA record natural and human-driven disturbances over the past 13 500 years in a cultural landscape.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41757490}, issn = {1751-7370}, support = {298726046//German Research Foundation/ ; //Research Training Group R3 - Resilience of Lake Ecosystems/ ; 290492639//International Continental Scientific Drilling Program/ ; //Elite Program for Postdocs, Baden-Württemberg Foundation/ ; 57450037//German Academic Exchange Service/ ; //MEiN Programme of the University of Konstanz/ ; //Doctoral Fund of the University of Konstanz/ ; }, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Lakes/microbiology ; *DNA, Ancient/analysis ; DNA, Bacterial/genetics ; Metagenomics ; DNA, Archaeal/genetics ; History, Ancient ; }, abstract = {Bacteria and archaea are under-characterized in palaeoecological studies, despite their ubiquity, high diversity, and tight integration with the abiotic, biotic, and human-influenced environments. The complexity of their assemblages and difficulties in separating living- from paleo-prokaryotes render research challenging. Here, we present an ancient metagenomic time series of prokaryotes from a sediment core of Lake Constance, spanning the last 13 500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and characterized the DNA damage of taxa as collectively increasing with time. By constructing co-abundance networks, we recognize major assemblage groups, containing both dead and living microbes, that show specific dynamics: short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods, and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa associated with various freshwater and soil environments persisted through millennia. By extricating different sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing nature- and human-caused long-term eco-evolutionary consequences.}, }
@article {pmid41757865, year = {2026}, author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y}, title = {Characterization of the dynamic microbiome evolution across thrips species.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70265}, pmid = {41757865}, issn = {1744-7917}, support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; }, abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.}, }
@article {pmid41757890, year = {2026}, author = {Tarasov, K and Zarubin, M and Yakhnenko, A and Gangapshev, A and Kravchenko, E}, title = {Metagenomic analysis of the biofilm community at the oxic-anoxic interface of a deep-underground saline spring at the Baksan Neutrino Observatory.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0210325}, doi = {10.1128/spectrum.02103-25}, pmid = {41757890}, issn = {2165-0497}, abstract = {In this work, the first-ever metagenomic study of the microbial community from the deep-underground saline spring located at the Baksan Neutrino Observatory (BNO) (Kabardino-Balkaria, Russia) is presented. Using the metagenomic approach, we obtained 19 metagenome-assembled genomes (MAGs) attributed to the phyla Pseudomonadota (the dominant phyla), Planctomycetota, Myxococcota, Nitrospirota, Gemmatimonadota, Armatimonadota, and Cyanobacteriota. Archaea are generally absent in the metagenome. The microbial community of the Baksan Neutrino Observatory demonstrates a high metabolic diversity, including carbon dioxide-fixing, methane-oxidizing, dinitrogen-fixing, nitrate- and iron-reducing, anammox, nitrifying, and predatory bacteria. Hydrogen, methane, ammonia, and reduced iron compounds, present in the ecosystem, provide energy for primary organic production. The abundance and diversity of bacteria capable of carrying out various stages of the nitrogen cycle suggest that nitrogen compounds are of great significance for microbial community metabolism. On the basis of the Genome Taxonomy Database Toolkit classification of MAGs and comparison to the closest RefSeq genomes, we have identified six new genera, with the proposed names-"Candidatus Jinrbaksania," "Candidatus Neutrinellum," "Candidatus Jinrextremum," "Candidatus Inrsubterrania," "Candidatus Inralta," and "Candidatus Neutrinobacter." Comparative analysis with metagenomes of microbial communities from the deep underground granitic sites and karst caves reveals that the BNO microbial community represents a unique transitional ecosystem on the boundary between the deep anoxic and surface aerobic biosphere.IMPORTANCEThe deep biosphere makes up 12-20% of the Earth's biomass and is poorly studied due to its inaccessibility. To date, only a few metagenomic studies of local deep biospheres have been performed in Russia. The Baksan Neutrino Observatory (BNO) is a deep-underground laboratory, with some abandoned tunnels. One of them hosts a mineral spring saturated with volcanic gases from the peripheral magma chamber of Mount Elbrus. The metagenomic analysis of the biofilm from this mineral spring has revealed the presence of unique microbial community whose composition occupies a transitional position between deep-underground microbial communities and communities of karst caves. We believe that this study of the microbial metagenome of the saline spring of the BNO will make a valuable contribution to understanding the composition and functioning of microbial communities formed at the oxic-anoxic interface.}, }
@article {pmid41757938, year = {2026}, author = {Hashimoto, K and Fukushima, K and Matsumoto, Y and Saito, H and Funauchi, A and Hamada, N and Yamauchi, J and Nitta, T and Motooka, D and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Komukai, S and Kumanogoh, A and Nakamura, S and Kida, H}, title = {Comparison of culture and culture-free methods for comprehensive identification of mycobacteria: a single-center prospective study.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0112825}, doi = {10.1128/jcm.01128-25}, pmid = {41757938}, issn = {1098-660X}, abstract = {The genus Mycobacterium, including Mycobacterium tuberculosis and over 200 nontuberculous mycobacteria (NTM), shows wide variability in clinical outcomes and drug susceptibility. Although culture-based identification remains the gold standard, slow mycobacterial growth delays diagnosis and treatment. In this study, we evaluated a novel culture-free method for subspecies-level identification directly from sputum. In this single-center prospective cohort study at Osaka Toneyama Medical Center, we analyzed 125 sputum samples from 115 patients with NTM pulmonary disease and 10 with non-NTM respiratory conditions. Samples were decontaminated using N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) or succinic acid. We compared the reference culture method (mycobacterial culture plus whole-genome sequencing) and a culture-free direct target capture sequencing method. Core genome multi-locus sequence typing identified subspecies in both workflows, covering 186 mycobacterial species, including M. tuberculosis. The 115 NTM cohort specimens yielded 57 smear-positive and 93 culture-positive results. The identified subspecies included 48 Mycobacterium avium subsp. hominissuis, 22 Mycobacterium intracellulare subsp. intracellulare, 5 subsp. chimaera, 7 Mycobacterium abscessus subsp. abscessus, 5 subsp. massiliense, 1 M. tuberculosis, and 5 other NTM species. The culture-free method showed a high identification rate for smear-positive specimens (75.4%) but a low identification rate for smear-negative specimens (13.9%). NALC-NaOH pretreatment resulted in higher accuracy (90.5%) than did succinic acid pretreatment (66.7%). Thus, our culture-free subspecies-level identification method achieved high accuracy, especially in alkaline-treated smear-positive sputum samples, achieving rates above 90%. This method is recommended in clinical practice for patients who require rapid diagnosis and timely initiation of appropriate treatment, bypassing time-consuming culture steps.IMPORTANCEAccurate identification of Mycobacterium species and subspecies is crucial for effective treatment, as drug susceptibility and clinical outcomes vary significantly among them. However, conventional diagnosis relies on culture-based methods that can take several weeks, critically delaying appropriate therapy. This study validates a novel culture-free method using target capture sequencing for the comprehensive, subspecies-level identification of over 186 mycobacterial species directly from sputum specimens. Our findings revealed the high accuracy of this approach for smear-positive specimens, especially with alkaline pretreatment. This rapid method is applicable in clinical settings and enables timely and precise treatment decisions, greatly benefiting patients who require urgent intervention.}, }
@article {pmid41758007, year = {2026}, author = {Nieves-Morales, R and Quiles-Pérez, CJ and Rivera-Lopez, EO and Torres-Zapata, I and Rodriguez-Ramos, J and Rios-Velazquez, C}, title = {Metagenomic libraries data sets from the hypersaline benthic microbial mats of the Fraternidad Lagoon, Puerto Rico, using an indirect DNA extraction method.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0150425}, doi = {10.1128/mra.01504-25}, pmid = {41758007}, issn = {2576-098X}, abstract = {Microbial mats are biofilm formations that reflect early Earth ecosystems. To investigate their microbial diversity, an indirect DNA extraction method was applied to benthic ephemeral microbial mats from Fraternidad Saltern Lagoon during rainy and dry seasons. This approach yields high molecular DNA, suitable for metabolic and diversity analysis.}, }
@article {pmid41758194, year = {2026}, author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L}, title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2638009}, pmid = {41758194}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antimetabolites/pharmacology/therapeutic use/pharmacokinetics ; Dysbiosis/chemically induced/microbiology ; Bacteria/metabolism/drug effects/genetics/classification ; Animals ; Metabolomics ; Neoplasms/drug therapy ; }, abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.}, }
@article {pmid41758250, year = {2026}, author = {Kumar, A and Bandyopadhyay, TK and Das, D}, title = {Bacterial laccases for green remediation of contaminants of emerging concern: from molecular cloning to metagenomic and computational insights.}, journal = {Biodegradation}, volume = {37}, number = {2}, pages = {}, pmid = {41758250}, issn = {1572-9729}, mesh = {*Laccase/metabolism/genetics/chemistry ; *Bacteria/enzymology/genetics ; Biodegradation, Environmental ; Metagenomics ; Cloning, Molecular ; *Bacterial Proteins/metabolism/genetics/chemistry ; Environmental Restoration and Remediation/methods ; *Water Pollutants, Chemical/metabolism ; }, abstract = {Contaminants of emerging concern (CECs) are increasingly recognized for their persistence, widespread occurrence, and potential risks to environmental and human health. Their frequent detection in wastewater, surface water, drinking water, and food chains underscores the urgent need for sustainable remediation strategies. Laccases, versatile multicopper oxidases, have demonstrated strong potential for degrading organic pollutants through oxidative mechanisms that transform complex contaminants into less toxic products. While fungal laccases have been extensively studied, bacterial laccases are gaining attention due to their structural simplicity, stability under alkaline conditions (pH 7.5-9.0), and limited requirement for post translational modifications. Recent studies indicate that bacterial laccases can transform approximately 60-80% of industrial dyes, a major class of CECs, even in complex wastewater matrices. Despite notable progress, broader application of bacterial laccases remains constrained by limited enzyme stability under industrial operating conditions, reduced catalytic performance under high salinity, extreme pH, and mixed pollutant environments, and frequent dependence on costly redox mediators, highlighting the need for more robust enzymes and sustainable mediator alternatives. This review summarizes recent advances in bacterial laccase research, with emphasis on structural and substrate specific insights, molecular cloning, heterologous expression, and optimized purification strategies. It also highlights emerging approaches such as metagenomics and machine learning for identifying robust, thermostable, and alkali resistant bacterial laccases suitable for large scale applications. Collectively, these advances support green chemistry principles and contribute to multiple United Nations Sustainable Development Goals by enhancing wastewater treatment efficiency, reducing energy and chemical inputs, and promoting sustainable waste valorization.}, }
@article {pmid41759061, year = {2026}, author = {Hong, S and Winkler, MH and Wang, ZW and Dhanasekar, A and Goel, R}, title = {Unveiling Metabolic Insights and Niche Differentiation of Microbial Communities in EBPR-Anammox Reactor through Integration of Long-Read Metagenomics and Metatranscriptomics.}, journal = {Environmental science & technology}, volume = {60}, number = {10}, pages = {7967-7982}, doi = {10.1021/acs.est.5c17958}, pmid = {41759061}, issn = {1520-5851}, mesh = {*Bioreactors/microbiology ; Metagenomics ; Biofilms ; Sewage/microbiology ; Phosphorus/metabolism ; }, abstract = {In this manuscript, we report niche differentiation among important groups of organisms involved in phosphorus and nitrogen cycling, and the interplay between relevant metabolic pathways carried out by these key organisms. We employed nanopore-based long-read and Illumina-based short-read sequencing techniques for metagenomics and metatranscriptomics, respectively, on samples collected from an integrated fixed film activated sludge (IFAS) bioreactor run in the conventional A[2]O mode under low dissolved oxygen (DO) conditions. Among the recovered metagenome-assembled genomes (MAGs), >90 MAGs from each community were high-quality, including 39 and 30 MAGs that were close-circularized, from the floc and biofilm communities, respectively, with no or minimal contamination. Some Candidatus Accumulibacter strains encoded for either full or partial denitrification. Ca. Accumulibacter were very efficient in aerobic and anoxic inorganic phosphorus (Pi) uptake, while the second highly enriched Ca. Accumulibacter was as competitive for denitrification metabolism. The potential of nitrous oxide (N2O) emissions in both the floc and biofilm communities was nearly 20 times higher in the aerobic zone than in the anoxic zone. As opposed to our initial hypothesis that slow growers will mostly reside in biofilms, the expression of ammonium monooxygenase (amoABC) was higher in flocs than in biofilm communities.}, }
@article {pmid41759241, year = {2026}, author = {Myers, PN and van Beijsterveldt, IALP and Snowden, SG and Eriksen, C and Nielsen, HB and Hughes, IA and Ong, KK and Hokken-Koelega, ACS and Koulman, A and Brix, S}, title = {Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106602}, doi = {10.1016/j.clnu.2026.106602}, pmid = {41759241}, issn = {1532-1983}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; *Breast Feeding ; *Infant Formula ; Female ; Lipidomics ; *Lipids/blood ; Male ; Prospective Studies ; Feces/microbiology ; *Infant Nutritional Physiological Phenomena ; Milk, Human ; }, abstract = {BACKGROUND & AIMS: Exclusive breastfeeding offers numerous health benefits. Despite advancements in formula, significant differences compared with breast milk remain. We aimed to assess how milk feeding type and volume at 3 months affect the infant plasma lipidome and gut microbiota.
METHODS: Infants were classified into exclusive breastfeeding (EBF), mixed feeding (MF), or exclusive formula feeding (EFF) groups based on feeding data collected prospectively across two European cohorts (n = 519). Lipidomics and shotgun metagenomics were applied to plasma and stool samples, respectively.
RESULTS: Feeding type explained major variation in both lipidomic and microbial profiles. Plasma lipids showed distinct signatures across groups, particularly in sphingomyelins and diacylglycerols. Microbiota diversity and species richness increased with formula exposure. Formula rich in intact whey protein was linked to higher S. thermophilus abundance in the infant gut. Random forest classification of feeding type using either lipidomic or gut microbiota features achieved high discriminatory accuracy (AUROC >0.90) in training and validation datasets.
CONCLUSION: Early nutrition is a critical determinant of the lipidome and gut microbiome during the breastfeeding phase.}, }
@article {pmid41759316, year = {2026}, author = {Zhang, J and Zhang, Z and Shen, Z and Yu, Z and Chen, J and Zeng, L and Li, D and Yan, X and Li, B and Wong, JWC}, title = {PDG_DB: A comprehensive database unveils environmental distribution patterns of plastic-degrading genes via large-scale multi-omic data analysis.}, journal = {Water research}, volume = {296}, number = {}, pages = {125619}, doi = {10.1016/j.watres.2026.125619}, pmid = {41759316}, issn = {1879-2448}, mesh = {*Plastics/metabolism ; Biodegradation, Environmental ; Multiomics ; }, abstract = {Plastic pollution has become a global environmental crisis, driving urgent research into plastic-degrading enzymes for achieving efficient green transformation and recycling of plastic waste. However, current plastic-degrading gene (PDG) databases remain fragmented and incomplete. Simultaneously, research has predominantly focused on laboratory-isolated strains with the limited exploration of the vast reservoir of PDGs in environmental metagenomes. To address these limitations, we employed large-scale environmental multi-omics analysis to systematically mine and characterize PDGs across diverse ecosystems. We constructed PDG_DB (https://github.com/Z-bioinfo/PDG_DB), a comprehensive PDG database containing 341 experimentally validated sequences categorized by substrate specificity. Large-scale multi-omics analysis across environmental samples identified 7,111 PDGs (3,612 non-redundant), with polyhydroxyalkanoate (PHAs) degrading genes predominating. Molecular docking revealed that novel putative PDGs for PHA degradation exhibited stronger binding affinity compared to known PDGs, demonstrating the necessity of mining novel enzymes from environmental sources. Most PDGs were bacterial, primarily from Pseudomonadota, with the genus Pseudomonas showing the broadest degradation range. Our global analysis of 5,466 datasets revealed high PDG abundance in East Asia, North Europe, America, and the oceans. Unexpectedly, drinking water systems harbored the highest PDG abundance, challenging assumptions about plastic contamination in potable water. PDG distribution varied by environment: soil favored genes for non-biodegradable plastics, while wastewater systems preferred those for biodegradable plastics. Metatranscriptomic analysis showed the highest PDG activity in marine environments. This work provides a comprehensive resource for PDGs, revealing distinctive global distribution patterns with drinking water systems as an unexpected reservoir. PDG_DB serves as a foundational database for identifying PDGs, facilitating future environmental monitoring and biotechnology applications.}, }
@article {pmid41759320, year = {2026}, author = {Yin, Y and Wu, H and French, CE and Lu, Z}, title = {Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies.}, journal = {Water research}, volume = {296}, number = {}, pages = {125614}, doi = {10.1016/j.watres.2026.125614}, pmid = {41759320}, issn = {1879-2448}, mesh = {*Triclosan/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics ; }, abstract = {The widespread presence of emerging contaminants, such as triclosan (TCS), in environmental systems raises significant concerns regarding their ecological risks, particularly the propagation of antibiotic resistance genes (ARGs). In this study, sequencing batch reactors (SBRs) were exposed to a TCS concentration gradient to simulate the accumulation of TCS in activated sludge and to elucidate its effects on microbial community structure, ARG dissemination, and horizontal gene transfer (HGT). Using a multi-omics approach that integrated 16S rRNA amplicon sequencing, short- and long-read metagenomics, and genome-scale metabolic modeling, we demonstrated that increasing TCS concentrations progressively reduced microbial diversity and stability. At lower TCS concentrations (0-1.0 mg/L), ARG-carrying bacteria were enriched, whereas at higher concentrations (10 mg/L), TCS eliminated ARG-carrying bacteria and selected for strains rich in mobile genetic element (MGE). Notably, HGT led to genome expansion of Acidomonas methanolica (from 3.75 Mb to 7.13 Mb), disrupting the microbial interaction networks within the community. Additionally, the introduction of a triclosan-degrading hydrogel-magnetic biochar-engineered strain composite mitigated the destabilizing effects of TCS stress on the microbial community, enhanced its resilience, and facilitated TCS degradation, thus reducing associated environmental risks. Our findings highlight how gradient TCS exposure reshapes microbial communities, promotes the dominance of MGE-enriched taxa, and has profound implications for the ecological and evolutionary dynamics of microbial communities in aquatic ecosystems. This study provides novel insights into the role of emerging contaminants in the propagation of resistance and microbial adaptation.}, }
@article {pmid41759554, year = {2026}, author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J}, title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0240725}, doi = {10.1128/spectrum.02407-25}, pmid = {41759554}, issn = {2165-0497}, abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.}, }
@article {pmid41759557, year = {2026}, author = {Yang, W and Shi, L and Li, X and Rao, F and Luo, R and Huang, C}, title = {Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0327625}, doi = {10.1128/spectrum.03276-25}, pmid = {41759557}, issn = {2165-0497}, abstract = {This study aimed to characterize the gut virome in children with allergic rhinitis (AR) and explore its interactions with immune markers and allergens. Metagenomic sequencing was performed on fecal samples from 16 AR and 17 healthy control (HC) children. Viral genes (VGs) were identified and taxonomically annotated using BLASTP against the NCBI NR database. Virome diversity, differential abundance, and correlations with IgE were analyzed using LEfSe, random forest, and Spearman correlation. While alpha diversity did not differ, beta diversity revealed subtle compositional trends. Taranisvirus was enriched in AR and positively correlated with total IgE (ρ = 0.4647, P = 0.045). Mitovirus and Duamitovirus were depleted in AR and negatively correlated with allergens. Virus-bacteria co-occurrence network analysis revealed a reconfigured ecological interactome in AR, characterized by pro-phage-centric associations that may disrupt mucosal immune homeostasis. Random forest identified total IgE, milk, and dust mite as top discriminators. This first study of the gut virome in pediatric AR reveals a pro-inflammatory phage enrichment and protective fungal virus depletion, implicating the virome in modulating Th2 immunity. These findings suggest a potential correlation between virome alterations and allergic diseases, which may inform future research on virome-targeted interventions.IMPORTANCEAllergic rhinitis is a prevalent childhood condition with a significant impact on quality of life, yet its pathogenesis is not fully understood. While the bacterial microbiome has been studied, the role of the gut virome remains largely unexplored. Our study provides the first evidence of gut virome dysbiosis in children with allergic rhinitis. We identified specific pro-inflammatory bacteriophages that are enriched and correlated with IgE levels, as well as protective fungal viruses that are depleted. These findings offer new perspectives on allergic disease pathogenesis by suggesting a potential role of the virome in modulating host immunity. This work not only opens a new avenue for understanding the environmental and microbial drivers of allergic diseases but also suggests the potential for novel virome-based diagnostics and therapeutic strategies, such as phage therapy, which could have a broad impact on clinical practice.This study is registered with ClinicalTrials.gov as ChiCTR2400085982.}, }
@article {pmid41759636, year = {2026}, author = {Liang, L and Su, S and Peng, L and Zhuang, H and Chen, Y and Cao, Y}, title = {Development of Mycobacterium tuberculosis post in vitro fertilization and embryo transfer: A case series derived from a multi-omics analysis and literature review.}, journal = {Microbial pathogenesis}, volume = {214}, number = {}, pages = {108408}, doi = {10.1016/j.micpath.2026.108408}, pmid = {41759636}, issn = {1096-1208}, mesh = {Humans ; Female ; *Fertilization in Vitro/adverse effects ; Pregnancy ; *Mycobacterium tuberculosis/genetics/isolation & purification/pathogenicity ; *Embryo Transfer/adverse effects ; Adult ; *Tuberculosis/microbiology ; *Pregnancy Complications, Infectious/microbiology ; Metagenomics ; Placenta/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Multiomics ; }, abstract = {The extensive progress in assisted reproductive technology has facilitated successful pregnancies through in vitro fertilization and embryo transfer (IVF-ET) for patients facing infertility. Pregnancy induces substantial endocrine and immune alterations that may diminish immune function, consequently heightening vulnerability to Mycobacterium tuberculosis (M.tb) infection or reactivation. Hematogenous disseminated pulmonary tuberculosis (TB), tuberculous meningitis, and potential congenital TB are serious complications that may arise after IVF-ET, posing significant risks to both maternal and fetal health. The clinical manifestations of TB during pregnancy frequently coincide with non-typical pregnancy symptoms, and the nonspecific characteristics of early-stage presentations render prompt diagnosis especially difficult. The existing literature on this subject is sparse, primarily consisting of isolated case studies involving individual participants, thereby yielding insufficient data and inadequate representations to comprehensively clarify this clinical emergency. This paper presents a case series of patients with normal immune function who developed hematogenous disseminated TB, including placental and central nervous system involvement, subsequent to IVF-ET. We showcased the multi-omic findings, including metagenomic sequencing and histopathological analyses, from patients with twin and singleton pregnancies and presented an extensive literature review. Additionally, we used metagenomic next-generation sequencing (mNGS) to detect pathogenic microorganisms in blood, bronchoalveolar lavage fluid (BALF), and cerebrospinal fluid (CSF) samples. Rare histopathological findings of placental TB were also documented, providing direct pathological evidence relevant to congenital TB. These findings expand the limited clinical evidence on TB following IVF-ET and underscore the importance of heightened clinical vigilance and multimodal diagnostic strategies in this high-risk population.}, }
@article {pmid41760689, year = {2026}, author = {Yarlina, VP and Tandra, JL and Indiarto, R and Andoyo, R and Harlina, PW and Ubaidillah, NHN and Lani, MN}, title = {Unraveling Tempeh through omics: a scoping review of fermentation pathways and functional health benefits.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00754-2}, pmid = {41760689}, issn = {2396-8370}, support = {No. 2245/UN6/N/PT.01.03/2025//Universitas Padjadjaran/ ; }, abstract = {Tempeh, a traditional Indonesian fermented soybean product, is widely recognized for its functional properties and for containing bioactive compounds produced by microbial fermentation. This study integrates recent advances in multi-omics technologies to elucidate the microbial community dynamics, enzymatic pathways, and metabolite transformation underlying Tempeh's health-promoting characteristics. A bibliometric analysis of studies published between January 2000 and August 2025, indexed in Scopus, PubMed,Web of Science, and ScienceDirect identified 36 relevant articles that met predefined inclusion criteria. Metagenomic and transcriptomic evidence highlights the important roles of Rhizopus species and associated Lactic acid bacteria in fermentation, supported by the presence of genes encoding key enzymes such as phytases, amylases, and proteases. Proteomic and peptidomic analyses have further identified bioactive short peptides exhibiting antioxidant and angiotensin-converting enzyme (ACE) inhibitory activities. Metabolomic profiling revealed elevated levels of amino acids, γ-aminobutyric acid (GABA), and isoflavone aglycones, compounds linked to various health benefits. Collectively, these multi-omics insights provide a mechanistic understanding of Tempeh's functional potential and highlight opportunities for innovation in fermentation optimization and clinical translation. Future integration of standardized fermentation protocols with targeted human studies will be essential to advance Tempeh from a traditional food to a globally recognized functional food product.}, }
@article {pmid41760690, year = {2026}, author = {Sammons, SL and Kuntz, TM and DiLullo, M and Morgan, XC and Martin, A and Hughes, ME and Rahman, T and Barroso-Sousa, R and Ogayo, ER and Giordano, J and Ryan, S and Waks, AG and Schlam, I and Ligibel, J and Lin, NU and Garrido-Castro, AC and Mittendorf, EA and Tolaney, SM}, title = {The landscape of the intestinal microbiome among patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ (DCIS).}, journal = {NPJ breast cancer}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41523-026-00922-3}, pmid = {41760690}, issn = {2374-4677}, support = {P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; Dana-Farber Cancer Institute project number 6395601//Massachusetts Life Sciences Center/ ; }, abstract = {The intestinal microbiome shapes immune responses and is associated with patient outcomes in cancer following immunotherapy. We evaluated differences between the intestinal microbiome profiles of patients with early-stage invasive breast cancer (BC) and ductal carcinoma in situ (DCIS) by subtype using whole genome metagenomic sequencing. There were no significant differences in microbiome composition between DCIS and invasive BC as measured by alpha diversity (p = 0.20, ANOVA) or beta diversity (p = 0.52, PERMANOVA). Within invasive BC, patients with hormone receptor-positive (HR +)/HER2 + BC differed significantly in beta diversity relative to other subtypes (p < 0.05), with differences in six species (q < 0.25). Bacteroides ovatus was significantly more abundant in patients with stage III BC vs. stage I (p = 0.0003). Functional pathway analysis using HUMAnN3 revealed stage-specific enrichment of amino acid biosynthesis and nucleotide-related pathways. Altogether, these findings highlight potential microbial signatures associated with BC subtype and stage.}, }
@article {pmid41761093, year = {2026}, author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA}, title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41761093}, issn = {1471-2105}, abstract = {PURPOSE: Gut microbiome dysbiosis is a critical determinant for autologous fecal microbiota transplantation (Auto-FMT) eligibility, yet current classification approaches rely predominantly on supervised learning with manually annotated sequencing labels, which are often scarce. This study proposes DynaBiome, a framework designed to predict gut dysbiosis by leveraging unsupervised learning and clinical phenotypic proxies as a scalable alternative to ground-truth genomic labeling.
METHODS: Our framework employs an LSTM autoencoder architecture to capture temporal microbiome dynamics within 14-day windows. The model reconstructs normal microbiome patterns, where high reconstruction errors signal potential dysbiosis. To ensure rigorous evaluation and prevent data leakage, the dataset was partitioned via a strict patient-level split. Unsupervised anomaly signals were refined via phenotypic proxy labels (e.g., fever, neutropenia) via weak supervision, and ensemble learning methods were applied to optimize classification performance.
RESULTS: The initial LSTM autoencoder successfully flagged dysbiotic sequences but required refinement to reduce false positives. Ensemble learning significantly enhanced predictive accuracy. The stacked ensemble (with Logistic Regression meta-learner) demonstrated optimal performance with an ROC AUC of 0.8908 and a Weighted F1-score of 0.7909. This approach significantly outperformed the standard One-Class SVM baseline (ROC AUC 0.6033), confirming the superiority of deep temporal modeling over static anomaly detection. Critically, the model achieved performance levels comparable to fully supervised baselines, confirming the efficacy of the proxy-label framework.
CONCLUSION: Integrating unsupervised temporal feature extraction with stacked ensemble methods provides a viable framework for dysbiosis prediction. These results demonstrate that leveraging phenotypic via weak supervision can effectively approximate supervised baselines, thereby reducing the reliance on comprehensive metagenomic annotations for longitudinal patient monitoring.}, }
@article {pmid41761378, year = {2026}, author = {Biggel, M and Oberhänsli, T and Kümmerlen, D and Walkenhorst, M and Stephan, R and Holinger, M}, title = {Diversity and abundance of antimicrobial resistance genes in manure from pig farms with varying antibiotic use: a long-read metagenomic sequencing approach.}, journal = {Porcine health management}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40813-026-00496-3}, pmid = {41761378}, issn = {2055-5660}, support = {04.1240.PZ//Swiss Expert Committee for Biosafety (SECB)/ ; }, }
@article {pmid41761979, year = {2026}, author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X}, title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {2}, pages = {48584}, doi = {10.31083/FBL48584}, pmid = {41761979}, issn = {2768-6698}, support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; }, mesh = {*Arsenic Trioxide/pharmacology/therapeutic use ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy ; Homeostasis/drug effects ; Humans ; *Bifidobacterium ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; *Tumor Microenvironment/drug effects/immunology ; *Antineoplastic Agents/therapeutic use/pharmacology ; Dysbiosis ; *Intestines/drug effects/microbiology/immunology ; *Probiotics/administration & dosage ; Disease Models, Animal ; }, abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.
METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.
RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.
CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.}, }
@article {pmid41762228, year = {2026}, author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X}, title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41762228}, issn = {1432-0991}, support = {82270598//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Lactobacillus/physiology ; *Ileum/metabolism/microbiology ; Mice ; *Gallstones/microbiology/prevention & control/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Male ; *Probiotics/administration & dosage ; Disease Models, Animal ; Colon/microbiology ; }, abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.}, }
@article {pmid41762314, year = {2026}, author = {Dabravolski, SA and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Orekhov, AN}, title = {A metagenomic perspective on microbial hydrocarbon degradation: uncovering novel pathways and community dynamics.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {5}, pages = {}, pmid = {41762314}, issn = {1573-2983}, support = {202760-2-000//RUDN University/ ; }, mesh = {Biodegradation, Environmental ; *Metagenomics ; *Hydrocarbons/metabolism ; Polycyclic Aromatic Hydrocarbons/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics ; }, abstract = {The microbial degradation of petroleum hydrocarbons is a fundamental biogeochemical process and a cornerstone of environmental bioremediation. While traditional culture-based studies have outlined the basic principles, the advent of metagenomics has revolutionised our understanding by revealing the full genetic and functional diversity of hydrocarbon-degrading communities in situ. This review synthesises the current state of knowledge on both aerobic and anaerobic hydrocarbon biodegradation, providing a critical comparative analysis of traditional versus multi-omics methodologies. We provide an in-depth examination of aerobic mechanisms, initiated by oxygenases (e.g., alkB, PAH-RHDα), and contrast them with the diverse array of anaerobic activation pathways, including fumarate addition (bssA) and the recently elucidated direct carboxylation pathway for polycyclic aromatic hydrocarbons (PAHs). Furthermore, we highlight groundbreaking metagenomic insights into anaerobic benzene degradation and the critical role of syntrophic networks driven by interspecies electron transfer. Finally, we present specific case studies demonstrating the translation of genomic data into practical bioremediation strategies, such as the rational design of synthetic consortia. This review charts these recent advances, highlights remaining knowledge gaps, and outlines future directions for harnessing multi-omics to translate genomic potential into effective, field-scale environmental solutions.}, }
@article {pmid41762333, year = {2026}, author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S}, title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41762333}, issn = {1573-0972}, }
@article {pmid41762461, year = {2026}, author = {Shen, S and Wang, L and An, X and Liu, H and Shi, M and Tu, Y and Ji, W and He, Z and Li, A}, title = {Basin governance coincides with lower MGE loads yet rewired ARG mobility: a hazard‑oriented, platform‑centric assessment.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141608}, doi = {10.1016/j.jhazmat.2026.141608}, pmid = {41762461}, issn = {1873-3336}, mesh = {*Drug Resistance, Microbial/genetics ; *Rivers/microbiology ; China ; Environmental Monitoring ; *Genes, Bacterial ; Metagenomics ; Microbiota ; }, abstract = {Antibiotic resistance genes (ARGs) serve as critical indicators for evaluating the ecological success of river restoration policies. We investigated the restructuring of the riverine resistome in the Yangtze River following the implementation of the "Ten-Year Fishing Ban" and the Yangtze River Protection Law. Using basin-wide surveys in the Jiangsu reach (2021 vs. 2023), we integrated shotgun metagenomics and RT-qPCR functional validation with a noise-filtering sampling design to assess how the removal of anthropogenic pressures reshaped resistance dissemination. Results show that policy-driven ecological recovery significantly altered microbial assembly mechanisms. While total ARG abundance declined, microbial communities shifted toward a more dispersal-dominated regime, with neutral model fits increasing from 0.817 to 0.913. Crucially, RT-qPCR analysis confirmed that the transcriptional activity of key resistance elements remained significantly elevated relative to a pristine baseline, suggesting persistent functional risks despite lower overall abundance. As localized selective pressures relaxed, the resistome transitioned toward integrated genetic platforms, evidenced by a significant rise in the mosaic index (MGI) from 12.81% to 22.50% (p < 0.05). Structural equation modeling (R2 = 0.766) identified a dominant sequential pathway from environmental co-selectors to mobile genetic elements and subsequently to ARGs, with intensified roles for integrons and insertion sequences (intI1, IS26). These findings demonstrate that policy success requires evaluation through both abundance-based and structural indicators. We propose a platform-centric surveillance framework incorporating the mosaic index as an early-warning tool for environmental agencies.}, }
@article {pmid41762466, year = {2026}, author = {Ma, Q and López, MJ and Zhang, S and Jin, L and Wei, D and Yang, J and Liu, J and Ruan, Z}, title = {Carbon source-dependent activation of herbicide-mixture degradation in a synthetic microbial community enriched from black soil.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141615}, doi = {10.1016/j.jhazmat.2026.141615}, pmid = {41762466}, issn = {1873-3336}, mesh = {*Herbicides/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Carbon/metabolism ; *Microbial Consortia ; Cyclohexanones/metabolism ; Atrazine/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; Sulfonylurea Compounds/metabolism ; Microbiota ; Pyridines ; }, abstract = {The extensive use of herbicides in agriculture has resulted in persistent soil contamination. Although microbial degradation of single herbicides has been extensively investigated, the responses and co-metabolism of microbial consortia to complex herbicide mixtures remain unclear. This study aimed to investigate the influence of a simple carbon source (glucose) on herbicide degradation by a natural microbial consortium (NMC) and identify key degraders for constructing an efficient synthetic microbial community (SynCom). An NMC enriched from herbicide-stressed agricultural black soil in Northeast China was inoculated into mineral salt media containing a mixture of herbicides (atrazine, nicosulfuron and mesotrione) as the sole carbon/nitrogen source, without (MSM) or with glucose supplementation (GSM). Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days. Integrated 16S rRNA gene sequencing and metagenomic analysis linked the glucose amendment to a specific shift in the microbial community structure and activation of central carbon metabolism (tricarboxylic acid [TCA] and glycolytic), which enhanced cellular energy supply and environmental acidification for co-metabolic degradation of herbicides. In contrast, metabolism in the MSM system was biased toward biosynthesis. Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa. Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase). A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system. These findings elucidate the role of labile carbon in driving the co-metabolism of complex herbicides and provide direct candidate strains and a construction strategy, facilitating practical bioremediation applications.}, }
@article {pmid41762491, year = {2026}, author = {Yan, S and Li, R and Shen, X and Li, Y and Zhang, L and Xu, M and Xie, S}, title = {Redox potential drives divergent microbial carbon fixation in mangrove wetland sediments, with ammonium exerting context-dependent effects.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119457}, doi = {10.1016/j.marpolbul.2026.119457}, pmid = {41762491}, issn = {1879-3363}, abstract = {Mangrove wetlands represent dynamic coastal interfaces where redox conditions and nutrient cycling shape microbial communities and their biogeochemical functions. However, tidal-driven siltation continuously transports sediment from low- to high-tide zones, altering sediment redox potential and nutrient content. The microbial responses to these changes, particularly the response mechanisms of carbon-fixing microorganisms, remain unclear. We integrated metagenomic and metatranscriptomic sequencing with [13]C and [15]N isotope labeling to examine how oxidation-reduction potential (ORP) and ammonium (NH4[+]) availability regulate microbial assembly and metabolism in mangrove sediments. ORP emerged as the primary determinant of microbial composition and diversity, while NH4[+] exerted variable effects on microbial traits. Under high ORP, CBBL-microorganisms predominantly utilized the cmmG CO2-concentrating mechanism, and carbon fixation rates decreased with increasing NH4[+] concentration. Under low ORP, CBBM-harboring genera dominated, primarily utilizing another mechanism cmmE, while NH4[+] had little effect and total organic carbon (TOC) exerted stronger control. ORP thus acts as the dominant environmental filter, with NH4[+] selectively affecting nitrifiers and carbon-fixing taxa. This was the first study to simultaneously measure ammonia oxidation and carbon fixation rate in mangrove sediments, revealing their mechanistic coupling. This work provides new mechanistic insights into the regulation of microbial metabolic potential in mangrove ecosystems and contributes to a broader understanding of their resilience and function in coastal biogeochemical cycles under fluctuating climate and environmental conditions.}, }
@article {pmid41762498, year = {2026}, author = {Jiang, PY and Tang, H and Tong, WK and Liu, J and Liu, K and Tang, W and Liu, JB and Gao, MT and Liu, N and Hu, J and Li, J}, title = {Interface modification of membrane substrates: Mitigating microbial interfacial adhesion and augmenting adsorptive capacity for seawater uranium recovery.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129080}, doi = {10.1016/j.jenvman.2026.129080}, pmid = {41762498}, issn = {1095-8630}, mesh = {*Seawater/chemistry ; *Uranium ; Adsorption ; }, abstract = {Seawater is endowed with vast reserves of high-value trace metals (gold, lithium, uranium) for resource recovery. However, their extremely low concentrations entail extensive, long-duration seawater processing in membrane-based systems, leading to pronounced microbial fouling and a substantial deterioration in adsorption efficiency. Given that practical membrane modules possess a multi-component architecture, this study mitigated microbial fouling via indigo modification of membrane supporting substrates, while maintaining the structural and functional integrity of the adsorptive membrane. This approach avoids the impairment of adsorption sites and porous structures induced by direct antimicrobial modification of the membrane. Column breakthrough experiments were employed to assess the fouling characteristics and severity of membrane modules in terms of macroscopic retention and structural evolution. Before modification, the membrane module exhibited interception rates of 79.8% and 77.3% for single strains and in-situ marine microbial communities (multiple strains), respectively, which were reduced to 45.6% and 57.1% after modification. Analysis using the dual-kinetic-site attachment-detachment model demonstrated that indigo-modified substrates reduced Langmuirian attachment and ripening, while the functional complementarity within microbial communities mitigated these effects. Metagenomic analysis confirmed that the modification selectively suppressed the attachment of microorganisms with strong adhesion and biofilm-forming ability. In a 28-day adsorption validation in real seawater, the modification increased the uranium adsorption capacity from 1.05 to 2.38 mg/g, effectively attenuating the performance decline induced by microbial contamination. The spatially decoupled integration of substrate anti-adhesion and membrane adsorption offers a new paradigm for membrane module design and optimization, extending its application potential in marine uranium recovery.}, }
@article {pmid41762508, year = {2026}, author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X}, title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129121}, doi = {10.1016/j.jenvman.2026.129121}, pmid = {41762508}, issn = {1095-8630}, mesh = {*Manure/microbiology ; Animals ; Swine ; Anaerobiosis ; *Metal-Organic Frameworks ; Drug Resistance, Microbial ; *Virome ; }, abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.}, }
@article {pmid41762837, year = {2026}, author = {Wang, Y and Zhang, X and Wu, Y and Sun, X and Zhang, X and Lv, J}, title = {Biodegradation pathway of organophosphate esters in sludge composting implications for environmental safety.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141622}, doi = {10.1016/j.jhazmat.2026.141622}, pmid = {41762837}, issn = {1873-3336}, mesh = {*Sewage/microbiology/chemistry ; Biodegradation, Environmental ; *Composting ; *Organophosphates/metabolism ; *Esters/metabolism ; Bacteria/metabolism ; *Soil Pollutants/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Soil Microbiology ; }, abstract = {Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation during sludge composting. In this study, under the stress of 100 mg/kg ∑7OPEs, three bacterial strains with degradation capabilities-Bacillus subtilis, Bacillus licheniformis, and Ralstonia pickettii-were screened and isolated, and a synthetic bacterial community (SynCom) was constructed. During 55 days sludge composting, the concentration of ∑7OPEs decreased significantly. In CK, TnBP degraded the fastest (> 90%). For the exogenous OPE-added groups strengthened with SynCom (T1B and T2B), the removal rates of TCPP and TPhP were nearly complete (> 93%). However, high concentrations of ∑7OPEs inhibited the degradation of compounds such as TCrP and EHDPP. Hydrolysis was identified as the preferentially initiated pathway for ∑7OPEs degradation during sludge composting. Functional enzyme such as phosphatase, as well as bacterial strains from the Rhodococcus and Paracoccus, synergistically participated in the degradation process. Multiple linear regression analysis confirmed that SynCom promoted ∑7OPEs removal by boosting phosphomonoesterase activity and enriching phosphatase-producing microorganisms. pH and total phosphorus (TP) emerged as critical environmental factors influencing this degradation. Composting significantly lowered OPE-associated ecological risks, ensuring the safe resource recovery of sludge. This study focused on the biological removal of OPEs during sludge composting. It first systematically evaluated the biodegradation efficiency of ∑7OPEs and clarified core metabolic pathways. Furthermore, key microbial communities and functional genes associated with ∑7OPEs degradation were identified, revealing their regulatory roles. It provides scientific support for controlling OPEs pollution and promoting sludge resource utilization.}, }
@article {pmid41763050, year = {2026}, author = {Cai, F and Wang, C and Liu, H and Shen, J and Wang, J and Yang, Y and Wang, X}, title = {Partitioning dynamics and microbial responses drive the fate of polycyclic aromatic hydrocarbons in a plateau lake.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129097}, doi = {10.1016/j.jenvman.2026.129097}, pmid = {41763050}, issn = {1095-8630}, mesh = {*Lakes/chemistry ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; China ; Environmental Monitoring ; Geologic Sediments ; Seasons ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent organic contaminants of concern in freshwater drinking-water sources, yet their environmental fate in hydrologically dynamic plateau lakes remains poorly constrained. Here, we investigated the multi-compartment distribution, apparent particle-water partitioning, microbial functional potential, and associated ecological and human-health risks of PAHs in Erhai Lake, a large subtropical plateau lake in southwestern China. PAHs were quantified simultaneously in the dissolved, suspended particulate, and surface-sediment phases across three seasons. Dissolved low-molecular-weight PAHs dominated the water column, exhibiting pronounced seasonal variability with summer peaks (12.9-49.8 ng L[-1]) driven by intensified tourism and hydrological inputs. In contrast, high-molecular-weight PAHs preferentially accumulated in sediments, forming depositional hotspots in the southern basin. Apparent organic-carbon-normalized partition coefficients (KOC,app) revealed that suspended particulates act as dynamic regulators of PAH transport and microbial accessibility. Metagenomic analysis revealed that the distribution of PAH-degradation-related functional genes co-varied with chemical partitioning patterns, suggesting potential microbial mediation of PAH fate. Ecological and human health risk assessments, including probabilistic Monte Carlo simulations, indicated that PAH-related risks remained within a low-risk regime across all seasons. Collectively, these findings provide a mechanistic framework for understanding how partitioning and microbial metabolism jointly regulate the fate of PAHs in plateau lakes, offering critical insights for the management of sensitive freshwater resources.}, }
@article {pmid41763967, year = {2026}, author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC}, title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ard.2026.01.018}, pmid = {41763967}, issn = {1468-2060}, abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).
METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.
RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.
CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.}, }
@article {pmid41764386, year = {2026}, author = {Mtetwa, HN and Amoah, ID and Mthethwa-Hlongwa, NP and Pieerneef, R and Kumari, S and Bux, F and Reddy, P}, title = {Decoding mycobacterial ecology in Sub-Saharan African wastewater: metagenomic and metatranscriptomic insights for tuberculosis surveillance.}, journal = {Journal of water and health}, volume = {24}, number = {2}, pages = {109-127}, pmid = {41764386}, issn = {1477-8920}, support = {96086//South African Medical Research Council/ ; }, mesh = {*Wastewater/microbiology ; Africa South of the Sahara/epidemiology ; Metagenomics ; *Tuberculosis/epidemiology/microbiology ; *Mycobacterium/genetics/isolation & purification/classification ; *Metagenome ; Humans ; }, abstract = {Tuberculosis (TB) remains a major public health challenge in sub-Saharan Africa, driven by high transmission, delayed diagnosis, and limited surveillance. This study presents one of the first integrated applications of shotgun metagenomic and metatranscriptomic sequencing to investigate Mycobacterium communities in wastewater across six TB-endemic countries: Cameroon, Ghana, Kenya, Nigeria, South Africa, and Uganda. Twelve untreated and treated wastewater samples were analysed to characterise taxonomic composition, strain-level diversity, and transcriptional activity. Metagenomic analyses revealed diverse Mycobacterium communities, including M. tuberculosis, M. canettii, M. bovis, and members of the M. avium complex. Metatranscriptomic data detected MTBC-associated transcripts, indicating transcriptional activity and/or persistence of MTBC RNA signals in wastewater, with higher signal predominance in influent samples, consistent with community-level shedding. Metagenome-assembled genomes (MAGs) recovered from South Africa, Cameroon, and Uganda showed >82% completeness and included zoonotic species. MTBC strains clustered into Lineages 1, 2, 4, and 6, with animal-adapted strains linked to livestock and rodents, highlighting One Health relevance. Overall, this dual-omics approach supports wastewater-based epidemiology as a scalable tool for TB surveillance in high-burden settings.}, }
@article {pmid41764388, year = {2026}, author = {Zhu, K and Amirali, A and Auch, B and Babler, KM and Biswas, P and Bowie, K and Choudhary, S and Currall, BB and Grills, GS and Healy, HG and Liachko, I and Lucaci, AG and Mason, CE and Sharkey, M and Shigeno Risse-Adams, O and Shukla, BS and Sisson, Z and Stevenson, M and Williams, SL and Zulli, A and Peccia, J and Solo-Gabriele, HM}, title = {Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.}, journal = {Journal of water and health}, volume = {24}, number = {2}, pages = {148-159}, pmid = {41764388}, issn = {1477-8920}, support = {//4Catalyzer/ ; U01DA053941/DA/NIDA NIH HHS/United States ; P30AI073961/NH/NIH HHS/United States ; }, mesh = {*Wastewater/microbiology ; *Metagenome ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; }, abstract = {The proliferation of antimicrobial resistance genes (ARGs) poses public health risks globally, with wastewater treatment plants (WWTPs) serving as dissemination hubs for horizontal gene transfer. In this study, we evaluated the potential of applying Hi-C sequencing coupled with metagenomic bioinformatics for surveillance of ARGs and other microbial fitness traits using samples from WWTPs. Hi-C sequencing has the advantage over other molecular approaches by directly associating genes conveying fitness to their host microbe, plus to their element type (in plasmids, phages, or within the core genome of its host microbe). Results from Hi-C analyses confirm results from more laborious approaches by showing that aminoglycoside resistance is disseminated by plasmids. Mercury resistance was found in Zoogloea bacteria. Resistance genes to quaternary ammonium compounds were found within bacteriophages. Results from this study provide proof-of-concept for the potential value of Hi-C metagenome sequencing in wastewater attribution studies by illustrating the breadth of information that can be obtained about the microbial community, the exchange of genes, and their interconnections. We believe that with further development, Hi-C sequencing can be integrated into routine monitoring of wastewater for the purpose of providing near-real-time information about the dissemination of fitness traits, including ARGs.}, }
@article {pmid41764576, year = {2026}, author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S}, title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41764576}, issn = {1674-9782}, support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; }, abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.
RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.
CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.}, }
@article {pmid41764643, year = {2026}, author = {Zeller, LM and Schorn, S and Nicolas-Asselineau, L and Zopfi, J and Ahmerkamp, S and Schubert, CJ and Lepori, F and Kuypers, MMM and Graf, JS and Milucka, J}, title = {Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag043}, pmid = {41764643}, issn = {1751-7370}, abstract = {Bacterial endosymbionts of the family Ca. Azoamicaceae obligately associate with anaerobic ciliates belonging to the class Plagiopylea. The symbionts' unique role for their host involves anaerobic respiration of nitrate and generation of ATP, analogous to the role of mitochondria in aerobic eukaryotes. As this symbiosis remains so far uncultured, insights into its functioning have been mainly inferred from environmental metagenomes. Here we investigated the distribution and environmental role of this symbiosis in the anoxic basins of two freshwater lakes Zug and Lugano (Switzerland) over a course of several years. We found that the environmental niche of the ciliate host is defined by the combined effects of sulfide, oxygen and nitrate, the latter of which is essential for the symbiont's respiratory function. Moreover, the distribution and abundances of ciliates with denitrifying endosymbionts in the water column suggests that they may substantially contribute to nitrate consumption in Lake Zug. Our microscopic analyses further demonstrated a coordinated division of the Candidatus Azoamicus ciliaticola symbionts and their ciliate hosts, implying a vertical inheritance of denitrifying symbionts. These observations offer new insights into the evolution of ciliates with denitrifying endosymbionts and their ecological role in oxygen-depleted lakewaters.}, }
@article {pmid41764831, year = {2026}, author = {Peng, X and Zhang, L}, title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {2}, pages = {117321}, doi = {10.1016/j.diagmicrobio.2026.117321}, pmid = {41764831}, issn = {1879-0070}, mesh = {Humans ; *Metagenomics/methods ; *Communicable Diseases/diagnosis/drug therapy/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; Computational Biology ; Anti-Bacterial Agents/therapeutic use ; Bacteria/genetics/drug effects ; }, abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.}, }
@article {pmid41764843, year = {2026}, author = {Das, N and Pandey, P}, title = {Striking a microbial balance: Rhizoremediation of crude oil-contaminated soils suppresses resistomes and reconstructs hydrocarbon-degrading microbial networks.}, journal = {The Science of the total environment}, volume = {1022}, number = {}, pages = {181586}, doi = {10.1016/j.scitotenv.2026.181586}, pmid = {41764843}, issn = {1879-1026}, mesh = {*Soil Pollutants/metabolism/analysis ; Biodegradation, Environmental ; *Petroleum/metabolism/analysis ; *Soil Microbiology ; *Hydrocarbons/metabolism ; *Petroleum Pollution ; Polycyclic Aromatic Hydrocarbons/metabolism ; Soil/chemistry ; }, abstract = {Integrated plant-microbe systems are crucial for restoring hydrocarbon- and heavy metal-contaminated soils. Here, Azadirachta indica inoculated with a hydrocarbon-degrading bacterial consortium (SynCom) was used in microcosm and field trials to remediate chronically oil-contaminated soils. SynCom treatment enhanced degradation of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) up to 99%, reduced heavy metal concentrations, and neutralized soil pH, while improving organic matter, soil aggregation, and nutrient mobilization (N, P, K). Metagenomic analyses revealed a shift from Proteobacteria to Actinobacteria, with a 10-fold reduction in antibiotic resistance genes, particularly multidrug resistance and efflux pump genes. Key functional taxa (Nocardioides, Bradyrhizobium japonicum, Rhodopseudomonas) were enriched, correlating with enhanced nutrient cycling, soil enzyme activity, and hydrocarbon degradation. Functional gene profiling indicated reduced oxidative stress and ecological recovery. This study demonstrates that targeted rhizoremediation effectively detoxifies soils while mitigating ARGs dissemination, offering a sustainable One Health-aligned strategy for environmental and public health protection.}, }
@article {pmid41764882, year = {2026}, author = {Huang, L and Feng, L and Sun, Y and Li, Z and Deng, L and Zhang, P and Li, X and Gao, D and Wang, Y and Deng, S and Shen, F and Fang, D}, title = {Oxygen stress drives overcompensation of carbon sources for enhanced polymer denitrification.}, journal = {Water research}, volume = {296}, number = {}, pages = {125631}, doi = {10.1016/j.watres.2026.125631}, pmid = {41764882}, issn = {1879-2448}, mesh = {*Denitrification ; *Oxygen ; *Carbon/metabolism ; Biofilms ; Nitrates ; Polymers ; Polyesters ; }, abstract = {Dissolved oxygen (DO) is traditionally considered as a strong inhibitor of denitrification. However, its impact on polymer-based denitrification, where carbon bioavailability is rate-limiting, remains poorly understood. Here, we investigated the response of a polycaprolactone (PCL)-supported biofilm system to long-term DO stress (2-8 mg/L). Contrary to conventional expectations, elevating DO from 2 to 8 mg/L significantly accelerated nitrate removal (from 8.06 to 10.50 mg N/L) rather than suppressing it. Stoichiometric modeling and metabolomic analysis revealed an oxygen-induced carbon release mechanism, where high DO stimulated the secretion of extracellular esterases and intensified the β-oxidation pathway, increasing polymer carbon release by 17.71 mg/L. This excess carbon overcompensated for aerobic consumption, effectively alleviating electron donor limitations. Metagenomics further confirmed a structural shift towards an oxygen-tolerant consortium, with significant enrichment of dual-function genera (e.g., Pseudoxanthomonas) and enhanced coupling of respiratory chain complexes (I-III). The biofilm achieved spatial decoupling, utilizing the outer aerobic layer for rapid hydrolysis and oxygen consumption to protect the inner anoxic denitrification zone. These findings overturn the strict anoxic requirement for denitrification, providing a robust strategy for advanced nitrate removal in oxygen-fluctuating tailwaters.}, }
@article {pmid41764931, year = {2026}, author = {Wang, G and Wei, J and Qiu, G and Guo, Z and Wang, W and Liu, X and Song, Y}, title = {Mechanism of activated carbon enhanced activated sludge (ACEAS) in treating recalcitrant chemical wastewater.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129058}, doi = {10.1016/j.jenvman.2026.129058}, pmid = {41764931}, issn = {1095-8630}, mesh = {*Sewage/chemistry ; *Wastewater/chemistry ; *Water Pollutants, Chemical ; *Waste Disposal, Fluid/methods ; Charcoal/chemistry ; Nitrobenzenes ; Biological Oxygen Demand Analysis ; Carbon ; }, abstract = {Recalcitrant chemical accident wastewater, especially nitrobenzene-containing wastewater, has posed a significant treatment challenge due to complex hazardous compounds as well as elevated toxicity. Activated carbon combined activated sludge processes can effectively remove hazardous organic pollutants from chemical wastewater. However, the interaction mechanism between activated carbon and activated sludge remains unclear. This study proposed the activated carbon enhanced activated sludge (ACEAS) process for treating nitrobenzene-containing wastewater. Combined with material characterization and metagenomic analysis, the removal efficiency of nitrobenzene was evaluated, and the interaction mechanisms between activated carbon and activated sludge was further investigated. The key findings include: The effluent nitrobenzene concentration in conventional activated sludge (AS) process was 6.5 and 9.2 times higher than in the original ACEAS (OS) and regenerated ACEAS (RS) processes, respectively. Without activated carbon replenishment, chemical oxygen demand (COD) removal efficiency in OS and RS processes increased by 10.19%-15.86% and 11.41%-14.60%, respectively, compared to AS process during long-term operation (6-24 h). Due to the formation of biofilms on the surface of activated carbon, and the content of C-O/C=O and C-N/C=N on OS increased by 13.2% and 17.3%, respectively, compared to original activated carbon (OC). Eventually, four enhanced mechanisms of activated carbon were proposed, each contributing to distinct degradation stages in the ACEAS system. In prophase, activated carbon might reduce toxicity and improve microbial degradation capacity by adsorption. During metaphase, biofilms on activated carbon surface further diminished adsorption/desorption effect. In the telophase, microbial carrier's fixation affected strengthens, reshaping microbial community structure, functional gene expression, and metabolic pathway selection, thereby enhancing activated sludge degradation efficiency.}, }
@article {pmid41764980, year = {2026}, author = {Xie, J and Hu, T and He, J and Cai, Y and Wu, Q and Li, L and Liu, H}, title = {Genome characterization and evolutionary analysis of a novel Anativirus from a wild Muscovy duck in Guangdong, China.}, journal = {Virology}, volume = {618}, number = {}, pages = {110849}, doi = {10.1016/j.virol.2026.110849}, pmid = {41764980}, issn = {1096-0341}, mesh = {Animals ; *Ducks/virology ; *Genome, Viral ; China ; Phylogeny ; *Evolution, Molecular ; Open Reading Frames ; *Bird Diseases/virology ; Animals, Wild/virology ; Viral Proteins/genetics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae/genetics/classification/isolation & purification ; }, abstract = {A novel member of the genus Anativirus was identified and characterized from a naturally deceased wild Muscovy duck (Cairina moschata) collected in Maoming, Guangdong Province, China. This strain, provisionally designated Anativirus GD2411, was detected through metagenomic next-generation sequencing (mNGS), which yielded a complete genome of 8,085 nucleotides. The genome comprises a single open reading frame (nt 413-7,873) encoding the canonical picornaviral polyprotein, flanked by a 5' untranslated region (UTR; 412 nt) and a 3' UTR (209 nt) with a poly(A) tail. Whole-genome nucleotide identity analysis revealed that GD2411 clustered with duck-origin strains, sharing 88.0% identity with CH01 and 81.2% with TW90, but only 50.6% with the chicken-derived strain CHK1. High amino acid conservation was observed across functional regions, particularly in 2C (≥91.9%), 3C (≥92.4%), and 3D (≥97.0%), reflecting the preservation of RNA-dependent RNA polymerase function. Phylogenetic analyses based on complete genomes and 3D protein sequences using maximum likelihood methods consistently placed GD2411 within the duck Anativirus clade, indicating a close evolutionary relationship with TW90 and CH01. Although an experimental infection model was not established, PCR screening revealed broad gastrointestinal distribution of the virus, with the highest viral load detected in the cecum, suggesting fecal-oral transmission as a primary route. These findings provide preliminary evidence of Anativirus infection in wild Muscovy ducks in southern China, though the limited sample size precludes definitive conclusions regarding host range expansion. The highly conserved 3D region is highlighted as a potential target for antiviral therapy or vaccine development.}, }
@article {pmid41765175, year = {2026}, author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C}, title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.}, journal = {Journal of endodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joen.2026.02.016}, pmid = {41765175}, issn = {1878-3554}, abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.
METHODS: Samples from 25 teeth with large (>8 mm) and 20 with small periapical lesions (<2 mm) were analyzed. Quantitative polymerase chain reaction, 16S next-generation and whole genome sequencing were used to assess microbial load, diversity, and composition. Functional predictions were performed using the Kyoto Encyclopedia of Genes and Genomes and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.
RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (P = .011), but comparable alpha diversity and number of species per group in 16S and whole genome analysis (P > .05). Lesion size showed significance by ANOSIM (P = .04) but not in PERMANOVA (P = .36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, P = .012; PERMANOVA R[2] = 0.063, P = .046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.
CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.}, }
@article {pmid41765316, year = {2026}, author = {Lyu, Y and Ye, Y and Zhang, C and Zhong, W and Zhu, L}, title = {Bisphenol A bis (diphenyl phosphate) disrupts tryptophan metabolism through microbiota dysbiosis to promote intestinal toxicity.}, journal = {Environmental research}, volume = {297}, number = {}, pages = {124140}, doi = {10.1016/j.envres.2026.124140}, pmid = {41765316}, issn = {1096-0953}, abstract = {Organophosphorus flame retardants (OPFRs) are associated with intestinal injury. Bisphenol A bis(diphenyl phosphate) (BDP), an emerging OPFR that presents widely in organisms and humans, may induce intestinal toxicity, yet the effect and underlying mechanism remains unclear. In this study, zebrafish were exposed to BDP at 2, 20 and 200 μg/L for 21 days. Distinct histopathological changes in the intestine of zebrafish were observed, and the relative expressions of mucus secretion and tight junction related genes (MUC-2, Occuludin a and ZO-1) were all downregulated. Through the integrated analysis combining metabolomics and metagenomics, the results demonstrated that BDP exposure downregulated the abundances of microbiota Peptostreptococcus, Clostridium, Bombilactobacillus and Sporolactobacillus in zebrafish intestines, to depress tryptophan metabolism and eventually reduce the abundances of tryptophan metabolites. As a result, the expression of AhR, an important receptor activated by tryptophan metabolites, was inhibited to downregulate IL-22 expression, promoting intestinal toxicity. In vivo experiment with indole-3-propionic acid supplement alleviated the pathological changes, which further confirmed that BDP destroyed microbiota-tryptophan metabolism homeostasis to interfere with the AhR-IL-22 axis, eventually promoted pathological toxicity in the intestines. This study highlights vulnerability of intestines to BDP, and provides first insight into the mechanism through which BDP threats intestinal health.}, }
@article {pmid41765557, year = {2026}, author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W}, title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.}, journal = {Journal of environmental sciences (China)}, volume = {162}, number = {}, pages = {573-583}, doi = {10.1016/j.jes.2025.05.044}, pmid = {41765557}, issn = {1001-0742}, mesh = {*Cadmium/metabolism ; *Bacillus cereus/metabolism/physiology ; *Oryza ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/analysis ; Soil Microbiology ; Rhizosphere ; }, abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.}, }
@article {pmid41765668, year = {2026}, author = {Nian, YP and Ning, SS and Li, SS and Yu, PB and Meng, Y and Zhao, X and Ren, RQ and Yan, J and Han, XY and Zheng, ZX and Zhang, QF and Wang, X and Zhang, Y}, title = {[Investigation and management of the first case of human infection with avian influenza A(H10N3) virus in northern China].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {47}, number = {2}, pages = {275-280}, doi = {10.3760/cma.j.cn112338-20250616-00397}, pmid = {41765668}, issn = {0254-6450}, mesh = {Humans ; China/epidemiology ; *Influenza, Human/epidemiology/virology ; *Influenza A virus/isolation & purification ; Animals ; Influenza in Birds/epidemiology/virology ; Male ; Poultry ; }, abstract = {Objective: To summarize and analyze the epidemiological characteristics and field investigation of the first case of human infection with avian influenza A(H10N3) virus in northern China and to provide reference for the investigation and management of human infection with animal-derived influenza in the future. Methods: Case epidemiological investigation, identification and medical observation of co-exposed people and close contacts, and tracing investigation and analysis of infection source were carried out. Samples were collected from the case, co-exposed persons, close contacts, poultry, and the external environment. Real-time fluorescent quantitative RT-PCR was used to detect influenza A virus. The positive samples were subjected to metagenomic sequencing and compared. Results: This is the first case of human infection with the avian influenza A(H10N3) virus in northern China, and a third-party laboratory performed the detection. The patient became ill on April 13, 2025, with no history of contact with similar cases prior to symptom onset but with a history of exposure to poultry. The macrogene test of bronchoalveolar lavage fluid was positive for avian influenza A(H10N3) virus on April 28, 2025. A total of 168 samples were collected from co-exposed individuals, close contacts, poultry, and the external environment, and all were negative for avian influenza A(H10N3) virus. Metagenomic sequencing analysis showed that the sequence had high homology with the human infection case of avian influenza A(H10N3) virus reported in Guangxi Zhuang Autonomous Region in December 2024. After taking emergency measures such as medical observation of close contacts, harmless treatment of poultry in the sick home, and disinfection of suspected exposure places, no secondary cases occurred. The case was cured and discharged on May 14. Conclusions: The source of the first human case of avian influenza A(H10N3) infection in northern China remains unclear, but no human-to-human transmission has been found. It is important to improve the sensitivity of surveillance for new subtypes of animal-derived influenza viruses, such as avian influenza A(H10N3), and to strengthen joint prevention and control between health and animal husbandry departments to support scientific approaches to preventing and controlling human infection with these viruses.}, }
@article {pmid41766220, year = {2026}, author = {Schwedhelm, C and Pinart, M and Forslund-Startceva, SK and Oluwagbemigun, K and Dötsch, A and Schlicht, K and Schwarz, F and Siampani, SM and Avraam, D and De Angelis, M and Bouwman, J and Brigidi, P and Caderni, G and Calabrese, FM and Cuadrat, RRC and De Filippo, C and De Filippis, F and Ercolini, D and Fabbrini, M and Laudes, M and Nöthlings, U and Özsezen, S and Sharon, I and Schulze, MB and Turroni, S and Vitali, F and Pischon, T and Nimptsch, K}, title = {Associations of Adiposity With Gut Microbiota Composition Among Adults-Results From a Federated Analysis of Individual Participant Data From Eight European Observational Studies.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {}, number = {}, pages = {e70106}, doi = {10.1111/obr.70106}, pmid = {41766220}, issn = {1467-789X}, support = {FKZ 01EA1906A//Bundesministerium für Bildung und Forschung/ ; 01EA1906B//Bundesministerium für Bildung und Forschung/ ; 01EA1906F//Bundesministerium für Bildung und Forschung/ ; BMBF//Bundesministerium für Bildung und Forschung/ ; //Fund for Scientific Research (FRS-FNRS, Belgium)/ ; //Research Foundation-Flanders (FWO, Belgium)/ ; //Institut National de la Santé et de la Recherche Médicale/ ; //Bundesministerium für Ernährung und Landwirtschaft/ ; //Ministero dell'Istruzione, dell'Università e della Ricerca/ ; //National Institute of Health Carlos III/ ; //the Netherlands Organization for Health Research and Development (ZonMw, the Netherlands)/ ; //Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie/ ; //Ministry of Science and Technology (Israel)/ ; //Formas (Sweden) and HDHL-Intimic Era-Net (EarlyFOOD)/ ; JTC-2017-7//Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"/ ; //European Union/ ; DZD Grant 82DZD00302//Ministerium für Ländliche Entwicklung, Umwelt und Landwirtschaft des Landes Brandenburg/ ; 442326535//National Research Data Infrastructure for Personal Health Data (NFDI4Health) by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; }, abstract = {Gut microbiota may contribute to the adiposity-associated disease risk, but human studies reported inconsistent associations of adiposity with gut microbiota composition. We examined associations of body mass index (BMI) with alpha diversity and relative microbial abundance at the phylum and genus taxonomic levels (based on 16S rRNA amplicon sequencing or metagenomics) among 7415 adults from eight European observational studies in a joint federated analysis of harmonized data using DataSHIELD. Higher BMI (per 5 kg/m[2]) was associated with lower alpha diversity (β: -0.05; 95% CI: -0.07, -0.03) and, on the phylum level, positively associated with Proteobacteria, but neither with Firmicutes nor Bacteroidetes nor their ratio, where high between-study heterogeneity was observed. On the genus level, BMI was inversely associated with the relative abundance of Faecalibacterium of the Firmicutes phylum (β: -0.11; 95% CI: -0.14, -0.07) but positively with the odds of detection of Dorea, Streptococcus, and Clostridium (all three Firmicutes) as well as Collinsella (Actinobacteria). This federated analysis of multiple studies found lower alpha diversity, alongside depleted Faecalibacterium, as well as higher odds of detection of Dorea, Streptococcus, Clostridium, and Collinsella with higher adiposity. By combining data from diverse study populations using harmonized data and statistical methods, our analysis partly overcomes sources of heterogeneity that may explain previously observed inconsistencies.}, }
@article {pmid41766731, year = {2026}, author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF}, title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73172}, pmid = {41766731}, issn = {2045-7758}, abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.}, }
@article {pmid41767535, year = {2026}, author = {Chen, J and Yang, J and Zhang, Y}, title = {Case Report: Rare pulmonary infection and cytomegalovirus retinitis revealed a case of lymphoma.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1732360}, pmid = {41767535}, issn = {2296-858X}, abstract = {BACKGROUND: Recurrent cytomegalovirus retinitis (CMVR) and rare opportunistic pulmonary infections may be the initial manifestations of underlying immunodeficiency caused by occult hematologic malignancy. Epstein-Barr virus-positive diffuse large B-cell lymphoma, not otherwise specified (EBV[+]DLBCL-NOS) is an aggressive lymphoma associated with immune dysfunction, predisposing patients to severe opportunistic infections, including CMVR. However, pulmonary co-infection with Tropheryma whipplei and Penicillium digitatum has not been previously described as a presenting feature of EBV[+] DLBCL-NOS.
CASE: A 66-year-old male presented with blurred vision and was diagnosed with CMVR, with profoundly low CD4[+] T-cell counts (102 cells/μL) and high cytomegalovirus (CMV) DNA levels in blood and aqueous humor. He initially responded to ganciclovir, but CMVR recurred five months later, accompanied by new pulmonary nodules. Despite negative conventional microbiological tests, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified co-infection with Tropheryma whipplei and P. digitatum. Broad-spectrum antimicrobial therapy led to partial clinical improvement, but pulmonary lesions persisted. PET-CT revealed hypermetabolic lung and lymph node lesions, and subsequent lung biopsy confirmed EBV[+] DLBCL-NOS. The patient's progressive immunodeficiency, recurrent CMVR, and refractory pulmonary infection were ultimately attributed to underlying lymphoma.
CONCLUSION: This case highlights that severe, unexplained immunodeficiency with recurrent CMVR and rare opportunistic pulmonary infections should prompt a high index of suspicion for underlying hematologic malignancy. mNGS and PET-CT are critical tools in the diagnostic workup, but definitive diagnosis relies on histopathological confirmation. Early recognition of such presentations can prevent delays in diagnosing aggressive lymphomas.}, }
@article {pmid41767718, year = {2026}, author = {Cao, M and Zhang, X and Huang, L}, title = {Advanced renal tuberculosis due to misdiagnosis as recurrent urinary tract infection: A case report.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02527}, pmid = {41767718}, issn = {2214-2509}, abstract = {Renal tuberculosis (RTB) lesions often initially localize to a specific part of the kidney, presenting with minimal clinical symptoms and a very slow disease progression, which makes the condition highly susceptible to misdiagnosis. We report an instructive case from the Second Affiliated Hospital of Zhejiang University School of Medicine, where a patient was ultimately diagnosed with advanced RTB after a 20-year diagnostic odyssey. The patient exhibited atypical clinical symptoms and was repeatedly diagnosed with recurrent urinary tract infection (UTI). Initial urinalysis revealed microscopic hematuria (52 RBCs/μL), pyuria (615 WBCs/μL), and 1 + proteinuria (0.7 g/L). A urine culture tested positive for Escherichia coli. Ultrasound imaging indicated a right renal calculus, and intravenous pyelography demonstrated significantly diminished right renal function. Suspicion for RTB was raised by CT findings and a positive tuberculosis infection T-cell spot (T-SPOT.TB) test. Acid-fast bacilli were consistently detected in two consecutive urine sediment examinations. The diagnosis was ultimately confirmed through metagenomic next-generation sequencing (mNGS) and postoperative pathological examination. This case underscores that the early diagnosis of RTB is challenging and requires a high index of clinical suspicion, comprehensive analysis of manifestations, and the strategic integration of modern diagnostic tools.}, }
@article {pmid41767950, year = {2026}, author = {Tang, L and Luo, Z and Gao, S and Lin, Z and Sun, M and Li, R and Gao, SH and Wu, G and Li, Y and Huang, L and Fan, L}, title = {A hot origin of dissimilatory sulfite reduction catalyzed by DsrAB in the Paleoarchean Era.}, journal = {mLife}, volume = {5}, number = {1}, pages = {108-121}, pmid = {41767950}, issn = {2770-100X}, abstract = {Dissimilatory sulfite reduction (DSR) has been essential to microbial energy metabolism in the biogeochemical sulfur cycle since the Paleoarchean Era. However, due to the lack of an integrated assessment of geological record and genomic data, the evolutionary origin of DSR remains elusive in terms of time, habitat, and genetic basis. In this study, we reconstructed the evolutionary pathways and the ancestral sequences of Dsr proteins by mining metagenomes ranging from mesothermal to hyperthermal environments. A phylogenetic analysis of the key catalytic enzyme, DsrAB, and other Dsr proteins indicates that the earliest and most basic functional cascade, DsrABCNM, emerged prior to the latest common ancestor of several basal branching DsrAB clusters encoded by bacteria and archaea. Using a molecular dating strategy that calibrates the protein tree with a species tree, we predicted that the DSR originated 3.508 billion years ago (Ga). This finding strongly confirms the earliest geological evidence of DSR (~ 3.47 Ga). Further predictions from ancestral sequence reconstruction indicate that the optimal catalytic temperature of DsrA at the time of DSR origin was approximately 73°C, which is consistent with the petrographic and geochemical evidence in early Archean hydrothermal deposits. After its hot origin, DsrA diversified into subclades that adapted to various temperature levels following the Great Oxidation Event. This is exemplified by the evolution of the reductive archaeal-type DsrA. Our results synchronize the molecular ages with the geological record, which advances our understanding of the earliest DSR systems and highlights the enzymatic adaptations of microbial life in the Archean biosphere.}, }
@article {pmid41768053, year = {2026}, author = {Lv, M and Tian, D and Wang, G and Hou, C and Fan, T and Li, W}, title = {Salinity gradients alter root-zone soil microbiome structure and nitrogen-related functional potential in alfalfa (Medicago sativa L.): a pot experiment.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1753229}, pmid = {41768053}, issn = {1664-462X}, abstract = {INTRODUCTION: Soil salinization constrains agricultural sustainability in arid and semi-arid regions. This study examined integrated soil-plant-microbe responses of alfalfa (Medicago sativa L.) to a salinity gradient.
METHODS: A pot experiment was conducted with control, low-, and moderate-salinity treatments. Root-zone soil and plants were sampled to measure soil EC, pH, and inorganic nitrogen forms, and to assess plant growth traits. Shotgun metagenomics was used to characterize microbial community composition and metagenome-inferred functional potential.
RESULTS: Salinity increased soil EC and pH and altered inorganic nitrogen forms, with higher NO3 [-]-N under moderate salinity and lower NH4 [+]-N under salinity compared with the control. Plant height peaked under low salinity, whereas fresh and dry biomass decreased under both salinity treatments. Microbial β-diversity differed among treatments, while α-diversity showed limited responses. Functional annotations indicated treatment-associated trends in nitrogen- and stress-related categories and KEGG level 3 pathways; however, most differences were not significant after FDR correction.
DISCUSSION: This integrative root-zone assessment links salinity-driven soil chemistry changes with alfalfa performance and suggests coordinated shifts in soil chemistry, microbiome structure, and plant growth under salinity stress.}, }
@article {pmid41768378, year = {2026}, author = {Li, J and Zeng, P and Mu, X and Cai, C}, title = {Clinical Characteristics and Risk Factors Analysis of Nontuberculous Mycobacterial Pulmonary Disease Complicated with Bronchiectasis.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {483326}, pmid = {41768378}, issn = {1178-6973}, abstract = {BACKGROUND: Nontuberculous mycobacteria pulmonary disease (NTM-PD) frequently coexists with bronchiectasis. This study aimed to compare clinical profiles and identify risk factors between NTM-PD patients with/without bronchiectasis and explore differences between rapid- vs slow-growing non-tuberculous mycobacteria (NTM) species.
METHODS: A retrospective analysis was conducted on patients diagnosed with NTM-PD and admitted to Beijing Tsinghua Changgung Hospital between April 2021 and April 2025. Among 496 inpatients with pulmonary diseases who underwent metagenomic next-generation sequencing (mNGS) analysis of bronchoalveolar lavage fluid, NTM were identified in 57 patients. Ultimately, 43 of these cases were confirmed and diagnosed as having NTM-PD. Relevant clinical data were collected, and the association between each variable and adverse outcomes was assessed using univariate and multivariate logistic regression analyses.
RESULTS: Among the 43 confirmed NTM-PD patients, 24 had concurrent bronchiectasis (NTM-PD with bronchiectasis group) and 19 did not (NTM-PD group). In terms of baseline characteristics, the NTM-PD with bronchiectasis had a significantly higher proportion of females (79.17% vs 31.57%, P=0.002) and lower BMI (19.46 vs 22.46, P=0.023). Slow-growing NTM (SGM, mainly Mycobacterium avium complex [MAC]) was more common in the NTM-PD with bronchiectasis group (70.83% vs 31.58%, P=0.010); rapid-growing NTM (RGM, mainly M. abscessus) was more prevalent in the NTM-PD group (57.89% vs 20.83%, P=0.013). The positive rate of T-SPOT.TB in the NTM-PD group was higher than that in the NTM-PD with bronchiectasis group (47.37% vs 8.33%, P=0.010). Multivariate logistic regression identified female sex as an independent risk factor for NTM-PD complicated with bronchiectasis (OR=17.784, 95% CI: 1.103-286.857, P=0.042), while T-SPOT.TB was not (OR=0.047, 95% CI: 0.002-1.341, P=0.074).
CONCLUSION: Female sex is an independent risk factor for NTM-PD complicated with bronchiectasis. NTM-PD patients with bronchiectasis are more likely to be infected with SGM (especially MAC), while those without bronchiectasis tend to have RGM (especially M. abscessus) infection.}, }
@article {pmid41768489, year = {2025}, author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Iwasaki, M and Dinassing, A and Senthilkumar, R and Preethy, S and Abraham, SJK}, title = {Randomised trial of Aureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation.}, journal = {BMJ nutrition, prevention & health}, volume = {8}, number = {2}, pages = {e000776}, pmid = {41768489}, issn = {2516-5542}, abstract = {OBJECTIVE: Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Anti-inflammatory, antifibrotic effects and enhancement of muscle regeneration biomarkers after oral consumption of Aureobasidium pullulans strain N-163-produced beta 1,3-1,6-glucan (Neu REFIX) having been demonstrated in clinical and preclinical studies of DMD; in this study, we have investigated the effects on the gut microbiome in patients with DMD.
DESIGN: Twenty-seven patients with DMD were included in the study (control (n=9), N-163 (n=18)). Whole-genome metagenomic sequencing was performed in pre-N-163 and post-N-163 intervention faecal samples of each of these participants.
RESULTS: After N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such as Roseburia and Faecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria and Alistipes.
CONCLUSION: Beneficial reconstitution of the gut microbiome after Neu REFIX beta-glucan administration and its safety have been confirmed. These outcomes correlating with the anti-inflammatory, anti-fibrotic effects along with increase in dystrophin in skeletal muscle and plasma, reported earlier make us recommend further in-depth exploration on its role in epigenetic manipulation which when found encouraging might help other genetic diseases as well.
TRIAL REGISTRATION NUMBER: CTRI/2021/05/033346.}, }
@article {pmid41768492, year = {2025}, author = {Vignal, L and de Lahondès, R and Gillibert, A and Tavolacci, MP and Prifiti, E and Formstecher, E and Ribet, D and Quillard, M and Coeffier, M and Déchelotte, P}, title = {Metagenomic analysis of salivary microbiota in patients with anorexia nervosa and association with functional digestive disorders (ORMICAN pilot study).}, journal = {BMJ nutrition, prevention & health}, volume = {8}, number = {2}, pages = {e001112}, pmid = {41768492}, issn = {2516-5542}, abstract = {BACKGROUND: Patients with anorexia nervosa (AN) have intestinal dysbiosis and are frequently affected by oral and upper gastrointestinal disorders. Until now, no metagenomic sequencing data were available on oral microbiota in AN.
DESIGN: This observational study enrolled 46 patients with restrictive/purging AN and 20 controls. Salivary samples were performed after fasting. DNA of oral microbiota from salivary samples was analysed by whole genome shotgun deep sequencing. The primary objective was to compare the diversity of oral microbiota between patients with AN and healthy individuals. Secondary endpoints were to assess the associations between the diversity of oral microbiota and the severity of functional digestive disorders, between patients with a restrictive type of AN and patients with a mixed/purging type and between the diversity of oral microbiota and the severity of AN.
RESULTS: We observed not only a significant decrease in the alpha diversity of oral microbiota in AN patients (4.47 (4.05; 4.75)) versus controls (4.81 (4.68; 5.04)) (p=0.001) but also in gene richness (p=0.00023). There was no significant correlation (95% CI) between oral microbiota diversity and functional digestive disorders nor between patients with a restrictive type of AN and patients with a mixed/purging type of AN, nor between the diversity of oral microbiota and the severity of AN. In addition, we observed four bacterial taxa that were decreased in AN patients.
CONCLUSION: Our study highlights a decreased diversity of oral microbiota in AN patients. Future larger studies may help identify the prognostic and therapeutic value of oral microbiota in AN.}, }
@article {pmid41768933, year = {2025}, author = {Ameer, A and Saleem, F and Keating, C and Afzal, F and Irshad, H and Ahmed, K and Sattar, S and Ijaz, UZ and Javed, S}, title = {Avian cecal microbiome response and resilience to Newcastle disease are dictated by breed background.}, journal = {Frontiers in systems biology}, volume = {5}, number = {}, pages = {1659648}, pmid = {41768933}, issn = {2674-0702}, abstract = {A wide range of viral infections threaten the long-term sustainability of poultry production. Newcastle disease (ND), caused by Newcastle disease virus (NDV), is endemic in most Asian countries, including Pakistan, causing 50%-100% mortality in young and mature chickens. Some local chicken breeds show resistance to certain diseases and have greater survival probability. The chicken gut microbiome is linked to immune response against infections and to production performance parameters. The present study aims to comprehend disease resistance patterns in multiple chicken breeds with respect to gut microbial communities. Day-old Naked Neck, Black Australorp, Rhode Island Red, white layer, and broiler chicks were raised on an antibiotic-free diet in a semi-controlled setup. Vaccinated and non-vaccinated birds were challenged with NDV. Disease onset was delayed in breeds other than broilers, in which disease symptoms appeared at day 3 post-challenge with maximum severity and mortality. Other breeds, irrespective of vaccination, survived through the challenge period. Naked Neck showed the least variation in clinical features and growth parameters. A lower diversity in broiler groups with a significant decrease after NDV challenge was revealed by 16S rRNA amplicon sequencing of cecal DNA. Furthermore, broiler cecal core microbiome membership was found to be more variable than other breeds. Moreover, differentially abundant genera were observed across treatment groups and breeds with a similar effect on the predicted metabolic pathways, indicating varied energy metabolism responses. Shotgun metagenomics revealed a higher abundance of functional genes, including antimicrobial resistance (AMR) genes, stress genes, virulence genes, and amino acid degradation genes in the broiler NDV-infected group compared to the control group. The gut microbiota in chickens affects immunity to infections, health, and productivity. Compared to broilers, local chicken breeds, specifically Naked Neck, are found to have high immune competence in resisting ND while maintaining most performance metrics. Broilers show lower alpha diversity with an unstable core microbiome. Therefore, stable core microbiome maintenance may help the birds cope with the viral infection. The results support the farming of resistant chicken breeds over broilers to reduce production losses from NDV outbreaks.}, }
@article {pmid41769339, year = {2026}, author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Sangtian, M and Panmontha, W and Bunlungsup, S and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sriswasdi, S and Viangteeravat, T}, title = {Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1751074}, pmid = {41769339}, issn = {2235-2988}, mesh = {Humans ; *Urinary Tract Infections/diagnosis/microbiology ; Thailand ; Tertiary Care Centers ; Retrospective Studies ; Female ; Male ; Middle Aged ; Sensitivity and Specificity ; Microbial Sensitivity Tests ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Young Adult ; Aged, 80 and over ; *Molecular Diagnostic Techniques/methods ; Urine/microbiology ; Southeast Asian People ; }, abstract = {BACKGROUND: The BIOTIA-DX platform (BDX), a commercially available clinical-grade mNGS-based test in the United States, has not been analytically validated for urinary tract infections (UTIs) in a Southeast Asian cohort, where microbial epidemiology and antimicrobial resistance (AMR) patterns differ significantly.
OBJECTIVE: Our primary objective was to evaluate the analytical performance and concordance with standard urine culture of the BIOTIA-DX platform in a Thai tertiary hospital setting, thereby assessing its transportability to a Southeast Asian population with distinct microbial epidemiology.
METHODS: We analyzed 398 retrospectively collected urine samples from patients with suspected UTI at a private hospital in Bangkok. Each sample was processed in parallel using standard-of-care urine culture and the BDX mNGS workflow. After excluding 30 samples with insufficient sequencing reads (<500 non-human reads), 368 samples (231 culture-positive, 137 culture-negative) were included. Diagnostic accuracy was assessed against culture, and genotypic AMR predictions were compared to phenotypic antimicrobial susceptibility testing (AST) N = 192.
RESULTS: The BIOTIA-DX platform demonstrated high analytical sensitivity at the sample level (98.7% [95% CI: 0.95-0.99]; 228/231 culture-positive samples detected) and organism level (94.6%; 229/242 culture-identified organisms correctly detected). Among 137 culture-negative samples, BIOTIA-DX detected microbial DNA in 98 samples (71.5%), identifying 264 organisms not detected by standard culture. These additional detections predominantly comprised anaerobic organisms (150/264, 56.8%) and fastidious species (54/264, 20.5%); however, the clinical significance of these detections (infection vs. colonization vs. contamination) could not be determined without clinical correlation. For AMR prediction, genotype-phenotype concordance rates were 94.1% for fluoroquinolone resistance in E. coli (96/102 resistant isolates correctly predicted), 91.4% for beta-lactams (106/116), 91.3% for aminoglycosides (21/23), and 81.5% for sulfamethoxazole/trimethoprim (75/92). Specificity and positive predictive value could not be calculated because organisms detected by BIOTIA-DX but not by culture could not be definitively classified as true positives or false positives without independent confirmation.
CONCLUSIONS: The BIOTIA-DX platform demonstrates robust analytical concordance with urine culture in a Thai patient population. Prospective clinical validation studies are needed to assess clinical utility and impact on patient outcomes, particularly in culture-negative and polymicrobial cases. This study represents the first analytical validation of this platform using Oxford Nanopore Technology and the first validation in Southeast Asia.}, }
@article {pmid41769343, year = {2026}, author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y}, title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1688580}, pmid = {41769343}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/complications ; *HIV Infections/microbiology/complications ; Male ; Female ; *Bacterial Translocation ; *Coinfection/microbiology/virology ; Middle Aged ; Adult ; Lipopolysaccharide Receptors/blood ; Lipopolysaccharides/blood ; Feces/microbiology ; SARS-CoV-2 ; Cohort Studies ; Severity of Illness Index ; Haptoglobins ; Protein Precursors/blood ; }, abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.
METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).
RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.
CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.}, }
@article {pmid41769388, year = {2026}, author = {Chang, ACG and Amaral, MWW and Keepers, K and Ikudaisi, C and Greenwood, M and Li, J and Hamsher, SE and Miller, SR and Kociolek, JP}, title = {An alternative technique for organelle genome recovery in diatoms using culture-independent, minimal-cell whole genome amplification.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20767}, pmid = {41769388}, issn = {2167-8359}, mesh = {*Diatoms/genetics ; *Genomics/methods ; *Genome, Mitochondrial ; *Genome, Chloroplast ; }, abstract = {BACKGROUND: This study presents an alternative method in diatom genomics using two raphid diatoms-Campylodiscus clypeus and Plagiotropis lepidoptera-whose organellar genome characteristics have remained unexplored due to cultivation constraints. Only a small fraction of the estimated 200,000 diatom species has been cultured in the laboratory. This research showcases the use of minimal-cell genomics as a viable alternative for studying diatoms and other eukaryotic microorganisms that do not respond well to traditional laboratory culture methods.
METHODS: Initial attempts to culture C. clypeus and P. lepidoptera were unsuccessful, hindering the acquisition of genomic data. To overcome these challenges, we employed minimal-cell whole genome amplification (mcWGA) techniques for two uncultured species, followed by metagenomic sequencing and assembly. This enabled direct genomic recovery from minimally isolated and pooled cells, eliminating the need for cultivation.
RESULTS: Using mcWGA approach, we successfully obtained the complete chloroplasts and mitochondrial genomes of C. clypeus and P. lepidoptera using only 8-12 viable cells isolated from fresh environmental samples. The plastome size of C. clypeus was 143,367 bp and mitogenome size was 46,274 bp, while P. lepidoptera has plastome and mitogenome sizes of 116,161 bp and 49,356 bp, respectively. The data generated provides a valuable resource for further research, highlighting the importance of culture-independent techniques in microbial genomics.}, }
@article {pmid41769651, year = {2026}, author = {Wang, L and Yu, Y and Shen, X and Li, X and Wang, D and Zhai, Y and Jiang, W and Zhao, W and Yu, Q and Liong, MT and Chen, D and Zhao, A}, title = {Bifidobacterium supplementation maintains gut microbiota stability and enhances well-being during short-term travel.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1724829}, pmid = {41769651}, issn = {2296-861X}, abstract = {BACKGROUND: International travel exposes individuals to abrupt environmental, dietary, and circadian changes that can disturb gut microbiota and overall well-being. While probiotics are known to support gastrointestinal and systemic health, their effects during short-term travel remain incompletely characterized in randomized trials.
METHODS: This randomized, double-blind, placebo-controlled study investigated whether a multi-strain Bifidobacterium probiotic could maintain gut microbiota stability and support health during a five-day trip from China to Japan. Forty healthy adults were randomly assigned to receive either probiotic (n = 22) or placebo (n = 18) daily from Day 1 to Day 4. Stool samples collected before departure (Day 0) and after return (Day 5) were analyzed by metagenomic sequencing, quantitative PCR, and fecal secretory immunoglobulin A (sIgA) assays. Participants completed validated questionnaires on gastrointestinal and respiratory symptoms, sleep quality (PSQI), anxiety (GAD-7), and well-being (WHO-5).
RESULTS: Compared with placebo, participants receiving the probiotic showed maintenance of microbial diversity (Chao1 and Fisher indices, both p = 0.044), prevented enrichment of potentially harmful taxa (Bilophila, Flavonifractor), and increased Bifidobacterium abundance. Clinically, the probiotic group reported fewer respiratory and systemic symptoms, including sore throat (p = 0.034) and fatigue (p = 0.043). Sleep quality also improved, with longer sleep duration (p = 0.023), fewer total occurrence days of PSQI >5 (p = 0.009), lower anxiety scores (p = 0.001) and higher WHO-5 well-being scores (p = 0.041). Functional profiling showed up-regulation of vitamin biosynthesis pathways (folate, biotin, retinol) and decreased antibiotic resistance gene prevalence.
CONCLUSION: Short-term probiotic administration demonstrated gut microbiota resilience and improved physiological and psychological stability during travel. Probiotics may serve as an accessible strategy to support well-being under transient environmental and lifestyle stress.
CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier NCT07163819.}, }
@article {pmid41769655, year = {2026}, author = {Ray, S and Shankaran, P}, title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1761992}, pmid = {41769655}, issn = {2296-861X}, abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.}, }
@article {pmid41770016, year = {2026}, author = {Martins, I and Silva, JM and Almeida, JR}, title = {HYMET: A Hybrid Metagenomic Pipeline for Accurate and Efficient Taxonomic Classification.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag024}, pmid = {41770016}, issn = {2047-217X}, abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a two-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor (LCA) classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.
RESULTS: Across seven CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93 s runtime and a mean peak memory of 6.24 GB. Performance remained stable under mutation rates up to 30% for most domains (F1 ≥ 0.8), with viral sequences showing the expected decline (F1 ≈ 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson r = 0.998, Bray-Curtis =0.04) across bacteria, fungi, and archaea.
CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.}, }
@article {pmid41770210, year = {2026}, author = {Du, Y and Wang, Y and Sun, F}, title = {Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.}, journal = {Current protocols}, volume = {6}, number = {3}, pages = {e70341}, pmid = {41770210}, issn = {2691-1299}, support = {EF-2125142//NSF/ ; }, mesh = {*Genome, Viral/genetics ; *Metagenomics/methods ; Metagenome ; Molecular Sequence Annotation/methods ; Computational Biology/methods ; *Viruses/genetics/classification ; }, abstract = {Metagenomic Hi-C (metaHi-C) links mobile genetic elements to their cellular hosts directly within complex microbial communities. Once shotgun and Hi-C libraries have been generated, however, the main challenges shift to the bioinformatics required for preprocessing, genome binning, taxonomic annotation, and network-level interpretation. Here, we present metaHi-C protocols that span from raw reads to downstream data analyses. Basic Protocol 1 describes quality control of shotgun and Hi-C reads, metagenomic assembly, Hi-C read mapping, and viral contig identification from assembled contigs. Basic Protocol 2 details the use of ViralCC to recover viral metagenome-assembled genomes (vMAGs) and infer virus-host linkages. Support Protocol 1 introduces NormCC and ImputeCC for normalization of raw Hi-C contacts and host genome binning. Support Protocols 2 and 3 describe taxonomic annotation of host MAGs with GTDB-Tk and viral bins with Virgo, respectively. Support Protocol 4 shows how to integrate these outputs in MetaHiCNet to generate cross-taxa and cross-bin Hi-C interaction networks. Together, these protocols provide a reproducible workflow for reconstructing viral and host genomes, assigning consistent taxonomies, and visualizing metaHi-C-derived virus-host interaction structure across diverse microbiomes. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preprocessing raw metagenomic Hi-C data Basic Protocol 2: Viral genome binning and virus-host interaction inference using ViralCC Support Protocol 1: Host genome binning using ImputeCC Support Protocol 2: Host MAG taxonomic annotation with GTDB‑Tk Support Protocol 3: Viral bin taxonomic annotation with Virgo Support Protocol 4: Visualization of virus-host interaction networks with MetaHiCNet.}, }
@article {pmid41770401, year = {2026}, author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J}, title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.}, journal = {Fish physiology and biochemistry}, volume = {52}, number = {2}, pages = {}, pmid = {41770401}, issn = {1573-5168}, support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; }, mesh = {Animals ; *Sulfinic Acids/pharmacology/administration & dosage ; Disulfides ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Animal Feed/analysis ; *Drug Resistance, Microbial/genetics ; Diet/veterinary ; *Fishes/growth & development/microbiology ; }, abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.}, }
@article {pmid41771404, year = {2026}, author = {Zhang, C and Zheng, L and Zhang, Q and Zhang, Y and Zheng, X}, title = {Synergistic removal of methanethiol and other odorant gases by a metabolically complementary synthetic consortia isolated from food waste.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134313}, doi = {10.1016/j.biortech.2026.134313}, pmid = {41771404}, issn = {1873-2976}, mesh = {*Odorants/analysis ; *Sulfhydryl Compounds/isolation & purification/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Gases/isolation & purification/metabolism ; *Food ; Hydrogen Sulfide ; Food Loss and Waste ; }, abstract = {Methanethiol (MeSH), a typical volatile sulfur compound, contributes significantly to environmental malodor and poses ecological risks. In this study, three bacterial strains capable of MeSH removal efficiencies exceeding 40% were isolated from food waste. These strains were taxonomically identified asAgrobacterium cavarae,Mycolicibacterium neoaurum, andPseudomonas qingdaonensis. Metagenomic annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that all strains possess key enzymes for the methionine and cysteine metabolism pathway, suggesting potential for MeSH degradation. In binary consortia, the combination of A. cavarae R1 and P. qingdaonensis CF (5:1 ratio) exhibited the optimal degradation performance, achieving removal efficiency of 87.2% for MeSH, 98.7% for H2S, and complete NH3 elimination (100%) after a 6-day cultivation. Among ternary consortia, the A. cavarae R1/M. neoaurum CD/ P. qingdaonensis CF combination at 3:2:1 and 3:1:2 ratios demonstrated superior removal efficiency for all three target odorants. Specifically, the 3:2:1 ratio consortium achieved 94.7% MeSH degradation, while the 3:1:2 ratio showd 91.7% NH3 removal efficiency. These results demonstrate the feasibility of using composite microbial agents for odor control in waste management systems.}, }
@article {pmid41771407, year = {2026}, author = {Zhao, Y and Zhang, X and Chen, X and Zhu, Z and Jiao, P and Ma, L and Li, Y}, title = {Evidence for Propioniciclava as a novel polyphosphate-accumulating organism and construction of its metabolic profile.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134320}, doi = {10.1016/j.biortech.2026.134320}, pmid = {41771407}, issn = {1873-2976}, mesh = {*Polyphosphates/metabolism ; Phosphorus/metabolism/isolation & purification ; Bioreactors/microbiology ; *Metabolome ; Glycogen/metabolism ; In Situ Hybridization, Fluorescence ; Metabolic Networks and Pathways ; }, abstract = {Enhanced biological phosphorus removal (EBPR) relies on polyphosphate-accumulating organisms (PAOs). This study identifies Propioniciclava as a novel putative PAO. High phosphorus release and uptake rates were achieved in two lab-scale Propioniciclava-dominated sequencing batch reactors (SBRs), reaching up to 2.37 and 2.10 mmolP/(gVSS·h), respectively. Metabolic pathway reconstruction for Propioniciclava was based on its most abundant metagenome-assembled genome (bin70), which accounted for 28.8% in SBR1 and 45.5% in SBR2. Functional annotation of bin70 revealed genes for phosphorus and glycogen metabolism but not for polyhydroxyalkanoate synthesis, suggesting a distinct storage strategy. Fluorescence in situ hybridization combined with 4',6'-diamidino-2-phenylindole (FISH-DAPI) staining provided evidence for intracellular polyphosphate granules. Metatranscriptomic analysis further highlighted genes related to phosphorus and glycogen synthesis being actively transcribed by Propioniciclava. The enrichment of Propioniciclava was crucially dependent on glucose. These findings expand the known diversity of PAOs and elucidate the metabolic profile of Propioniciclava, enhancing our understanding of EBPR microbiology.}, }
@article {pmid41771597, year = {2026}, author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R}, title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e100158}, pmid = {41771597}, issn = {2044-6055}, mesh = {Humans ; *Kidney Transplantation ; *Frailty/etiology/physiopathology ; Longitudinal Studies ; Aged ; Adult ; Middle Aged ; Female ; Male ; }, abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.
METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged ≥40 years; n=50) and Group B (patients aged ≥40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged ≥65 years (or ≥55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150 bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.
ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.}, }
@article {pmid41771902, year = {2026}, author = {Qian, Y and Xu, S and He, X and Lai, Y and Zhang, Y and Mo, C and Ai, P and Yang, X and Xiao, Q}, title = {Gut ecosystem dysfunction in parkinson's disease: deciphering faecal metabolome-metagenome links for novel diagnostic panels.}, journal = {NPJ Parkinson's disease}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41531-026-01299-7}, pmid = {41771902}, issn = {2373-8057}, support = {81901283//National Natural Science Foundation of China/ ; 81801254//National Natural Science Foundation of China/ ; 82171246//National Natural Science Foundation of China/ ; 22YF1440200//Shanghai Sailing Program/ ; 22QA1405700//the Shanghai Rising-Star Program/ ; 2018B030337001//Key Field Research and Development Program of Guangdong Province/ ; SHDC2020CR3012A//Clinical Research Plan of SHDC/ ; 2022YFE0210100//National Key Research and Development Program of China/ ; }, abstract = {Gut ecosystem dysfunction is implicated in Parkinson's disease (PD), but integrative faecal metabolome-metagenome links are undefined. We explored these interactions in Chinese PD patients to develop diagnostic panels. Targeted faecal metabolomics (LC‒MS/MS) was performed on 132 PD and 113 healthy controls (HCs) and shotgun metagenomics was integrated for 39 PD/HC pairs. We identified 33 significantly altered faecal metabolites in PD (FDR-P < 0.05). A novel 12-metabolite panel could distinguish PD from HCs. Multi-omic integration revealed gut ecosystem dysfunction manifests via co-disruptions in microbial genes (e.g., amino acid metabolism genes) and metabolites. Critically, a combinatorial diagnostic panel integrating faecal metabolites and microbial gene markers achieved exceptional PD detection (AUC = 0.961, 95% CI = 0.923-0.998). This study deciphers metabolome-metagenome links driving gut dysfunction in PD, identifying amino acid metabolism as a core perturbed pathway. The novel diagnostic panels provide mechanistic insights and clinical tools for PD precision diagnosis.}, }
@article {pmid41772715, year = {2026}, author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD}, title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41772715}, issn = {2049-2618}, support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Caloric Restriction ; *Bacteria/virology/genetics/classification ; Longevity ; Genome, Viral ; Metagenome ; Male ; Longitudinal Studies ; Female ; }, abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.
RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.
CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.}, }
@article {pmid41772733, year = {2026}, author = {Buscaglia, M and Castillo-Inaipil, W and Schulz, F and Guajardo-Leiva, S and Iriarte, JL and Aparicio-Rizzo, P and Masotti, I and Díez, B}, title = {Unveiling the viral frontier in a warming world: temperature as a key ecological driver of viral diversity in subantarctic Chilean Patagonia fjords.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41772733}, issn = {2524-6372}, support = {21190726//ANID/ ; AUB1900003//ANID/ ; DG_06-20//INACH/ ; 151500003//ANID-FONDAP/ ; 1523A0002//ANID-FONDAP/ ; CIMAR25F//CONA-SHOA/ ; ICN2021_044//ANID - Millennium Science Initiative Program/ ; }, abstract = {BACKGROUND: The fjords of Chilean Patagonia (~ 41.5-55.9 °S) lie at the forefront of global warming, where rising temperatures threaten to disrupt microbial processes central to ocean productivity and carbon cycling. Despite their ecological relevance, the diversity and environmental drivers of viral communities, both giant viruses and prokaryotic viruses, remain poorly understood in high-latitude fjords.
RESULTS: Here, we leveraged metagenomics across a 500 km latitudinal gradient in Chilean Patagonia (4-10 °C; salinity 18-33 PSU) to decode the structure and distribution of marine viral communities. We recovered 126 giant viruses (polB sequences dereplicated at 100% average nucleotide identity) and 9213 prokaryotic viruses (viral contigs dereplicated at 95% average nucleotide identity), primarily affiliated with Prasinoviridae (proposed genus g177, order Algavirales) and Caudoviricetes, respectively. Consistent with global-scale studies, temperature emerged as the strongest driver structuring viral communities, outpacing the effects of salinity, depth, dissolved oxygen, chlorophyll-a, and geography. Viral diversity was consistently higher in the northern warmer waters (7.5-10.4 °C), while southern colder sites (4.0-7.4 °C) harbored less diverse and compositionally distinct communities. Giant viruses shift from Pandoravirales and AG_04 (Algavirales) at lower temperatures to increasing dominance of IM_01 (Imitervirales) and Prasinoviridae (AG_01) in warmer habitats. Prokaryotic virus communities also displayed strong temperature structuring, with additional influence from salinity.
CONCLUSIONS: Together, our findings underscore the environmental sensitivity of viral communities in subpolar marine systems and highlight their vulnerability to climate-driven changes. Given the critical role of viruses in microbial turnover, nutrient cycling, and ecosystem resilience, shifts in their diversity and structure may have far-reaching consequences for biogeochemical fluxes and food web dynamics in the fjords of Chilean Patagonia.}, }
@article {pmid41773230, year = {2026}, author = {Li, X and Feng, Q and Yu, H}, title = {A Rare Case of Concurrent Tropheryma Whipplei and Pneumocystis Jirovecii Pneumonia in a Patient During Endocrine Therapy for Breast Cancer.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {580235}, pmid = {41773230}, issn = {1178-6973}, abstract = {Tropheryma whipplei (TW), a rare Gram-positive bacterium, is an uncommon cause of pulmonary infection, typically being reported in the context of gastrointestinal or neurological Whipple's disease. We present a case of a patient receiving endocrine therapy and ovarian suppression for breast cancer who developed a concurrent pulmonary infection with both Pneumocystis jirovecii (PJ) and TW. The diagnosis was secured through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, which successfully identified both pathogens. Following the initiation of targeted antimicrobial therapy, the patient exhibited significant clinical and radiological improvement.}, }
@article {pmid41773424, year = {2026}, author = {Valdés-Varela, L and Goyache, I and Virto, R and Sáinz, N and López-Yoldi, M and Sánchez-Vicente, A and López-Giral, N and Gil, AG and Milagro, FI and Aranaz, P}, title = {Companilactobacillus alimentarius CNTA 209 alleviates diet-induced obesity in mice through adipose tissue browning and gut barrier modulation.}, journal = {Food & function}, volume = {17}, number = {6}, pages = {2851-2870}, doi = {10.1039/d5fo04242a}, pmid = {41773424}, issn = {2042-650X}, mesh = {Animals ; *Obesity/metabolism ; *Probiotics/administration & dosage/pharmacology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Male ; *Adipose Tissue, Brown/metabolism ; Rats ; Rats, Wistar ; *Lactobacillaceae/physiology ; }, abstract = {The use of probiotics with health-promoting effects has emerged as a promising therapeutic strategy for managing obesity and metabolic syndrome. In this study, we characterized the probiotic properties of a novel strain, Companilactobacillus alimentarius CNTA 209, and investigated its potential anti-obesity effects and safety in rodent models. C. alimentarius exhibited sensitivity to all tested antibiotics, resistance to simulated gastric and intestinal conditions in vitro, and functional activities including β-galactosidase activity and short-chain fatty acid (SCFA) production. C. alimentarius supplementation mitigated liver damage induced by a high-fat, high-fructose diet and significantly reduced adiposity in obese C57BL/6 mice by enhancing brown adipose tissue metabolic activity. Metagenomic analysis revealed a beneficial modulation of gut microbiota composition, associated with improved intestinal barrier function. A comprehensive toxicological assessment conducted in Wistar rats confirmed the safety of the strain at a dose of 1 × 10[9] CFU per animal per day for oral administration. This study provides the first documented evidence of anti-obesity and metabolic benefits conferred by a strain of C. alimentarius, positioning CNTA 209 as a novel and safe candidate for the development of probiotic-based interventions targeting obesity and related metabolic disorders.}, }
@article {pmid41773475, year = {2026}, author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M}, title = {Correction to "Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation".}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {9}, pages = {8027}, doi = {10.1021/acs.jafc.6c01914}, pmid = {41773475}, issn = {1520-5118}, }
@article {pmid41773588, year = {2026}, author = {Sun, S and Subramaniyan, S and Ranjani, G and Cid Gomes, L and Bernin, D and Bayer, T and Bornscheuer, UT and Hakkarainen, M and Syrén, PO}, title = {Polyurethane Cascade Depolymerization by a Combination of Thermal Pretreatment and Enzymatic Hydrolysis.}, journal = {ChemSusChem}, volume = {19}, number = {5}, pages = {e202502633}, pmid = {41773588}, issn = {1864-564X}, support = {CTS 23:2626//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 2021-02509//Svenska Forskningsrådet Formas/ ; NNF23OC0086236//Novo Nordisk Fonden/ ; NNF25OC0100562//Novo Nordisk Fonden/ ; }, mesh = {Hydrolysis ; *Polyurethanes/chemistry/metabolism ; *Polymerization ; *Carboxylic Ester Hydrolases/metabolism/chemistry ; *Temperature ; }, abstract = {Enzymatic depolymerization of postconsumer polyurethanes (PURs) offers a promising route for sustainable plastic waste management. However, the complex chemistry of PURs containing carbamate, ether, and ester bonds poses a challenge for such a biotechnological process. Here, we explored the deconstruction of a commercial polyether-polyester-PUR through a cascade depolymerization approach, in which a low-temperature thermal pretreatment (180°C, 4 h) was combined with tandem enzymatic hydrolysis. Heat treatment modified the polymer's physicochemical properties, enabling the cutinase HiC from Humicola insolens to cause more than 8% weight loss of the treated PUR films, versus less than 2% of the untreated control after 48 h incubation. Furthermore, the addition of the metagenomic urethanase SP2 completed the one-pot enzymatic cascade, achieving not only depolymerization to the constituent monomer, 4,4'-methylenedianiline (MDA), but also a nearly 3-fold increase in MDA yield compared to using SP2 alone. Docking studies highlighted HiC's specificity toward ester bonds in the PUR polymeric units, and two HiC variants further enhanced degradation within 24 h. Altogether, this work lays the foundation for future investigation and process design for the depolymerization of polyether-polyester-PURs and related materials by cascade enzymatic reactions.}, }
@article {pmid41773858, year = {2026}, author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M}, title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0222025}, doi = {10.1128/spectrum.02220-25}, pmid = {41773858}, issn = {2165-0497}, abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.
IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.}, }
@article {pmid41774204, year = {2026}, author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M}, title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41774204}, issn = {1432-0991}, mesh = {*Microbiota ; Humans ; *Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Environmental Microbiology ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial ; }, abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.}, }
@article {pmid41774281, year = {2026}, author = {Kapoor, V and Sanchez-Vicente, S and Donovan, W and Park, J and Nagapurkar, A and Gokden, A and Shrivastava, P and Horn, E and Briese, T and Lipkin, WI and Tokarz, R}, title = {Adaptation of custom capture sequencing panels to the Oxford Nanopore MinION platform.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41774281}, issn = {1573-4978}, support = {75A50122C00012//Biomedical Advanced Research and Development Authority/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods/instrumentation ; Humans ; *Sequence Analysis, DNA/methods ; Nanopores ; Metagenomics/methods ; *Nanopore Sequencing/methods ; Animals ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Next generation sequencing (NGS) remains underutilized in clinical microbiology applications despite providing broad pathogen spectrum detection superior to other molecular methods. This is primarily because of lower sensitivity of metagenomic NGS (mNGS) compared to PCR, lengthy turn-around times, cost, and complexity of data analysis. Capture sequencing is a technique that can mitigate some of the limitations of mNGS. Using probes that are engineered to selectively bind and pull down desired nucleic acids, capture sequencing enriches for targets of interest and can result in up to a 10,000-fold increase in sensitivity compared to mNGS. In this study, we describe the application of capture sequencing on Oxford Nanopore Technology's portable sequencer, the MinION MK1C.
METHODS: We examined the performance of VirCapSeq-VERT and TBDCapSeq, two distinct capture sequencing assays that target vertebrate viruses and tick-borne pathogens, respectively. Both assays were originally established on the Illumina platform. To enable sequencing on the MinION instrument, we developed a modified hybrid workflow using our established library preparation and capture protocol for Illumina, followed by the addition of the ONT sequencing adaptor. In tests using contrived and clinical samples, we compared sensitivity thresholds and sequencing output, including pathogen genome coverage and relevant read counts.
RESULTS: The addition of capture enrichment to MinION NGS provided significant improvement in pathogen detection when compared to mNGS. Assessment of assay performance on pathogen-positive samples revealed equivalent sensitivity on the MinION MK1C and Illumina NextSeq. We found that the elevated read counts and sequencing depth generated by Illumina NGS were offset by the greater read length obtained on the MinION MK1C and resulted in comparable pathogen genome coverage between the two platforms.
CONCLUSION: This study demonstrates the utility for employment of VirCapSeq and TBDCapSeq on different sequencing platforms and suggest the potential of the MinION platform for broad-spectrum clinical diagnostics.}, }
@article {pmid41775000, year = {2026}, author = {Mammeri, M and Obregon, D and Chevillot, A and Abuin-Denis, L and Skičková, Š and Kratou, M and Wu-Chuang, A and Maitre, A and Christine, J and Polack, B and Cabezas-Cruz, A and Adjou, KT}, title = {Yeast probiotic protects gut microbiota diversity and metabolic potential against Cryptosporidiosis-induced disruption in goat kids.}, journal = {Veterinary parasitology}, volume = {343}, number = {}, pages = {110729}, doi = {10.1016/j.vetpar.2026.110729}, pmid = {41775000}, issn = {1873-2550}, mesh = {Animals ; Goats ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Cryptosporidiosis/parasitology/prevention & control ; Male ; *Goat Diseases/parasitology/prevention & control/microbiology ; *Saccharomyces cerevisiae ; Cryptosporidium parvum/physiology ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/veterinary/prevention & control ; }, abstract = {Cryptosporidiosis, caused by Cryptosporidium parvum, is a major cause of enteric disease and gut microbiota disruption in neonatal ruminants. It can lead to impaired growth, increased susceptibility to pathogens, and long-term gut dysfunction. In this study, we investigated whether supplementation with a live yeast probiotic (Saccharomyces cerevisiae Sc47) could help preserve gut microbiota resilience and functional homeostasis during an experimental C. parvum oral infection in goat kids. Thirty male French Alpine goat kids were assigned to three groups: uninfected control (healthy), infected, and infected with yeast supplementation. Longitudinal 16S rRNA gene sequencing, network analysis, and functional metagenomic predictions were used to assess microbial diversity, community composition, co-occurrence patterns, and metabolic potential, with a focus on short-chain fatty acid (SCFA) biosynthesis. Infection induced marked dysbiosis, characterised by a substantial reduction in microbial richness and a widespread loss of SCFA-producing commensals and metabolic functions. In contrast, yeast supplementation significantly reduced oocyst excretion by more than 84% throughout the experiment, attenuated pathogen-induced community shifts, and maintained beneficial genera such as Butyricicoccus and members of the Oscillospiraceae family. Furthermore, network analysis revealed that probiotic treatment preserved microbial association structures and reduced community fragmentation. Consistent with these findings, functional profiling showed the retention of pathways involved in carbohydrate metabolism, amino acid biosynthesis, and SCFA production, suggesting enhanced microbiota resilience. These findings demonstrate that S. cerevisiae supplementation can mitigate infection-associated dysbiosis by controlling pathogenic overgrowth while sustaining commensal bacterial stability and functional capacity. This highlights its potential as a microbiota-targeted strategy to support gut health in neonatal ruminants.}, }
@article {pmid41775040, year = {2026}, author = {Liu, T and Sun, X and Huang, D and Kong, T and Huang, W and Lin, Z and Wang, Z and Li, B and Sun, W}, title = {Differential patterns of antibiotic resistance, virulence, and dissemination risks in floating and sedimented plastispheres.}, journal = {Water research}, volume = {296}, number = {}, pages = {125644}, doi = {10.1016/j.watres.2026.125644}, pmid = {41775040}, issn = {1879-2448}, mesh = {*Geologic Sediments/microbiology ; Virulence ; *Drug Resistance, Microbial/genetics ; Plastics ; Rivers ; China ; Virulence Factors/genetics ; }, abstract = {The plastisphere, a unique ecological niche on plastic surfaces, enriches microbial antibiotic resistance genes (ARGs) and virulence factors (VFs), posing environmental and health risks. Although aquatic sediment is a major sink for plastic contaminants, the resistance, virulence and dissemination potentials of sedimented plastispheres remain poorly characterized compared to floating plastics. Through investigation of metagenomes from two sites in the Pearl River in China, one of the world's plastic pollution hotspots, we report that water plastisphere showed 2.4 and 3.6 times more ARG and VF genes than those in sediment plastisphere and surrounding environments, together with higher mobile genetic element (MGE) abundances and a denser ARG-VF co-occurrence network (5,879 vs. 2,874 edges; density 0.043 vs. 0.025), indicating enhanced horizontal gene transfer potential. These differences coincide with contrasting ARG/VF assembly mechanisms, with deterministic and stochastic assembly processes dominating ARG/VF profiles in water and sediment plastispheres, respectively. Genome-resolved analyses further revealed that dominant plastisphere populations harbored multiple ARGs and VFs, with 41 MAGs predicted with pathogenicity capacities, most of which belonged to the families Mycobacteriaceae, Aeromonadaceae, Moraxellaceae, and Pseudomonadaceae. Notably, these taxa have been repeatedly reported as common plastisphere members across diverse ecosystems, suggesting that elevated resistance and virulence in floating plastispheres may be a widespread phenomenon across aquatic ecosystems. Together, our findings demonstrate that floating plastics act as dynamic vectors of antimicrobial resistance and pathogenicity, as well as their dissemination potentials, highlighting water-sediment transition may reduce these ecological risks within the plastisphere.}, }
@article {pmid41775186, year = {2026}, author = {Geromino, P and LeMoine, CM and Drahun, I and Cassone, BJ}, title = {Co-supplementation of a polyethylene diet for improved fitness of Galleria mellonella larvae.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141617}, doi = {10.1016/j.jhazmat.2026.141617}, pmid = {41775186}, issn = {1873-3336}, mesh = {Animals ; Larva/growth & development/drug effects ; *Moths/growth & development/physiology ; *Polyethylene/metabolism ; Diet ; Gastrointestinal Microbiome ; }, abstract = {A growing number of plastivore insects have been discovered that readily consume and biodegrade various petro plastics, including LDPE. The caterpillar larvae of Galleria mellonella are capable of breaking down the polymers at expedited rates; however, feeding on LDPE as a sole nutrient source is inefficient and detrimentally impacts larval survival, growth, and development. The objective of our study was to improve fitness parameters and feeding activities of LDPE-fed larvae through the addition of various macro- and micronutrients. Each co-supplementation recovered fitness and consumption to some extent in comparison to pure LDPE; however, artificial sources produced outcomes that were well below those of the caterpillar's natural diet, regardless of the combination. Co-supplementation of LDPE, honeycomb, and corn syrup was the most successful, with larval fitness and consumption approximating their natural diet. To provide mechanistic insights into this recovery, qPCR and metagenomics analyses indicated the co-supplementation promoted greater gut bacterial abundance and species richness and evenness. In addition, GC-MS analyses identified notable differences in their fat body metabolic profiles that may contribute to slower developmental rates. We also assessed the capability of the larvae to eliminate food wastes, which showed promise and could represent a potential co-supplement source for LDPE biodegradation.}, }
@article {pmid41775197, year = {2026}, author = {Lin, L and Su, Z and Yang, X and Yang, F and Zhang, L and Adyari, B and Yang, X and Liu, S and Hu, A}, title = {Impacts of tributaries and sewage effluents on antibiotic resistance genes and pathogens in an urban river.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141641}, doi = {10.1016/j.jhazmat.2026.141641}, pmid = {41775197}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Sewage/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; Cities ; China ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) within urban rivers presents an increasingly public health threat. This study utilized shotgun metagenomics to assess the distribution, drivers, and risks associated with ARGs and ARG-carrying pathogens (APs) in the Xiaoqing River, focusing on impacts from sewage treatment plant (STP) effluents and tributaries. Results demonstrated significantly elevated ARG and AP abundance and diversity in urban segments and STP effluents relative to upstream and downstream areas. Macrolide-lincosamide-streptogramin resistance genes dominated the urban river resistome. Tributaries were characterized by elevated concentrations of ARGs and identified as important reservoirs. STP effluents introduced APs, including Acinetobacter johnsonii, Enterobacter asburiae and Escherichia coli. Although overall ARG pollution decreased downstream, 44.8% of ARG subtypes and clinically relevant APs persisted, with downstream E. coli strains notably carrying an 8-fold higher ARG load. Mobile genetic elements showed a strong correlation with ARG propagation (R[2] > 0.60, P < 0.001), which may be facilitated by erythromycin and clarithromycin. Semi-quantitative source tracking analysis indicated that tributaries and STP effluents likely represent nonnegligible contributors to ARGs and APs in the urban river. This study demonstrates that sustained urban and tributary discharges drive resistome dissemination, posing persistent risks that require integrated riverine antimicrobial resistance management.}, }
@article {pmid41775198, year = {2026}, author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z}, title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141645}, doi = {10.1016/j.jhazmat.2026.141645}, pmid = {41775198}, issn = {1873-3336}, mesh = {China ; *Rivers/microbiology/chemistry ; *Anti-Bacterial Agents/analysis/pharmacology ; Wetlands ; *Bacteria/genetics/drug effects ; Geologic Sediments ; Genes, Bacterial ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Water Microbiology ; Environmental Monitoring ; }, abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.}, }
@article {pmid41775266, year = {2026}, author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J}, title = {Competition and compromise between exogenous probiotics and native microbiota.}, journal = {Cell systems}, volume = {17}, number = {3}, pages = {101516}, doi = {10.1016/j.cels.2025.101516}, pmid = {41775266}, issn = {2405-4720}, mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; Feces/microbiology ; Bifidobacterium animalis ; Mice, Inbred C57BL ; Dietary Fiber ; Male ; Bifidobacterium ; }, abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.}, }
@article {pmid41775298, year = {2026}, author = {Luo, J and Yang, S and Feng, Q and Zou, X and Wu, Y and Wang, F}, title = {Triazine-induced extracellular polymeric substance disruption drives metabolic reprogramming and enhanced volatile fatty acid production in anaerobic sludge fermentation.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134322}, doi = {10.1016/j.biortech.2026.134322}, pmid = {41775298}, issn = {1873-2976}, mesh = {*Triazines/pharmacology ; *Sewage/microbiology ; *Fatty Acids, Volatile/biosynthesis/metabolism ; *Fermentation/drug effects ; Anaerobiosis/drug effects ; *Extracellular Polymeric Substance Matrix/metabolism/drug effects ; RNA, Ribosomal, 16S/genetics ; Molecular Docking Simulation ; Metabolic Reprogramming ; }, abstract = {The accumulation of antimicrobial contaminants in waste-activated sludge (WAS) posed challenges to anaerobic fermentation processes, with mechanistic impacts on volatile fatty acids (VFAs) production remaining poorly understood. 1,3,5-triazine (triazine), a widely detected triazine-based antimicrobial agent, paradoxically enhanced VFAs production in a concentration-dependent manner, achieving maximum yields of 1771 mg COD/L (18.4-fold increase compared with control). Enhanced production was accompanied by a distinct metabolic shift from propionate to acetate dominance (from 38.7 to 54.3%), driven by systematic disruption of extracellular polymeric substances (EPS), especially proteins. Molecular docking revealed that triazine induced conformational instability and structural damage in proteins through hydrogen bonding and hydrophobic interactions. Meanwhile, the increase in ammonium nitrogen concentration under triazine stress provided further confirmation of the hydrolysis of proteins, providing readily fermentable substrates for VFAs production (particularly acetate). High-throughput 16S rRNA sequencing uncovered concentration-dependent microbial community restructuring, characterized by enrichment of proteolytic bacteria (Petrimonas) and acetate producers (Anaerovorax), concurrent with the suppression of methanogens. Functional metagenomic analysis using PICRUSt2 revealed upregulation of proteolytic enzymes (e.g., EC:3.4.16.4) and acetyl-CoA synthesis genes (e.g., PDHA), facilitating enhanced protein hydrolysis and acetate biosynthesis. Critically, triazine stress activated quorum sensing and two-component regulatory systems, with luxS expression increasing 5.7-fold, promoting metabolic coordination and stress resilience rather than community collapse. Partial least squares path modeling confirmed that substrate availability (λ = 0.459) served as the primary driver of VFAs accumulation, mediated by microbial community adaptation (λ = 0.560). These findings unveil how antimicrobial stress enhanced resource recovery via EPS-mediated metabolic reprogramming.}, }
@article {pmid41775307, year = {2026}, author = {Li, Y and Pan, J and Li, Y and Zhao, Z and Zhang, Y}, title = {Direct interspecies electron transfer-based methanogenic aggregate: A survival strategy to overcome defensive attack from type VI secretion system during syntrophic cooperation.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134329}, doi = {10.1016/j.biortech.2026.134329}, pmid = {41775307}, issn = {1873-2976}, mesh = {Electron Transport ; *Methane/metabolism ; Sewage/microbiology ; Bioreactors/microbiology ; Anaerobiosis ; }, abstract = {Physically tight structure of methanogenic aggregates formed by syntrophic microbes that exchange electrons via interspecies hydrogen/formate transfer (IHT/IFT) can activate defensive attack from type VI secretion system (T6SS), which has been recognized as the primary cause for poor stability. Direct interspecies electron transfer (DIET) may alleviate the technical bottleneck of proximity-triggered defensive attack from T6SS, since syntrophic microbes function long-distance electron transfer via electrically conductive pili (e-pili) or its displayed c-type cytochromes. Here, three up-flow anaerobic sludge blanket reactors, respectively with ethanol, propionate, and butyrate as a sole substrate, were used to culture DIET- and IHT/IFT-based aggregates. DIET-based aggregates were generally larger and exhibited a looser, porous structure compared to IHT/IFT-based aggregates. However, rheological behavior showed that they possessed higher rigidity and toughness, attributed to the structural support of the conductive pili network. 3D reconstruction and imaging of a single DIET-based aggregate by nano-industrial computed tomography showed that syntrophic microbes did not display a pronounced localized aggregation pattern. Conductivity-temperature/pH response showed that the DIET-based aggregates exhibited a metallic-like conductance similar to that found in e-pili. Meanwhile, the surface-enhanced Raman spectra showed that the intensities of characteristic peaks associated with c-type cytochromes in DIET-based aggregates were higher than those in IHT/IFT-based aggregates. Analysis of metagenomic and metaproteomic data showed that in DIET-based aggregates expression of key proteins of T6SS was suppressed. These results demonstrated that in DIET-based aggregates syntrophic microbes did not aggregate to form a physically tight structure, eluding defensive attack from T6SS and strengthening their stabilities.}, }
@article {pmid41775707, year = {2026}, author = {Wang, J and Wang, S and Li, T and Hou, W and Deng, Y}, title = {A watershed-scale potential pathogenic bacteria dataset from the Yangtze River Basin.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06983-0}, pmid = {41775707}, issn = {2052-4463}, support = {42277104//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbial safety is fundamental to ensuring water quality, particularly in the Yangtze River Basin, China's most critical drinking water source. Despite its ecological and economic importance, the basin faces significant anthropogenic pressures, including wastewater discharge, which may elevate the risk of pathogenic contamination. However, fragmented sampling efforts and limited coverage have hindered a systematic understanding of pathogenic microbial diversity and distribution across this vast ecosystem. A novel bioinformatic pipeline leveraging Genome-Specific Markers to accurately identify and quantify potential pathogenic taxa in metagenomic data was applied to 625 publicly available metagenomes, spanning water, sediments, and riparian soils along the 6,300 km Yangtze River continuum. We reconstructed a potential pathogen catalog comprising 403 taxa, largely expanding the pathogen diversity in the large river ecosystem. We also generate the Richness distribution maps of potential pathogens for water, sediments and soils along Yangtze River. The basin-scale pathogen inventory not only establishes a baseline for potential pathogenic bacteria communities in the Yangtze Basin but also serves as a reference library for quick biosurveillance and risk management from genomic resolution.}, }
@article {pmid41775798, year = {2026}, author = {Nearman, A and Lamas, ZS and Niño, EL and Fine, J and Mayack, C and Seshadri, A and Boncristiani, D and Huang, WF and Evans, JD and Chen, YP}, title = {Metagenomic and gene expression patterns in declining commercial honey bee colonies.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42605-w}, pmid = {41775798}, issn = {2045-2322}, support = {FSA25IRA0012292//Farm Service Agency/ ; 8130-0960//Animal and Plant Health Inspection Service/ ; }, }
@article {pmid41775849, year = {2026}, author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM}, title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41775849}, issn = {2045-2322}, abstract = {UNLABELLED: Environmental DNA (eDNA) metabarcoding is an emerging and versatile tool in biodiversity research. With recent advances in field sampling techniques, this approach becomes increasingly suited for application in tropical ecosystems where biodiversity monitoring gaps remain significant and species detection is particularly challenging. Using amphibians as a model, we harness eDNA metabarcoding in 52 localities in the Tropical Andean biodiversity hotspot to rapidly trace elusive, threatened, or presumed extinct species as a baseline for conservation action. Metabarcoding ‘bycatch’ of non-target species further revealed specific environmental threats through the detection of invasive species and pathogens, thus facilitating integrative conservation assessments despite the incompleteness of reference data and the vast species richness hampering biodiversity assessments in complex tropical communities. Consequently, we call for more intense employment of eDNA metabarcoding in conservation to rapidly bridge critical knowledge gaps on elusive species or declining populations in tropical biodiversity hotspots.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41937-x.}, }
@article {pmid41776033, year = {2026}, author = {Yu, Q and Liu, H and Shi, H and Abdrakhmanov, Y and Shen, J and Zhang, C and Dong, Z and Zong, L and Si, L and Dai, L and Li, Y}, title = {Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models.}, journal = {Nature biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {41776033}, issn = {2157-846X}, abstract = {Identifying evolutionarily remote antimicrobial peptides (AMPs) is crucial for discovering underexplored clinical candidates to combat antibiotic resistance. Existing experimental and computational methods are limited by their reliance on sequence identity to known AMPs, missing distant homologues. Here we introduce HMD-AMP, a protein language model-based approach for AMP discovery. HMD-AMP outperforms previous methods in identifying evolutionarily distant AMPs and enables the discovery of unknown and highly potent AMPs from metagenomic data. Applied to host and gut microorganism genomes of nine mammals, HMD-AMP revealed over 37 million predicted AMPs. Of 91 high-confidence sequences experimentally validated, 74 showed strong antibacterial activity and 48 were evolutionarily remote from known AMPs. Four of these AMPs exhibited broad-spectrum antibacterial activity at low effective concentrations and showed low toxicity, with the most potent peptide demonstrating therapeutic efficacy in a mouse model of peritoneal Escherichia coli infection. This study introduces an effective strategy to uncover AMPs.}, }
@article {pmid41776310, year = {2026}, author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA}, title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.}, journal = {Nature aging}, volume = {6}, number = {3}, pages = {682-702}, pmid = {41776310}, issn = {2662-8465}, support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; T32 AG052374/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; *Ovary/physiology ; *Fecal Microbiota Transplantation ; Mice ; *Aging/physiology ; Mice, Inbred C57BL ; Transcriptome ; *Menopause ; Metagenomics ; Fertility ; }, abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.}, }
@article {pmid41776502, year = {2026}, author = {Tümmler, B and Schulz, A and Minso, R and Alfeis, N and Tamm, S and Rademacher, J and Ringshausen, FC}, title = {CFTR activity in nasal potential difference of adults with idiopathic bronchiectasis.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03599-1}, pmid = {41776502}, issn = {1465-993X}, }
@article {pmid41776697, year = {2026}, author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X}, title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00533-0}, pmid = {41776697}, issn = {2524-4671}, }
@article {pmid41777069, year = {2026}, author = {Zamperin, G and Palumbo, E and Castellan, M and Marciano, S and Fusaro, A and Monne, I}, title = {Metagenomic sequencing of zoonotic viruses: evaluation of a CRISPR-Cas-based rRNA depletion system.}, journal = {Veterinaria italiana}, volume = {62}, number = {2}, pages = {}, doi = {10.12834/VetIt.3908.38985.2}, pmid = {41777069}, issn = {1828-1427}, mesh = {*CRISPR-Cas Systems ; Animals ; *Metagenomics/methods ; *RNA, Ribosomal/genetics ; *Zoonoses/virology ; Genome, Viral ; }, abstract = {Pathogen-agnostic diagnostics are crucial for the early detection of emerging viruses. Shotgun metagenomic sequencing enables unbiased detection of viral genomes but is frequently constrained by the abundance of host and microbial ribosomal RNA (rRNA), which reduces sensitivity and increases sequencing costs. CRISPR-Cas9-based rRNA depletion has emerged as an alternative to enzymatic methods; however, its performance for the characterization of zoonotic viruses across diverse animal hosts and tissues remains underexplored. We compared CRISPR-Cas9 (Jumpcode CRISPRclean™ Plus) and RNase H-based enzymatic depletion (Ribo-Zero Plus, Illumina) using 12 samples positive for rabies lyssavirus, influenza A virus, West Nile virus or norovirus, from multiple host species and tissues, including both high-quality and degraded RNA. CRISPR-Cas9 efficiently reduced rRNA content (14.5%) but recovered fewer viral reads than Ribo-Zero, which achieved up to 60.7× enrichment. Both methods produced complete viral consensus genomes when RNA quality and viral load were sufficient. However, based on the data generated here, enzymatic depletion currently remains more efficient and cost-effective for viral metagenomics. Further optimization of CRISPR-Cas9 workflows could enhance its utility for viral surveillance and diagnostics.}, }
@article {pmid41777393, year = {2026}, author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D}, title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1685007}, pmid = {41777393}, issn = {1664-462X}, abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.}, }
@article {pmid41777539, year = {2026}, author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B}, title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771459}, pmid = {41777539}, issn = {1664-302X}, abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).
METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.
RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2] = 0.032, p = 0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.
DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.}, }
@article {pmid41777547, year = {2026}, author = {Maisto, L and Telegrafo, C and Rubino, F and Santamaria, M and Traka, MH and Tullo, A and Bouwman, J and Sbisà, E and Balech, B}, title = {Multifaceted human gut microbiome data associated with health and nutrition.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1722500}, pmid = {41777547}, issn = {1664-302X}, abstract = {The microbiome, also considered the hidden organ, is a fundamental ecosystem directly associated with the disease and health status of the human body. With the availability of high-throughput DNA sequencing technologies, a growing number of studies from clinical and experimental (observation and intervention) samples are constantly revealing new findings on the relationship between human organs and their microbiomes. In such a context, diet and nutrition are among the key factors influencing microbiome composition, richness, and functional behavior. In this review, we illustrate how microbiome-related data and associated metadata are in recent times scattered across primary and specialized databases with different levels of curation, annotation, and standardization, limiting, to some extent, the possibility of deep data discovery, reuse, alignment, and harmonization. Therefore, we describe the way Findable, Accessible, Interoperable, and Reusable (FAIR) data principles would enhance the onset of novel scientific hypotheses and potential microbiome-targeted therapies by improving the standardization policies in data sources. Accordingly, using advanced semantic classification and data mining technologies based on suitable and comprehensive ontologies, annotations of studies present in source databases or in scientific literature would further improve the data and metadata enrichment, integration and alignment relevant to microbiome data associated with health, disease and nutrition.}, }
@article {pmid41778161, year = {2026}, author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z}, title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1755982}, pmid = {41778161}, issn = {1664-2392}, mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; }, abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.
METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.
RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).
DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.}, }
@article {pmid41778495, year = {2026}, author = {Lu, J and Bi, H and Zhang, R and Liu, X and Wang, B and Wu, J and Lee, JK and Kalia, VC and Gong, C}, title = {Pesticide Biodegradation Catalyzed by a Cold-Adapted Acetylxylan Esterase Identified from a Metagenome-Assembled Genome.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {10}, pages = {8187-8197}, doi = {10.1021/acs.jafc.5c13419}, pmid = {41778495}, issn = {1520-5118}, mesh = {Biodegradation, Environmental ; Metagenome ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Pesticides/metabolism/chemistry ; Cold Temperature ; *Acetylesterase/genetics/metabolism/chemistry ; Enzyme Stability ; Substrate Specificity ; }, abstract = {This study identified a putative cold-adapted acetylxylan esterase in Glutamicibacter soli Em07 via a metagenome-assembled genome. The gene encoding this enzyme was cloned and heterologously expressed in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the protein has a molecular weight of 33.24 kDa. Using 1-naphthyl acetate as a substrate, the enzyme activity was optimal at 20 °C and pH 9. Furthermore, the enzyme exhibited excellent cold adaptation, alkali resistance, and salt tolerance. It demonstrated OCP pesticide-degrading activity: 66.48% degradation of carbaryl, 92.14% of cypermethrin, and 97.78% of malathion, underscoring its strong potential in environmental remediation. Notably, this esterase emerged as the first to simultaneously possess cold adaptation, alkali resistance, and salt tolerance. These results positioned the enzyme as a promising candidate for bioremediation strategies in multiextreme environments. Further research will investigate its activity on other persistent organic pollutants.}, }
@article {pmid41778780, year = {2026}, author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S}, title = {Beyond bacilli: integrating the microbiome into the TB research agenda.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2638004}, pmid = {41778780}, issn = {1949-0984}, mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; }, abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.}, }
@article {pmid41778788, year = {2026}, author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N}, title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0097125}, doi = {10.1128/spectrum.00971-25}, pmid = {41778788}, issn = {2165-0497}, abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.}, }
@article {pmid41778823, year = {2026}, author = {Shean, RC and Tardif, KD and Rangel, A and Dutrschi, J and Bogumil, D and Cruse, A and Hernandez, S and Iremadze, N and Pollock, S and Lipson, D and Bradley, BT}, title = {Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0187425}, doi = {10.1128/spectrum.01874-25}, pmid = {41778823}, issn = {2165-0497}, abstract = {Clinical metagenomic next-generation sequencing (mNGS) is a diagnostic tool allowing near-universal pathogen detection directly from clinical specimens. Despite promising clinical data, broad adoption of mNGS has been hindered by high cost and reduced sensitivity relative to targeted nucleic acid amplification tests (NAATs). Recently, Ultima Genomics introduced the UG 100 NGS platform which advertises 10 billion reads per $2,400 sequencing wafer. By lowering costs and improving sequencing depth, the historical value proposition of mNGS may be improved. This study evaluates the UG 100 sequencer's ability to generate reads for metagenomic pathogen detection from cerebrospinal fluid specimens. Ultima reads demonstrated 93% (26/28) positive agreement with orthogonal test results and 63% (10/16) negative agreement against a syndromic panel for meningitis and encephalitis. Near full-length genomes were recovered for three organisms (human herpesvirus-1 [HSV-1], Streptococcus pneumoniae, and Haemophilus influenzae), with the ability to detect putative antimicrobial resistance genes for H. influenzae. Recovery of Borrelia burgdorferi reads (6.1 reads per million [RPM] and 9.03 RPM) was achieved from clinical samples with late cycle threshold values (39.7 and 43.0, respectively). Limit of detection (LoD) studies demonstrated detection of HSV-1 and S. pneumoniae reads at concentrations of 50 genomes/mL each, which is below the reported LoD for the orthogonal NAATs used in this study. Reducing sequencing costs and improving the analytical sensitivity remove two major hurdles for mNGS adoption by clinical laboratories. While these results are preliminary, they demonstrate a future in which mNGS may be more widely implemented.IMPORTANCEClinical metagenomic next-generation sequencing has struggled to gain wider adoption for nearly a decade, due in part to its high cost and reduced performance versus targeted molecular assays. This study demonstrates the ability of the UG100 sequencing platform to reduce per-base metagenomic sequencing costs while producing reads that maintain high positive agreement with existing molecular assays. Further improvements to cost and analytical performance may shift clinical metagenomics from an expensive test of last resort to a front-line diagnostic for identifying infections.}, }
@article {pmid41779028, year = {2026}, author = {Ladd-Wilson, SG and Fawcett, RW and Park, SY and Venkatasubrahmanyam, S and Lindner, MS and Davis, S and Spry, A and Singleton, J and Karpathy, SE and Paddock, CD}, title = {Rickettsia lanei Rickettsiosis, Oregon, USA, 2025.}, journal = {Emerging infectious diseases}, volume = {32}, number = {4}, pages = {}, doi = {10.3201/eid3204.251962}, pmid = {41779028}, issn = {1080-6059}, abstract = {Using metagenomic sequencing, we identified a patient infected with Rickettsia lanei who was initially diagnosed with Rocky Mountain spotted fever (RMSF), a clinically similar disease caused by infection with R. rickettsii. Our investigation highlights the importance of clinical, epidemiologic, and laboratory partnerships to leverage the discovery of novel pathogens.}, }
@article {pmid41780079, year = {2026}, author = {Zhao, B and Xu, Y and Li, F and Song, S and Liu, Z and Liu, J and Liu, Z and Chen, X and Zhou, M and Zhao, L and Wang, X}, title = {Cyclosporine A ameliorates ulcerative colitis by inhibiting cellular senescence, modulating the JAK2-STAT3/NF-κB signaling pathway, and regulating the gut microbiota-metabolite axis.}, journal = {International immunopharmacology}, volume = {175}, number = {}, pages = {116452}, doi = {10.1016/j.intimp.2026.116452}, pmid = {41780079}, issn = {1878-1705}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/pathology/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; STAT3 Transcription Factor/metabolism ; *Cyclosporine/therapeutic use/pharmacology ; Signal Transduction/drug effects ; Janus Kinase 2/metabolism ; Cellular Senescence/drug effects ; NF-kappa B/metabolism ; Mice ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; Humans ; Disease Models, Animal ; *Immunosuppressive Agents/pharmacology/therapeutic use ; }, abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease characterized by immune dysregulation, compromised intestinal barrier integrity, and disruptions in the microbiota-metabolite axis. Current clinical management of UC remains limited, underscoring the need for novel therapeutic approaches. Cellular senescence is increasingly recognized as a significant contributor to the pathogenesis of this disease. Senescent cells promote inflammatory responses via the sustained release of pro-inflammatory mediators such as IL-6, IL-1β, and TNF-α. Conversely, persistent inflammation drives further cellular senescence, establishing a self-amplifying cycle that exacerbates disease progression. Additionally, gut microbiota dysbiosis (reduced Akkermansia abundance) and metabolic abnormalities (disrupted bile acid metabolism) may further compromise intestinal barrier integrity. Cyclosporine A (CsA), a classical immunosuppressant, has unclear mechanisms in UC, particularly regarding its potential effects on senescence and the microbiota-metabolite axis. In this investigation, using a dextran sulfate sodium (DSS)-induced UC model, we demonstrated that CsA significantly alleviated DSS-induced acute colitis in mice and senescence-associated pathological changes. Multi-omics analyses integrating network pharmacology, transcriptomics, metabolomics, and metagenomics demonstrated that CsA likely exerts its therapeutic effects through inhibition of the JAK2-STAT3/NF-κB signaling pathway. This leads to reduced release of pro-inflammatory cytokines, modulation of intestinal microbiota composition and metabolite profiles, and enhanced intestinal barrier function.These findings elucidate new mechanisms by which CsA improves DSS-induced colitis in mice through anti-senescence effects and microbiota-metabolic regulation, providing potential therapeutic targets for UC.}, }
@article {pmid41780235, year = {2026}, author = {Xin, Y and Liu, LH and Liu, L and Chen, SH and Zheng, YM and Zhao, QB}, title = {Seasonal variation regulates the efficacy of phytoremediation strategies on the rhizosphere resistome in urban river ecosystems.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141647}, doi = {10.1016/j.jhazmat.2026.141647}, pmid = {41780235}, issn = {1873-3336}, mesh = {*Rhizosphere ; Biodegradation, Environmental ; Seasons ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Ecosystem ; }, abstract = {Phytoremediation, as a representative nature-based solution, holds significant potential for mitigating the dissemination of antibiotic resistome in urban rivers, which is vital for safeguarding public health and aquatic ecosystems. However, the performance and mechanisms of different phytoremediation strategies (hydroponic or substrate-based strategies) in influencing the rhizosphere resistome across seasonal variation remain poorly understood. This study combined in-situ plant cultivation with metagenomic sequencing and statistical modelling to elucidate rhizosphere resistome dynamics in different phytoremediation strategies. The results showed that the phytoremediation strategies exerted limited influence on the composition and diversity of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). Instead, the above parameters were predominantly regulated by seasonal variation and generally exhibited higher abundances during winter (4.07 ×10[-4]-2.92 ×10[-2]) than summer (3.35 ×10[-4]-2.26 ×10[-2], ANOSIM: R>0.12, P < 0.05). Nonetheless, phytoremediation strategies still led to distinct patterns for the specific resistome (P < 0.05). The relative abundance of specific VFGs was also significantly higher in the substrate-based strategy (7.21 ×10[-4]-8.82 ×10[-4]) than the hydroponic strategy (5.87 ×10[-4]-7.98 ×10[-4]), particularly during summer. The key ARB, such as those belonging to Bacteroidota, showed higher relative abundance in the hydroponic strategy (2.28 ×10[-2]-6.23 ×10[-2]) than substrate-based strategy (1.12 ×10[-2]-3.65 ×10[-2]) across seasonal variation. Mechanistically, rhizosphere exudate-derived dissolved organic matter mediated ARG dynamics by regulating bacterial communities, MGEs, and VFGs (P < 0.05). This study delineates strategy-specific controls of hydroponic and substrate-based phytoremediation on ARG dissemination across seasonal variations, delivering actionable protocols for nature-based solutions optimization in urban rivers.}, }
@article {pmid41780243, year = {2026}, author = {Sun, Y and Chen, R and van den Broek, S and Wen, J and Li, Y and Zeng, X and Su, S and Garland, G}, title = {Transmission and migration of antibiotic resistance genes following agricultural fertilization in sloping croplands.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141666}, doi = {10.1016/j.jhazmat.2026.141666}, pmid = {41780243}, issn = {1873-3336}, mesh = {*Fertilizers ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Agriculture ; China ; *Genes, Bacterial ; Soil/chemistry ; Gene Transfer, Horizontal ; Crops, Agricultural ; Metagenome ; Soil Pollutants/analysis ; Manure ; }, abstract = {Livestock manure, a major anthropogenic source of antibiotic resistance genes (ARGs) in agricultural soils due to residual veterinary antibiotics, is commonly used as a nutrient-rich fertilizer on sloping cropland. However, the role of landscape features, particularly topographic heterogeneity in shaping ARG transmission and migration remains poorly understood. In this study, we analyzed 76 metagenomes from five environmental habitats collected along three sloping cropland routes in the Dongting Lake region of China. Soil shared 276 ARG subtypes with other habitats, indicating manure fertilization on slopes facilitates ARGs diffusion across ecosystem. ARG abundance exhibited strong spatial patterns in soil samples, associated with distance from fertilized zones and buffer strips. In fertilized highland soils, mobile genetic elements (MGEs), such as transposases and Insertion Sequence Common Region (ISCRs), were significantly correlated with ARG abundance, indicating active horizontal gene transfer. In unfertilized-lowland soils, ARG composition was primarily influenced by heavy metals, particularly arsenic and cadmium. Source-tracking analysis showed that up to 70.3% of microbes migrated downslope via gravitational runoff, facilitating long-distance ARG dispersal. Risk assessment revealed higher ecological than human health risks, with high-risk ARGs linked to crop pathogens. Our findings highlight the need for landscape-based ARG management strategies within the One Health framework.}, }
@article {pmid41780383, year = {2026}, author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X}, title = {Enhancing methane production in anaerobic digestion of food waste by Fe-MOF and Fe-MOF-derived carbon composites: Insights into properties, multi-omics analyses, and mechanisms.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129181}, doi = {10.1016/j.jenvman.2026.129181}, pmid = {41780383}, issn = {1095-8630}, mesh = {*Methane ; Anaerobiosis ; Iron/chemistry ; Carbon/chemistry ; Metal-Organic Frameworks/chemistry ; Multiomics ; Food Loss and Waste ; }, abstract = {In this work, Fe-MOF and Fe-MOF-derived carbon composites (Fe-MDCs) derived at 300, 500, and 700 °C were first applied in anaerobic digestion to achieve efficient renewable energy production from food waste. The enhancement mechanism of methane yield was further explored using metagenomic and metaproteomic analysis. The results showed that compared with the control group, methane yield was enhanced by 9.66%-13.99%, 16.21%-23.56%, and 7.99%-19.84% in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups, respectively. Among them, Fe-MDC-500 possessed superior electronic conductivity and a higher specific surface area, which was beneficial for improving methane production by facilitating interspecies electron transfer and providing abundant surface sites for microbial attachment. Metagenomic analysis demonstrated that the functional microorganisms, key genes related to methane metabolism, and the activity of corresponding coenzymes were increased in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups. The poor syntrophic interaction resulted in the lowest methane yield under Fe-MOF-300 addition. Metaproteomic analysis indicated that the expressions of proteins related to quorum sensing system, transcription, and translation were also up-regulated, indicating that Fe-MDC-500 potentially promoted microbial communication among methanogenic and symbiotic microorganisms, ultimately boosting the metabolic activity of anaerobic digestion system. Meanwhile, the expressions of vital proteins involved in enzyme synthesis and catalytic bioconversion, including RNA polymerase, Ribosome, and Aminoacyl-tRNA biosynthesis, were significantly upregulated. This research clarified the mechanism of exogenous materials enhanced methane production by elucidating the key metabolic pathways and functional genes, which provided valuable insights for optimizing energy recovery system.}, }
@article {pmid41780389, year = {2026}, author = {Du, Y and Zhao, S and Gao, Y and Yan, Y and Kong, Y and Meng, W and Lu, X and Zheng, S and Mu, H and Chen, X and Kong, Q}, title = {The synergistic effect of algal-bacterial granular sludge in a sequencing batch reactor with tetracycline-containing synthetic livestock and poultry breeding wastewater.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129178}, doi = {10.1016/j.jenvman.2026.129178}, pmid = {41780389}, issn = {1095-8630}, mesh = {Animals ; *Tetracycline ; *Wastewater ; Livestock ; *Sewage/microbiology ; Bioreactors ; Poultry ; Bacteria ; Waste Disposal, Fluid/methods ; Anti-Bacterial Agents ; }, abstract = {The concentration of environmental antibiotics, along with their ecological risk, has increased due to the continuous accumulation of livestock and poultry breeding wastewater (LPBW). In this study, two sequencing batch reactors (SBRs) were established-one equipped with algal-bacterial granular sludge (ABGS) and the other with aerobic granular sludge (AGS)-to investigate the treatment performance of tetracycline containing synthetic LPBW. Pollutant removal efficiency and underlying mechanisms were determined by analyzing the physiological and biochemical properties, dynamic changes in the microbial community, and the fate of antibiotic resistance genes (ARGs). Compared to AGS, ABGS resulted in faster granulation and greater lipid production. Exposure to tetracycline significantly altered the contents of extracellular polymeric substances (EPS) and chlorophyll. During the cultivation stage, the removal efficiencies of TN and TP by ABGS were 7.01% and 1.52% higher, respectively, than those by AGS. However, after tetracycline was added, the TN and TP removal efficiencies of ABGS decreased by 0.77% and 6.91%, respectively, compared to those of AGS. The tetracycline removal efficiency of ABGS reached 86.32%, which was 4.49% greater than that of AGS. Metagenomic analysis revealed that the relative abundances of Pseudomonas and Stenotrophomonas (key tetracycline-degrading bacteria) in ABGS were 36.61% and 66.82% greater, respectively, than those in AGS. After tetracycline was added, the relative abundances of tetracycline-related ARGs (tetX and MuxB) increased by 36.01% and 61.68%, respectively, in AGS but decreased by 53.98% and 5.71%, respectively, in ABGS. In this study, ABGS exhibited outstanding performance in enhancing the removal of pollutants from tetracycline-containing synthetic LPBW in SBR systems.}, }
@article {pmid41780396, year = {2026}, author = {Xia, R and Shi, T and Liu, W and Li, G and Zhi, S and Luo, W and Xu, Z}, title = {Genome-resolved metagenomic insights into cornstalks-mediated reduction of pathogens and antibiotic resistomes during passively aerated static composting of swine manure.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129185}, doi = {10.1016/j.jenvman.2026.129185}, pmid = {41780396}, issn = {1095-8630}, mesh = {*Manure/microbiology ; *Composting ; Animals ; Swine ; Zea mays ; Drug Resistance, Microbial ; Anti-Bacterial Agents ; Metagenomics ; }, abstract = {Passively aerated static composting is widely adopted for livestock manure treatment; however, its efficacy in eliminating antibiotic resistance genes (ARGs) and pathogens is often inadequate due to ineffective oxygen diffusion to restrict organic biodegradation and thus the formation of thermophilic condition. Despite extensive research on aerobic composting, the optimal amendment strategy and mechanistic role of crop stalks in shaping ARG dynamics during passively aerated static composting of swine manure remain unclear. Here, cornstalks and swine manure were representatively selected to elucidate how their passively aerated static composting was successfully initiated to improve ARG elimination using genome-resolved metagenomics and multivariate statistical analysis. Results show that adding 10% cornstalks significantly enhanced antibiotic resistome removal by improving composting properties (e.g. moisture content and oxygen permeability) and increasing temperature (above 65 °C). This improvement effectively inactivated bacterial hosts of ARGs and restrict horizontal gene transfer (HGT). Under these conditions, cornstalk addition promoted thermal inactivation of ARG hosts (e.g. Actinomycetota), particularly pathogenic antibiotic-resistant bacteria (e.g. Corynebacterium), thereby suppressing HGT. More importantly, chromosomally encoded mobile genetic elements (rather than plasmids and viruses) dominated HGT during composting. The transfer of multidrug, bacitracin, and macrolide-lincosamide-streptogramin resistance genes was primarily facilitated by intra-phylum HGT events, particularly within Bacillota. Cornstalk addition significantly accelerated inactivation of pathogens and ARG hosts (e.g. macrolide-lincosamide-streptogramin resistant bacteria), resulting in an increased removal of over 49.0% for both. These findings provide mechanistic insights into the optimization of passively aerated static composting for safe agricultural reuse of livestock manure.}, }
@article {pmid41780408, year = {2026}, author = {Wu, H and Qi, F and Huo, Y and Li, R and Ye, M and Topp, E and Qiao, M and Zhu, Y}, title = {Feed additives increase soil risk from antibiotic resistance genes via distinct horizontal gene transfer pathways.}, journal = {Environment international}, volume = {209}, number = {}, pages = {110174}, doi = {10.1016/j.envint.2026.110174}, pmid = {41780408}, issn = {1873-6750}, mesh = {*Gene Transfer, Horizontal ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; *Soil Pollutants/analysis ; Animal Feed ; }, abstract = {Non-antibiotic components of feed additives can enter farmland soils via livestock manure and accumulate persistently in agroecosystems, presenting potential environmental risks. We established soil microcosms, integrated metagenomes with viromes, and applied a contig-based horizontal gene transfer (HGT)-resolution pipeline to partition vector-level contributions, to assess how saccharin, copper, and their co-contamination affect soil gene flow and health risk. Results indicate divergent vector responses under additive stress: phage-host associations increased under saccharin (82 pairs vs. control 29 pairs), whereas copper strengthened plasmid-host associations. With saccharin, phage nucleotide diversity rose while synonymous nucleotide diversity declined, consistent with stronger purifying selection atop enhanced mutation supply, whereas copper increased lysogeny. Saccharin significantly elevated HGT frequency (∼50% increase), expanded donor-recipient phylogenetic span (class-level P < 0.05), and raised the phage-mediated share (∼100% increase). Copper primarily modestly increased the plasmid-mediated contribution (Cu 2.7%, HS 1.9%). Two-factor analyses revealed a significant antagonistic interaction between saccharin and copper, reducing overall HGT across taxonomic ranks under co-exposure. Although total ARG abundance did not change significantly, the health-risk index increased under saccharin, driven by enhanced ARG-MGE co-occurrence. Under co-contamination, auxiliary metabolic genes were enriched, suggesting phage-conferred metabolic empowerment that mitigates stress, partly explaining the antagonism. Altogether, our findings reveal that feed additives reshape vector-specific gene mobility and ARG risk, and they underpin a three-tiered risk-assessment framework that progresses from mere abundance to network-structured mobility and finally to mobility drivers incorporating phylogenetic transfer distance, offering a more mechanistic basis for soil-health management.}, }
@article {pmid41780450, year = {2026}, author = {Li, Z and Li, X and Jiao, B and Yang, Y and Wang, H and Gu, L and Ai, H and Cheng, H and Cheng, S}, title = {Redox oscillations in riparian zone stimulate carbon loss by enhancing microbial respiration.}, journal = {Water research}, volume = {296}, number = {}, pages = {125672}, doi = {10.1016/j.watres.2026.125672}, pmid = {41780450}, issn = {1879-2448}, mesh = {Oxidation-Reduction ; *Carbon/metabolism ; Soil Microbiology ; Soil/chemistry ; Iron ; Ecosystem ; }, abstract = {Redox oscillations within riparian ecosystems emerge as a critical threat to carbon sequestration, yet the mechanistic coupling between abiotic drivers and microbial metabolism remains elusive. Through controlled incubation experiments, we demonstrate that redox-oscillating conditions significantly reduce microbial carbon use efficiency (CUE), thus accelerating carbon loss compared to static oxic or anoxic conditions. Mechanistically, redox oscillations drove the cycling of iron (Fe) species, thereby reducing the amorphous Fe pool and liberating mineral-associated organic carbon (MAOC) composed of substantial biodegradable organic substrates (e.g., lipids and proteins). Concurrently, hydroxyl radicals (•OH) generated during Fe(II) oxidation depolymerize complex aromatic organic matter into labile forms. Integrated metagenomic and metabolomic analyses further demonstrated that redox oscillations significantly reshaped soil metabolite profiles and microbial community. In particular, microbial catabolic pathways such as pentose phosphate pathway and the tricarboxylic acid (TCA) cycle were activated to efficiently mineralize newly available substrate. Together, these results identify a coupled abiotic-biotic "prime and burn" mechanism in which Fe-driven substrate reorganization primes microbial differentiation toward enhanced respiration. This study highlights redox-oscillating zones as potential carbon leakage hotpots in the terrestrial carbon sink.}, }
@article {pmid41780551, year = {2027}, author = {Wolf, J and Goggin, KP and Inaba, Y and Allison, KJ and Ahmed, AA and Maron, G and Ferrolino, J and Lazure, L and Kohler, C and Brenner, A and Sun, Y and Tang, L and Gonzalez-Pena, V and Rubnitz, JE and Gawad, C and Margolis, EB and Thomas, P}, title = {Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101312}, doi = {10.1016/j.lanmic.2025.101312}, pmid = {41780551}, issn = {2666-5247}, abstract = {BACKGROUND: Patients receiving myelosuppressive chemotherapy or haematopoietic cell transplantation are at high risk for life-threatening bloodstream infections. A novel pre-emptive treatment paradigm guided by pathogen detection before symptoms appear might reduce this risk, but no validated screening test is available. This study evaluated the sensitivity and specificity of plasma microbial cell-free DNA metagenomic sequencing (mcfDNA-Seq) for predicting bloodstream infections in children and adolescents receiving therapy for high-risk leukaemia.
METHODS: In this prospective cohort study, between Aug 9, 2017, and Feb 28, 2022, leftover clinical plasma samples were prospectively collected up to once per day from patients who were younger than 25 years, receiving care for leukaemia at St Jude Children's Research Hospital (Memphis, TN, USA), and at high risk for life-threatening bloodstream infections. mcfDNA-Seq was used to identify pathogen DNA in blood samples obtained during the 7 days before to 1 day after bloodstream infection onset, and in control samples from the same population in the absence of fever or infection. The testing laboratory was masked to sample status. Primary outcomes were predictive sensitivity of mcfDNA-Seq for detecting the expected bloodstream infection pathogen during the 3 days preceding the day of bloodstream infection onset, with a prespecified favourable sensitivity of 50%, and predictive specificity of mcfDNA-Seq in control samples. Exploratory analyses comprised assessing sensitivity and specificity restricted to bacteria or common bloodstream infection pathogens, and after applying a data-derived DNA fragment concentration cutoff; estimating the predictive sensitivity on each of the 7 days before bloodstream infection onset; identifying clinical characteristics that affected predictive sensitivity or specificity; and examining the clinical relevance of additional organisms identified by mcfDNA-Seq during bloodstream infection episodes. Diagnostic sensitivity was also assessed on samples collected on the day of, or day after, diagnosis of bloodstream infection. This study is registered with ClinicalTrials.gov, NCT03226158.
FINDINGS: 94 evaluable bloodstream infections occurred in 60 (38%) of 158 enrolled participants; 19 episodes were previously described in the pilot phase of this study. The predictive sensitivity of mcfDNA-Seq was 51·9% (95% CI 40·5-63·1) for all bloodstream infection episodes, 53·8% (42·2-65·2) for bacterial infection only, and 51·9% (40·5-63·1) when applying a DNA fragment concentration cutoff of 140 molecules per μL. Sensitivity was lowest at day -7 and increased daily until the day of diagnosis. Diagnostic sensitivity was 81·3% (95% CI 71·0-89·1) for all bloodstream infection episodes and 83·1% (72·9-90·7) for bacterial infections only. Predictive specificity was 82·7% (95% CI 76·0-88·2), but improved to 88·9% (83·0-93·3) for common bloodstream infection pathogens, and to 93·8% (88·9-97·0) when also applying the DNA fragment concentration cutoff. Predictive sensitivity was higher in participants with acute lymphoblastic leukaemia (adjusted odds ratio [aOR] 11·1 [1·7-74·2] vs those with acute myeloid leukaemia), and it was lower in polymicrobial infections (aOR 0·0 [0·0-0·2] vs monomicrobial Gram-positive infections). Clinical false-positive results were positively associated with gastrointestinal disturbance alone (p=0·037) or combined with recent administration of high-dose cytarabine (p=0·012). Additional organisms identified by mcfDNA-Seq that were not identified by blood culture were less likely than expected organisms to have an increasing DNA concentration during the days preceding bloodstream infection diagnosis.
INTERPRETATION: mcfDNA-Seq can detect causative pathogens before the onset of some bloodstream infection episodes in profoundly immunocompromised patients. Predictive specificity might be improved by restricting results to a subgroup of relevant organisms, excluding patients with high risk of false-positive results, or applying a higher concentration cutoff. Clinical trials are needed to evaluate mcfDNA-Seq-guided pre-emptive therapy for preventing life-threatening bloodstream infections in patients with high risk.
FUNDING: The National Cancer Institute, American Lebanese Syrian Associated Charities, St Jude Children's Research Hospital, and Karius.}, }
@article {pmid41781852, year = {2026}, author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC}, title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04878-z}, pmid = {41781852}, issn = {1471-2180}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, }
@article {pmid41781872, year = {2026}, author = {Tian, N and Liu, M and Zhao, Y and Lian, Y and Jin, M and Yang, F}, title = {Gut microbiota dysbiosis and metabolic reprogramming in pediatric migraine: a multi-omics analysis revealing diagnostic biomarkers.}, journal = {The journal of headache and pain}, volume = {27}, number = {1}, pages = {}, pmid = {41781872}, issn = {1129-2377}, support = {2022 Budget Approval No. 180 of Hebei Provincial Department of Finance//Provincial Medical Outstanding Talents Project funded by the Provincial Government in 2022/ ; Grant No. 20260868//Hebei Provincial Medical Science Research Project funded by the Health Commission of Hebei Province/ ; 2026 Hebei Provincial Introduction of Foreign Intelligence Project//Hebei Provincial Department of Science and Technology/ ; }, abstract = {BACKGROUND: Numerous studies have identified disruptions in the gut microbiota of patients with migraine, and the role of the gut–brain axis in the pathogenesis and development of migraine has been established. The incidence of migraine in children increases with age, yet the intestinal microbiota in pediatric migraine has been inadequately investigated. Therefore, we aim to investigate the composition, functional characteristics, and metabolite profiles of the gut microbiota in children with migraine.
METHODS: We recruited 30 children with migraine and 30 healthy controls aged 5–14 years from Hebei Province, China, and collected 60 fresh fecal samples. Metagenomic sequencing was performed to obtain species abundance profiles and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotations of gene sequences. Non-targeted metabolomic analysis was applied to assess differential changes in gut microbiota metabolites between children with migraine and healthy controls.
RESULTS: The abundance of gut microbiota species was significantly reduced in children with migraine (P = 0.001), and was associated with migraine presence (R[2] = 0.051, P = 0.001). Bacteria within Pseudomonadota were significantly enriched in the gut flora of children with migraine, with Escherichia coli being the most abundant species. The propionic acid, the arginine and proline metabolism pathways were significantly upregulated in children with migraine (P < 0.05). In contrast, the porphyrin metabolism pathway, amino acid biosynthesis pathway, and arginine biosynthesis pathway were significantly down-regulated (P < 0.05). The intestinal lipopolysaccharide biosynthetic pathway showed diagnostic potential for pediatric migraine, with an Area Under the Curve (AUC) of 0.75 (95% CI: 0.63–0.87). Intestinal metabolites were also dysregulated in children with migraine; notably, Docosahexaenoyl Ethanolamide (DHEA) and kynurenic acid were significantly depleted (P < 0.05).
CONCLUSION: This study revealed an association between gut microbiota and its metabolite in children with migraine, suggesting that the potential pathogenic role of gut microbiota may be mediated by the functions of Pseudomonadota and Escherichia coli and by the levels of metabolites derived from them. Furthermore, this study provides strong evidence for the diagnostic potential of kynurenic acid in pediatric migraine and supports future targeted metabolite research.
GRAPHICAL ABSTRACT: [Image: see text]
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s10194-026-02315-0.}, }
@article {pmid41781883, year = {2026}, author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J}, title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04902-2}, pmid = {41781883}, issn = {1471-2180}, support = {32171607//National Natural Science Foundation of China/ ; }, }
@article {pmid41781897, year = {2026}, author = {Liu, D and Yu, S and Tian, X and Wang, Z and Lu, Y and Dai, Y and Hu, C and Ma, X and Mao, M and Xue, L and Yi, Z and Zhang, G and Li, S and Wang, Q and Zhang, Z and Tian, Z}, title = {Epidemiological investigation of an acute gastroenteritis outbreak associated with norovirus GΙΙ.17[P17] in a cross-border travel group - Shanghai Port, China, 2024.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-12978-4}, pmid = {41781897}, issn = {1471-2334}, support = {2024HK149//General Administration of Customs Project/ ; 2022YFC2302800//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Norovirus is a leading cause of acute gastroenteritis and spreads efficiently in closed, mobile cohorts such as organized travel groups. This case is notable for the real-time detection and genomic confirmation of a cross-border outbreak at a port of entry, including near-identical Norovirus GΙΙ.17[P17] genomes and documented asymptomatic carriage, illustrating the practical value of integrated metagenomic surveillance in border health operations.
CASE PRESENTATION: On July 21, 2024, 26 travelers arrived at Shanghai Port after a 12-day group tour in Europe. Clinical interviews identified 15 individuals (57.7%) with diarrhea, nausea, dizziness, and abdominal pain; no hospitalizations occurred. On-site anal swab testing was negative for SARS-CoV-2, influenza A and B, Vibrio cholerae, and Escherichia coli. RT-qPCR detected Norovirus GII in 10 samples (38.5%), including two asymptomatic individuals. Metagenomic sequencing generated near-complete genomes for all RT-qPCR-positive samples, which were 99.9-100% identical and classified as Norovirus GΙΙ.17[P17], confirming a cross-border outbreak within the travel cohort. Prompt public health response measures were initiated by Shanghai Customs and CDC authorities.
CONCLUSIONS: This case demonstrates the feasibility and impact of rapid, genomically informed surveillance at the border for detecting and characterizing travel-associated enteric virus outbreaks. The findings underscore the need for robust port-of-entry monitoring, rapid diagnostics, and integrated genomic analysis to mitigate transmission in group travel settings.}, }
@article {pmid41781966, year = {2026}, author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X}, title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04231-6}, pmid = {41781966}, issn = {1477-3155}, support = {32272514//National Natural Science Foundation of China/ ; }, abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.}, }
@article {pmid41782011, year = {2026}, author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J}, title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02368-y}, pmid = {41782011}, issn = {2049-2618}, support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.
RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.
CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.}, }
@article {pmid41782139, year = {2026}, author = {Mao, K and Zang, Y and Wang, C and Yang, W and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Liang, H and Xu, L and Qu, M and Li, Y}, title = {Rumen microbiota-associated stress alleviation by creatine pyruvate in newly received cattle: a multi-omics study.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02365-1}, pmid = {41782139}, issn = {2049-2618}, support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; No. 3230810//the National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; }, abstract = {BACKGROUND: Stress experienced by newly received cattle is a significant challenge in the beef industry, frequently resulting in weakened immune responses and impaired growth. The rumen microbiota is essential to host health, and its imbalance can exacerbate stress. This study investigates the mechanisms by which creatine pyruvate (CrPyr) mitigates stress in newly received cattle through multi-omics approaches, including metagenomics, metabolomics, in vitro and in vivo experiments, and rumen microbiota transplantation (RMT) in mice.
RESULTS: Our results revealed that CrPyr significantly reduces stress-related hormones (cortisol and adrenocorticotropic hormone) and inflammatory markers (IL-6, IL-1β, and TNF-α), and enhanced antioxidant capacity (SOD: 57.38 versus 46.93 U/mL, P < 0.05; GSH-Px: 305.87 versus 217.07 U/mL, P < 0.05; T-AOC: 9.62 versus 7.66 U/mL, P < 0.05). Metagenomic analysis demonstrated that CrPyr increased Prevotella abundance, a key rumen bacterium involved in volatile fatty acid (VFA) production, and enriches metabolic pathways associated with energy metabolism (ATP synthesis, and pyruvate metabolism) and antioxidant defense (glutathione metabolism, FC = 1.08, P < 0.05). In vitro and in vivo experiments, as well as RMT studies in mice, further validate these findings, demonstrating that CrPyr promote VFA synthesis and increased ATP production through the electron transport phosphorylation pathway.
CONCLUSIONS: CrPyr modulates the abundance of ruminal Prevotella in transport-stressed cattle to enhance glutathione and VFA metabolism and to accelerate ATP and nucleotide synthesis, thereby alleviating stress in newly received cattle. This multimodal approach established CrPyr as an effective nutritional intervention that improves rumen function and increases livestock productivity. Video Abstract.}, }
@article {pmid41782849, year = {2026}, author = {Fang, T and Hu, P and Zhang, Y and Hu, B and Miao, Q}, title = {Chronic Mycobacterium kansasii Pleural Infection Mimicking Metastatic Breast Cancer: A Seven-Year Diagnostic Odyssey and the Critical Role of Metagenomic Sequencing.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {580064}, pmid = {41782849}, issn = {1178-6973}, abstract = {INTRODUCTION: Nontuberculous mycobacteria such as Mycobacterium kansasii can mimic malignancy on imaging and pathology, leading to prolonged diagnostic uncertainty and inappropriate anticancer therapy.
CASE REPORT: A 76-year-old woman with remote right breast carcinoma (mastectomy and adjuvant therapy in 1996) had a persistent right chest-wall lesion with rib changes and encapsulated pleural effusion repeatedly interpreted as metastatic disease from 2017 to 2023, despite multiple biopsies showing only fibrous hyperplasia. In August 2024, fever and cough prompted re-evaluation. PET-CT demonstrated a hypermetabolic pleura-adjacent lesion (SUVmax 10.8) without distant metastases. Plasma metagenomic next-generation sequencing (mNGS) yielded a low-level M. kansasii signal; pleural fluid mNGS identified 146 reads (94% relative abundance), later confirmed by culture. Targeted anti-NTM therapy stabilized the infection; however, the patient developed severe varicella-zoster virus infection and cardiac complications and subsequently died. The death was attributed to these complications rather than the progression of the M. kansasii infection.
CONCLUSION: Chronic M. kansasii pleural infection can masquerade as metastatic breast cancer for years. PET-CT alone is insufficient to distinguish infection from malignancy; careful imaging review combined with unbiased mNGS can establish the diagnosis and avert unnecessary anticancer therapy. Multidisciplinary collaboration is essential for timely recognition and management.}, }
@article {pmid41783251, year = {2026}, author = {Nibbering, B and Nooij, S and Harmanus, C and Sanders, IMJG and Miedema, IM and Ducarmon, QR and Vossen, RHAM and Kloet, SL and Ardis, CK and Britton, RA and Yousefi, F and Bayne, J and Charavaryamath, C and Law, A and Murphy, ML and Sponseller, B and Burrough, ER and Ramirez, A and Mooyottu, S and Opriessnig, T and Kuijper, EJ and Roestenberg, M and Smits, WK}, title = {Characterization of the clade 4 non-toxigenic C. difficile isolate L-NTCD03 carrying the cfr(B) gene.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag010}, pmid = {41783251}, issn = {2633-6685}, abstract = {Clostridioides difficile infection (CDI) is a toxin-mediated gastro-intestinal disease. Yet, C. difficile is a phylogenetically diverse species that includes many non-toxigenic strains. In general, these are understudied, despite having significant potential impact for our understanding of the colonization process and as therapeutic modalities. Here, we present an in-depth characterization-including the complete genome sequence-of the non-toxigenic C. difficile strain L-NTCD03. This strain belongs to PCR ribotype 416, clade 4 and multilocus sequence type 39. It is resistant to multiple antimicrobials, but not those used for treatment of CDI. We validated the relevance of the cfr(B) gene from this strain in antimicrobial resistance to clindamycin, linezolid, retapamulin, and streptogramin A. We found the L-NTCD03 strain to be non-toxic in various assays. Altogether, L-NTCD03 is a promising candidate for developing into a live biotherapeutic product.}, }
@article {pmid41783404, year = {2026}, author = {Liu, D and Ma, Y and Ma, Q and Huang, H and Li, T and Wang, J and Zhang, J and Cheng, X and Ge, X and Chen, Y and Zhang, Y}, title = {Clinical pathogen profiles and lung microbiome features in lung infection patients and concurrent cancer: insights from metagenomics next-generation sequencing.}, journal = {Open life sciences}, volume = {21}, number = {1}, pages = {20251220}, pmid = {41783404}, issn = {2391-5412}, abstract = {Pulmonary infections in immunocompromised cancer patients present significant diagnostic and therapeutic challenges. From Dec 2021 to Aug 2023, 85 patients with pulmonary infection were enrolled and categorized into a cancer group (CP, n = 20) and a non-cancer control group (NCP, n = 18). Pathogen detection was performed using both mNGS and culture and lung microbiome analysis was conducted. mNGS demonstrated a significantly higher pathogen detection rate than culture (P < 0.0001). The CP group exhibited older age (P < 0.001), elevated neutrophil counts (NE) and higher procalcitonin (PCT) levels compared to the NCP group. Furthermore, fungal pathogens were significantly more prevalent in the CP group (P = 0.046). Both cancer status and advanced age were independent influencing factors for the detection of pulmonary fungi. Pulmonary microbiome analysis revealed no significant differences in α-diversity or β-diversity between groups. These findings indicate that mNGS offers superior sensitivity over culture. Cancer-related pulmonary infections present a distinct pathogen profile characterized by a higher prevalence of fungal pathogens. This underscores the need for enhanced clinical vigilance, especially among elderly cancer patients.}, }
@article {pmid41783570, year = {2026}, author = {Lin, H and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Zhang, XH and Moreau, JW}, title = {Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.}, journal = {Marine life science & technology}, volume = {8}, number = {1}, pages = {206-220}, pmid = {41783570}, issn = {2662-1746}, abstract = {UNLABELLED: Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair hgcAB encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. "Blue holes" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, Nitrospina and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00332-7.}, }
@article {pmid41784027, year = {2026}, author = {Mekonnen, YT and Indio, V and Lucchi, A and Manfreda, G and Serraino, A and De Cesare, A}, title = {Detection of Chlamydia ibidis in the neck skin microbiome of broiler carcasses at the end of slaughter.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.14726}, pmid = {41784027}, issn = {2239-7132}, abstract = {Chlamydia is the etiological agent of chlamydiosis in wild and domestic birds, mammals, and humans. In this study, Chlamydia reads were detected in the microbiome of the neck skin of 76 broiler carcasses collected in the same slaughterhouse at the end of the chilling tunnel. The carcasses originated from four different flocks of female Ross 308, reared in two broiler houses located in Northern Italy. One flock from each poultry house was sampled in 2019 and one flock in 2023. The carcass neck skin microbiome was investigated by shotgun metagenomic sequencing. Chlamydia reads displayed a mean relative abundance of 7.38%, with significant differences between carcasses obtained from the two poultry houses, sampled at both sampling times. Chlamydia ibidis was the prevalent species among time points and poultry houses. The zoonotic potential of C. ibidis and foodborne transmission have never been demonstrated. However, it is known that the genus Chlamydia has "spore"-like extracellular forms able to survive for months outside the host. Therefore, the presence of C. ibidis reads on broiler carcasses at the end of the chilling tunnel deserves further investigation. The results of this study highlight the feasibility of microbiome investigations to detect unexpected biological hazards in foods.}, }
@article {pmid41784373, year = {2026}, author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A}, title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0369125}, doi = {10.1128/spectrum.03691-25}, pmid = {41784373}, issn = {2165-0497}, abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.}, }
@article {pmid41784805, year = {2026}, author = {Shen, J and Gao, J and Gao, L and Yan, D and Wang, Y and Meng, J and Li, H and Chen, D and Wu, J}, title = {Melatonin ameliorates autistic-like behaviors by restoring gut microbiota-derived tryptophan metabolites.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41784805}, issn = {1420-9071}, support = {2023-MS-310, 2019-BS-098//Natural Science Foundation of Liaoning Province/ ; LJKQZ2021149//Scientific Research Fund of Liaoning Provincial Education Department/ ; }, abstract = {UNLABELLED: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive stereotyped behavior. Disrupted microbiota‒gut‒brain axis (MGBA) signaling contributes to the pathology of ASD and cognitive disability. Melatonin (MT), a naturally occurring compound, has shown potential in ameliorating core symptoms of ASD and mitigating gut microbiota dysbiosis, yet the underlying mechanism is poorly understood. This study aimed to investigate whether exogenous melatonin improves behavioral deficits in valproic acid (VPA)-exposed male offspring rats, and the modulation of gut microbiota-derived tryptophan metabolites. In prenatal VPA-induced model rats, microbial diversity and construction was analyzed through metagenomic sequencing, targeted-metabolomics and transcriptomics were conducted to explore related metabolic pathways and molecular profiles. We identified 7 gut bacterial genus causally associated to ASD: Faecali-bacterium, Lachnospiraceae, Ruminococcaceae, Butyricimonas, and Bacteroides exhibited protection, whereas Erysipelotrichaceae and Clostridia enhanced risk. The exacerbation of Erysipelotrichaceae and Clostridia by VPA versus restoration of Faecalibacterium, Butyricimonas, Bacteroides and Bifidobacterium by melatonin, which are known to participate in tryptophan metabolism. Correspondingly, systemic metabolomics pointed to melatonin’s restoration of tryptophan metabolic disorders (IDO1-kynurenine, TPH1/2-serotonin-melatonin, and Indole-3-propionic acid (IPA)) induced by VPA, paralleled the rectification of microglial reactivity, synaptic proteins, dendritic morphology, and hippocampal neurogenesis. These molecular profiles were further integrated by transcriptomics, highlighted tryptophan-derived neurotransmitters and neuroactive ligand-receptor interaction, contributing to enhanced social and cognitive behaviors under melatonin intervention. Based on multi-omic analysis, our findings underscore key bacteria and metabolites contributing to neurological and immune dysfunction in VPA-exposed rats, providing novel targets for possible therapeutics of melatonin.
GRAPHICAL ABSTRACT: [Image: see text]
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06163-8.}, }
@article {pmid41785052, year = {2026}, author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S}, title = {MDPD reveals specific microbial signatures in human pulmonary diseases.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41785052}, issn = {1477-4054}, mesh = {Humans ; *Lung Diseases/microbiology ; *Microbiota ; *Databases, Factual ; Bacteria/classification/genetics ; Machine Learning ; }, abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.}, }
@article {pmid41785249, year = {2026}, author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR}, title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.}, journal = {PLoS computational biology}, volume = {22}, number = {3}, pages = {e1013185}, pmid = {41785249}, issn = {1553-7358}, mesh = {Humans ; *Mouth/microbiology ; Infant ; *Microbiota/genetics ; Female ; Phylogeny ; Metagenome/genetics ; Metagenomics ; Male ; Streptococcus/genetics/classification ; Longitudinal Studies ; Computational Biology ; }, abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.}, }
@article {pmid41785480, year = {2026}, author = {Shekarriz, S and Vigod, SN and Bianco, T and Bala, A and Hao, C and Allard, JP and Hota, S and Poutanen, S and Surette, MG and Taylor, VH}, title = {The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.}, journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie}, volume = {}, number = {}, pages = {7067437261420877}, pmid = {41785480}, issn = {1497-0015}, abstract = {BackgroundThe gut microbiome has been proposed as a potential modifiable target to treat mental illness. This double-blind randomized control trial investigated fecal microbiota transplant (FMT) in bipolar disorder (BD) to assess efficacy, safety, and feasibility. The primary outcome evaluated the effectiveness of standard approved therapy for BD depression + FMT in individuals not responding to standard treatment, measured by change in the Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to week 24. Secondary outcomes included FMT's impact on anxiety, global function, side-effects, and safety. The feasibility of this novel intervention was also assessed. Microbial analysis utilized whole-genome shotgun metagenomic sequencing, comparing outcomes between allogenic (donor) and autologous (participants own) FMT.MethodsA total of 35 participants (28 women and 7 men) with at least moderate depressive-phase BD (MADRS) were randomized to receive either allogenic FMT (n = 17) or autologous FMT (n = 18) via colonoscopy and were followed for 24 weeks.ResultsMADRS scores significantly improved from baseline to the last visit in both treatment arms. There was no significant difference between allogenic FMT (16.74-point improvement) and autologous FMT (15.4-point improvement) regarding clinical efficacy (t = -0.47, p-value = .64, 95% confidence interval [CI] = -7.3-4.6). Microbiota analysis showed that allogenic FMT let to a bacterial profile similar to the healthy donor and increased bacterial diversity at the 6-month mark, whereas those receiving autologous FMT did not. The intervention was well tolerated with no significant adverse events. Recruitment, randomization, and retention metrics support feasibility of a larger trial.ConclusionFeasibility and tolerability data indicate further investigation into microbial manipulation in BD is warranted. The absence of efficacy differences between the two types of FMT, despite microbial change, highlights the importance of a true placebo in future studies, as well as the importance of understanding exactly what bacteria are linked to improvements. ClinicalTrials.gov, NCT0327922.}, }
@article {pmid41785576, year = {2026}, author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I}, title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.}, journal = {The Science of the total environment}, volume = {1023}, number = {}, pages = {181623}, doi = {10.1016/j.scitotenv.2026.181623}, pmid = {41785576}, issn = {1879-1026}, mesh = {Aerosols/analysis ; Cities ; *Environmental Monitoring ; Seasons ; *Air Microbiology ; Canada ; *Air Pollutants/analysis ; Socioeconomic Factors ; }, abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.}, }
@article {pmid41785649, year = {2026}, author = {Dong, W and Ye, T and Zhang, Z and An, L and Peng, Y and Chen, Y and Zhang, Y and Ke, L and Chen, S and Zhao, S and Hu, Y}, title = {Quorum sensing-associated acid adaptation in bacterial communities during pit fermentation of sauce-flavor Baijiu.}, journal = {International journal of food microbiology}, volume = {453}, number = {}, pages = {111715}, doi = {10.1016/j.ijfoodmicro.2026.111715}, pmid = {41785649}, issn = {1879-3460}, mesh = {Fermentation ; *Quorum Sensing ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Fermented Foods/microbiology ; Food Microbiology ; Lactic Acid/metabolism ; *Acids/metabolism ; Adaptation, Physiological ; Hydrogen-Ion Concentration ; }, abstract = {Sauce-flavor Baijiu is produced by multi-round solid-state fermentation under progressively increasing acidity, yet how bacterial communities adapt to this extreme acid stress and whether quorum sensing (QS)-associated features are involved remain unclear. Here, fermented grains from eight pit-fermentation rounds under both traditional and mechanized processes were analyzed by metagenomic sequencing and physicochemical profiling. The traditional process showed higher moisture, stronger and faster acidification, greater lactic acid accumulation, and more rapid depletion of reducing sugars and starch than the mechanized process. These conditions coincided with a sharper decline in bacterial α-diversity and convergence toward a community overwhelmingly dominated by Acetilactobacillus jinshanensis (>90%) in the traditional process, whereas the mechanized process maintained higher diversity and a multi-species core dominated by A. jinshanensis, Lactobacillus acetotolerans, Bacillus, and actinomycetes. Canonical correspondence analysis identified acidity (lactic acid) as a major environmental factor associated with these divergent trajectories. QS gene profiling revealed process-specific signatures, with the LuxS/AI-2-associated module being the most abundant QS-related feature and significantly enriched in the traditional process. Functional annotation uncovered coordinated enrichment of acid-adaptation genes (ATPF1A, clpP, ATPF1B, dnaK, and groEL) during mid-to-late stages under high acidity. Network analysis further highlighted tighter co-associations among A. jinshanensis, QS modules, and acid-adaptation genes, supporting a community-level QS-associated functional framework for ecological convergence. Collectively, this study links LuxS/AI-2-associated features to acid-adaptation capacity and A. jinshanensis dominance in high-acidity environment. These findings provide ecological insight into microbial resilience in high-acidity solid-state fermentations and offer QS-informed perspectives for future targeted validation in Baijiu production.}, }
@article {pmid41786226, year = {2026}, author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF}, title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134333}, doi = {10.1016/j.biortech.2026.134333}, pmid = {41786226}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Oxygen/metabolism ; *Nitrites/metabolism ; Bioreactors/microbiology ; *Autotrophic Processes ; Bacteria/metabolism/genetics ; Water Purification/methods ; Genes, Bacterial ; }, abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.}, }
@article {pmid41786734, year = {2026}, author = {Gao, M and Delgado-Baquerizo, M and Xiong, C and Sáez-Sandino, T and Wang, J and Liang, J and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK}, title = {Dominance and natural suppression of bacterial plant pathogens across global soils.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70233-5}, pmid = {41786734}, issn = {2041-1723}, support = {DP230101448//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Soils are the primary environmental reservoir of plant pathogens impacting food production and ecosystem productivity worldwide. Yet, some soils can also suppress pathogens through environmental and microbial regulation. Here we integrate 1602 soil metagenomes from 59 countries with a greenhouse experiment to identify 32 dominant pathogens, including Ralstonia solanacearum, Clavibacter michiganensis, and Streptomyces europaeiscabiei. Pathogen hotspots occur primarily in warm ecosystems and agricultural soils, whereas higher soil microbial diversity, increased soil organic carbon and colder climatic conditions are associated with lower pathogen prevalence. Non-pathogenic Streptomyces spp., arbuscular mycorrhizal fungi, and biosynthetic gene clusters encoding terpenes and polyketides are associated with reduced pathogen prevalence. Predictive modelling suggests that several dominant bacterial pathogens are likely to increase in prevalence under future climate scenarios, particularly in tropical and subtropical regions. By identifying global drivers of dominant pathogens and their suppression, this study provides a foundation for improved surveillance and management of plant disease risks under climate change.}, }
@article {pmid41786735, year = {2026}, author = {Wen, Y and Gao, M and Wang, Z and Liu, X and Zhang, Y and Lin, G and He, P and Yang, H and Xiao, Y and Lyu, W}, title = {Dietary copper-driven colonic dysbiosis mediates oxidative stress and butyrate deficiency to facilitate the spread of resistome in pigs.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00949-1}, pmid = {41786735}, issn = {2055-5008}, support = {10417000025CE0615G//State Key Laboratory for Managing Biotic and Chemical Threats to the Safety of Agro-products/ ; 32372907//National Natural Science Foundation of China/ ; LR25C170001//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {Copper-induced transmission of antimicrobial resistance has been well documented in livestock farming environments, but the in vivo mechanisms driving fecal resistome development remain unclear. Here, 120 mg/kg CuSO4 and copper-peptide were supplemented to piglets, and the fecal resistome development was first analyzed by metagenomic sequencing. In this study, dietary CuSO4 drove abundant and diverse ARGs and MRGs. Following CuSO4 deprivation, ARGs and copper resistance exhibited a persistent promotion, whereas most MRGs rapidly declined. The resistance development was characterized by abundant MGEs. This phenomenon expanded the multiple-antibiotic resistance reservoir in fecal community, which was preferentially harbored by pathogens. Furthermore, dietary CuSO4 disturbed colonic homeostasis, characterized by impaired epithelial integrity and reduced butyrate-producing bacteria abundance, which coincided with an oxidative stress environment and increased prevalence of multiple-resistant pathogens, such as Escherichia coli and Enterococcus spp. In vitro validation further supported these associations, showing that butyrate supplementation and hypoxic conditions alleviated Cu[2+]-induced ROS generation and reduced the frequency of ARGs conjugative transfer. Overall, this study suggests that dietary inorganic copper may contribute to microbial disturbances linked to oxidative stress and potentially facilitate antimicrobial resistance transmission among pathogens, highlighting organic copper as a sustainable alternative for mitigating resistance risks in farmed animals.}, }
@article {pmid41786764, year = {2026}, author = {Franciosa, I and Castelnuovo, G and Cantele, C and Cardenia, V and Bo, S and Ponzo, V and Goitre, I and Pontonio, E and Tortarolo, D and Verni, M and Bugianesi, E and Cordero, F and Beccuti, M and Cocolin, L and Ferrocino, I}, title = {Gut microbiome modulation by cricket, pea, and whey protein using the SHIME in vitro simulator.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00785-9}, pmid = {41786764}, issn = {2396-8370}, support = {D17G22000150001//NODES funding from the MUR - M4C2 1.5 of PNRR, funded by the European Union - NextGenerationEU, Mission 4 Component 1.5 - ECS00000036/ ; }, abstract = {Entomophagy is increasingly popular, and Acheta domesticus offers an ecologically sustainable protein alternative, but the effects on the human gut microbiome need further investigation. In this study, we investigated the impact of the intake of three isolated proteins: pea (plant), whey (animal), and cricket (insect) on gut microbiome of a single-donor using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Cricket protein intake was associated with potential beneficial taxa such as Bifidobacterium and Lactobacillus, genes related to vitamin biosynthesis and bacteriocin transport, and short and medium-chain fatty acids. Pea protein intake was associated with Faecalibacterium and Slackia, while whey protein with Butyricimonas and Lactobacillus. Metagenomic analysis revealed that pea intake led to increased lysine degradation genes, promoting SCFAs production. Each protein has its own unique characteristics that may contribute positively to gut health. Specifically, cricket protein intake appears to have beneficial effects, promoting the growth of potentially beneficial taxa and enhancing short-chain fatty acid production. The results of this study indicate that cricket protein does not exhibit any detrimental effects compared to pea and whey proteins.}, }
@article {pmid41786809, year = {2026}, author = {Nagy, NA and Laczkó, L and Freytag, C and Tóth, RB and Nagy, SV and Sramkó, G and Barta, Z}, title = {Draft genomes of two Lethrus species.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06978-x}, pmid = {41786809}, issn = {2052-4463}, abstract = {The superfamily Scarabaeoidae is a species-rich and diverse group within the order Coleoptera. The members of this taxon are of interest due to the diversity of their feeding and mating behaviour, and their ecological importance. Despite the size of the superfamily, only a few genomes have been published, leaving a large gap in our understanding of the evolution of these beetles. To reduce this gap, we generated third-generation sequencing data to describe the first genome assembly of Lethrus scoparius and to improve the assembly of Lethrus apterus. The genome of L. scoparius consists of 2,873 contigs with an N50 value of 301,243 bp. BUSCO analysis revealed 98.1% complete ortholog hits in the Endopterygota ortholog database. For the L. apterus genome, we were able to assemble 886 scaffolds with an N50 value of 1,378,308 bp and a complete BUSCO hit of 96.8%. We assigned functions to 15,252 genes in L. scoparius and 15,520 in L. apterus. These genomes may contribute to understanding the evolution of the superfamily.}, }
@article {pmid41786830, year = {2026}, author = {Nowak, RG and Gough, E and Holm, JH and Hu, F and Akinyombo, K and Okudo, C and Ozumba, PJ and Jonathan, EC and Tiamiyu, AB and Kokogho, A and Adebajo, SB and Shoyemi, E and Baral, SD and Lombardi, K and Peel, S and Lim, JN and Gaydos, CA and Manabe, YC and Sears, CL and Shardell, M and Ravel, J and Crowell, TA and Tuddenham, S}, title = {Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42119-5}, pmid = {41786830}, issn = {2045-2322}, support = {R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R01MH099001/MH/NIMH NIH HHS/United States ; }, }
@article {pmid41787122, year = {2026}, author = {Panagiotou, K and Geesink, P and Köstlbacher, S and de Zwaan, GH and Ettema, TJG}, title = {Diversity, ecology, cell biology and evolution of the Asgard archaea.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41787122}, issn = {1740-1534}, abstract = {The Asgard archaea are a clade of archaea that was first discovered through metagenomic surveys of marine sediments. The past decade has witnessed a substantial expansion of their genomic diversity, revealing diverse metabolic repertoires and providing insights into their ecological interactions and function. Notably, comprehensive phylogenomic analyses, together with the identification of numerous eukaryotic signature proteins in Asgard archaeal genomes, have provided compelling evidence that Asgard archaea had a central role in the emergence of eukaryotes. Studies have reported the characterization of cultured Asgard archaeal representatives, uncovering unique cell biological characteristics hinting at thus far undescribed lifestyles. Here, we review the current state of the research field focusing on these intriguing microorganisms and outline future research directions aiming to resolve their ecology, cell biology and evolution.}, }
@article {pmid41787125, year = {2026}, author = {Schleper, C and Rodrigues-Oliveira, T}, title = {Asgard archaea: have we found our microbial ancestors?.}, journal = {The EMBO journal}, volume = {45}, number = {6}, pages = {1836-1851}, pmid = {41787125}, issn = {1460-2075}, support = {W1257//Austrian Science Fund (FWF)/ ; EFP 25//Austrian Science Fund (FWF)/ ; }, mesh = {*Archaea/genetics/ultrastructure ; *Biological Evolution ; Cell Cycle ; *Eukaryota ; Genome, Archaeal ; Metagenomics ; Organelle Biogenesis ; Protein Biosynthesis ; Symbiosis ; Transcription, Genetic ; }, abstract = {The discovery of Asgard archaea about a decade ago has greatly reshaped our understanding of archaeal evolution and the origin of eukaryotes. Asgards are currently thought to be the closest prokaryotic relatives of eukaryotes and to represent the archaeal host lineage that participated in the endosymbiotic event leading to the first eukaryotic cell. The presence of numerous eukaryotic signature proteins in Asgard genomes supports this view and provides important insights into the deep evolutionary roots of eukaryotic cellular complexity. However, the close relationship between archaea and eukaryotes had been observed for decades, based on features that are shared in different molecular processes. This review discusses the discovery of Asgard archaea in the broader context of archaeal molecular and cellular biology and highlights how earlier findings foreshadowed their emergence. Primarily targeted at newcomers to the field, the review provides an overview of evolutionary innovations across the Archaea domain and discusses molecular and cellular features of cultivated Asgard strains in light of previous archaeal research.}, }
@article {pmid41787208, year = {2026}, author = {Fiola, TE and Rathore, RS and Akinbi, GO and Mwashote, B and Badisa, VLD and Chen, G and Ibeanusi, V}, title = {Investigation of water quality and microbial diversity in Mississippi's major land resource area.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41787208}, issn = {1614-7499}, support = {NR204423XXXXC125-F1-SA1-21//U.S. Department of Agriculture/ ; TOA/PO-NO: 0000663592//U.S. Department of Energy/ ; DE-EM0005308//U.S. Department of Energy/ ; 0000005948//U.S. Department of Energy/ ; }, abstract = {The purpose of this research is to assess the quality of water in the Nesbit farm, which is located in the Major Land Resource Area (MLRA) in Mississippi, United States of America. This is a land resource area that faces a high risk of nutrient runoff. This research did an in-depth analysis of the quality of water in the Nesbit farm in the MLRA in Mississippi in the United States of America. This research will help to address the problems associated with the quality of water in this region by using physicochemical analysis, microbial community analysis, water quality index analysis, and geospatial analysis. The quality of water in this region, the problems associated with the quality of water in this region, and the microbial communities for grazing land management are taken into consideration in this research. The results for water temperature were obtained as (32.23 ± 0.39 °C), slightly acidic pH values ranging from (6.23-6.52), heavy metals were below the permissible limits for water as per the World Health Organization. Total dissolved solids were in the range of (1.4-1.6 mg/L), and the levels of dissolved oxygen were low (2.49-3.45 mg/L), indicating organic enrichment. Nitrate (0.11-6.36 mg/L), phosphate (0.03-0.15 mg/L) were high in concentration. The WQI of Nesbit farm water quality was 7.35, which shows that water quality is excellent in spite of localized stressors. The principal component analysis showed that the first two components explained 85.7% of the variance, and the major contributing parameters were chloride and pH. The Pearson correlation analysis indicated that there is a positive correlation between lead, total dissolved solids, chloride, and nitrate, which could be related to runoff. The metagenomics analysis indicated that Proteobacteria (30-35%) and Bacteroidetes (13-17%) are dominant species, which could be related to low organic matter. The study has provided valuable insight into water quality for Mississippi grazing land, which could be useful for effective management and conservation of natural resources.}, }
@article {pmid41787261, year = {2026}, author = {Dühr, H and Pärnänen, K and Kucháriková, N and Werner, P and Pershagen, G and Lahti, L and Alenius, H and Bergström, A and Ruuskanen, MO and Fyhrquist, N}, title = {Lifestyle associates with unique resistome and microbiome signatures in children.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41787261}, issn = {1471-2180}, abstract = {BACKGROUND: Antibiotic resistance is a global health crisis that is not solely explained by antibiotics usage. However, environmental and lifestyle contributions to antimicrobial resistance (AMR) in children are not well understood, especially compared to adults. As the gut functions as a reservoir for antibiotic resistance genes (ARGs), the aim of this study was to better understand the influence of lifestyle on the gut microbiome and resistome using shotgun-metagenomic sequencing data of Swedish children from the PARSIFAL (Prevention of Allergy Risk factors for Sensitization In children related to Farming and Anthroposophic Lifestyle) study.
RESULTS: Farm children exhibited high proportions of unique bacterial species and differentially abundant ARGs linked to the farm environment, and similar differences were found in anthroposophic children. Age, breastfeeding duration, and obesity significantly influenced the overall resistance load, independently of lifestyle. Despite limited statistical power, our findings suggest that lifestyle and environment both shape the microbiome and resistome of children.
CONCLUSIONS: This study corroborates the possible influence of the farm environment on the gut microbiome and resistome, revealing a highly individualized repertoire of low-abundance microbes and ARGs in farm children. Additionally, associations of age, obesity and the duration of exclusive breastfeeding with ARG load were found in a currently understudied age range. Overall, this study raises the need for further research on rare species and ARGs as well as their transmission dynamics in relation to the environment.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04665-2.}, }
@article {pmid41787302, year = {2026}, author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W}, title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12725-8}, pmid = {41787302}, issn = {1471-2164}, support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; }, }
@article {pmid41788258, year = {2026}, author = {Keles, E and Celik, O}, title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.}, journal = {Microbial cell (Graz, Austria)}, volume = {13}, number = {}, pages = {117-130}, pmid = {41788258}, issn = {2311-2638}, abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.}, }
@article {pmid41788574, year = {2026}, author = {Liang, ZW and Guan, YH and Lv, Z and Yang, SC and Zhao, M and Chen, JW}, title = {Metagenomics reveals an interaction among rhizosphere microbial community, soil properties and active ingredients in a medicinal crop Panax notoginseng.}, journal = {Journal of ginseng research}, volume = {50}, number = {2}, pages = {100918}, pmid = {41788574}, issn = {1226-8453}, abstract = {BACKGROUND: This study aimed to examine the effects of intensive cultivation practices on the rhizosphere microecology of Panax notoginseng. Additionally, we sought to compare these practices with an understory cultivation model that was intended to mimic native growth conditions, with the objective of improving the quality of Radix Notoginseng.
METHODS: The total saponin and active ingredient content in both cultivation methods were quantified using high-performance liquid chromatography (HPLC). The nutrients of the rhizosphere soils associated with both cultivation methods (understory cultivated P. notoginseng rhizosphere soil [UCPS] and intensive cultivated P. notoginseng rhizosphere soil [ICPS]) were analyzed. The microbial communities present in UCPS and ICPS were characterized using metagenomic sequencing.
RESULTS: The underground biomass accounted for 71.21 % and 74.00 % of the total biomass in understory cultivated P. notoginseng (UCPn) and intensively cultivated P. notoginseng (ICPn), respectively. The total saponin content in the main root of UCPn was found to be 109.24 ± 3.40 mg/g, compared to 91.31 ± 5.82 mg/g in ICPn. The concentration of medicinal ingredients (ginsenoside Rb1 + ginsenoside Rg1 + notoginsenoside R1) in UCPn was 10.83 %, while ICPn exhibited a higher concentration of 13.39 %. Microbial biomarkers identified in UCPS include Bradyrhizobium, Pseudomonas, and Paraburkholderia, which are associated with nitrogen cycling processes. In contrast, Variovorax and Sphingobium were predominant in ICPS, contributing to phosphorus metabolism.
CONCLUSION: Rhizosphere soil microbial biomarkers influence soil carbon nutrition, which directly impacts the quality of UCPn. The quality of ICPn is primarily determined by phosphorus-related biomarkers, with indirect influences from carbon and nitrogen nutrition.}, }
@article {pmid41788684, year = {2026}, author = {Cao, W and Li, R and Zhang, H and Zhang, T and Pan, H and Sun, W and Wang, L and Ke, J and Petersen, JD and Zhang, P}, title = {Exploratory multi-omics analysis of gut microbiota and fecal metabolites in relation to serum S-equol levels in older adults with osteoporosis from a tropical community: a pilot study.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1784894}, pmid = {41788684}, issn = {2296-861X}, abstract = {BACKGROUND: Osteoporosis (OP) is a multifactorial skeletal disorder influenced by host metabolism, inflammation, and gut microbiota-derived metabolites such as S-equol. However, the interplay between intestinal microbiota, S-equol production, and host metabolic profiles in OP remains incompletely understood.
OBJECTIVE: To conduct a preliminary multi-omics investigation integrating metagenomic and metabolomic analyses to identify gut microbiota and metabolite biomarkers associated with serum S-equol levels in older adults with OP.
METHODS: A cross-sectional study was conducted in 39 community-dwelling adults aged ≥50 years in Haikou, China. Participants were grouped into OP and control groups based on lumbar spine T-scores, using a cut-off value of ≤ - 2.5 to define osteoporosis. Serum biomarkers (S-equol, inflammatory cytokines, oxidative stress indicators) were assessed by ELISA. Fecal samples underwent metagenomic sequencing and untargeted metabolomics. LEfSe, Spearman correlation, machine learning, and KEGG enrichment were used to explore microbiota-metabolite-bone health axes.
RESULTS: Serum S-equol levels were significantly lower in the OP group compared to controls (3,561 ± 304 vs. 3,855 ± 469 pg/mL, p = 0.026), whereas most inflammatory markers were comparable between groups, apart from a modest increase in IL-1β in OP. Metagenomic analysis revealed a lower relative abundances of key SCFA-producing taxa in OP (e.g., Faecalibacterium prausnitzii, Roseburia hominis, Bacteroides uniformis). Metabolomic profiling identified distinct alterations in amino acid and tryptophan pathways, with KEGG analysis highlighting disruptions in glycerophospholipid, glycine-serine-threonine, and choline metabolism. Discriminative metabolites (e.g., Gln-Val-Ile-Asp., 5-oxooctanoic acid) showed diagnostic potential (AUC > 0.75). S-equol levels positively correlated with these beneficial microbes and with amino acid-related metabolites (e.g., D-tryptophan, 3-indoleacrylic acid, N-methylglutamate). Network and heatmap analyses illustrated differences in microbial-metabolite association patterns between groups.
CONCLUSION: In conclusion, low levels of serum S-equol in older adults with osteoporosis were associated with distinct changes in gut microbiota composition and fecal metabolic profiles in this pilot study.}, }
@article {pmid41789009, year = {2026}, author = {Cao, HT and Sun, RJ and Qian, QY and Yang, D and Sun, YY and Zhao, LY and Zhang, GY and Zhang, MD and Gu, H and Cao, HW and Wang, B and Huang, YW and Yang, YL}, title = {Molecular characterization and evolutionary dynamics of a recombinant PDCoV strain in a swine diarrhea epidemic with SADS-CoV co-infection.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1749819}, pmid = {41789009}, issn = {2297-1769}, abstract = {Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus that poses a significant threat to the swine industry. In this study, a novel PDCoV strain, designated PDCoV-ZJHZ2024, was identified from fecal samples of diarrheic pigs in China. Metagenomic analysis revealed co-detection of PDCoV and swine acute diarrhea syndrome coronavirus (SADS-CoV), with the microbial community predominantly composed of bacteria and characterized by abnormal enrichment of Bacillus cereus and pronounced gut microbiota dysbiosis. Genomic analyses demonstrated that PDCoV-ZJHZ2024 has undergone independent recombination events involving the ORF1b region and the spike (S) gene, accompanied by cross-regional genetic exchange, highlighting the critical role of recombination in PDCoV evolution and diversification. Codon usage analysis further indicated that codon preferences in this strain are primarily shaped by natural selection, potentially conferring enhanced translational efficiency in the host. Collectively, these findings underscore the evolutionary adaptability and transmission potential of PDCoV-ZJHZ2024 and provide new insights into PDCoV evolutionary dynamics, thereby informing future surveillance efforts and prevention strategies in swine populations.}, }
@article {pmid41789433, year = {2026}, author = {Eldholm, V and Straume, D and Brynildsrud, OB}, title = {Assessing sequencing-based pathogen surveillance of a recreational swimming area in Oslo, Norway.}, journal = {Access microbiology}, volume = {8}, number = {2}, pages = {}, pmid = {41789433}, issn = {2516-8290}, abstract = {Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occasional wastewater contamination. Restricted water exchange also allows for occasional summer heat spells with elevated water temperatures. Thus, infections stemming from wastewater contamination and seasonal opportunistic pathogens are potential health threats to recreational users of the fjord. In this pilot study, we assess the suitability of sequencing-based surveillance for the detection of pathogens at a popular urban location for recreational water activities, employing both long- and short-read sequencing platforms, paired with selective culturing. We find both metagenomic and full-length 16S sequencing to be promising tools for surveillance of seasonal opportunistic Vibrio pathogens. Furthermore, we identified Rhodoferax abundance to be a potentially attractive indicator of sewage contamination using low to medium-depth full-length 16S sequencing. Selective plating revealed minimal abundance of culturable extended-spectrum β-lactam-resistant bacteria, of which none were detected by metagenomic sequencing. Metagenomic analyses did, however, pick up several other β-lactamases in various bacterial taxa, including some that were closely related to those identified by selective plating and sequencing.}, }
@article {pmid41789894, year = {2026}, author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N}, title = {Gut virome and metabolic associations in patients with acute pancreatitis.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0140025}, pmid = {41789894}, issn = {2379-5077}, mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; Male ; Female ; *Pancreatitis/virology/metabolism/microbiology ; Middle Aged ; Adult ; Metagenomics ; Case-Control Studies ; Acute Disease ; Aged ; }, abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.}, }
@article {pmid41789915, year = {2026}, author = {Chen, S and Li, Y and Xue, J and Hao, Y and Shaalan, MGA and Ghallab, EHS and Guo, Z and Jin, S and Fang, Y and I M Khater, E and Li, S}, title = {Metagenomic sequencing reveals viral diversity of mosquitoes from Egypt: co-circulation of multiple insect-specific viruses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0213525}, doi = {10.1128/spectrum.02135-25}, pmid = {41789915}, issn = {2165-0497}, abstract = {UNLABELLED: Mosquito-borne virus surveillance is pivotal for investigating mosquito viromes, facilitating understanding of viral evolutionary histories and genetic diversity. Natural viral communities in mosquitoes include not only insect-specific viruses (ISVs) but also viruses infecting symbiotic microorganisms. In this study, a total of 654 mosquito samples-encompassing species from the Aedes and Culex genera-were collected from Egypt and subjected to metagenomic sequencing analysis. Over 130 virus species were identified, grouped into 35 families or equivalent taxonomic ranks. Detected ISVs included Culex flavivirus (CxFV), Kustavi Toti-like virus, Hanko Toti virus 5, Culex phasma-like virus (CPLV), Culex Iflavi-like virus 1, Culex Iflavi-like virus 4, Guadeloupe Culex rhabdovirus (GCRV), and Sarawak virus, confirming concurrent ISV circulation in Egyptian mosquitoes. Phylogenetic analyses of these ISVs revealed their closest evolutionary affinities to viral genome sequences originating from the Middle East, Europe, Oceania, and Asia. Specifically, Egyptian CxFV strains exhibited a closer genetic relationship with the tropical lineage within the Latin American/Caribbean/Africa genotype. Furthermore, our study uncovered 10 putative novel viruses, which are distributed across seven viral families: Amagaviridae, Chrysoviridae, Mitoviridae, Totiviridae, Virgaviridae, Narnaviridae, and Orthomyxoviridae. Collectively, our findings emphasize the necessity for more in-depth investigations into arthropod viromes-encompassing both mosquitoes and ticks-in Egypt, as well as in neighboring African and Middle Eastern countries. Such research is critical for enhancing our understanding of viral diversity and evolutionary biology, elucidating their roles in mosquito-pathogen-host interactions, and exploring their potential as biocontrol agents against vector-borne diseases of public health importance.
IMPORTANCE: Mosquito-borne viruses are estimated to cause over 100 million human infections annually, making surveillance of these pathogens increasingly crucial amid growing international travel and trade. Egypt, situated in northeastern Africa, serves as a geopolitical and geographical hub connecting Asia, Europe, and Africa-a unique location that complicates the surveillance of mosquito-borne viruses. Arboviruses persist in nature through cyclical transmission between arthropod vectors (e.g., mosquitoes, ticks, and midges) and susceptible vertebrate hosts. Despite this, systematic investigations into mosquito viromes remain relatively scarce in Egypt. The present study aimed to explore the genetic diversity and evolutionary relationships of mosquito-associated viruses in Egypt using metaviromic sequencing. Our findings significantly expand the current knowledge of both known and previously uncharacterized mosquito-associated viruses in the region, while also providing complete genome sequences of several viruses that may infect arthropods or vertebrates, and potentially interfere with the replication of pathogenic arboviruses.}, }
@article {pmid41789917, year = {2026}, author = {Chen, D and Zhang, Z and Wang, S and Li, W and He, Y and Zhang, W and Sun, W and Chen, M and Zou, S and Qian, X}, title = {Differential assembly and functional roles of bacterial communities in coniferous and mixed conifer-broadleaf forest soils.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0062725}, doi = {10.1128/msphere.00627-25}, pmid = {41789917}, issn = {2379-5042}, abstract = {Forest soils harbor a diverse array of bacteria that play a crucial role in nutrient cycling. However, the differential effects of coniferous versus mixed conifer-broadleaf forests on the distribution of both abundant and rare bacterial taxa remain poorly understood. In this study, we integrated 16S rRNA gene amplicon sequencing with metagenomic shotgun sequencing to conduct a comparative analysis of soil bacterial communities in a conifer plantation and an adjacent mixed conifer-broadleaf forest, specifically examining their community structure, assembly mechanisms, co-occurrence networks, and functional potential. Both abundant and rare taxa showed significant differences in community composition between the two forest types. Soil pH and organic matter content significantly influenced the total and abundant bacterial communities, while available phosphorus and potassium were key determinants of rare community composition. Co-occurrence network analysis revealed that abundant communities formed highly clustered, simplified networks, contrasting with more fragmented and keystone-rich networks in rare communities. Null model analyses indicated that community assembly was largely driven by stochastic processes, with ecological drift accounting for about 80% of the variation in total and rare communities, and dispersal limitation explaining nearly 72% of the variation in abundant communities. Functional predictions indicated that bacterial communities in mixed forests were enriched in pathways linked to glycosylation, carbohydrate degradation, and nitrogen fixation, while coniferous forests favored pathways related to autophagy, signaling, and stress responses. This study highlights the complementary roles of abundant and rare bacterial taxa in forest soil ecosystems and underscores the importance of preserving mixed forests to sustain microbial functional diversity.IMPORTANCEForest soils host a complex web of common and rare bacteria that quietly regulate nutrient cycles. By comparing pure conifer stands with mixed conifer-broadleaf forests, we found that abundant species underpin essential functions while rarer microbes fill specialized niches. Acidity and nutrients strongly influence which bacteria thrive; mixed stands favored microbes that break down carbohydrates and fix nitrogen, whereas conifer soils supported organisms adapted to stress and nutrient-poor conditions. These findings emphasize the importance of preserving diverse forest ecosystems for soil health, carbon storage, and effective forest management strategies in climate change adaptation.}, }
@article {pmid41789923, year = {2026}, author = {Yao, J and Yang, C and Wang, H and Zhang, C and Meng, J}, title = {Metagenomic analysis of gut bacteria in different developmental instars of Spodoptera litura.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0208125}, doi = {10.1128/spectrum.02081-25}, pmid = {41789923}, issn = {2165-0497}, abstract = {Spodoptera litura is a globally distributed agricultural pest across Asia and Australia (EPPO database, https://gd.eppo.int/taxon/PRODLI/distribution), whose gut microbiota significantly influences host feeding, digestion, immunity, and development. We used whole metagenomic sequencing to analyze the diversity and functional roles of gut bacteria at different developmental stages (eggs, first to sixth instar larvae, pupae, and adults). Findings revealed that Pseudomonadota predominated at the phylum level, with notable differences across instars: Bacillota was dominant in young larvae, whereas Verrucomicrobiota was added in older larvae, eggs, pupae, and adults. At the genus level, Pseudomonas dominated, Enterococcus was prevalent in larvae, and Piscirickettsia was prevalent in eggs, pupae, and adults. Metagenomic analysis identified numerous carbohydrate-active enzymes (CAZy database) aiding in plant cell wall polysaccharide digestion. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated differential gene expression in metabolism and xenobiotic degradation across instars, with metabolic gene annotation levels declining as development progressed. Detoxification-related enzyme genes were predominantly expressed in early instar larvae and adults, uncovering microbial origins of these enzymes.IMPORTANCEOur study provides evidence that the gut microbiota significantly modulates the physiology of Spodoptera litura, with profound effects on its dietary habits, metabolic processes, and host fitness. Using whole metagenomic sequencing, we analyzed gut bacteria across different life stages. At the phylum level, Pseudomonadota and Bacillota were dominant, while at the genus level, Pseudomonas was the most abundant taxon. Metagenomic analysis identified enzymes aiding in plant cell wall digestion. Kyoto Encyclopedia of Genes and Genomes analysis showed varying gene expression in metabolism and detoxification, with higher expression in early instar larvae and adults. This research enhances understanding of S. litura gut microbiota-host interactions and supports novel pest control strategies targeting gut microbiota.}, }
@article {pmid41789948, year = {2026}, author = {Yadav, S and Yang, T and MacLean, MA and El-Naggar, MY}, title = {Metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 from Southern California marine sediments.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0002526}, doi = {10.1128/mra.00025-26}, pmid = {41789948}, issn = {2576-098X}, abstract = {Cable bacteria conduct long-distance electron transport in sediments but are not yet isolated in pure culture. We report the metagenome-assembled genome of Candidatus Electrothrix sp. NPCB-01 from Newport Bay, California. This 3.46-Mb genome encodes sulfur oxidation, nitrogen and carbon metabolism, and nickel homeostasis genes, expanding resources for these electroactive microbes.}, }
@article {pmid41790075, year = {2026}, author = {Kong, C and Jin, Y and Guo, F and Yang, Y and Liu, G and Chen, Z and Li, J and Wang, Q and Ma, Y}, title = {Revealing the Antagonistic Interactions of Faecalibacterium prausnitzii and Bacteroides fragilis in Colorectal Cancer.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.12.030}, pmid = {41790075}, issn = {1528-0012}, abstract = {BACKGROUND & AIMS: Maladaptation of host-microbe metabolic interactions plays a crucial role in development of colorectal cancer (CRC). However, remains a lack of comprehensive studies using multi-omics analysis to illustrate host-microbe metabolic interactions in CRC.
METHODS: We collected and analyzed 440 stool samples from a discovery cohort in Shanghai China (255 patients with CRC and 185 healthy controls). Each sample was subjected to metagenomic sequencing and nontargeted liquid chromatography mass spectrometry. Fresh-frozen specimens of tumors and matched adjacent normal mucosae were extracted from 62 patients with CRC, and whole exome sequencing and RNA sequencing were performed to explore host genomic patterns and host-microbe metabolic interactions. Finally, relationships detected in the discovery cohort were validated against independent cohorts, organoid models, and mice experiments.
RESULTS: The relationship between disrupted microbial homeostasis and CRC progression is characterized by Bacteroides fragilis enrichment and reduction of Faecalibacterium prausnitzii. F prausnitzii metabolizes tryptophan into picolinic acid (PIA) via the enzyme 2-amino-3-carboxymuconate semialdehyde decarboxylase, with PIA exerting an antagonistic effect on enterotoxigenic B fragilis-mediated tumor progression. Mechanistically, enterotoxigenic B fragilis up-regulates the expression of genes associated with poor differentiation and recurrence, namely TCERG1 and CKAP2, and PIA induces tumor cell apoptosis by down-regulating these 2 genes. Independent validation cohorts and murine models corroborated that a tryptophan-rich diet effectively elevates circulating PIA levels, suggesting its potential as an anticancer dietary intervention.
CONCLUSIONS: Our research characterized a representative microbe-metabolite-host regulatory pathway occurring in CRC, namely the F prausnitzii-PIA-TCERG1/CKAP2 axis antagonizing enterotoxigenic B fragilis-induced CRC progression. As a treatment option, we highlight the therapeutic potential inherent in a tryptophan-rich diet and in manipulating microbial composition targeting the F prausnitzii-PIA axis to prevent CRC.}, }
@article {pmid41790111, year = {2026}, author = {Kumar, K}, title = {Cultivation of yet-to-be cultured microorganisms: advances, strategies, and prospects.}, journal = {Journal of applied microbiology}, volume = {137}, number = {3}, pages = {}, doi = {10.1093/jambio/lxag066}, pmid = {41790111}, issn = {1365-2672}, mesh = {Bioreactors/microbiology ; *Bacteria/growth & development/isolation & purification/genetics ; Coculture Techniques ; Metagenomics/methods ; *Microbiological Techniques/methods ; }, abstract = {More than 99% of microorganisms in the natural environment are not readily culturable using standard laboratory techniques. These microbes can be reservoirs of novel metabolites and biomolecules having pharmaceutical applications against bacterial infections, chronic diseases, and antibiotic resistance. Given this, our work is a comprehensive synthesis of recent advances in understanding, detection, and cultivation of "yet-to-be cultured" (YTBC) microbes. We highlight physiological traits that restrict their domestication under standard laboratory conditions. Some of the factors that may influence are their metabolic dormancy, specialized nutrient demands, siderophore-mediated iron acquisition, microbial signaling, and interspecies interactions. The review discusses various strategies, such as simulated natural environments, co-culture, and advanced bioreactor systems, which can be implemented to cultivate them. We reviewed recent metagenomic approaches and single-cell isolation methods, including label-based techniques (e.g. fluorescence in situ hybridization), label-free approaches such as Raman-activated cell sorting, and high-throughput tools like flow cytometry. We also examined culture-dependent approaches, including co-cultivation with helper strains with a special emphasis on bioreactor-based systems, diffusion chamber, hollow-fiber membrane chamber, high-throughput isolation chip (iChip), and encapsulation. Overall, this review provides a roadmap to unlock the biotechnological potential of YTBC microbes by outlining new technologies, methodological trends, and important knowledge gaps.}, }
@article {pmid41790499, year = {2026}, author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T}, title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.}, journal = {Microbial genomics}, volume = {12}, number = {3}, pages = {}, pmid = {41790499}, issn = {2057-5858}, mesh = {*Vitamin B 12/metabolism/biosynthesis/genetics ; *Mesorhizobium/genetics/metabolism ; *Synechococcus/genetics/metabolism/growth & development ; Metagenomics/methods ; *Microbial Interactions ; Microbial Consortia/genetics ; Transcriptome ; Gene Expression Profiling ; Multiomics ; }, abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.}, }
@article {pmid41790792, year = {2026}, author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT}, title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0344114}, pmid = {41790792}, issn = {1932-6203}, mesh = {*Soil Microbiology ; Bangladesh ; *Bacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Gardens ; Soil/chemistry ; Biodiversity ; }, abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.}, }
@article {pmid41790828, year = {2026}, author = {Carrillo, A and Hageman, E and Chittick, L and Mackey, AI and Ndlovu, KS and Tian, F and Gilbert, NE and Muratore, D and Vik, D and LeCleir, GR and Sun, C and Jang, HB and Pavan, RR and Weitz, JS and Wilhelm, SW and Sullivan, MB}, title = {Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts.}, journal = {PLoS biology}, volume = {24}, number = {3}, pages = {e3003474}, pmid = {41790828}, issn = {1545-7885}, mesh = {Atlantic Ocean ; *Viruses/genetics/isolation & purification/classification ; *Seawater/virology ; Population Dynamics ; Bermuda ; Ecosystem ; Metagenome ; }, abstract = {Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.}, }
@article {pmid41790921, year = {2026}, author = {Wang, J and Jiang, B}, title = {Utilizing metagenomic next-generation sequencing to diagnose central nervous system infections after craniotomy.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {2}, pages = {263-270}, doi = {10.3855/jidc.21771}, pmid = {41790921}, issn = {1972-2680}, mesh = {Humans ; *Craniotomy/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Prospective Studies ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology ; Adult ; *Metagenomics/methods ; Aged ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; *Postoperative Complications/diagnosis/microbiology ; Adolescent ; }, abstract = {INTRODUCTION: Postoperative central nervous system (CNS) infections in craniotomy patients diagnosed through clinical signs and cerebrospinal fluid (CSF) bacterial culture, pose a challenge due to the morbidity and mortality of bacterial meningitis. The objective of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosing CNS infections post craniotomy.
METHODOLOGY: A prospective study compared mNGS with traditional diagnostics from January 2021 to October 2023. Patients with suspected post-craniotomy intracranial infections were enrolled, following guidelines and regulations.
RESULTS: mNGS and traditional culture diagnosed 111 patients with suspected intracranial infections. mNGS showed higher sensitivity (62.5% vs. 25%). Traditional culture excelled in specificity and positive predictive value. Of the 18 mNGS-positive samples, 12 were culture-negative. mNGS detected pathogens such as Candida albicans (2 cases), Enterobacter cloacae (1 case), Enterococcus faecalis (1 case), Klebsiella pneumoniae (2 cases), Pseudomonas aeruginosa (1 case), Staphylococcus aureus (2 cases), Staphylococcus epidermidis (2 cases), and Streptococcus haemolyticus (1 case). Some pathogens were likely missed due to prior antibiotic use and fastidious growth requirements. Physicians adjusted treatments based on mNGS pathogen detection for culture-negative patients. Empirical therapy continued for patients with negative results until more diagnostic information was available.
CONCLUSIONS: mNGS detects post-neurosurgery CNS infections, especially hard-to-cultivate microorganisms. While mNGS has advantages, traditional culture's higher positive predictive value confirms infections and remains indispensable. Combining mNGS with traditional methods provides a comprehensive diagnostic strategy, aiding physicians in accurately identifying infections, reducing misdiagnosis, and offering personalized treatment plans to improve outcomes and quality of life.}, }
@article {pmid41791253, year = {2026}, author = {Fu, CX and Cai, JJ and Liu, JL and Qiu, GY and Chen, XD and Zhang, JB and Qiao, M and Tong, WB and Guo, B}, title = {Mechanistic investigation of the associations between bacterial community composition and cadmium distribution in Zizania latifolia.}, journal = {Ecotoxicology and environmental safety}, volume = {312}, number = {}, pages = {119972}, doi = {10.1016/j.ecoenv.2026.119972}, pmid = {41791253}, issn = {1090-2414}, mesh = {*Cadmium/metabolism/analysis ; *Soil Pollutants/metabolism/analysis ; Rhizosphere ; *Bacteria/metabolism/classification/genetics ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; *Poaceae/microbiology/metabolism ; Plant Leaves/metabolism/microbiology ; *Microbiota ; }, abstract = {The role of bacteria in external niches regulating cadmium (Cd(II)) in plant tissues remains unclear. We explored Cd(II) profiles and identified bacterial contributors among phyllosphere, rhizoplane, and rhizosphere of four Zizania latifolia varieties through integrated metagenomic and chemical analyses. Zizania latifolia accumulated Cd(II) in leaves (0.06-0.77 mg/kg), roots (0.73-1.57 mg/kg), and rhizosphere (0.43-3.15 mg/kg), respectively. The highest enrichment coefficient (leaf-Cd(II)/soil-Cd(II)) was observed in Genotype 3 (0.6). Among top 10 genus-level bacteria, Enterococcus in phyllosphere, Streptomyces and Dechloromonas in rhizoplane, and Bradyrhizobium, Pseudolabrys, Mycobacterium, and Dechloromonas in rhizosphere were significantly related to Cd(II). Enterococcus adsorbed Cd(II) by extracellular polysaccharides and precipitated Cd(II) sulfide. Rhizoplane and rhizosphere bacteria absorbed Cd(II) by cell-surface functional groups, and fixed Cd(II) through synthesizing polyphosphate and driving Fe (II) oxidation. Additionally, 64.4%-80% of bacteria were shared between rhizoplane and rhizosphere, 5.5%-6.9% between rhizoplane and phyllosphere, and 4.4%-6.1% between rhizosphere and phyllosphere. Metagenomic analysis indicated that Cd(II) disturbed bacterial secretion system and amino acid metabolic pathways. These findings provided comprehensive insights into interrelationships between Cd(II) and bacteria in leaves, roots, and rhizosphere of Zizania latifolia, offering valuable foundations for developing targeted strategies to mitigate Cd(II) accumulation in aquatic vegetables.}, }
@article {pmid41791469, year = {2026}, author = {Ma, J and Liu, J and Guo, Z and Zhu, M and Chai, Z and Jiang, F and Li, Z and Liang, Z and Jiang, Z}, title = {Characteristics of the microbial carbon pump in kelp farming areas and the impact of artificial reefs: A metagenomic and ecological perspective.}, journal = {Environmental research}, volume = {297}, number = {}, pages = {124166}, doi = {10.1016/j.envres.2026.124166}, pmid = {41791469}, issn = {1096-0953}, abstract = {The microbial carbon pump (MCP) can transform labile dissolved organic carbon (LDOC) into recalcitrant dissolved organic carbon (RDOC), yet how sedimentary MCP efficiency is regulated by natural gradients of organic carbon input remains unclear. In this study, we investigated sediments in a kelp farming environment, leveraging the contrast between artificial reef (AR) areas and adjacent non-reef (NR) areas. We combined full-length 16S rRNA sequencing, metagenomics, and fluorescent dissolved organic matter (FDOM) characterization to compare microbial processing under these contrasting depositional regimes. Elevated LDOC inputs in the AR zones were associated with reshaped community metabolic profiles and with enhanced turnover and potential formation of RDOC. High substrate availability was linked to coordinated metabolic functional potential, in which increased genetic potential for upstream catabolism covaried with genomic features indicative of expanded acetyl-CoA supply potential. This putative metabolic overflow was more strongly associated with the mevalonate (MVA) pathway than with the alternative methylerythritol phosphate pathway, consistent with a potential routing toward isoprenoid and terpenoid backbone biosynthesis and the formation of carboxyl-rich alicyclic molecule (CRAM) precursors. Genome-resolved reconstructions further suggested metabolic complementarity among taxa, with predicted cross-feeding interactions that could help sustain carbon processing in MVA-enriched copiotrophs. Overall, humic-like FDOM signals co-vary with organic loading driven by artificial reefs, indicating that these engineering interventions serve as controllable levers, providing a scientific basis for optimizing the carbon sink function of marine ranching through strategic artificial reef deployment.}, }
@article {pmid41791723, year = {2026}, author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M}, title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70264}, doi = {10.1111/1462-2920.70264}, pmid = {41791723}, issn = {1462-2920}, support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; }, mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; }, abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.}, }
@article {pmid41791848, year = {2026}, author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ}, title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337478}, pmid = {41791848}, issn = {1468-3288}, abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.
OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.
DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.
RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).
CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.}, }
@article {pmid41792155, year = {2026}, author = {Benoit, G and James, R and Raguideau, S and Alabone, G and Goodall, T and Chikhi, R and Quince, C}, title = {High-quality metagenome assembly from nanopore reads with nanoMDBG.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69760-y}, pmid = {41792155}, issn = {2041-1723}, support = {BBX011089/1,BBS/E/ER/230002C,BB/CSP1720/1,BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 872539, 956229, 101047160 and 101088572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables. We present nanoMDBG, an evolution of metaMDBG, which supports the latest ONT reads through an error correction pre-processing step in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. Critically, the latest ONT technology can now produce comparable MAG construction results as those obtained using PacBio HiFi at the same sequencing depth.}, }
@article {pmid41792508, year = {2026}, author = {Li, M and Li, Y and Li, C and Liu, A and Liu, Y and Li, Y and Xiao, J and Zhang, D and Jin, Y and Wang, G and Pang, X and Jiang, K and Yin, Y}, title = {Dynamic reorganisation of intratumoural bacterial florae during colorectal cancer progression.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {41792508}, issn = {1532-1827}, support = {81874235/82030081//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits distinct bacterial community compositions compared to healthy mucosae, which intimately correlate with CRC clinical outcomes. There is a lack of explanation for the inducements of microbiota remodelling.
METHODS: FISH experiments and 16S rRNA sequencing were conducted to determine the inducements of various bacterial colonisation within tissues. Community cultivation was conducted to estimate the capacity of tumours to remodel bacterial communities. Metagenomic analyses were utilised to determine the remodelled communities of CRC with distant metastasis. Scratch tests and three-dimensional (3D) cultivation were employed to investigate the influence of specific taxa on tumour cell behaviours.
RESULTS: Colorectal tumours exhibit heterogeneous and individualised preferences in constantly remodelling intratumoural bacterial florae. Various degrees of colorectal gland differentiation within tumours cause heterogeneous intratumoural bacterial colonisation. CRC progression further alters bacterial community composition. Particularly, Prevotella is significantly enriched in the newly established communities colonising the primary foci of metastatic CRC. Furthermore, Prevotella intermedia (P. intermedia) promotes the invasion, migration, and ectopic tumorigenesis of CRC cells.
CONCLUSIONS: Individual evaluation of the preference of tumours in microbiota may pave the way to the development of CRC therapeutic strategies, and Prevotella is an emerging genus worthy of clinical attention.}, }
@article {pmid41792922, year = {2026}, author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD}, title = {Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41792922}, issn = {1751-7370}, support = {1755402//NSF Division of Integrative Organismal Systems/ ; 1755353//NSF Division of Integrative Organismal Systems/ ; 2439853//NSF Graduate Research Fellowship Program/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Amino Acids, Essential/metabolism/biosynthesis ; *Peromyscus/microbiology/metabolism ; Diet ; Muscle, Skeletal/metabolism ; Dietary Proteins/metabolism ; Mice ; Carbon Isotopes/analysis ; *Bacteria/metabolism/classification/genetics ; }, abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.}, }
@article {pmid41793806, year = {2026}, author = {Qi, J and Song, Y and Luo, S and Zhu, M and Fu, F and Feng, Y and Mei, W and Feng, H and Li, X and Song, C}, title = {Soil water and inorganic nitrogen contents drive soil microbial carbon fixation during wetland reclamation and restoration.}, journal = {Water research}, volume = {297}, number = {}, pages = {125666}, doi = {10.1016/j.watres.2026.125666}, pmid = {41793806}, issn = {1879-2448}, abstract = {Wetlands are critical terrestrial carbon sinks, playing a vital role in mitigating global warming by fixing substantial atmospheric carbon dioxide. To explore how wetland reclamation and restoration affect soil microbial carbon fixation, we sampled soils from five land-use types in western Jilin Province, China: undisturbed natural reed wetland, reclaimed rice paddy and upland field, restored agricultural drainage wetland and naturally restored wetland after farmland abandonment. We analyzed the effects of wetland reclamation and restoration on microbial communities, metabolic pathways, and carbon fixation potential. Results showed Proteobacteria (31.81 %), Actinobacteria (27.08 %), and Acidobacteria (15.12 %) dominated carbon-fixing microbes, with the reductive tricarboxylic acid cycle and dicarboxylate/4-hydroxybutyrate cycle as major carbon-fixing pathways. The natural wetland had the highest carbon fixation potential, with a mean value of 1.58 mg·kg[-1] across the 0-15 cm topsoil layer and 15-30 cm subsoil layer, which was 1.30 to 4.02 times that of the reclaimed wetlands and restored wetlands. Among reclaimed sites, the rice paddy retained soil microbial community similarity to the natural wetland with complex, stable microbial networks. Compared to the naturally restored wetland, the agricultural drainage-restored wetland showed superior restoration outcomes, including microbial communities more similar to the natural wetland, higher network stability, and greater carbon fixation potential. Soil water and inorganic nitrogen contents were core drivers regulating carbon fixation via RubisCO activity and microbial metabolic pathways. This result highlights that the key to wetland restoration lies in prioritising hydrological regulation and nitrogen management, thereby enhancing microbial carbon fixation potential.}, }
@article {pmid41793822, year = {2026}, author = {Li, P and Wang, Y and Bao, Z and He, X and Wang, S and Su, X and Nie, W and Xu, F and Zhou, H and Li, H and Xu, B}, title = {Metagenomics-based insights into the microbial community composition and quality characteristics development potentiality in traditional dry-cured ham.}, journal = {International journal of food microbiology}, volume = {453}, number = {}, pages = {111705}, doi = {10.1016/j.ijfoodmicro.2026.111705}, pmid = {41793822}, issn = {1879-3460}, mesh = {Animals ; Metagenomics ; Swine ; *Meat Products/microbiology/analysis ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Volatile Organic Compounds/analysis/metabolism ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Food Microbiology ; Peptides ; }, abstract = {The objective of this study was to elucidate the formation mechanisms of quality characteristics in traditional dry-cured ham. The microbial community composition in three types of dry-cured ham was analyzed using metagenomics technology. Volatile flavor profiles were characterized via gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS), while peptide profiles were determined using liquid chromatography-mass spectrometry (LC-MS). Based on metagenomic data, biosynthetic pathways of volatile flavor compounds and bioactive peptides in dry-cured hams were reconstructed. Key microorganisms identified include Staphylococcus equorum, Staphylococcus saprophyticus, Aspergillus glaucus, Aspergillus ruber, Debaryomyces hansenii, and Debaryomyces fabryi. Using GC-MS and GC-IMS, 25 volatile compounds were identified in dry-cured ham, with branched-chain compounds exhibiting higher odor activity values (OAVs). LC-MS analysis identified 203 microbial-derived peptide fragments, predominantly possessing angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase-IV (DPP-IV) inhibitory, and antioxidant activities. Further investigation into the contribution of microbial communities to the characteristic quality attributes revealed that Staphylococcus species promote the formation of 3-methyl-butanal via branched-chain amino acid transaminase (BCAT) and 3-hydroxy-2-butanone via acetolactate synthase (ALS). With regard to functional bioactive peptides, Staphylococcus indirectly contributes to the synthesis of NPPKFD, DLEE, and KRQKYD via glutamyl endopeptidase activity. Additionally, proteins derived from Aspergillus glaucus (actin-related protein 5) and Staphylococcus equorum (chromosome segregation protein) serve as direct precursors for bioactive peptides, yielding potential sequences such as KNSKDPVSI and LEDDI. This study provides evidence indicating the role of microbial communities in shaping the quality characteristics of dry-cured ham.}, }
@article {pmid41793859, year = {2026}, author = {Brito, B and Frost, M and Webster, J and To, J and Kirkland, P}, title = {Quantifying the impact of sequencing depth and reference genome choice on metatranscriptomic detection of four bovine RNA viruses.}, journal = {Research in veterinary science}, volume = {204}, number = {}, pages = {106125}, doi = {10.1016/j.rvsc.2026.106125}, pmid = {41793859}, issn = {1532-2661}, abstract = {Metatranscriptomic sequencing enables untargeted detection of RNA viruses across clinical and environmental contexts. Evaluating this approach through metrics such as limits of detection and genome coverage, in direct comparison with established molecular tools like qRT-PCR, is essential for understanding its potential diagnostic utility. In the present study, we assessed the detection performance of metatranscriptomic sequencing for four bovine respiratory RNA viruses: Bovine coronavirus (BCoV), Bovine nidovirus (BNV), Influenza D virus (IDV), and Bovine viral diarrhea virus-1 (BVDV-1) in nasal swabs, using reference-based mapping. Sequencing depth (1, 10, and 20 million (M) reads) and reference genome choice (NCBI RefSeq and study-assembled) were systematically varied to quantify their effects on viral read recovery and genome coverage. For BNV and BCoV, sequencing at ≥10 M reads was sufficient for metatranscriptomic detection of samples that were qRT-PCR positive at high Ct values (up to 40), but recovering high genome completeness was only achieved for samples with Ct < 30. IDV detection was less sensitive: several qRT-PCR-positive samples (Ct 29.6-34.5) yielded no mapped reads even at 20 M. BVDV-1 recovery was strongly reference-dependent; mapping to study-assembled genomes markedly increased read counts and coverage compared with NCBI RefSeq, reflecting divergence between field strains and the standard reference sequence. A low number of mapped reads was observed in several qRT-PCR-negative BVDV-1 pools when using the NCBI RefSeq, consistent with potential misclassification of host-derived sequences. By quantitatively linking qRT-PCR Ct values, sequencing depth, and reference divergence, the present study outlines methodological considerations that may guide future applications of metatranscriptomics into veterinary diagnostics.}, }
@article {pmid41793868, year = {2026}, author = {Wang, M and Yu, G and Zhang, Y and Ren, J and Chen, W and Li, Q and Cong, P}, title = {Seasonal dynamics and environmental regulation of pathogenic bacteria in the Weihe River Basin.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141646}, doi = {10.1016/j.jhazmat.2026.141646}, pmid = {41793868}, issn = {1873-3336}, mesh = {*Rivers/microbiology/chemistry ; Seasons ; *Water Microbiology ; *Bacteria/genetics/pathogenicity/isolation & purification ; China ; Environmental Monitoring ; }, abstract = {Waterborne pathogen transmission poses a significant global environmental health risk. This study employs metagenomic sequencing combined with co-occurrence network analysis, redundancy analysis (RDA), and partial least squares path modeling (PLS-PM) to investigate the distribution and transmission risk of pathogens in the Weihe River Basin. The study identified 232 pathogenic species in the Weihe River's main and tributary waters, with core pathogens (such as Pseudomonas aeruginosa and Salmonella enterica) consistently present across all hydrological periods. RDA analysis indicated temperature, salinity, nitrate-nitrogen, and chlorophyll-a are key environmental factors driving pathogen community structure. The PLS-PM model reveals significant seasonal variations in the association patterns between mobile genetic elements (MGEs) and pathogens. During the high-water period, MGEs showed the strongest correlation with pathogens, suggesting that pathogens are the primary hosts of MGEs. MGEs-mediated horizontal gene transfer may drive pathogen dissemination during this period. During the normal-water period, MGEs primarily facilitated the transfer of virulence factors (VFs), enhancing the potential pathogenicity of pathogens. During the low-water period, environmental factors promoted the spread of MGEs while inhibiting the expression of virulence genes, leading to a reduction in pathogen virulence. Co-occurrence networks further demonstrate that during the high-water period, MGEs closely linked key VFs, such as Capsule, with enteric pathogens; network connectivity decreased significantly during the normal-water period, maintaining only limited associations; during the low-water period, functional VFs were frequently co-occurring with opportunistic pathogens. This study provides scientific evidence and management references for pathogen risk assessment and control in river basins.}, }
@article {pmid41793890, year = {2026}, author = {Dong, M and Zhang, Q and Wang, Y and Wang, S and Feng, G and Qi, H}, title = {Restructuring tilth layers suppresses cotton Verticillium wilt through the niacinamide-mediated enrichment of beneficial Pseudomonas.}, journal = {Microbiological research}, volume = {307}, number = {}, pages = {128491}, doi = {10.1016/j.micres.2026.128491}, pmid = {41793890}, issn = {1618-0623}, mesh = {Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Verticillium/drug effects ; Soil Microbiology ; *Gossypium/microbiology ; *Niacinamide/metabolism/pharmacology ; *Pseudomonas/metabolism/drug effects/growth & development ; Metabolomics ; Microbiota ; Plant Roots/microbiology ; Metagenomics ; }, abstract = {Restructuring tilth layers (RTL) is an innovative tillage practice that involves the vertical exchange of topsoil and subsoil while the deeper layer is loosened, and this practice has been verified to significantly reduce the incidence of cotton Verticillium wilt. However, the ecological mechanisms underlying disease suppression remain unclear. In this study, we integrated field experiments, metagenomic sequencing, untargeted metabolomics, and functional validation to elucidate the effects of RTL on the rhizosphere ecosystem from the perspectives of microbe and metabolite interactions. RTL significantly altered the diversity and composition of the rhizosphere microbial communities and increased their network complexity and stability. Linear discriminant analysis effect size (LEfSe) revealed that RTL promoted the enrichment of beneficial taxa such as Pseudomonas, Lysobacter, and Mesorhizobium. Metabolomic profiling revealed that the abundance of niacinamide was 19.11-fold higher (P < 0.05) in the RTL rhizosphere than in the control rhizosphere. Exogenous supplementation and antagonistic assays demonstrated that niacinamide stimulated Pseudomonas enrichment and activation in the rhizosphere. Although niacinamide did not have direct antifungal activity, its coapplication with Pseudomonas reduced the disease index of Verticillium wilt by 81.89%. Overall, RTL suppresses Verticillium wilt through two pathways, by establishing a more stable and complex microbial network and regulating rhizosphere metabolite composition, particularly niacinamide accumulation, which drives the colonization and activation of defense mediated by beneficial microbes, forming an ecological defense mechanism that links metabolite signaling, microbial response, and pathogen suppression.}, }
@article {pmid41793958, year = {2026}, author = {Li, X and Sun, Z and Lin, L and Deng, T and Xu, M}, title = {Attenuation of sulfamethoxazole and associated antimicrobial resistome by enriched electroactive microbial consortia.}, journal = {Environment international}, volume = {209}, number = {}, pages = {110182}, doi = {10.1016/j.envint.2026.110182}, pmid = {41793958}, issn = {1873-6750}, mesh = {*Sulfamethoxazole/metabolism ; *Microbial Consortia ; Biofilms ; Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/metabolism ; }, abstract = {Electroactive biofilms with the capacity of extracellular electron transfer (EET) have shown great promise for mitigating antibiotics and antibiotic resistance genes (ARGs). However, detailed interactions between antibiotics and electroactive microorganisms, along with ARGs dissemination dynamics within the electroactive consortia, remained poorly understood. In this study, stable electroactive microbial consortia were enriched, and their influences on the fates of sulfamethoxazole (SMX) and associated ARGs were systematically investigated. The results showed the enriched consortia could degrade SMX effectively within a wide concentration range through co-metabolism which was stimulated by their electrogenic respiration. Moreover, with accelerated SMX removal, the abundances of associated ARGs including sul1 and sul2 in the consortia decreased significantly due to alleviated SMX-induced selective pressure and probably weakened horizontal gene transfer mediated by mobile genetic elements (e.g., IS91 and tnpA). Degrader isolation and metagenomic analysis identified the core EET-proficient genera (e.g., Geobacter and Alcaligenes) as essential for the accelerated co-metabolism biodegradation of SMX, whereas the proliferation of other bacteria with limited or no EET capacity (e.g., Hydrogenophaga, Burkholderia, Comamonas, Desulfovibrio and Pseudomonas) was closely linked to the ARGs dissemination. This work provides a mechanistic elucidation of how electroactive microbial consortia stimulate antibiotic degradation and attenuate ARGs proliferation, offering strategic insights for risk control of the resistome during wastewater treatment.}, }
@article {pmid41794383, year = {2026}, author = {Wannaiampikul, S and Lee, B and Chen, J and Prentice, KJ and Ayansola, R and Xu, A and Santosa, S and Pantopoulos, K and Sweeney, G}, title = {Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {110327}, doi = {10.1016/j.jnutbio.2026.110327}, pmid = {41794383}, issn = {1873-4847}, abstract = {BACKGROUND: Metabolic Syndrome (MetS) presents a global health challenge, characterized by obesity, hypertension, dyslipidemia, and insulin resistance. Despite recognition of the gut microbiome's role in metabolic health, there remains scope for defining association of unique microbes with clinical status. Unique genetic, dietary, and lifestyle factors may influence gut microbial composition and circulating metabolites, and consequently susceptibility to MetS. By identifying specific microbial and metabolomic signatures associated with MetS, we aim to uncover potential targets for reducing the disease burden.
METHODS: We correlate comprehensive clinical parameters with fecal metagenomics and untargeted serum metabolomics to delineate population-specific characteristics from 142 individuals with MetS (N=97) or control (CTRL; N=45).
RESULTS: Microbiome species-level alpha diversity was reduced in MetS compared to CTRL. After adjustment for sex, age, BMI, and intensity of statin usage, we identified 20 MetS-related species. A co-abundant network analysis revealed Eubacterium eligens, enriched in the CTRL population, with the highest node degree. Serum metabolomics identified 106 significantly differentially regulated metabolites. N-arachidonoyl dopamine (NADA), an endocannabinoid implicated in GABAergic signaling, was the most significantly altered, enriched in CTRL and correlated with E. Eligens. sPLS-DA modeling revealed that E. eligens and D. formicigenerans species cluster together with metabolites NADA and tetrahydrocorticosterone (THB), representing defining characteristics distinguishing MetS in this population.
CONCLUSIONS: Our data reveal a distinct multi-omic signature of MetS, characterized by a significant reduction in E. eligens and D. formicigenerans abundance, and in circulating NADA and THB levels.}, }
@article {pmid41794459, year = {2026}, author = {Cai, J and Huang, A and You, L and Wang, Z and Huang, C and Huang, R and Li, Y and Liang, T and Zhang, F and Wu, Q and Wang, J and Zhu, Z and Ding, Y}, title = {Neomycin-sensitive gut bacteria-derived brassicasterol mediates the anti-obesity effects of Cordyceps militaris polysaccharide.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118574}, doi = {10.1016/j.foodres.2026.118574}, pmid = {41794459}, issn = {1873-7145}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Obesity/prevention & control/drug therapy ; Diet, High-Fat/adverse effects ; Mice ; *Neomycin/pharmacology ; Mice, Inbred C57BL ; *Cordyceps/chemistry ; Male ; *Anti-Obesity Agents/pharmacology ; Anti-Bacterial Agents/pharmacology ; Liver/metabolism ; *Fungal Polysaccharides/pharmacology ; Lipid Metabolism/drug effects ; }, abstract = {Diet-based modulation of the gut microbiota has emerged as a promising strategy to alleviate obesity and its related complications. Our previous study demonstrated that polysaccharide derived from Cordyceps militaris (CMP) exerts anti-obesity effects, yet the specific mechanism linking gut microbiota to its metabolic impact remains unclear. Herein, we utilized murine models with distinct gut microbial profiles created via antibiotic cocktails to investigate these mechanisms. The protective effects of CMP against high-fat diet (HFD)-induced obesity and associated metabolic disturbances were substantially impaired in mice depleted of neomycin-sensitive gut bacteria. Metagenomic analyses further established that CMP required these bacteria to restore gut microbial homeostasis. Notably, we observed that CMP elevated hepatic levels of brassicasterol in a manner dependent on neomycin-sensitive gut bacteria. Brassicasterol treatment alone replicated the anti-obesity effects of CMP, as indicated by reduced body weight gain, improved lipid and glucose metabolism, and decreased inflammation. Through transcriptomic and functional analyses, we identified hepatic Apoa4 as a key downstream effector of brassicasterol. Our results indicated that brassicasterol upregulated Apoa4, facilitating lipid transport and suppressing inflammation both in vitro and in vivo. Collectively, our findings indicate that CMP exerts its anti-obesity effects through a neomycin-sensitive gut bacteria-brassicasterol-Apoa4 pathway. This work expands the mechanistic understanding of CMP and highlights a novel microbiota-metabolite-host regulatory axis for dietary intervention in metabolic disorders.}, }
@article {pmid41794462, year = {2026}, author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V}, title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118577}, doi = {10.1016/j.foodres.2026.118577}, pmid = {41794462}, issn = {1873-7145}, mesh = {*Fermentation ; *Vitis/microbiology ; *Wine/microbiology/analysis ; *Mycobiome ; Italy ; Metabolomics/methods ; Greece ; Saccharomyces cerevisiae/metabolism ; Metagenomics/methods ; Food Microbiology ; Metabolome ; Kluyveromyces/metabolism ; Multiomics ; }, abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.}, }
@article {pmid41794791, year = {2026}, author = {Song, Z and Li, R and Liang, L and Zhang, M and Wang, H and Bu, H and Zhang, Y}, title = {Varicella zoster virus-related myelitis: a case series and literature review.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03123-3}, pmid = {41794791}, issn = {1743-422X}, support = {No. H2023206903//the National Science Foundation of Hebei Province/ ; }, abstract = {INTRODUCTION: Varicella zoster virus (VZV) is a human neurotropic herpesvirus that remains latent in the dorsal root ganglia and can reactivate to cause herpes zoster. In immunocompromised patients, reactivation may lead to severe neurological complications such as encephalitis, meningitis, myelitis, and neuropathy. However, varicella zoster virus-related myelitis (VZVM) is relatively rare, particularly in immunocompetent adults. The pathogenesis may involve direct viral invasion of the spinal cord parenchyma during the acute phase or a postinfectious immune-mediated inflammatory response.
CASE PRESENTATIONS: This report describes three patients with VZVM(one woman ages 49 years and two men age 60 and 56 years), none of whom presented with a typical rash. Two patients (cases 1 and 2) developed encephalomyelitis at disease onset, characterized by fever, impaired consciousness, and long-segment spinal cord lesions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) detected VZV nucleic acid in both cases. In case 3, the patient initially developed VZVM complicated by cerebral venous sinus thrombosis. After an interval of approximately 40 days, delayed thoracic myelitis developed, and repeated CSF mNGS testing yielded negative results. All three patients received intravenous antiviral therapy; two additionally received low-dose corticosteroids combined with intravenous immunoglobulin, and one received intravenous methylprednisolone. During follow-up, one patient achieved full recovery of lower-limb motor function, whereas two patients remained paraplegic.
CONCLUSIONS: VZVM presents with diverse clinical manifestations and may occur without the typical vesicular rash. It can develop either during the initial phase of VZV infection or as a delayed complication. Early magnetic resonance imaging and CSF molecular testing support timely diagnosis. Prompt and adequate antiviral therapy combined with immunomodulatory treatment may improve neurological outcomes.}, }
@article {pmid41794977, year = {2026}, author = {Yaikhan, T and Wongsurawat, T and Jenjaroenpan, P and Thaipisuttikul, I and Chayakulkeeree, M and Tribhuddarat, C and Nitayanon, P and Peizner, MT and Tansirichaiya, S and Kamolvit, W and Surachat, K}, title = {Evaluating long-read metagenomics for bloodstream infection diagnostics: a pilot study from a Thai Tertiary Hospital.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41794977}, issn = {2045-2322}, support = {B13F660074//the NSRF through the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; MED6801076S//the National Science Research and Innovation Fund (NSRF) and Prince of Songkla University, Thailand/ ; }, abstract = {UNLABELLED: Bloodstream infections (BSIs) are life-threatening and require rapid, accurate pathogen characterization to guide antimicrobial therapy. Conventional culture-based diagnostics offer limited insight into the genetic basis of antimicrobial resistance (AMR) and virulence. In this study, we applied Oxford Nanopore Technology (ONT) metagenomic sequencing directly to 40 positive blood culture bottles collected at Siriraj Hospital, Thailand (2022 and 2025). Long-read data enabled species identification, AMR marker detection, virulence profiling, and plasmid replicon analysis. Diverse Gram-negative and Gram-positive pathogens were identified, including ESBL-producing Escherichia coli, carbapenem-resistant Klebsiella pneumoniae, Enterococcus spp., and Staphylococcus spp. Comprehensive genomic profiling revealed complex resistance mechanisms, multiple virulence factors related to adhesion, biofilm formation, and toxin production, and diverse plasmid types associated with horizontal gene transfer (HGT). This study demonstrates the value of ONT-based metagenomics as a faster workflow that is blood culture-dependent but subculture-independent, enabling species identification and AMR gene detection within 6–8 h, compared with 5–7 days for conventional methods, while supporting integrated genomic characterization for diagnostics, infection control, and regional AMR surveillance.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41247-2.}, }
@article {pmid41795336, year = {2026}, author = {Hao, J and Zhang, YT and Li, X and Dai, X and Xu, Y}, title = {Water-evaporation-induced efficient high-temperature aerobic fermentation of food waste.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134368}, doi = {10.1016/j.biortech.2026.134368}, pmid = {41795336}, issn = {1873-2976}, mesh = {*Fermentation ; Aerobiosis ; *Water/chemistry ; *Hot Temperature ; *Food ; *Waste Products/analysis ; Food Loss and Waste ; }, abstract = {Aerobic fermentation is an effective approach for reducing, stabilising, and recovering resources from food waste. However, its performance is often constrained by poor oxygen transfer within the fermentation substrate. In this study, we investigated the inductive mechanism of water evaporation enhancing aerobic fermentation of food waste. It was observed that water evaporation, as the primary driving force, promoted microscale moisture redistribution and pore structure optimization, leading to an 84.8% (p < 0.01) increase in the average pore diameter and an 8.7% (p < 0.01) increase in porosity. As a result, a significant increase in the oxygen mass transfer coefficient (+250.1%) was achieved within the food waste. This improved microenvironment steered microbial community succession toward thermophilic functional groups dominated by Bacillus and Diutina, prolonging the thermophilic phase by 167% (p < 0.05) and facilitating the degradation of major organic components. Among them, the degradation rate of lipids was significantly increased by 57.1% (p < 0.01). Consequently, the humic substance content in the fermentation product increased by 18.8% (p < 0.05) and the corresponding germination index increased by 41.4% (p < 0.05). These results were further confirmed by the metagenomic analysis, which indicated that water evaporation induced the significant enrichment of functional genes associated with the tricarboxylic acid cycle and electron transport chain in the aerobic fermentation. These findings offer new mechanistic insights into leveraging microscale moisture regulation to optimize aerobic bioconversion.}, }
@article {pmid41795395, year = {2026}, author = {Chen, Z and Kerfahi, D and He, X and Zhang, X and Zhang, P and Gao, G and Gao, K and Hall-Spencer, JM and Adams, JM and Lin, X}, title = {Ocean acidification reduces diatom and photosynthetic gene abundance on plastic in an coastal bay mesocosm experiment.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107917}, doi = {10.1016/j.marenvres.2026.107917}, pmid = {41795395}, issn = {1879-0291}, mesh = {*Seawater/chemistry ; *Diatoms/physiology ; *Plastics ; *Photosynthesis/genetics ; China ; Hydrogen-Ion Concentration ; Bays/chemistry ; *Water Pollutants, Chemical/analysis/toxicity ; Ecosystem ; Carbon Dioxide ; Ocean Acidification ; }, abstract = {Discarded plastics are accumulating in the global ocean and posing threats to marine life. The plastisphere - the community colonizing plastic surfaces - profoundly influences the environmental behavior of plastic, affecting its degradation and entry into marine food webs. Ocean acidification (OA) due to anthropogenic CO2 emissions, is also threatening marine ecosystems, but the effect of OA on the structure and ecological functions of plastisphere communities remain poorly understood. Here, using a mesocosm experiment, we investigated the effects of OA on the plastisphere colonizing floating PET plastic bottles. The study was conducted using subtropical eutrophic coastal water from Southern China under two CO2 conditions: increased CO2 to 1000 μatm (HC) and ambient CO2 410 μatm (LC). Metagenomic sequencing of the plastic samples, after exposure for 32 days, showed striking changes in relative abundance of eukaryotes and bacteria caused by HC. There was a 75.3 % decrease in eukaryote read abundances at high CO2, most strikingly a 95.6% decrease in the relative abundance of diatoms. In addition, the relative abundance of genes involved in photosystem II light reactions and pigment synthesis decreased under high CO2 conditions. This suggests that OA could reduce the photosynthetic potential of the plastisphere. Shifts in plastisphere community structure and potentially diminished photosynthesis under OA could influence food chains within plastisphere, plastic degradation, transportation, and carbon cycling involving plastics. Overall, our results suggest that OA can alter the functional ecology of the plastisphere, with potential implications for marine biogeochemical processes and food web dynamics in subtropical eutrophic coastal water.}, }
@article {pmid41795412, year = {2026}, author = {Zhang, T and Yang, L and Xie, F and Xing, M and Zhang, H and Song, X and Ai, L}, title = {Docynia delavayi (Franch.) Schneid polyphenols: Optimization of ultrasound-assisted extraction and bioactivity study.}, journal = {Ultrasonics sonochemistry}, volume = {128}, number = {}, pages = {107804}, pmid = {41795412}, issn = {1873-2828}, abstract = {Docynia delavayi is a polyphenol-rich indigenous plant from China, known for its medicinal and edible properties. However, its bioactivities have been scarcely studied. This study aimed to establish an efficient ultrasound-assisted extraction (UAE) process for isolating D. delavayi polyphenols (DDP) and to systematically assess their bioactivities. Single-factor assays combined with response surface methodology were employed to determine optimal UAE conditions for DDP: 43% ethanol, 460 W ultrasonic power, 21 mL/g liquid-to-solid ratio, and 41 min extraction. In vitro evaluation showed that DDP exhibited excellent antioxidant (DPPH radical scavenging IC50 = 3.75 μg/mL) and carbohydrate digestion enzyme (α-Glucosidase and α-Amylase) inhibitory activity. Moreover, DDP also exhibited inhibitory effects on Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Salmonella. Metagenomic analysis revealed that DDP promoted species associated with short-chain fatty acid synthesis, such as Flavonifractor plautii and Eubacterium sp., while reducing pathogenic bacteria, including Shigella sonnei and Klebsiella pneumoniae. Untargeted metabolomics analysis showed that DDP modulated the intestinal metabolic profile and enriched pathways involved in Fatty acid biosynthesis, Fatty acid metabolism, and Fatty acid elongation in mitochondria. We believe that DDP, owing to its remarkable biological activity, may exhibit significant prebiotic effects, thereby modulating the gut microbiota and metabolic network, ultimately improving host health. This study elucidated an efficient UAE process and the diverse biological activities of DDP, providing an experimental foundation for its development as a natural functional ingredient and supporting high-value utilization of medicinal and edible plant resources.}, }
@article {pmid41795563, year = {2026}, author = {Chen, J and Zhou, Z and Liu, D and Yao, Y}, title = {Kaolinite-mediated dual enhancement of tetracycline degradation and methane recovery in anaerobic digestion of contaminated sludge: Microbial community reshaping and metabolic pathway regulation.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141659}, doi = {10.1016/j.jhazmat.2026.141659}, pmid = {41795563}, issn = {1873-3336}, abstract = {Tetracycline (TC) residues in waste-activated sludge (WAS) inhibit key microbial guilds, destabilizing anaerobic digestion (AD). Conventional AD systems rarely achieve both effective antibiotic detoxification and energy recovery. This study investigates the use of kaolinite, a low-cost mineral with superior stability and surface adsorption properties compared to montmorillonite, as an additive for TC-spiked WAS treatment. At an optimal dosage of 0.2 g·L[-1] , kaolinite increased specific methane yield to 44.4 L·kg VS[-1] , a 4.0-fold enhancement over the control, while improving TC removal by 55%. LC-HRMS identified eleven TC transformation products through three main degradation pathways: hydroxylation, N-dealkylation, and ring cleavage. Metagenomic sequencing showed kaolinite selectively enriched syntrophic taxa (Anaerolinea, Hydrogenispora) and the methanogen Methanosarcina, while upregulating genes involved in extracellular electron transfer (e.g., mhcA), methanogenesis (mcrA), and antibiotic resistance/detoxification (tetW, tetX). Network analysis revealed a shift from competitive to mutualistic interactions, enhancing community resilience under TC stress. Mechanistically, kaolinite acts as a "physicochemical buffer and microbial-activity regulator", stabilizing the microenvironment and promoting efficient methanogenesis through direct interspecies electron transfer. These combined effects improve both pollutant removal and methane production, demonstrating a promising approach for optimizing AD in antibiotic-laden sludge management.}, }
@article {pmid41795600, year = {2026}, author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Wei, K and Tahir, M and Zhong, J}, title = {Multi-Omics Reveals Phenethyl Acetate and Its Producer Lactiplantibacillus plantarum as Key Drivers of Enhanced Palatability in Alfalfa Silage.}, journal = {Microbial biotechnology}, volume = {19}, number = {3}, pages = {e70332}, pmid = {41795600}, issn = {1751-7915}, support = {32201467//National Natural Science Foundation of China/ ; XDA26040201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2025KJHZ0041//Science and Technology Program of the Inner Mongolia Autonomous Region/ ; }, mesh = {*Medicago sativa/microbiology/chemistry/metabolism ; *Silage/microbiology/analysis ; Fermentation ; *Flavoring Agents/metabolism ; Taste ; *Acetates/metabolism ; Amino Acids/analysis/metabolism ; *Lactiplantibacillus plantarum/metabolism ; *Lactobacillaceae/metabolism ; Multiomics ; }, abstract = {High-quality silage enhances palatability and feed intake; however, the effects of co-fermentation with flavouring agents and lactic acid bacteria (LAB) on its flavour quality, core microbiota, and taste-active amino acids remain unclear. This study investigated the effects of fermentation using Lactiplantibacillus plantarum (LP) alone or in combination with phenethyl acetate (LPP) on the flavour profile of alfalfa silage and its subsequent influence on feed intake. Both LP and LPP significantly improved fermentation quality versus control (CK), with markedly higher feed intake-LP > CK and LPP > LP. Key flavour compounds, including dimethyl trisulfide, 4-ethylphenol and β-damascenone, were significantly increased in the LP alone group. Contrarily, essential taste-related amino acids including aspartic acid, alanine, proline, histidine, isoleucine, and valine were decreased, except for arginine. These metabolic shifts collectively contributed to enhanced feed intake. The addition of LPP increased phenylethyl alcohol, benzyl alcohol and hexanal, and decreased arginine, contributing to enhanced palatability. Aryl alcohol dehydrogenase, proline aminopeptidase, histidine dehydrogenase, and branched-chain amino acid transaminase from LP played a crucial role in the formation of phenylethyl alcohol, proline, histidine and isoleucine during fermentation. These results provide insights into how LAB and flavouring agents jointly regulate flavour development in high-quality alfalfa silage.}, }
@article {pmid41796197, year = {2026}, author = {Sujeeth, NK and Dharani Bommi, KB and Manojkumar, S and Angayarkanni, J and Gnanadesigan, M}, title = {Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41796197}, issn = {2045-2322}, abstract = {UNLABELLED: In this research, the rhizosphere soil microbiome diversity of mangrove trees such as Avicennia marina, Ceriops tagal & Rhizophora apiculata and salt marsh halophytes Suaeda maritima, Suaeda monoica and Sesuvium portulacastrum from Karankadu mangroves of Tamil Nadu, India was investigated. The collected sample was profiled by 16S rRNA Illumina NovaSeq 6000 platform sequencing of V3–V4 amplicon region by metagenomic approach to investigate the bacterial communities related with the different mangrove species. Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. Bacteria were the most abundant domain followed by Archaea and Eukaryota; Proteobacteria, Actinobacteria, Firmicutes, Fibrobacterota, Chlorobiota, and Bacteroidota were found to be predominant phyla present in all samples; Unculturable environmental microbes were also detected, particularly abundant in S. maritima and S. monoica samples. Staphylococcus aureus, Vibrio parahaemolyticus, Klebsiella pneumoniae, Salmonella enterica, Streptomyces griseocarneus were the most abundant species observed in this study. The variations in bacterial community structure across these ecosystems may be influenced by the distinct environmental conditions of each sampled mangrove habitat. For the first time, our findings highlight the richness of microbial diversity in the Karankadu mangroves, providing essential baseline data and revealing differences between mangrove trees and halophytes. This study offers valuable insights for further investigation into the mechanisms governing rhizosphere microbiome interactions with their host environment.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42270-z.}, }
@article {pmid41796809, year = {2026}, author = {He, J and Zhang, A and Wang, L and Ping, Q and Gao, P and Liu, Y}, title = {Aging attenuates threat: how moderate aging of microplastics suppresses antibiotic resistance gene proliferation during sludge anaerobic digestion.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134342}, doi = {10.1016/j.biortech.2026.134342}, pmid = {41796809}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Microplastics ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Polypropylenes ; *Genes, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Microplastics (MPs) are known to promote antibiotic resistance gene (ARG) dissemination in waste activated sludge; however, most existing evidence is based on unaged MPs, and the influence of aging degree remains poorly understood. This study systematically investigated how varying aging degrees of polyethylene (PE) and polypropylene (PP) MPs modulate ARG profiles and transfer mechanisms during anaerobic digestion. The results demonstrated a non-monotonic effect of aging degree on ARG proliferation, with moderate aging of MPs showing the strongest attenuation of ARG promotion. Under moderate carbonyl indices (CI) of 0.104 for PE-MPs and 0.219 for PP-MPs, the average reduction of the most affected ARGs reached 40% and 50%, respectively, compared with the unaged MPs. Metagenomic analysis further revealed that moderate aging of MPs reduced both the abundance and diversity of ARGs stimulated by unaged MPs. Mechanistically, unaged MPs induced multiple biological responses. These included enrichment of dominant ARG-hosting genera within Proteobacteria and Chloroflexi, elevated oxidative stress, increased membrane permeability, and activation of horizontal gene transfer (HGT) pathways, including the type IV secretion system (T4SS), quorum sensing (QS), and two-component systems (TCS). Conversely, aging weakened these microbial signaling and stress responses at moderate aging degrees but led to a rebound at higher aging degrees, thereby modulating HGT potential in a non-monotonic manner. These findings indicate that aging of sludge-relevant MPs (PE and PP) fundamentally alters their ecological impact on the sludge resistome, highlighting the necessity of incorporating aging dynamics into the risk assessment of MPs in engineered ecosystems.}, }
@article {pmid41797015, year = {2026}, author = {Jeon, J and Lee, DH and Kim, JH and Choi, Y and Jin, YK and Hong, JK and Lee, YM}, title = {Methanotrophic community structure and metabolic potential in the sulfate-methane transition zone of the ARAON mounds, Arctic Chukchi Sea.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107959}, doi = {10.1016/j.marenvres.2026.107959}, pmid = {41797015}, issn = {1879-0291}, mesh = {*Methane/metabolism ; Sulfates/metabolism ; Arctic Regions ; *Microbiota ; Archaea/metabolism ; Geologic Sediments/microbiology ; Bacteria/metabolism ; Oxidation-Reduction ; }, abstract = {Anaerobic oxidation of methane (AOM) mediated by archaea is a pivotal process for methane consumption in gas seepage-associated sediments. Despite its importance in regulating methane flux, the ecological roles and metabolic potential of microbial communities involved in AOM remain poorly understood in Arctic regions. In this study, we investigated the microbial community structures and methanotrophic signatures in sediments from gas hydrate-bearing and non-gas hydrate-bearing sites in ARAON Mounds (AMs) and reference sites. Microbial communities in AMs were distinct from those in reference sites, with high relative abundances of Euryarchaeota (45.5 ± 11%), Lokiarcheota (35 ± 6.1%), and Atribacterota (50.1 ± 23.3%). Anaerobic methanotrophic archaea (ANME) showed site- and depth-specific distributions, with ANME-1a, ANME-1b, and ANME-2c predominating the sulfate-methane transition zone (SMTZ) of the gas hydrate-bearing sites, and ANME-1a prevailing at non-gas hydrate-bearing sites. Sulfate-reducing bacteria (SRB) affiliated with Seep-SRB1 co-occurred with ANME-1a and ANME-1b within the AMs. Metagenome-assembled genomes (MAGs) of ANME-1b and ANME-2c recovered from the SMTZ of the gas hydrate-bearing site (AM6) harbored key AOM-related genes, and their putative syntrophic bacterial partner, ETH-SRB1, possessed essential genes for sulfate reduction. Additionally, Lokiarchaeota and Atribacterota MAGs encoded genes involved in protein degradation, fermentation, and hydrogen metabolism, indicating their possible roles in methane cycling. Collectively, these results reveal distinct microbial assemblages and their functional genomic traits, suggesting niche specialization associated with methane oxidation potential at the SMTZ of the gas hydrate-bearing site.}, }
@article {pmid41797140, year = {2026}, author = {You, G and Jin, H and Wu, M and Li, Y and You, X and Huang, C and Xu, Y and Hou, J}, title = {Insights into antibiotic resistance gene dynamics during Tanfloc-induced flocculation-storage process for cyanobacteria removal in an algae-laden drinking water source.}, journal = {Journal of environmental management}, volume = {403}, number = {}, pages = {129223}, doi = {10.1016/j.jenvman.2026.129223}, pmid = {41797140}, issn = {1095-8630}, mesh = {*Drinking Water/microbiology ; Flocculation ; *Cyanobacteria ; *Drug Resistance, Microbial/genetics ; Water Purification/methods ; }, abstract = {Tannin-based flocculants (TA) are increasingly promoted as green polymeric alternatives for cyanobacteria removal in algae-laden drinking water sources, yet their potential to influence antibiotic resistance gene (ARG) dissemination during subsequent flocculation-storage remains unclear. This study compared TA with polyaluminum chloride (PACl) to assess ARG fate in both supernatant and cyanobacteria-laden drinking water sludge throughout flocculation and 8-day storage. Results showed that TA achieved over 97% removal efficiency for both cyanobacteria and ARGs at a low dosage of 20 mg/L, outperforming PACl. Moreover, TA treatment led to markedly reduced release of microcystin-LR and dissolved organic matter (DOM) after storage. Nevertheless, elevated biomass within TA-induced flocs promoted ARG proliferation, primarily due to enhanced production of triplet-state DOM and suppression of carotenoid synthesis. Metagenomic evidence indicated elevated abundances of CAZyme genes (e.g., GH43, CE4, CE1, GH9, CE11), highlighting an increased functional potential for TA-associated polymer breakdown and consequent weakening of the floc coating after 8 days, which in turn promoted ARG escape from flocs. Meanwhile, increased motility of phycosphere-associated antibiotic-resistant bacteria (e.g., Pseudomonas) promoted ARG transfer into the supernatant, accompanied by enrichment of mobile genetic elements and virulence factor genes, which collectively amplified ecological risks. These findings underscore that ARG release and dissemination should be explicitly integrated into safety assessments of TA-based cyanobacteria control, and they provide mechanistic guidance for mitigating ARG hazards in algal-affected drinking water supplies.}, }
@article {pmid41797187, year = {2026}, author = {Tang, Z and Liu, X and Yang, J and Zhang, F and Shan, X and Liu, Y and Li, F and Lu, S and Xi, B}, title = {Unraveling the redox-driven mechanisms of viral-bacterial interactions in modulating the fate of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134358}, doi = {10.1016/j.biortech.2026.134358}, pmid = {41797187}, issn = {1873-2976}, mesh = {Oxidation-Reduction ; *Bacteria/genetics/drug effects/metabolism ; *Drug Resistance, Microbial/genetics ; Wetlands ; Bioelectric Energy Sources/microbiology ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial/genetics ; Wastewater/microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants in wastewater systems, where heterogeneous redox conditions regulate microbial community assembly and ARG dissemination. However, how within-system redox gradients generated by electrochemical configurations structure bacterial and viral processes and ultimately control ARG dynamics remains unclear. Here, we established a vertical-flow wetland (VW), a direct-current powered VW (DW), and a microbial fuel cell-coupled VW (MW), and performed metagenomic analyses of substrates adjacent to anodes and cathodes to resolve spatial ARG patterns and mechanisms. Across all systems, 478 ARG subtypes from 26 classes were detected, dominated by sulfonamide, multidrug, and tetracycline resistance genes. Electrochemical operation substantially reduced total ARG abundance, with inhibition efficiencies of 49% in DW and 73% in MW and suppressed high-risk genes such as sul1, sul2, tetG, and bacA. Pronounced divergence occurred between anodic and cathodic microenvironments, with ARG levels averaging 0.419 and 0.229 copies per cell, respectively. Redox differentiation reshaped ARG host composition, microbial diversity, ecological networks, virus-host interactions, and metabolic strategies. Cathodic reductive zones were enriched in viral auxiliary metabolic genes linked to folate pathways, potentially alleviating sulfamethoxazole-driven selection, whereas anodic oxidative environments favored outer-membrane porins and mobile genetic elements, coinciding with elevated ARG abundance and greater horizontal transfer potential. Collectively, these results highlight redox-driven microbial metabolism, viral auxiliary functions, and MGE-mediated mobility as key regulators of ARG fate in electrochemical wetlands and provide guidance for engineering redox-optimized systems to mitigate ARG dissemination.}, }
@article {pmid41797508, year = {2026}, author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W}, title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71656}, pmid = {41797508}, issn = {1530-6860}, support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Gallstones/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; Aged ; Multiomics ; Amidohydrolases ; }, abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.}, }
@article {pmid41797768, year = {2026}, author = {Dai, M and Pang, L and Hu, M and Meng, J and Ji, C and Sheng, L and Zhang, W}, title = {Case report: Be alert to parvovirus infection in patients with unexplained anemia after cerebral hemorrhage surgery.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1700344}, pmid = {41797768}, issn = {2296-858X}, abstract = {BACKGROUND: Human parvovirus B19 (PVB19) is a highly prevalent single-stranded DNA virus that infects a large proportion of the global population. It can involve multiple organ systems, leading to a broad spectrum of clinical manifestations. While most infections in immunocompetent individuals are mild and self-limiting, PVB19 can occasionally cause severe and diverse complications.
CASE PRESENTATION: We report a rare case of an immunocompetent patient who experienced unexplained clinical deterioration following surgical evacuation of an intracerebral hemorrhage. The patient presented with refractory anemia, impaired consciousness, fever, seizures, and progressive dysfunction of the cardiac, hepatic, and renal systems. Metagenomic next-generation sequencing revealed high levels of PVB19 DNA in the cerebrospinal fluid, blood, and pleural effusion. The patient was treated with intravenous immunoglobulin (IVIG) therapy and supportive care. Following treatment, improvements were observed in consciousness, mobility, and anemia. However, renal function failed to recover and ultimately progressed to renal failure, necessitating renal replacement therapy.
CONCLUSION: This case underscores the potential severity of PVB19 infection following cerebral hemorrhage surgery, particularly when accompanied by unexplained anemia. Accurate diagnosis requires a high index of suspicion and the use of advanced diagnostic tools. Management primarily involves IVIG therapy and supportive care. This case highlights the importance of expanding the differential diagnosis in postoperative patients presenting with unexplained anemia and multi-organ dysfunction, as early recognition of atypical infections may improve clinical outcomes.}, }
@article {pmid41797781, year = {2026}, author = {Zhang, X and Li, W and Zhao, S and Han, Y and Ma, W and Jiang, Z and Ma, Y and Zhang, G and Wang, J and Jia, H and Guo, S and Cui, N}, title = {Fulminant amebic colitis complicated by appendiceal perforation and massive abdominal hemorrhage: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1760895}, pmid = {41797781}, issn = {2296-858X}, abstract = {INTRODUCTION: Fulminant amebic colitis complicated by intestinal perforation or massive intra-abdominal hemorrhage is uncommon but associated with extremely high mortality. In non-endemic regions, diagnosis is frequently delayed because early manifestations resemble bacterial appendicitis or perforated peritonitis.
CASE PRESENTATION: We report a fatal case of Entamoeba histolytica infection presenting with appendiceal perforation, septic shock, and recurrent intra-abdominal bleeding. Surgery revealed extensive transmural necrosis, deep ulcers, and exposure of submucosal vessels. Metagenomic next-generation sequencing (mNGS) of blood and peritoneal drainage fluid was performed, followed by histopathological confirmation. Despite emergent appendectomy, bowel resection, and prompt initiation of anti-amebic therapy, the patient developed refractory septic shock and recurrent intra-abdominal hemorrhage, resulting in death.
CONCLUSION: mNGS can facilitate early recognition of severe amebiasis when conventional diagnostic modalities are uncertain, particularly in non-endemic settings. Fulminant amebic colitis complicated by perforation or hemorrhage carries a poor prognosis. Timely clinical suspicion and early anti-amebic therapy are essential to improve outcomes.}, }
@article {pmid41798955, year = {2026}, author = {Xiao, Y and Zhang, T and Chen, Q and Zhang, Y and Chen, B and Wang, M and Zhang, Y and Huang, M and Su, Y and Guo, J}, title = {Multi-omics analysis reveals the mechanism of verbenalin in treating gout via modulating purine metabolism, gut microbiota, and inflammatory pathways.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1761558}, pmid = {41798955}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Purines/metabolism ; Disease Models, Animal ; *Gout/drug therapy/metabolism ; Inflammation/drug therapy/metabolism ; Signal Transduction/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Hyperuricemia/drug therapy ; Rats, Sprague-Dawley ; Metabolomics/methods ; Arthritis, Gouty/drug therapy/metabolism ; Multiomics ; }, abstract = {BACKGROUND: Gout is a prevalent metabolic disorder characterized by hyperuricemia and inflammation. Verbenalin, an iridoid glycoside from Verbena officinalis, possesses anti-inflammatory properties; however, its therapeutic potential and underlying mechanisms in gout remain underexplored.
OBJECTIVE: This study aimed to evaluate the pharmacological effects and elucidate the molecular mechanisms of verbenalin in a rat model of gout.
METHODS: Hyperuricemia and acute gouty arthritis were induced in rats using potassium oxonate/hypoxanthine and monosodium urate, respectively. Verbenalin was administered orally for 7 days. Therapeutic efficacy was assessed via physical symptom scores (inflammation, gait, swelling), renal/hepatic function indices, and histopathology. Furthermore, a multi-omics strategy integrating transcriptomics, metagenomics, and metabolomics, combined with Western blotting, was employed to investigate the pharmacological mechanisms.
RESULTS: Verbenalin treatment significantly alleviated joint inflammation and swelling while improving gait scores. It effectively lowered serum uric acid (UA), creatinine, and BUN levels, inhibited hepatic xanthine oxidase (XOD) activity, and promoted urinary UA excretion. Histopathological damage in the joints, kidneys, and liver was markedly mitigated. Mechanistically, verbenalin downregulated the expression of urate transporters (URAT1, GLUT9) and inflammatory mediators (NLRP3, IL-1β) by inhibiting the PI3K-AKT and MAPK signaling pathways. Multi-omics analysis further revealed that verbenalin restored gut microbiota diversity and modulated purine metabolism, correlating with reduced UA levels.
CONCLUSION: These findings demonstrate that verbenalin may exert anti-gout effects through the potential synergy of modulating purine metabolism, shifting gut microbiota composition, and suppressing PI3K-AKT and MAPK inflammatory signaling pathways. This study provides a preliminary scientific basis for further investigation into verbenalin as a prospective multi-target therapeutic candidate.}, }
@article {pmid41799583, year = {2026}, author = {Ofuchi, T and Hu, Q and Omachi, K and Kanemitsu, K and Otsu, H and Yonemura, Y and Tobo, T and Baba, Y and Iwatsuki, M and Mimori, K}, title = {Intratumoral Fusobacterium nucleatum Drives Cancer-Associated Fibroblasts Enrichment and Immune Exclusion in Esophageal Squamous Cell Carcinoma.}, journal = {Annals of gastroenterological surgery}, volume = {10}, number = {2}, pages = {611-620}, pmid = {41799583}, issn = {2475-0328}, abstract = {BACKGROUND: Fusobacterium nucleatum, an oral commensal bacterium, has been increasingly recognized for its oncogenic role in gastrointestinal malignancies. In esophageal squamous cell carcinoma (ESCC), F. nucleatum has been implicated in promoting tumor progression and facilitating immune evasion. However, its relationship with stromal remodeling and the tumor microenvironment (TME) remains unclear.
METHODS: We performed integrative analyses using metagenomic profiling and transcriptomic deconvolution, and histopathological assessment of 93 The Cancer Genome Atlas (TCGA)-ESCC cases and an independent cohort of 126 resected tumors. F. nucleatum status was determined by microbial abundance and quantitative Polymerase Chain Reaction (q-PCR).
RESULTS: F. nucleatum-positive tumors showed significant enrichment of TNFα/NF-κB signaling and reduced CD8[+] T cell infiltration. Stromal analysis revealed a marked increase in cancer-associated fibroblasts (CAFs) in F. nucleatum-positive tumors, confirmed by transcriptomic deconvolution and α-SMA immunohistochemistry. Notably, immunohistochemical analysis demonstrated increased nuclear localization of NF-κB p65, indicating F. nucleatum-induced NF-κB activation in tumor cells. Clinically, among elderly patients with poor performance status, the prevalence of F. nucleatum positivity was significantly higher.
CONCLUSION: F. nucleatum may contribute to the progression of ESCC by inducing NF-κB-mediated inflammatory signaling in tumor cells and promoting CAFs activation. Its presence may facilitate immune exclusion and tumor invasion through stromal remodeling. Furthermore, F. nucleatum positivity may reflect broader host vulnerability, particularly in frail elderly individuals. These findings highlight F. nucleatum as a potential biomarker of tumor immune dynamics and suggest the importance of maintaining good oral hygiene to reduce F. nucleatum colonization.}, }
@article {pmid41799605, year = {2026}, author = {Suzuki, Y and Osumi, W and Taniguchi, K and Kato-Kogoe, N and Sakaguchi, S and Nakamura, S and Imai, Y and Nakano, T and Ueno, T and Lee, SW}, title = {Comparison of Pre- and Postoperative Gut Microbiota Diversity in Patients With Rectal Cancer Undergoing Stoma Creation and Closure.}, journal = {Annals of gastroenterological surgery}, volume = {10}, number = {2}, pages = {492-501}, pmid = {41799605}, issn = {2475-0328}, abstract = {AIM: To investigate the impact of temporary stoma creation and its subsequent closure on gut microbiota composition and diversity in patients undergoing rectal cancer surgery.
METHODS: Nineteen patients with primary rectal cancer who underwent curative surgery were enrolled and divided into two groups: stoma (n = 10, all underwent temporary ileostomy) and non-stoma (n = 9). Fecal samples were collected preoperatively and 6 months postoperatively. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Alpha diversity (observed operational taxonomic units and Shannon index) and beta diversity (UniFrac distances) were compared between time points. Taxonomic shift was identified using Linear discriminant analysis Effect Size (LEfSe).
RESULTS: In the stoma group, alpha diversity significantly decreased after surgery (p = 0.049), and beta diversity analyses revealed significant changes in microbial composition (PERMANOVA; unweighted p = 0.026; weighted p = 0.046). LEfSe analysis identified an increased abundance of potentially pathogenic genera (e.g., Enterococcus and Eggerthella) and a decreased abundance of short-chain fatty acid-producing genera (e.g., Megamonas and Anaerostipes). These changes persisted for at least 6 months after stoma closure. In contrast, the non-stoma group showed no significant alterations in microbial diversity or composition over time.
CONCLUSION: Temporary stoma creation in rectal cancer surgery induces persistent alterations in gut microbiota; these alterations are characterized by reduced diversity and a shift toward a dysbiotic profile with increased pathogenic and decreased beneficial taxa. These findings highlight the potential need for microbiota-targeted strategies to mitigate long-term dysbiosis in patients undergoing stoma-related procedures.}, }
@article {pmid41799966, year = {2026}, author = {Habuding, X and Chen, J and Zhu, J and Wang, G and Ma, L and Abulikemu, T}, title = {Integrated metagenomic and culturomic strategies to mine and validate beneficial rhizosphere Actinobacteria from lavender.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1745076}, pmid = {41799966}, issn = {1664-462X}, abstract = {INTRODUCTION: The lavender industry faces significant constraints from soil salinization and continuous cropping obstacles. However, systematic exploration and functional analysis of beneficial rhizosphere microbial resources, particularly Actinobacteria, remain inadequate.
METHODS: To address this, we integrated metagenomic and culturomic strategies to investigate the rhizosphere and endophytic microbiomes in saline-alkaline lavender cultivation areas in Huocheng, China (soil pH ~8.04, salt ~0.074%). Metagenomic functional annotation and soil factor correlation analysis guided a subsequent culturomics approach to isolate strains. Isolates were screened for plant growth-promoting (PGP) traits, and selected strains were evaluated in pot inoculation experiments with Arabidopsis thaliana.
RESULTS: High-throughput sequencing revealed that Actinomycetota dominated the microbial communities, with Streptomyces and Nocardioides as key genera. Metagenomic analysis showed the community was enriched with functional genes related to saline-alkaline stress response, secondary metabolite synthesis, and nutrient cycling, whose distribution correlated significantly with soil pH and salinity. From this resource, 10 actinobacterial strains with multiple PGP traits (e.g., P-solubilization, siderophore production, IAA, ACC deaminase, and nitrogenase activity) were obtained. Pot experiments confirmed that these saline-alkaline-derived actinobacteria, both as single strains and as a bacterial consortium (C4 + A1), significantly promoted the growth of A. thaliana.
DISCUSSION: This study achieves a closed-loop verification from in silico functional prediction to empirical validation of beneficial strains. It provides the first systematic elucidation of the functional adaptation mechanisms of the lavender rhizosphere actinobacterial community under saline-alkaline stress and identifies elite microbial resources with both stress tolerance and PGP functions. The findings offer novel microbial agents and a theoretical foundation for developing specialized inoculants to mitigate saline-alkaline obstacles in lavender cultivation.}, }
@article {pmid41800013, year = {2026}, author = {Walia, T and Srivastava, N and Shetty, RM and Rana, V}, title = {Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review.}, journal = {International journal of clinical pediatric dentistry}, volume = {19}, number = {2}, pages = {278-284}, pmid = {41800013}, issn = {0974-7052}, abstract = {AIM AND BACKGROUND: The oral cavity harbors a diverse microbiota that significantly influences oral health and disease. Conventional microbiological techniques have limitations in detecting the full range of microbial species, particularly those that are uncultivable. Metagenomics, through culture-independent, high-throughput sequencing methods, offers a comprehensive approach to studying oral microbial diversity. This narrative review aims to evaluate the role of metagenomics in exploring the oral microbiome and its association with dental diseases.
METHODS: This review systematically synthesized current literature and research on metagenomic technologies, including 16S ribosomal RNA (rRNA) sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics. It highlighted their principles, diagnostic capabilities, and limitations in analyzing microbial communities in caries, endodontic infections, and periodontitis. It also reviewed auxiliary tools such as quantitative polymerase chain reaction (qPCR), microarrays, fluorescence in situ hybridization (FISH), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and discussed the integration of artificial intelligence (AI) in metagenomic data interpretation.
RESULTS: Metagenomic studies have expanded the scope of known microbial species involved in dental caries beyond Streptococcus mutans, highlighting the contributions of Lactobacillus, Veillonella, Actinomyces, and Candida albicans. In endodontics, resistant species such as Enterococcus faecalis, Porphyromonas endodontalis, and Fusobacterium nucleatum are implicated in persistent infections. In periodontitis, a dysbiotic microbial shift has been associated with the presence of complex microbial consortia, including red and orange complex bacteria.
CONCLUSION: Metagenomics is a powerful diagnostic tool that provides an in-depth characterization of the complex microbial ecosystem of the oral cavity. It offers diagnostic potential through early and accurate detection of pathogenic shifts, promotes personalized treatment planning, and opens avenues for the development of potential biomarkers of disease progression.
CLINICAL SIGNIFICANCE: The integration of metagenomics into dental practice can revolutionize caries risk assessment, treatment precision, and disease prevention strategies. Although challenges such as high cost, data complexity, and lack of standardization remain, ongoing advancements in sequencing technologies and bioinformatics are expected to enhance its accessibility and clinical relevance.
HOW TO CITE THIS ARTICLE: Walia T, Srivastava N, Shetty RM, et al. Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review. Int J Clin Pediatr Dent 2026;19(2):278-284.}, }
@article {pmid41800387, year = {2026}, author = {Gupta, S and Quarato, V and Lai, W and Kobel, CM and Aho, VTE and Vera-Ponce de León, A and La Rosa, SL and Sandve, SR and Pope, PB and Hvidsten, TR}, title = {OmniCorr: an R-package for visualizing putative host-microbiome interactions using multi-omics data.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag057}, pmid = {41800387}, issn = {2635-0041}, abstract = {Holo-omics leverages omics datasets to explore the interactions between hosts and their associated microbiomes. Although the generation of omics data from matching host and microbiome samples is steadily increasing, there remains a scarcity of computational tools capable of integrating and visualizing this data to facilitate the prediction and interpretation of host-microbiome interactions. We present OmniCorr, an R package designed to: (i) manage the complexity of omics data by clustering co-varying features (e.g. genes, proteins, and metabolites) into modules, (ii) visualize correlations of these modules across different omics layers, host-microbiome interfaces, and metadata, and (iii) identify statistically significant associations indicative of putative host-microbiome interactions. OmniCorr's utility is demonstrated using datasets from two systems: (i) Atlantic salmon, integrating host transcriptomics with metagenomics and metatranscriptomics to explore dietary impacts, and (ii) cattle, combining host proteomics with metaproteomics to investigate methane emission variability. Availability and implementation: OmniCorr is freely available at https://github.com/shashank-KU/OmniCorr.}, }
@article {pmid41800416, year = {2026}, author = {Bustos, ML and Song, K and Brochu, HN and Zhang, Q and Iyer, LK and Icenhour, CR}, title = {Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1707004}, pmid = {41800416}, issn = {1664-302X}, abstract = {INTRODUCTION: The nasopharyngeal microbiome plays a critical role in respiratory health and disease and is a major focus of metagenomic research. However, inconsistent reporting practices across studies limit reproducibility, dataset usability, and cross-study integration, thereby reducing the overall scientific value of publicly available nasopharyn.
METHODS: A systematic review was conducted to evaluate the impact of non-standardized reporting on reproducibility, usability, and integration of nasopharyngeal metagenomic datasets. A total of 988 studies were screened, and 227 manuscripts met predefined inclusion and exclusion criteria for full-text review. Methodological reproducibility, metadata completeness, and compatibility between reported laboratory methods and deposited datasets were assessed. Reproducible datasets were further analyzed to evaluate the interchangeability of nasopharyngeal aspirates and nasopharyngeal swabs.
RESULTS: Only 78 studies (34%) contained methods sections sufficient for reproducibility, and of these, 33 studies (15%) provided analytically sufficient metadata to support secondary analysis. Mismatches between reported laboratory methods and deposited datasets were identified in 4% of studies. These deficiencies were primarily attributed to incomplete methodological reporting, inaccessible or insufficient metadata, and incompatible file formats. Comparative analysis of reproducible datasets demonstrated significant differences in microbial profiles between nasopharyngeal aspirates and nasopharyngeal swabs, confirming that these specimen types are not interchangeable within a study.
DISCUSSION: The findings demonstrate that inadequate reporting standards substantially impair the reproducibility, reuse, and integration of nasopharyngeal metagenomic data. The observed methodological and metadata inconsistencies limit the reliability of downstream analyses and cross-study comparisons. Standardized reporting guidelines are urgently needed to improve transparency, ensure reproducibility, and enhance the integrative potential of nasopharyngeal microbiome research. Adoption of comprehensive and consistent reporting practices would significantly strengthen the scientific rigor and utility of metagenomic studies in this field.}, }
@article {pmid41800425, year = {2026}, author = {Huangfu, H and Pu, J and Jiao, M and Zhou, H and Fan, Q and Deng, H and Ling, Q and Luo, X and Xu, J}, title = {Unveiling the RNA viral diversity in three organs of the Asian house shrew (Suncus murinus) from Tropical Hainan, China: a previously underappreciated key zoonotic reservoir.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1738936}, pmid = {41800425}, issn = {1664-302X}, abstract = {Shrews represent an important reservoir of diverse human-pathogen viruses with implications for human infectious diseases. As the most populous shrew species, the Asian house shrew-Suncus murinus (Su. murinus) is widely distributed across South and Southeast Asia-particularly tropical and subtropical regions-yet its virome remains poorly studied. In this study, we collected 249 Su. murinus from 18 cities/counties (excluding Sansha) across Hainan Island and conducted RNA sequencing on gut, spleen, and lung tissues. We identified 192 RNA viruses, comprising 120 known viral species and 72 novel viruses, including key zoonotic viral families: Arenaviridae, Hantaviridae, Paramyxoviridae etc. We assembled 102 complete and nearly complete genomes. Notably, 64 known viruses exhibited cross-species transmission potential, including 57 with spillover risk and 7 human-pathogenic viruses: Mammarenavirus choriomeningitidis (LCMV), Henipavirus (HeV), Wenzhou virus (WENV), Langat virus (LGTV), Amur virus (AMRV), Influenza A virus (H1N1), and Rotavirus A (RVA). Additionally, AMRV, LGTV, and LCMV were reported here for the first time in Su. murinus based on metagenomic detection. Our phylogenetic and RT-PCR results indicate Su. murinus is a candidate reservoir for Langya-like henipavirus. Collectively, our study reveals tropical populations of Su. murinus are a previously underappreciated reservoir of viral diversity, underscoring their key role in zoonotic emergence and necessitating surveillance in tropical regions.}, }
@article {pmid41800589, year = {2026}, author = {Juan, DR and Dilanaz, A and Camila, RV and Fernando, DG and Pedro, SR and Ana, MB and Ricardo, U and Barrie, JD and Mario, V and Díez, B and Matías, C and Pedro, T and Alejandra, G and Francisco, I and Raquel, Q}, title = {Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag048}, pmid = {41800589}, issn = {1751-7370}, abstract = {Extreme acidic environments represent natural laboratories for investigating the mechanisms of microbial community assembly, yet the ecological processes structuring these communities remain incompletely understood. Here, we investigate how spatial partitioning, hydrodynamics, and colonization history shape microbial succession in a unique sulfur-rich, acidic river of volcanic origin in northern Patagonia. We combined 16S rRNA gene profiling and shotgun metagenomics with a multi-scale experimental framework encompassing water column fractionation and colonization assays under native and controlled conditions. Microbial diversity was strongly influenced by spatial fractionation, with free-living communities exhibiting higher richness and temporal variability than particle-associated assemblages. Water flow modulated community structure, increasing evenness in free-living fractions under high-flow conditions, but had limited impact on particle-attached communities. Colonization of sulfur-beads followed a structured successional trajectory, with autotrophic sulfur oxidizers dominating early stages and heterotrophs adapted to biofilm lifestyles increasing over time. Ex situ recolonization assays revealed strong priority effects, with initial colonizers determining successional trajectories. Turnover analyses revealed that the balance among stochastic and deterministic assembly processes shifted across communities with pronounced stochasticity in the water column and flow-dependent effects in free-living communities, while biofilm associated communities on sulfur-beads exhibited stronger contribution of deterministic selection. These ecological patterns were mirrored by functional differentiation, with gene enrichment analyses revealing adaptive signatures of substrate attachment and resource acquisition. By integrating fine-scale environmental variation with colonization dynamics, this study reveals how microscale habitat structure and temporal fluxes jointly modulate microbial community assembly rules, offering a nuanced framework to dissect ecological processes in extreme systems.}, }
@article {pmid41800893, year = {2026}, author = {Ge, T and Zhao, T and Ruan, Y and Ye, L and Xiao, Y and Xiao, F and Li, Y and Li, X and Wang, R and Hu, H and Lu, C and Sun, H and Zhang, C and Yu, G and Zhang, T}, title = {Dysbiosis of fecal virome in pediatric Crohn's disease and its dynamic changes during infliximab therapy.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0148925}, doi = {10.1128/msystems.01489-25}, pmid = {41800893}, issn = {2379-5077}, abstract = {UNLABELLED: The gut virome is an emerging but underexplored component of the human microbiota, especially in pediatric Crohn's disease (CD). This study aimed to characterize the fecal virome in children with CD and evaluate its association with clinical response to infliximab (IFX) therapy. A total of 85 participants, including 60 pediatric CD patients and 25 healthy controls (HC), were recruited. Among the CD patients, 53 received ≥3 IFX infusions, 41 achieved remission (IFX-R), and 12 did not (IFX-NR). Viral-like particles in fecal samples were enriched and profiled by metagenomic sequencing, while bacterial communities were assessed via 16S rRNA gene sequencing. Pediatric CD patients exhibited significantly reduced viral richness and altered viral community compared to HCs. Functional analyses revealed that CD patients exhibit a shift in fecal virome function from DNA repair to viral replication and assembly. Trans-kingdom correlations were disrupted in CD, particularly between Torque teno viruses and beneficial bacteria, such as Blautia. An integrated machine learning model combining viral and bacterial markers achieved a certain level of diagnostic accuracy for pediatric CD (area under the curve [AUC] = 89.3%). IFX treatment influences the gut virome, with remission associated with higher abundances of Microviridae and Siphoviridae, while Anelloviridae, Myoviridae, and Podoviridae were enriched in IFX-NR at baseline. These findings suggest the virome as a potential biomarker for predicting clinical outcome in pediatric CD, offering a novel avenue for disease diagnosis and personalized treatment strategies.
IMPORTANCE: Crohn's disease (CD) in children poses a growing clinical challenge, with increasing incidence and variable response to biologic therapies such as infliximab (IFX). While gut bacterial dysbiosis has been extensively studied, the role of the gut virome in pediatric CD remains largely unexplored. This study provides the first longitudinal characterization of the fecal virome in children with CD undergoing IFX therapy. We reveal distinct viral community patterns, functional alterations, and virus-bacteria interactions in pediatric CD patients. Notably, integration of virome and bacteriome profiles enhances diagnostic accuracy, offering a promising avenue for predictive biomarker development. Furthermore, virome changes may be associated with the IFX treatment outcomes in children with CD. These findings highlight the gut virome as a critical but overlooked dimension of host-microbiome interactions in pediatric CD, with potential implications for personalized therapy and mechanistic understanding of treatment resistance.}, }
@article {pmid41801284, year = {2026}, author = {Wang, J and Ge, H and Liu, Y and Huang, C and Zhang, L and Yu, Y and Xu, L and Fang, H}, title = {Earthworm gut microbiome promotes biodegradation of albendazole in soil.}, journal = {Crop health}, volume = {4}, number = {1}, pages = {}, pmid = {41801284}, issn = {2948-1945}, support = {2023YFD1902903//National Key Research and Development Program of China/ ; 42177252//National Natural Science Foundation of China/ ; 2023C02039-01//Leading Goose" R&D program of Zhejiang Province of China/ ; }, abstract = {The excretion of the anthelmintic drug albendazole (ALB) from treated animals into the soil, as well as its widespread application as a fungicide, poses a serious ecological risk to the soil environment. In this study, we investigated the degradation of ALB in soil and its bioaccumulation in earthworms, changes in the microbiome and degradation genes, and the effect of zinc oxide nanoparticles on the degradation and enrichment behaviors of ALB and microbial community structure and function. Our findings showed that ALB selectively enriched specific albendazole degradation genes (i.e., hmr and ami) in the earthworm, preferentially activating the pathways associated with sulfur reduction, amination of ALB sulfone, and hydroxylation of ALB. Metagenomic analysis revealed that the relative abundances of ppo, xylA, cutC, and nfsl in the earthworm gut were 0.19-52.64-fold higher in the ALB treatment than in the control, indicating their potential dominance in ALB biodegradation. Network analysis further identified potential bacterial hosts carrying biodegradation genes and albendazole degradation genes. Notably, Sphaerobacter, Saccharothrix, Actinomadura, and Nocardia were recognized as potential dual hosts of biodegradation genes and albendazole degradation genes, displaying a 0.05-1.32-fold elevation in relative abundance in ALB-treated earthworm guts compared to the control. Additionally, ZnO nanoparticles were found to reduce ALB bioaccumulation in earthworms and accelerate its dissipation in soil. These findings provide novel insights into the bioremediation mechanisms of pesticides in soil-earthworm ecosystems.}, }
@article {pmid41801404, year = {2026}, author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH}, title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {75}, number = {4}, pages = {}, pmid = {41801404}, issn = {1432-0851}, support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; }, mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Middle Aged ; Aged ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prospective Studies ; *Neoplasms/drug therapy/immunology/mortality ; Melanoma/drug therapy/immunology ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; }, abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.}, }
@article {pmid41802510, year = {2026}, author = {Gou, X and Shen, Y and Liu, F and Wang, Y and Zong, Y and Qu, D and Ren Zeng, C and Nhamdriel, T and Kuang, T and Fan, G}, title = {Swertia chirayita ameliorates MAFLD by improving intestinal microenvironment and hepatic lipogenesis.}, journal = {Journal of ethnopharmacology}, volume = {364}, number = {}, pages = {121471}, doi = {10.1016/j.jep.2026.121471}, pmid = {41802510}, issn = {1872-7573}, mesh = {Animals ; *Lipogenesis/drug effects ; *Liver/drug effects/metabolism/pathology ; Male ; Rats ; *Swertia/chemistry ; *Plant Extracts/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Diet, High-Fat/adverse effects ; Intestines/drug effects ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Metabolic-associated fatty liver disease (MAFLD) is emerging as a very serious threat to human health. The search for effective remedies for MAFLD from natural herbs is gaining increasing attention. Swertia chirayita (SC) is a famous herb in China, India, and Nepal. It has long been employed within the traditional Tibetan medical system for managing hepatic disorders. Nevertheless, the therapeutic impacts and possible mechanisms of SC in the context of MAFLD are unclear.
AIM OF THE STUDY: This present investigation was designed to research the pharmacological influence and potential mechanisms of SC in MAFLD rats. We conducted a particular examination of its effects on the intestinal microenvironment and hepatic lipogenesis.
MATERIALS AND METHODS: The pharmacological effects of SC were evaluated in MAFLD rats established through a 12-week high-fat diet (HFD) feeding. After 8 weeks of SC administration, biochemical assessments were conducted for body fat, liver function, glucose metabolism, lipid parameters, and inflammatory factors. The main chemical constituents of SC and three short-chain fatty acids (SCFAs) in rat feces were quantitatively analyzed by HPLC. Furthermore, targeted metabolomics, transcriptomics, metagenomics, and Western blotting were employed to investigate possible mechanisms by which SC improves MAFLD.
RESULTS: Treatment with SC significantly ameliorated excessive fat accumulation and insulin resistance in MAFLD rats. It also improved hepatic enzyme activities (AST and ALT), several lipid metrics (TG, TC, and LDL-C), and liver histopathological changes. Moreover, SC attenuated systemic inflammation, as shown by decreased circulating IL-1β, TNF-α, LPS, and IL-6. Metagenomic profiling revealed that SC administration helped reestablish the dysregulation of multiple types of gut microbiota (bacteria, fungi, archaea, and viruses) in MAFLD rats. It improved microbial diversity, community composition, and transkingdom correlations. In addition, SC enhanced gut barrier function by raising the amount of butyric acid, acetic acid, and propionic acid and upregulating the expression of several ZO-1, occludin, and claudin-1. Liver transcriptomic analysis suggested that SC could regulate the metabolism of bile acids (BAs). Importantly, targeted metabolite analysis and western blotting demonstrated that SC improved bile acid dysfunction in MAFLD rats. In particular, SC increased TCDCA, TCA, and DCA, thereby activating the FXR/FGF15 signaling axis. This activation then controlled the production of SHP and SREBP-1c proteins in the hepatic, thereby inhibiting hepatic lipogenesis to improve MAFLD.
CONCLUSIONS: SC has shown a good therapeutic effect on MAFLD by improving intestinal microenvironment and hepatic lipogenesis. Specifically, it improves the imbalance of multiple types of gut microbiota, restores disrupted transkingdom interactions, promotes creation of beneficial SCFAs and bile acid, protects the intestinal barrier, and inhibits hepatic lipogenesis by regulating the BAs/FXR/FGF15 and SHP/SREBP-1c signaling pathways.}, }
@article {pmid41802644, year = {2026}, author = {Wang, X and Feng, X and Zhou, Z and Li, M and Zhang, R}, title = {A pre-LECA origin of giant viruses as revealed by polymerase-based time tree.}, journal = {Molecular phylogenetics and evolution}, volume = {220}, number = {}, pages = {108602}, doi = {10.1016/j.ympev.2026.108602}, pmid = {41802644}, issn = {1095-9513}, abstract = {The viral phylum Nucleocytoviricota (NCLDV) infects a wide range of eukaryotic hosts and exhibits genome complexities and virion sizes comparable to prokaryotes, blurring the boundaries between cellular life and viral entities. Despite significant advances from large-scale metagenomic surveys and identification of endogenous viral elements that expand our understanding of NCLDV's genomic diversity and host range, their evolutionary origin remains contentious. Here, we utilize DNA-directed DNA polymerase (DNAP) and RNA polymerase (RNAP), conserved markers across eukaryotes, prokaryotes, and NCLDVs, to leverage abundant eukaryotic fossils for dating the origins of NCLDVs. Phylogenetic analyses showed that NCLDV's DNAP and RNAP consistently form deep branches separate from their eukaryotic homologs. Molecular dating analyses further indicated that both DNAP and RNAP in NCLDV originated before the emergence of last eukaryotic common ancestor (LECA), findings which are robust across various dating settings. Notably, the estimated origin based on RNAP was older compared to DNAP, underscoring the need to identify additional orthologues shared with eukaryotes. Collectively, our findings represent the first attempt, to the best of our knowledge, to establish a reliable temporal framework for NCLDV evolution, supporting a pre-LECA origin of ancestral NCLDVs and suggesting a prolonged co-evolutionary history with their (proto-)eukaryotic hosts during eukaryogenesis.}, }
@article {pmid41802657, year = {2026}, author = {Ma, R and Jia, B and Zhang, X and Zhao, Z and Zhao, F and Liong, MT and Ali, A and Abd Hamid, IJ and Hasan, TH and Taib, F and Sun, Z}, title = {Bifidobacterium longum subsp. infantis B8762 modulates the infant gut-lung axis via microbial and metabolic reprogramming.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108431}, doi = {10.1016/j.micpath.2026.108431}, pmid = {41802657}, issn = {1096-1208}, abstract = {Respiratory and gastrointestinal infections are leading causes of morbidity in children. Increasing evidence highlights the gut-lung axis as a key regulatory interface influencing infection susceptibility. Bifidobacterium longum subsp. infantis B8762 (B8762) has shown clinical efficacy in reducing such infections, but its mechanistic basis remains unclear. In a randomized, double-blind, placebo-controlled study involving 115 infants (probiotic group: n = 57, placebo group: n = 58; aged 6-12 months), fecal metagenomic sequencing was performed to assess microbial and functional changes after four weeks of B8762 supplementation (0.5 × 10[10] CFU/day). B8762 significantly altered the gut microbial structure (β-diversity, P < 0.05) without affecting α-diversity. The intervention enriched beneficial taxa including Bifidobacterium longum, Eubacterium limosum, and Roseburia hominis, while reducing potential pathogens such as Staphylococcus aureus and Candida parapsilosis (P < 0.05). Functionally, B8762 upregulated metabolic pathways involved in coenzyme A and L-tryptophan biosynthesis and enhanced predicted production of immunoregulatory metabolites including butyrate, inosine, and chenodeoxycholic acid. In summary, this study suggests that B8762 modulates the pediatric gut microbiota toward a composition and metabolic profile that supports mucosal barrier integrity and systemic immune regulation. These findings provide mechanistic insight into its protective role against respiratory and gastrointestinal infections in children, supporting its use as a targeted gut-lung axis probiotic intervention.}, }
@article {pmid41803086, year = {2026}, author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L}, title = {Water mass specific genes dominate the Southern Ocean microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41803086}, issn = {2041-1723}, support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; //France Génomique/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; //Laboratoire d’Excellence” LabexMER/ ; }, mesh = {*Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Antarctic Regions ; *Bacteria/genetics/classification ; Sulfonium Compounds/metabolism ; Arctic Regions ; Plankton/genetics ; Phylogeny ; }, abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.}, }
@article {pmid41803098, year = {2026}, author = {Zhu, Y and Sun, M and Chen, B and Liu, X and Yang, G and Li, X}, title = {Diagnostic Value of Cerebrospinal Fluid Metagenomics Next-generation Sequencing in Neurobrucellosis in Children: Erratum.}, journal = {The Pediatric infectious disease journal}, volume = {45}, number = {4}, pages = {384}, pmid = {41803098}, issn = {1532-0987}, }
@article {pmid41803498, year = {2026}, author = {Zhou, H and Sun, R and Nie, X and Xia, L and Dong, H and Liu, Y and Hou, S and Dong, W and Zhu, X and Yao, Y and Zhao, GP and Lu, S and Wang, Y and Yang, C}, title = {A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41803498}, issn = {2058-5276}, support = {82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31925001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073152//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241227//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030045//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Targeting the gut microbiota is a promising strategy to enhance the efficiency of cancer immunotherapy; however, success has been limited. Here we combined metagenomic analysis and in silico prediction to identify bacterial species associated with immunotherapy response in patients with non-small-cell lung cancer. We constructed a defined consortium (RCom) of 15 bacterial species, most of which were isolated from responder patient faeces, associated with improved clinical response to anti-programmed cell death protein 1 (PD-1) treatment. Metabolic models and in vitro experiments revealed that RCom is a stable and cooperative community, and in vivo experiments showed that RCom engrafts and produces immunomodulatory metabolites. Oral administration of RCom improved the anti-tumour activity of anti-PD-1 by increasing the intratumoural infiltration and cytotoxic function of CD8[+] T cells in syngeneic tumour models and across mice with heterogeneity in baseline gut microbiota composition. RCom supplementation also limited anti-PD-1 resistance in mice conferred by faecal microbiota transplantation from individual non-responsive patients. These findings suggest that RCom is a potential adjuvant to improve responsiveness to anti-PD-1 therapy in cancer.}, }
@article {pmid41803682, year = {2026}, author = {Shen, Z and Zhang, Z and Gao, J and Chen, J and Xu, Q and Li, D and Zeng, L and Cheng, D and Wang, K and Zhang, J and Wong, JWC}, title = {Microbial succession accompanies increased antibiotic resistance risk during grass carp (Ctenopharyngodon idella) spoilage under ambient household conditions.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04924-w}, pmid = {41803682}, issn = {1471-2180}, support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 22206107//National Natural Science Foundation of China/ ; 2023ZT10L060//Program for Guangdong Introducing Innovative and Entrepreneurial Teams of China/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; }, abstract = {Understanding fish spoilage mechanisms under household storage conditions is critical for food safety in regions with limited cold chain infrastructure, where ambient storage remains common practice. This study investigated the spoilage dynamics, microbial succession, and antibiotic resistance gene (ARG) proliferation in grass carp stored under simulated household conditions at 13.0 ± 3.4 °C using three packaging scenarios. The biogenic amine index (BAI) of fish exceeded 50 mg/kg within 16 h, marking early spoilage onset. After 64 h, K-values surpassed 60%, TVB-N exceeded the safety limit of 20 mg/100 g, and BAI reached over 220 mg/kg, indicating advanced spoilage. 16S rRNA amplicon sequencing demonstrated dramatic microbial community shifts from Cyanobacteriota-dominated fresh samples to Pseudomonadota-dominated spoilage communities, with Aeromonas emerging as the primary specific spoilage organism (SSO), increasing from 0.001% to 67.2% at 64 h. Pathogen abundance escalated from 0.06% to 72.2% in muscle tissues, posing substantial food safety risks. Distinct microbial community structures were observed across tissue types (muscle vs. gut) and packaging treatments, with storage time exerting the strongest selective pressure on community composition. Metagenomic analysis revealed progressive ARG enrichment, with surface samples exhibiting 2.6-fold higher total ARG abundance and 3.8-fold greater ARG type richness compared to the fresh gut baseline by 24 ~ 64 h. Rapid ARG enrichment was detected during early spoilage (24 h), representing a critical food safety concern. Notably, carbapenem resistance genes (e.g., OXA-12, cphA6) were substantially enriched, underscoring the high risk posed by these clinically relevant resistance genes. These findings demonstrate that grass carp stored under ambient household conditions maintain acceptable quality for < 16 h, necessitating immediate consumption or cold chain implementation to ensure food safety and minimize ARG dissemination.}, }
@article {pmid41803729, year = {2026}, author = {Tian, J and Jiang, Y and Ye, N and Zhang, Y}, title = {A case of uveitis and retinal vasculitis induced by varicella-zoster virus: vitrectomy treatment and literature review.}, journal = {BMC ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12886-026-04710-2}, pmid = {41803729}, issn = {1471-2415}, support = {20260814//Medical Science Research Project of Hebei/ ; 20260814//Medical Science Research Project of Hebei/ ; 20260814//Medical Science Research Project of Hebei/ ; }, }
@article {pmid41803767, year = {2026}, author = {Maeda, K and Tamura, Y and Nagai, Y and Kariya, Y and Katsuta, H and Ajiro, N and Yoshida, H and Han, Y and Hashimoto, S and Chikamatsu, K and Takaki, A and Matsumoto, Y and Fatimah, RM and Tanaka, M and Nakamura, S and Iida, T and Mitarai, S and Nagai, T}, title = {Non-tuberculous Mycobacterial pulmonary disease due to novel mycobacterium: Mycobacterium habikinoensis: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-12857-y}, pmid = {41803767}, issn = {1471-2334}, }
@article {pmid41803907, year = {2026}, author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM}, title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41803907}, issn = {2049-2618}, support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundación Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracción de talento investigador César Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; French Guiana ; Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Metals/pharmacology ; Male ; Female ; Adult ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenome ; *Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.
RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.
CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.}, }
@article {pmid41804366, year = {2026}, author = {Jiang, W and Luo, M and Jiang, M and Yang, J and Qin, L and Yang, Z and Xue, F and Long, Z and Zhao, L and Long, H}, title = {Clinical Features and Risk Factors for Severe Disease in 57 Cases of Chlamydia psittaci Pneumonia: A Retrospective Study.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {584050}, pmid = {41804366}, issn = {1178-6973}, abstract = {BACKGROUND: This study aimed to analyze the clinical features of Chlamydia psittaci (C. psittaci) pneumonia and identify risk factors for severe patients to facilitate early diagnosis and treatment.
METHODS: In this retrospective analysis, we collected and summarized the clinical data of 57 patients with C. psittaci pneumonia confirmed by metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS), who were admitted to the First Affiliated Hospital of Guilin Medical University between July 2020 and August 2025. Patients were further divided into a severe group (n=23) and a non-severe group (n=34) for comparative analysis of their clinical characteristics.
RESULTS: The mean age of the patients was 58.68 ± 12.36 years. Common symptoms included fever, cough/sputum, fatigue, dyspnea, and neurological and gastrointestinal symptoms. The severe group had a significantly higher incidence of fatigue, dyspnea, and neurological and gastrointestinal manifestations. Laboratory findings revealed that most patients had normal or mildly elevated white blood cell counts with lymphopenia, alongside significantly elevated levels of C-reactive protein (CRP), procalcitonin (PCT), and erythrocyte sedimentation rate (ESR). Anemia, hypoalbuminemia, and abnormalities in liver enzymes, myocardial enzymes, and electrolytes were also commonly observed. The predominant chest computed tomography finding was consolidation, with pleural effusion present in 59.6% of all patients and occurring more frequently in the severe group. Multivariate analysis identified CRP as an independent risk factor for severe C. psittaci pneumonia, while albumin and platelet count were protective factors.
CONCLUSION: Pneumonia patients presenting with non-specific influenza-like symptoms should raise clinical suspicion for C. psittaci pneumonia. Particular vigilance for potential progression to severe disease is warranted in male patients, the elderly, those with underlying comorbidities, and individuals presenting with neurological or gastrointestinal symptoms. Elevated CRP, hypoalbuminemia, and thrombocytopenia serve as significant predictors of severe C. psittaci pneumonia.}, }
@article {pmid41804664, year = {2026}, author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B}, title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70278}, doi = {10.1111/1462-2920.70278}, pmid = {41804664}, issn = {1462-2920}, support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; }, mesh = {Biodegradation, Environmental ; *Composting ; *Microplastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Polymers/metabolism/chemistry ; *Soil Microbiology ; Microbiota ; Polyesters/metabolism ; *Soil Pollutants/metabolism ; Soil/chemistry ; }, abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.}, }
@article {pmid41804674, year = {2026}, author = {Liu, D and Luo, M and Li, M and Chen, C and Chen, S and Wu, Y and Zhang, G and Gao, Y and Hong, Y and Zhou, Q and Li, X and Zhou, S and Wu, Y and Zhao, Y and Zhang, Y and Yin, J}, title = {Dynamic interaction between Escherichia coli enterotoxins and bacteriocins.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.70488}, pmid = {41804674}, issn = {1742-4658}, support = {2023YFD1401400//the National Key R&D Program of China/ ; 32471200//the National Natural Science Foundation of China/ ; kq2208167//the Natural Science Foundation of Changsha/ ; xjt [2021] 346//the postgraduate joint training base project in Hunan Province/ ; 2023JJ10029//the Natural Science Foundation for Distinguished Young Scholars of Hunan Province/ ; }, abstract = {The intestinal microbiota constitutes a crucial defense barrier against pathogenic invasion; however, the molecular mechanisms enabling pathogens to evade or modulate this defense remain poorly understood. Here, we established a coculture model combining the commensal Escherichia coli Y18J, isolated from the piglet gut, and the enterotoxigenic E. coli (ETEC) strain W25K to investigate microbe-pathogen interactions. Our findings reveal a bidirectional regulatory mechanism between Y18J and W25K mediated by bacteriocin and toxin signaling. Colicin B/M produced by Y18J upregulates the expression of heat-stable enterotoxin (ST) in W25K during the early phase of coculture, while ST suppresses colicin B/M synthesis in Y18J. At later stages, colicin B/M stimulates heat-labile enterotoxin (LT) expression, which in turn enhances colicin B/M production. Notably, LT markedly reduces intestinal colonization of W25K(ST[-]LT[+]) in murine hosts. Leveraging metagenomic and bioinformatic analyses, we further identified a Ligilactobacillus strain within the murine gut microbiota capable of producing multiple bacteriocins that effectively inhibit W25K colonization. Transcriptomic profiling of Y18J revealed glutamine synthetase as a pivotal regulator of colicin B/M-mediated antagonism. Mechanistic investigations demonstrated that ST suppresses colicin B/M expression through the cGMP signaling pathway, whereas LT enhances it via the cAMP signaling pathway. Collectively, these findings uncover a dual regulatory mechanism through which bacterial enterotoxins modulate probiotic antimicrobial activity, providing new insights into the molecular dialog between commensal and pathogenic bacteria. This study establishes a conceptual framework for developing microbiota-based strategies to prevent and control enteric infections.}, }
@article {pmid41805117, year = {2026}, author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE}, title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {10}, pages = {8268-8283}, doi = {10.1021/acs.jafc.5c15254}, pmid = {41805117}, issn = {1520-5118}, mesh = {Soil Pollutants/chemistry/metabolism ; Microbiota ; Bacteria/chemistry/metabolism ; Rhizosphere ; Biodegradation, Environmental ; *Soil Microbiology ; *Glycine max/growth & development/metabolism/microbiology ; }, abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.}, }
@article {pmid41805177, year = {2026}, author = {Pereira, AC and Cortez, F and Chaves, G and Nanetti, E and Leite, RB and Mendes, MC and Oliveira, I and Abreu, H and Martins, M and Keller-Costa, T and Costa, R}, title = {Thirteen metagenome-assembled genomes of Paraglaciecola chathamensis associated with the farmed red seaweeds Porphyra dioica and Porphyra umbilicalis.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0149625}, doi = {10.1128/mra.01496-25}, pmid = {41805177}, issn = {2576-098X}, abstract = {We report 13 metagenome-assembled genomes (MAGs) of Paraglaciecola chathamensis (Gammaproteobacteria) retrieved from farmed Atlantic Nori (Porphyra spp.) across several developmental stages. MAGs encode proteins involved in host-microbe interactions, nutrient acquisition, nitrogen and cofactor metabolism, stress resilience, and genome plasticity, illuminating the possible roles of Paraglaciecola in the Porphyra holobiont.}, }
@article {pmid41805398, year = {2026}, author = {Bouderka, F and López-García, P and Deschamps, P and Zhou, Y and Krupovic, M and Gutiérrez-Preciado, A and Ciobanu, M and Bertolino, P and David, G and Moreira, D and Jardillier, L}, title = {Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages.}, journal = {mBio}, volume = {}, number = {}, pages = {e0002526}, doi = {10.1128/mbio.00025-26}, pmid = {41805398}, issn = {2150-7511}, abstract = {Patescibacteriota form a very diverse and widely distributed phylum of small bacteria inferred to have an episymbiotic lifestyle. However, the prevalence of this lifestyle within the phylum and its host specificity remain poorly known due to the scarcity of cultured representatives. Here, we describe a complex system consisting of a patescibacterium, its gammaproteobacterial hosts, and their respective phages based on enrichment cultures and metagenomic data from two shallow, geographically close, freshwater ecosystems. The patescibacterium Strigamonas methylophilicida sp. nov. defines a new genus within the family Absconditicoccaceae. It grows as an epibiont on cells of methanotrophic species of the gammaproteobacterial family Methylophilaceae. Strigamonas cells grow tightly attached to the host, sometimes forming stacks that connect two host cells. Despite a surprisingly large genome (1.9 Mb) compared to many other Patescibacteriota, S. methylophilicida lacks many essential biosynthetic pathways, including the complete biosynthesis of phospholipids, amino acids, and nucleic acids, implying a dependence on the host to obtain these molecules. We also identified and assembled the complete genomes of one patescibacterial phage that might represent a new virus family within the class Caudoviricetes, and two Methylophilaceae phages predicted to have head-tailed and filamentous virions, respectively. The patesciphage uses a modified genetic code similar to that of its host and encodes four tRNA genes, including the suppressor tRNA gene for the UGA stop codon, which is reassigned to glycine in many Patescibacteriota. Our results confirm a prevalent episymbiotic lifestyle in Absconditicoccaceae and further suggest a clade-specific adaptation of this patescibacterial family for gammaproteobacterial hosts.IMPORTANCEPatescibacteriota are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes; however, their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. By combining targeted cultivation with genomic and microscopy analyses, we reveal previously unrecognized host lineages and expand the known viral diversity infecting this major, but still poorly known, bacterial phylum. We describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family, previously found to infect only photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its methylotrophic hosts, including one phage that uses a modified genetic code matching that of the patescibacterium, which shows a specific viral adaptation to infect Absconditicoccaceae hosts. Our findings reveal a previously unrecognized patescibacteria-methylotrophs-phages tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.}, }
@article {pmid41805951, year = {2026}, author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM}, title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41805951}, issn = {1432-184X}, abstract = {Shotgun metagenomics is an approach increasingly applied to investigate microbial succession and functional potential in complex fermented food systems, including cocoa bean fermentation. In this study, we used Illumina-based shotgun metagenomic sequencing to characterize microbial community dynamics and metabolic potential across two post-harvest cocoa processing routes (R1 and R2) in Boyacá, Colombia, encompassing both fermentation and drying stages. Cocoa beans were sampled at defined time points during fermentation and subsequent natural drying, and non-host metagenomic reads were subjected to taxonomic classification and functional annotation to assess fungi, bacteria, and viruses. A clear multi-ecological succession was observed throughout post-harvest processing. Fungal communities shifted from a yeast-dominated profile, mainly Saccharomyces and Pichia during fermentation, to the emergence of the filamentous fungus Aspergillus during drying. Bacterial populations transitioned from diverse Enterobacteriaceae in early fermentation to a near-complete dominance of Acetobacter, which persisted throughout the drying phase. Viral communities also displayed structured successional patterns, with Lambdavirus and Punavirus prevalent in early fermentation, followed by Spbetavirus, Lafunavirus, and Pemunavirus during later stages and drying. Functional analyses revealed high metabolic potential for carbohydrate, energy, and amino acid metabolism during early fermentation, followed by a marked reduction in later stages, indicating a metabolic slowdown. Core metabolic functions were retained during drying at substantially lower activity levels. This integrated metagenomic analysis links microbial structure to functional potential and provides a scientific basis for optimizing starter cultures and post-harvest processing strategies to enhance cocoa quality and safety.}, }
@article {pmid41806005, year = {2026}, author = {Dong, X and Zhang, T and Tang, B and Zeng, Q and Hu, Z and Huang, P and Xiong, X and Wang, X and Dong, W and Cai, Y}, title = {Microbial and metabolic profiles in autism spectrum disorder with atopic dermatitis in children.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02037-1}, pmid = {41806005}, issn = {2191-0855}, }
@article {pmid41806446, year = {2026}, author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C}, title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.}, journal = {The Science of the total environment}, volume = {1025}, number = {}, pages = {181655}, doi = {10.1016/j.scitotenv.2026.181655}, pmid = {41806446}, issn = {1879-1026}, mesh = {*Microbiota ; *Porifera/microbiology ; Antarctic Regions ; Animals ; Archaea ; Biodiversity ; Ecosystem ; Bacteria ; }, abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.}, }
@article {pmid41806753, year = {2026}, author = {Wang, R and Liu, Z and Zhang, Q and Lian, J and Meng, H}, title = {Performance of oxic/anoxic process for treating aniline wastewater and gaseous N2O emission characteristics under low dissolved oxygen conditions.}, journal = {Journal of environmental management}, volume = {403}, number = {}, pages = {129250}, doi = {10.1016/j.jenvman.2026.129250}, pmid = {41806753}, issn = {1095-8630}, mesh = {*Wastewater/chemistry ; *Aniline Compounds ; Oxygen ; Water Pollutants, Chemical ; Bioreactors ; Nitrous Oxide ; Waste Disposal, Fluid/methods ; }, abstract = {In the biological treatment of aniline wastewater, the influence mechanism of dissolved oxygen (DO) concentration on the degradation of pollutants and N2O emission remains unclear. In this study, three A/O reactors were constructed to treat aniline wastewater, with the aerobic stage was operated under distinct low DO conditions: R1 (0.2-1.0 mg/L, ultralow oxygen), R2 (0.3-1.5 mg/L, lower oxygen), and R3 (0.4-2.0 mg/L, low oxygen). The results showed that as DO concentration increased, the removal rates of aniline, COD and NH4[+]-N improved slightly, whereas TN removal rate decreased significantly. During one operating cycle, cumulative gaseous N2O emissions were lowest in R2 and highest in R3. Therefore, considering pollutants removal, N2O emission and energy conservation, the lower oxygen control strategy (0.3-1.5 mg/L) was recommended. The metagenomic data revealed the enrichment of the aniline-degrading bacteria CAADHD01, and denitrifying bacteria JABWCM01, UBA12294, and Thauera in all reactors. The metabolic pathways of aniline and nitrogen were inferred. Aniline degradation primarily occurred via the meta-cleavage pathway, and nitrogen transformation involved assimilation, nitrification, and denitrification, while nitrification was inhibited by aniline. At the lower oxygen level (R2), the abundance of hao (hydroxylamine oxidoreductase gene) was lowest, and that of nosZ (nitrous oxide reductase gene) was highest, leading to lowest N2O emission. This study provides valuable strategies for N2O reduction during the biological treatment of aniline wastewater.}, }
@article {pmid41806901, year = {2026}, author = {Yin, Z and Ping, H and Li, C}, title = {Associations between Antibiotic and Metal Resistance Genes in Geothermal Springs.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124235}, doi = {10.1016/j.envres.2026.124235}, pmid = {41806901}, issn = {1096-0953}, abstract = {Metals, particularly toxic heavy metal(loid) pollutants, have been widely reported to facilitate the co-selection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in contaminated environments. However, in natural geogenically metal-rich systems such as geothermal springs-often considered pristine environments analogous to early Earth-the occurrence of ARGs and their associations with MRGs remain poorly understood. Here, we investigated ARGs and MRGs distribution patterns in China's largest geothermal field using metagenomic and metatranscriptomic analyses. ARGs were detected in all studied geothermal springs, with total abundances ranging from 52.80 to 668.12 TPM. Macrolide-lincosamide-streptogramin (MLS), bacitracin, and rifamycin resistance genes were the most abundant ARGs. Significant associations between ARGs and MRGs were observed across the geothermal springs, as evidenced by Mantel tests and Procrustes analysis. For instance, bacitracin (R = 0.96, P = 1.06E-05) and rifamycin (R = 0.95, P = 3.41E-05) resistance genes exhibited strong positive correlations with arsenic (As) resistance genes. Metagenome-assembled genomes (MAGs) analyses further identified putative key drivers mediating the linkage between ARGs and MRGs (e.g., Thiomonas and Tepidimonas). Metatranscriptomic data confirmed the active transcription of ARGs, MRGs, and mobile genetic elements (MGEs). Collectively, this study provides a systematic understanding of the distribution patterns of ARGs in pristine geothermal springs and highlights their associations with MRGs.}, }
@article {pmid41806991, year = {2026}, author = {Martinez-Tellez, B and Schönke, M and Kovynev, A and Garcia-Dominguez, E and Ortiz-Alvarez, L and Verhoeven, A and Gacesa, R and Vich Vila, A and Ducarmon, QR and Jimenez-Pavon, D and Gomez-Cabrera, MDC and Weersma, RK and Smits, WK and Giera, M and Ruiz, JR and Rensen, PC}, title = {Roseburia inulinivorans increases muscle strength.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336980}, pmid = {41806991}, issn = {1468-3288}, abstract = {BACKGROUND: Gut bacteria have been implicated in a wide range of health conditions, yet their potential role in preventing and treating muscle-wasting disorders remains largely unexplored.
OBJECTIVE: We aimed to investigate whether specific gut microbial species are associated with muscle strength and to explore underlying mechanisms linking the gut microbiota to muscle health.
DESIGN: We conducted metagenomic analyses in cohorts of younger and older adults extensively phenotyped for muscle strength. Associations were tested between bacterial taxa and performance measures. Causality was assessed by oral supplementation of candidate species in antibiotic-treated mice. Metabolomic profiling and muscle phenotyping were performed to elucidate mechanisms.
RESULTS: The relative abundance of Roseburia inulinivorans, but not other Roseburia species, was positively associated with multiple strength measures including handgrip, leg press and bench press in humans. Supplementation of R. inulinivorans in mice significantly enhanced forelimb grip strength, whereas other Roseburia species had no effect. Metabolomic analyses revealed that R. inulinivorans reduced amino acid concentrations in the caecum and plasma, while activating the purine and pentose phosphate pathway in muscle. These changes coincided with increased muscle fibre size and a shift from type I to type II fibres. Accordingly, we observed that the relative abundance of R. inulinivorans is lower in older adults compared with young adults.
CONCLUSION: R. inulinivorans emerges as a species-specific modulator of muscle strength, linking gut microbiota to muscle metabolism and function. These findings support its potential as a probiotic candidate for nutraceutical interventions targeting age-related muscle-wasting diseases.
TRIAL REGISTRATION NUMBER: NCT02365129.}, }
@article {pmid41807455, year = {2026}, author = {Bi, D and Wu, Y and Ji, G and Zhu, X and Li, H and Xie, R and Gao, Y and Deng, Z and Han, D and Qin, H and Wei, Q}, title = {Integrating ANI and phylogenies for re-evaluation of Fusobacterium taxonomy and disease associations.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70540-x}, pmid = {41807455}, issn = {2041-1723}, support = {82572576//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072236//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072634//National Natural Science Foundation of China (National Science Foundation of China)/ ; SHDC2020CR2069B//Shanghai Hospital Development Center (SHDC)/ ; }, abstract = {The genus Fusobacterium encompasses significant pathogens implicated in diseases spanning from infections to cancer. However, taxonomic ambiguities persist within the genus, particularly concerning Fusobacterium nucleatum (sensu lato). Through genus-wide average nucleotide identity (ANI) and phylogenetic analyses of 540 Fusobacterium genomes, we identify an ANI gap (93.38%-93.89%) for species delineation, leading to comprehensive taxonomic revisions that resolve these ambiguities. We further establish gyrB and rpoB as high-resolution taxonomic markers with phylogenies consistently supporting the revised taxonomy. Leveraging these markers, we develop B&B, a general strategy for precise species identification without whole-genome sequencing, and validate its accuracy in clinically relevant strains. Integrating the revised taxonomy with genomic/metagenomic toolkits demonstrate broad utilities, reinterpreting key colorectal cancer-associated species. This work establishes a unified taxonomic framework and enables standardised species classification for Fusobacterium isolates and microbiomes, highlighting the genetic divergence among Fusobacterium species and providing the taxonomic precision essential for advancing Fusobacterium-related research.}, }
@article {pmid41808169, year = {2026}, author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J}, title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.}, journal = {Microbial cell factories}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12934-026-02977-0}, pmid = {41808169}, issn = {1475-2859}, support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; }, }
@article {pmid41808525, year = {2026}, author = {Jiménez, DJ and Rosado, AS}, title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70272}, pmid = {41808525}, issn = {1462-2920}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Microbiota ; *Polyethylene Terephthalates/metabolism ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biocatalysis ; *Bacteria/enzymology/genetics ; }, abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.}, }
@article {pmid41808728, year = {2026}, author = {Pereira, MH and Tyagi, S and Mohanty, A and Garg, S and Kumar, A}, title = {Metagenomic studies reveal diverse microbial community in the developmental stages of highly adaptable malarial vector Anopheles stephensi liston.}, journal = {3 Biotech}, volume = {16}, number = {4}, pages = {124}, pmid = {41808728}, issn = {2190-572X}, abstract = {UNLABELLED: Anopheles stephensi, a highly adaptable malaria vector species, continues to expand its range from South Asia to Sub-Saharan Africa, posing a serious global public health concern. In India, it serves as the principal urban vector of both Plasmodium falciparum and P. vivax. Conventional control measures reliant on chemical insecticides have raised issues of resistance, highlighting the need for alternative strategies such as microbiota-mediated vector control. This study aimed to test the hypothesis that a subset of bacterial taxa persist across developmental stages of An. stephensi, representing potential candidates for transstadial transmission and future paratransgenic manipulation. Using both culture-based data and next-generation sequencing (NGS) approaches targeting the 16 S rRNA gene (V3-V4 region), we characterized bacterial communities from breeding water, larvae, pupae, and adult mosquitoes (male and female) collected in Goa, India. Across all developmental stages, Proteobacteria and Firmicutes were the dominant phyla, while 15 bacterial genera formed the putative core microbiome shared by ≥ 80% of stages at ≥ 0.1% abundance. Among these, Pseudomonas (adult males: 11.5%, pupae: 3.2%), Exiguobacterium, Acinetobacter, Psychrobacter, and Asticcacaulis were consistently detected, together contributing approximately 30% of total microbial composition. Alpha diversity indices indicated higher richness and evenness in pupae and adults than in larvae, suggesting microbial enrichment during metamorphosis. Beta diversity and PCoA analyses clustered pupal and adult stages distinctly from larvae and breeding water, confirming selective microbial retention through development. These findings reveal that An. stephensi harbors a stable, stage-spanning core microbiome dominated by metabolically versatile genera with potential for transstadial persistence. The dominance of Pseudomonas across life stages supports its candidacy for paratransgenic applications aimed at disrupting malaria transmission. This work provides the first integrated culture-NGS baseline of An. stephensi microbiota from India, offering essential insight for microbiome-based vector control strategies.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04739-6.}, }
@article {pmid41808765, year = {2026}, author = {Rivera-Sánchez, ES and Salinas-García, M and Viviano, E and Villaró-Cos, S and Lafarga, T}, title = {Effect of salinity on growth and microbial diversity in cultures of Scenedesmus almeriensis produced at a pilot scale.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1753183}, pmid = {41808765}, issn = {2296-4185}, abstract = {Introduction: Freshwater scarcity represents a major constraint for the sustainable industrial-scale cultivation of microalgae. This study investigates the feasibility of producing Scenedesmus almeriensis using seawater in 3.1 m[3] tubular photobioreactors under winter-spring conditions. The appearance of algal predators represents a significant challenge in industrial facilities, and this research also explores whether seawater can serve as a strategic water source for more resilient and efficient production systems. Methods: Biomass productivity and microbial diversity were compared between freshwater and seawater-based cultures under batch and semi-continuous regimes at dilution rates of 0.1, 0.2, and 0.3 day[-1]. The production was carried out in duplicate using identical tubular photobioreactors. Analytical determinations included measuring biomass concentration, chlorophyll fluorescence, and oxygen production via photorespirometry. Microbial diversity was assessed through microscopy and metagenomic analysis (18S and 16S rDNA) to identify taxonomic classifications and potential biotic contaminants. Results and Discussion: Maximum biomass concentrations reached 0.60 and 2.15 g·L[-1] in freshwater and seawater, respectively. Production using seawater led to a higher biomass productivity (0.18 g·L[-1]·day[-1]) compared to freshwater (0.06 g·L[-1]·day[-1]) at a fixed dilution rate of 0.1 day[-1]. Seawater cultures exhibited greater stability and higher photosynthetic efficiency, with Scenedesmus dominating up to 70% of the microalgal community due to reduced contamination by zooplankton, fungi, and ciliates. In contrast, freshwater cultures were rapidly degraded by rotifers and anaerobic fungi, leading to a culture crash when dilution rates were increased. These findings highlight the potential of seawater to act as a biological barrier against contaminants while significantly reducing freshwater requirements in industrial microalgae production.}, }
@article {pmid41809220, year = {2026}, author = {Wishahi, M}, title = {Gut microbiotas attributed to disorders and diseases of the gastrointestinal tract, colorectal cancer, bladder cancer: Geographical factors, inflammation, metabolic toxic.}, journal = {World journal of gastrointestinal pharmacology and therapeutics}, volume = {17}, number = {1}, pages = {115573}, pmid = {41809220}, issn = {2150-5349}, abstract = {Recently, there were several publications that attributed gut microbiota (GM) to various gastrointestinal tract functional disorders and diseases, including inflammatory bowel diseases, colon cancer, pancreatic cancer, and diverticulosis. GM is attributed to the initiation of urinary tract diseases and bladder carcinoma (BCa). The concern is whether GM is dysbiotic or protective. We explored the studies on GM contribution to colorectal cancer and BCa. Selected studies from different geographical regions on tissue samples or faecal samples from patients with colorectal cancer and controls. The results showed diverging results of microbiota abundance, genus, class, and phylum. These data indicated that other factors of environmental, diet, ethnic, and personal factors are contributors to GM in the initiation of inflammation and tumors. GM are not inhabitants in the urinary tract; it is postulated that GM attributes to BCa via the circulating metabolic toxins in the initiation of tumorigenesis and BCa.}, }
@article {pmid41809269, year = {2026}, author = {Pei, J and Chen, L and Pushparaj, R and Huang, P and Pan, G and Sun, C and Gao, X and Zhang, L and Manirujjaman, M and Huang, CK and Ting, PS and Deng, Z and Chen, S and Zhang, X and Vatsalya, V and McClain, CJ and Feng, W}, title = {High-dose taurine supplementation exacerbates alcohol-associated liver disease by inducing gut microbiota dysbiosis and bile acid dysregulation in mice.}, journal = {eGastroenterology}, volume = {4}, number = {1}, pages = {e100321}, pmid = {41809269}, issn = {2976-7296}, abstract = {BACKGROUND: β-aminoethanesulfonic acid (taurine) is a conditionally essential amino acid that plays critical roles in bile acid (BA) conjugation, antioxidative defence and metabolic regulation. Previous studies showed that faecal taurine level was reduced in patients with alcohol-associated liver disease (ALD), suggesting that taurine supplementation may have beneficial effects. This study aimed to determine whether oral taurine supplementation prevents the development of ALD in mice and to elucidate the underlying mechanisms.
METHODS: A total of 8-week-old male mice were subjected to a chronic-plus-binge ALD model. Taurine was administered orally via the diet for ten days before and during ethanol exposure. Faecal 16S ribosomal RNA metagenomic analysis, liver RNA sequencing and BA profiling were performed.
RESULTS: High-dose taurine supplementation (3 g/kg body weight/day) was associated with worsened ethanol-induced liver injury, as indicated by increased serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, hepatic steatosis, apoptosis and inflammation. At the molecular level, high-dose taurine treatment was associated with reduced Cpt1a expression, altered expression of genes involved in fatty acid β-oxidation and lipogenic gene Fasn, and decreased expression of Baat, accompanied by changes in taurine-conjugated BA profiles. These alterations were accompanied by changes in BA composition and intestinal FXR-associated gene expression. Taurine supplementation was also associated with shifts in gut microbial composition, including enrichment of hydrogen sulfide-producing bacteria, increased microbial H2S production, impaired intestinal barrier-related parameters and increased bacterial translocation to the liver, paralleling enhanced hepatic inflammatory responses. In contrast, low-dose taurine supplementation (0.2 g/kg body weight/day) was associated with improved liver phenotypes, including reduced steatosis, lower serum ALT and AST levels, decreased Fasn expression and enhanced BA conjugation. Collectively, these results indicate a dose-dependent association between taurine supplementation and ALD-related outcomes.
CONCLUSIONS: Our findings suggest that high-dose taurine supplementation is associated with unfavourable alterations in gut microbiota composition, intestinal barrier integrity, BA metabolism and hepatic taurine-related pathways in ALD, coinciding with exacerbated liver injury. In contrast, low-dose taurine supplementation was associated with improved hepatic outcomes. These results highlight the importance of dose considerations in taurine supplementation and support the concept that taurine may exert divergent effects on ALD depending on the administered dose.}, }
@article {pmid41809628, year = {2026}, author = {Zhang, W and Tang, Y and Luo, R and He, J and Yan, J and Long, F and Li, L}, title = {Altitudinal changes induce responses in Coptis chinensis Franch. rhizomes: endophytic communities, metabolite types, and alkaloid contents.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1777206}, pmid = {41809628}, issn = {1664-462X}, abstract = {Coptis chinensis Franch. is a perennial medicinal plant with huge economic and social benefits, but how altitude affects the accumulation of bioactive compounds through microbial ecosystems remains unexplored. This study examined how microbial communities at different altitudes influence the bioactive components of Coptis chinensis, to help identify beneficial microorganisms for application to its rhizomes. Samples of Coptis chinensis were cultivated at four different altitudes in Shizhu, Chongqing. To characterize the phytochemical profile of Coptis chinensis, nine specific alkaloids were quantified by High Performance Liquid Chromatography (HPLC) and Ultraviolet-Visible Spectrophotometry (UV-Vis), with Liquid Chromatography-Mass Spectrometry (LC-MS) subsequently employed to characterize differential metabolite accumulation at each altitude. Microbial community structure in the rhizomes was analyzed by metagenomic sequencing. Results indicated that the contents of groenlandicine, coptisine, berberine, and total alkaloids increased with altitude, with the total alkaloid content rising from 15.97% at 907 m to 17.82% at 1698 m (P < 0.01). Analysis revealed 912 differential metabolites, with distinct accumulation patterns at different altitudes. Microbial diversity in the rhizomes also varied by altitude, with significant shifts in Mucoromycota, Pseudomonadota, Rhizophagus, and Mesorhizobium populations. Moreover, the relative abundance of these microorganisms was intricately linked to alkaloid content. High altitude significantly enhances alkaloid accumulation in C. chinensis, and this effect is primarily mediated by the enrichment of beneficial endophytes, which promote the biosynthesis of target alkaloids via optimizing nitrogen utilization and inducing the expression of key enzymes.}, }
@article {pmid41809656, year = {2026}, author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M}, title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {251}, number = {}, pages = {10894}, pmid = {41809656}, issn = {1535-3699}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology ; *Probiotics/administration & dosage/therapeutic use ; *Bifidobacterium bifidum/physiology ; Male ; Female ; Adult ; Middle Aged ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.}, }
@article {pmid41809703, year = {2026}, author = {Suvvari, TK and Kodakandla, R and Kandi, V}, title = {Redefining the diagnostic pathway for pulmonary nocardiosis: The imperative for early metagenomic sequencing.}, journal = {World journal of radiology}, volume = {18}, number = {2}, pages = {119080}, pmid = {41809703}, issn = {1949-8470}, abstract = {In this article, we comment on the pivotal article by Wang et al. We focus on the critical intersection of advanced imaging and molecular diagnostics highlighted by their findings. The study delineates specific high-risk computed tomography patterns, notably consolidation with nodules/cavities, particularly in immunocompromised hosts or patients with bronchiectasis, that should serve as immediate red flags for pulmonary nocardiosis. Traditionally, diagnosis has relied on slow-growing cultures, leading to dangerous therapeutic delays. This editorial argues that the presence of these defined radiologic signatures may represent an important step toward refining the diagnostic pathway for pulmonary nocardiosis. Rather than a confirmatory last resort, metagenomic next-generation sequencing should be deployed as a first-line investigative tool following high-suspicion imaging. We propose a concrete, integrated diagnostic algorithm where imaging triage triggers parallel processing with metagenomic next-generation sequencing and conventional microbiology. This synergy of morphology and metagenomics promises to expedite species-specific diagnosis, guide timely targeted therapy, and ultimately improve outcomes for patients with this challenging and often elusive infection.}, }
@article {pmid41809936, year = {2026}, author = {Su, M and Luo, Y and Huan, X and Xi, C and Yang, L and Zhong, H and Liu, F and Zhang, Q and Liu, Q and Wang, X and Cao, Y and Wang, M and Ta, F and Wang, B and Ai, J and Zhao, C and Zheng, J and Luo, S}, title = {Application of Droplet Digital PCR in Sputum Samples in Myasthenia Gravis Patients with Pneumonia.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {588779}, pmid = {41809936}, issn = {1178-6973}, abstract = {BACKGROUND: Due to the rapid progression of the pneumonia in patients with Myasthenia gravis (MG), faster pathogen detection techniques are needed. The droplet digital polymerase chain reaction (ddPCR) has the ability to detect pathogens in about 3 h. Thus, this study focused on application of ddPCR in sputum samples in the MG patients with pneumonia and analyzed the association between ddPCR and other laboratory results.
METHODS: We prospectively enrolled 22 MG inpatients with pneumonia and collected 24 sputum samples. All samples were analyzed using traditional culture, ddPCR and metagenomic next-generation sequencing (mNGS) in parallel. Clinical outcomes during hospitalization were documented.
RESULTS: Among the 24 sputum samples collected from 22 MG patients, ddPCR achieved a 100% positivity rate with the identification of bacteria in all 24 samples, while mNGS also demonstrated a high detection rate, identifying bacteria in 23 of 24 samples (95.8%), and additionally detecting viral and fungal pathogens across multiple cases. In 4 patients with negative sputum culture results, pathogens were identified by both ddPCR and mNGS.
CONCLUSION: The ddPCR demonstrated rapid and sensitive identification of predefined bacterial targets and drug-resistance genes, making it suitable for initial diagnostic screening and timely clinical decision-making in MG patients with pneumonia. The speed of ddPCR detection is faster than mNGS and traditional culture, and the results are similar to mNGS and culture, with good consistency.}, }
@article {pmid41809988, year = {2026}, author = {Parks, DH and Newell, RJP and Ginn, AN and Bowerman, KL and Alsheikh-Hussain, A and Fang, L and Shah, S and MacDonald, S and Wimpenny, T and Evans, P and Arias Guzman, NE and Pribyl, AL and Tyson, GW and Hugenholtz, P and Krause, L and Newcombe, J and Griffin, P and Wehrhahn, MC and Angel, NZ and Wood, DLA}, title = {Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1759322}, pmid = {41809988}, issn = {2235-2988}, mesh = {*Feces/microbiology/virology ; *Metagenomics/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Bacteria/genetics/isolation & purification/classification ; *Molecular Diagnostic Techniques/methods ; Virulence Factors/genetics ; Viruses/genetics/isolation & purification ; Reproducibility of Results ; }, abstract = {BACKGROUND: Robust identification of pathogens is essential for managing patients with symptomatic infection, yet conventional diagnostic methods focus on a subset of the most prevalent pathogens and genes. Metagenomic next-generation sequencing (mNGS) is a powerful technology that can comprehensively and simultaneously assess a broader range of pathogens and genes in a sample. This study evaluates the clinical (22 targets), analytical (19 targets), and in silico (176 targets) performance of a faecal mNGS assay on clinically relevant bacterial, eukaryotic, viral, virulence factor (VF) and antimicrobial resistance (AMR) genes.
METHODS: Diagnostic performance was evaluated relative to conventional pathology testing using 510 clinical faecal samples from patients presenting with gastrointestinal symptoms. Contrived samples were used to assess analytical performance and establish the assay's limit of detection by adding cells to a faecal matrix. In silico faecal samples containing targets reflecting the limit of detection of the assay were used to evaluate performance across all 176 targets.
RESULTS: Clinical specificity was ≥96% (≥99% for all but Adenovirus F), and median pathogen sensitivity was 91%. VF and AMR gene detection was less sensitive (median 58.7%). The assay was highly reproducible in biological triplicates (27,656/27,808 calls concordant; 99.5%). Importantly, broad mNGS coverage increased diagnostic yield, with 256/510 (50.2%) samples containing one or more additional targets not reported by standard care, and 181/510 (35.5%) containing AMR genes, including carbapenemases. In silico benchmarking showed strong performance for all 176 targets down to analytically defined detection limits.
CONCLUSIONS: The faecal mNGS assay performed competitively with existing diagnostic techniques while substantially expanding actionable detection in a single assay. These results support stool mNGS as a high-yield second-line or syndromic test for gastrointestinal infection, enabling improved recognition of rare pathogens, co-infections, and resistance determinants.}, }
@article {pmid41810030, year = {2026}, author = {Karr, AF and Ruane, R}, title = {Effects of Training Data Quality on Classifier Performance.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {41810030}, issn = {2331-8422}, abstract = {We describe extensive numerical experiments assessing and quantifying how classifier performance depends on the quality of the training data, a frequently neglected component of the analysis of classifiers. More specifically, in the scientific context of metagenomic assembly of short DNA reads into "contigs," we examine the effects of degrading the quality of the training data by multiple mechanisms, and for four classifiers-Bayes classifiers, neural nets, partition models and random forests. We investigate both individual behavior and congruence among the classifiers. We find breakdown-like behavior that holds for all four classifiers, as degradation increases and they move from being mostly correct to only coincidentally correct, because they are wrong in the same way. In the process, a picture of spatial heterogeneity emerges: as the training data move farther from analysis data, classifier decisions degenerate, the boundary becomes less dense, and congruence increases.}, }
@article {pmid41810234, year = {2026}, author = {Yang, G and He, S and Wang, J and Yu, S and Zhang, S and Fan, W}, title = {Cryptococcus neoformans infection presenting as a mediastinal mass in an immunocompetent child with parrot exposure: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1771746}, pmid = {41810234}, issn = {2296-858X}, abstract = {Cryptococcus neoformans typically causes pulmonary or central nervous system (CNS) infections, but mediastinal mass as its primary manifestation is rare-especially in immunocompetent children with pet parrot exposure. This study reports a 7-year-old girl who presented with recurrent fever and a mediastinal mass secondary to Cryptococcus neoformans infection, with a 5-month history of daily contact with parrot feces. Conventional diagnostic tests (e.g., fungal culture, serology) were negative, and the diagnosis was confirmed by targeted metagenomic next-generation sequencing (tNGS) of bronchoalveolar lavage fluid (BALF). The patient received a three-phase antifungal regimen: induction with amphotericin B + flucytosine, consolidation with fluconazole, and maintenance with low-dose fluconazole. After one year of treatment, the mediastinal mass nearly resolved, and no recurrence was observed. A literature review, supplemented with specific cases of parrot-associated Cryptococcus neoformans infection, highlights that parrot exposure is an underrecognized risk factor for pediatric cryptococcosis, and tNGS significantly improves diagnostic efficiency for atypical extrapulmonary manifestations. This case emphasizes the importance of inquiring about pet bird exposure in children with unexplained mediastinal masses and fever, and supports the use of tNGS for early, non-invasive diagnosis.}, }
@article {pmid41810244, year = {2026}, author = {Zhou, F and Zhang, Y and Liu, Y and Mou, Y and Chen, J}, title = {Streptococcus suis meningitis in an elderly man: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1735413}, pmid = {41810244}, issn = {2296-858X}, abstract = {BACKGROUND: Streptococcus suis is a zoonotic pathogen that resides in pigs. It can be transmitted to humans through several routes, including contact with sick or carrier pigs via broken skin or mucous membranes and consumption of undercooked pork products. Streptococcus suis often causes severe clinical symptoms such as meningitis, sepsis, and shock.
CASE PRESENTATION: A 66-years-old male butcher was admitted to the hospital with a sudden high fever and disturbance of consciousness, and he remained in a state of persistent restlessness. The neurological examination findings were as follows: he was poorly cooperative with the examinations of higher cortical functions and cranial nerves, uncooperative with the examination of limb muscle strength, and unable to cooperate with the examinations of sensation and ataxia. He presented with nuchal rigidity, with a distance of four finger breadths between the chin and chest, and Kernig's sign was positive. The patient was diagnosed with Streptococcus suis meningitis based on the results of Metagenomic Capture sequencing, cerebrospinal fluid culture, and blood culture. Considering the patient's critical condition, he had received empirical treatment with cephalosporin in the previous hospital, but the therapeutic effect was not satisfactory. Moreover, in this region, there is a phenomenon of decreased sensitivity in Streptococcus pneumoniae to penicillin and third-generation cephalosporins. Therefore, the patient received antibiotic treatment with vancomycin (1 g) intravenously every 12 h. Concurrently, he was administered mannitol to reduce intracranial pressure and ulinastatin for anti-inflammatory effects and immune enhancement. Subsequently, vancomycin 20 mg was administered by intrathecal injection. The patient's condition improved, and he was discharged from the hospital. There was no special discomfort during follow-up.
CONCLUSION: This case report describes the diagnosis and treatment process of Streptococcus suis meningitis. It proposes an antibiotic treatment plan centered on vancomycin. Intrathecal injection of antibiotics may provide an effective treatment option for severe patients and offer a treatment choice for drug-resistant bacterial infections in the central nervous system. It was also pointed out that Metagenomic Capture sequencing can reduce host gene interference and increase the detection rate of pathogens. This case aims to enhance clinicians' understanding of the disease and provide a reference for early identification and standardized treatment.}, }
@article {pmid41810372, year = {2026}, author = {Ding, SC and Yu, J and Liao, T and Ahmann, LS and Yao, YY and Ho, C and Wang, L and Pinsky, BA and Gu, W}, title = {Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41810372}, abstract = {BACKGROUND: Circulating cell-free DNA (cfDNA) has become a valuable analyte for molecular testing, but requires specialized collection tubes or immediate processing. We investigated the feasibility of using residual plasma from heparin separators, which are routinely used in clinical chemistry, as an accessible and underutilized source for cfDNA biobanking and testing.
METHODS: We analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing tube comparison across EDTA, Streck, and heparin separators (n = 5) and a clinical-handling simulation that paired EDTA and heparin separator tubes and delayed processing at room temperature versus 4°C (n = 6). We also analyzed matched EDTA and heparin separator plasma samples from viral PCR-positive patients (Hospital Cohort; n =38). Whole-genome sequencing and genome-wide enriched methylation sequencing were performed to evaluate concordance across multiple benchmarks, including metagenomics, chromosomal copy number, methylome, and fragmentomics.
RESULTS: Under immediate processing, heparin separator plasma showed high concordance with EDTA and Streck plasma for methylation patterns (Pearson's r = 0.92-0.93, Spearman's ρ=0.65-0.70) and fragmentation features (n = 5). In the clinical-handling simulation, cfDNA integrity in heparin separators was comparable to that in EDTA at 4°C (n=6). In the Hospital Cohort, heparin separators showed a strong concordance with matched EDTA tubes for viral detection (n=38, Pearson's r=0.96), copy number alteration profiling (n=6, Pearson's r=0.96-1.00), and methylation patterns (n=12, r=0.83-0.93).
CONCLUSION: Hospital residual plasma from routine clinical chemistry tests that are processed within a short pre-centrifugation window and refrigerated can provide a vast, untapped resource for cfDNA biobanking and potential testing.}, }
@article {pmid41810379, year = {2026}, author = {Anzà, S and Rosa, BA and Herzberg, MP and Lee, G and Herzog, ED and Zhao, P and England, SK and Ndao, IM and Martin, J and Smyser, CD and Rogers, CE and Barch, DM and Hoyniak, C and McCarthy, R and Luby, J and Warner, BB and Mitreva, M}, title = {Simplifying Daily Cortisol Cycle Analysis: Validation and Benchmarking of the Cortisol Sine Score Against Cosinor and JTK_CYCLE models.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41810379}, abstract = {The daily cortisol cycle is a critical indicator of hypothalamic-pituitary-adrenal (HPA) axis function. The current analytical approaches produce several outputs difficult to integrate into simple statistical models, clinical workflows, and ML/AI pipelines requiring single-value inputs. We developed the Cortisol Sine Score (CSS), a model-free scalar metric that quantifies daily cortisol exposure by computing a weighted sum of cortisol measurements across the day, using sine-transformed time-of-day weights. The CSS produces positive values for morning-dominant patterns, negative values for evening-shifted profiles, and near-zero values for flattened rhythms characteristic of chronic stress and circadian disruption. We validated the CSS performance in 3,006 samples from 501 pregnant women enrolled in the March of Dimes program, with cortisol values measured at 6 time points per day collected during the second trimester of pregnancy. The CSS showed strong correlations with observed and model-estimated amplitude and acrophase from Cosinor regression and JTK_CYCLE approaches, with excellent classifying performance (AUC=0.89, high versus low). The CSS successfully captured established associations between social disadvantage and cortisol dysregulation, and demonstrated utility in predicting gut microbiome composition in metagenomic analyses. Importantly, the CSS maintains excellent fidelity to the full 6-sample protocol with as few as 3-4 daily measurements. The 4-sample protocol achieves great performance (r = 0.952, MAE = 0.087) while reducing participant burden. The 06:00 time point was identified as essential for accurate CSS quantification. The CSS bridges the gap between circadian analysis and practical implementation by providing a simple, interpretable, and robust assessment of cortisol daily cycle in large-scale epidemiological studies, clinical screening, and biomedical sensors.}, }
@article {pmid41810553, year = {2026}, author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ}, title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70264}, pmid = {41810553}, issn = {2045-8827}, support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovación/ ; }, mesh = {Humans ; *Glycoside Hydrolases/metabolism/genetics ; *Polysaccharides/metabolism ; Infant ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; Substrate Specificity ; Infant, Newborn ; }, abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.}, }
@article {pmid41811526, year = {2026}, author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S}, title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.}, journal = {Cancer causes & control : CCC}, volume = {37}, number = {4}, pages = {}, pmid = {41811526}, issn = {1573-7225}, support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Adult ; Metagenomics/methods ; Risk Factors ; Finland/epidemiology ; Metagenome ; Diet ; }, abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.
METHODS: Our data included 1,228 adults aged 25-64 years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.
RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p < 0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (β 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (< 0.0001).
CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.}, }
@article {pmid41811805, year = {2026}, author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L}, title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0344050}, pmid = {41811805}, issn = {1932-6203}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Adenoma/microbiology/metabolism/pathology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Case-Control Studies ; Aged ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.
OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.
MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.
RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K₂) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.
CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K₂ biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.}, }
@article {pmid41812751, year = {2026}, author = {Prabhakar, S and Rajeev, AC and Sankappa, NM and Harsha, R}, title = {High-throughput metagenomic profiling of functional and resistome features in estuarine microplastic microbiomes.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124159}, doi = {10.1016/j.envres.2026.124159}, pmid = {41812751}, issn = {1096-0953}, abstract = {Microplastics (MPs) are now recognized as persistent pollutants in aquatic ecosystems, providing unique surfaces for microbial colonization and acting as vectors for the spread of pathogens, antibiotic resistance, and virulence factors. Estuarine systems, due to their dynamic hydrology and proximity to anthropogenic activity, are particularly vulnerable to MP accumulation and associated microbial risks. This study presents the first comprehensive metagenomic investigation of MP-associated microbial communities across five estuaries spanning the northern and southern coastal regions of Karnataka, India. MPs were isolated, characterized, and the extracted total DNA from the MPs was subjected to high-throughput sequencing and comprehensive bioinformatic analyses. Taxonomic, functional, and resistance gene profiling were performed to evaluate microbial diversity, ecological roles, and potential public health implications. The findings revealed distinct regional differences in microbial community structure and functional potential, with evidence of clinically relevant pathogens, antibiotic resistance genes, and virulence determinants within the plastisphere. These results highlight the role of MPs as reservoirs and vectors for microbial risks in estuarine ecosystems. By linking microbial diversity of MPs with environmental and anthropogenic influences, this work provides crucial baseline data for monitoring and managing estuarine health. It also underscores the urgent need for integrated strategies to mitigate plastic pollution and its cascading ecological and public health impacts.}, }
@article {pmid41812803, year = {2026}, author = {Bao, Z and Ji, X and Liu, Q and Zhang, L}, title = {Light-driven N-doped carbon quantum dots facilitate microbial chain elongation: Bridging process enhancement to functional metagenomics.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134393}, doi = {10.1016/j.biortech.2026.134393}, pmid = {41812803}, issn = {1873-2976}, mesh = {*Quantum Dots/chemistry ; *Carbon/chemistry ; *Light ; *Nitrogen/chemistry ; *Metagenomics/methods ; Fatty Acids/biosynthesis/metabolism ; Oxidation-Reduction ; Caproates ; }, abstract = {Microbial chain elongation (CE) converts low-value substrates into medium-chain fatty acids (MCFAs), but its efficiency is often constrained by limited electron availability and incomplete elongation from C4 to C6 products. This study demonstrates that nitrogen-doped carbon quantum dots (NCQDs), under visible light irradiation, significantly improved CE performance and product selectivity. At 1.5 g/L NCQDs, caproate concentration increased to 3.76 g/L, representing a 276% improvement over the control, while butyrate accumulation decreased, indicating enhanced elongation toward longer-chain products. Electrochemical characterization showed that NCQDs exhibited visible light absorption, a 2.31 eV bandgap, measurable photocurrent responses, and reduced charge-transfer resistance, reflecting enhanced redox activity at the system level. Metagenomic analysis revealed increased relative abundance of Bacillus and enrichment of functional genes associated with reverse β-oxidation and fatty acid biosynthesis pathways. In addition, quorum sensing-related genes (LuxI, LuxR, RpfF) and Hnd hydrogenase-associated gene clusters were enriched, indicating enhanced functional potential for microbial coordination and redox-related metabolism. These coordinated shifts in electrochemical behavior, microbial community composition, and functional gene abundance were consistent with improved caproate production and metabolic selectivity. This work provides an effective hybrid photochemical-microbial strategy associated with enhanced MCFAs production and offers a promising approach for waste valorization into value-added biochemicals.}, }
@article {pmid41812817, year = {2026}, author = {Freitas, JF and Oliveira, TT and Agnez-Lima, LF}, title = {Longitudinal wastewater metagenomics reveals distinct environmental and anthropogenic associations with resistance, virulence, and viral communities.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {397}, number = {}, pages = {127943}, doi = {10.1016/j.envpol.2026.127943}, pmid = {41812817}, issn = {1873-6424}, abstract = {Urban wastewater systems are reservoirs of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs), increasingly recognized as emerging environmental pollutants. However, longitudinal evidence linking tourism-related human mobility to its dynamics remains limited in the Southern Hemisphere. We evaluated whether tourism seasonality, used as a proxy for transient population load, is associated with changes in the wastewater resistome, virulome, and virome in Natal (Northeast Brazil). Using year-long shotgun metagenomics (June 2021-May 2022) of 24 monthly pooled metagenomes (12 composites × 2 replicates) from three wastewater treatment plants, we observed differential enrichment patterns despite stable bacterial community composition dominated by Aliarcobacter. Redundancy analysis (RDA) demonstrated that the model for bacterial community explained 40.1% of the total variance (F = 1.79, p = 0.039), with tourism showing marginal effects. In contrast, precipitation was not significant (p = 0.262). RDA also revealed that precipitation was associated with ARG distribution (p = 0.027) and that VFG composition was associated with international tourism (p = 0.002). ARGs were more abundant during high-precipitation periods, whereas VFGs showed higher relative abundance during international tourism peaks. Metagenome-assembled genomes (n = 95) revealed 33 multidrug-resistant hosts, including understudied taxa such as Tolumonas and the family Aquaspirillaceae, harboring plasmids (e.g., IncFIB(K)). Co-occurrence networks showed that viruses were positively correlated with ARGs and negatively correlated with VFGs, except for crAssphage, which was associated with virulence traits. These findings reveal distinct environmental and human mobility factors underlying wastewater microbial dynamics. We underscore the importance of integrating longitudinal metagenomics into seasonally adjusted surveillance frameworks to mitigate antimicrobial resistance as an emerging form of environmental pollution.}, }
@article {pmid41813810, year = {2026}, author = {Top, FK and Gaye, A and Boussiengui, GL and Sall, Y and Sall, NC and Camara, D and Ba, M and Ndiaye, NKD and Seye, AO and Ndiaye, NK and Diallo, B and Sagne, SN and Mbanne, M and Diagne, MM and Faye, O and Fall, G and Sow, B and Loucoubar, C and Ndiaye, EHM and Diop, B and Sall, AA and Dia, N and Faye, O and Sow, A and Faye, M}, title = {The 2024 Mpox surveillance in Senegal uncovers a large circulation of Chickenpox.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44066-7}, pmid = {41813810}, issn = {2045-2322}, abstract = {During preparedness activities in Senegal to the 2024 Mpox Public Health Emergency of International Concern, a study was conducted to assess the prevalence of Varicella-Zoster virus among patients suspected of having Mpox. Samples, including skin swabs, serum, and nasopharyngeal swabs, were collected from 103 patients who presented with Mpox-like symptoms. Molecular testing via qPCR revealed that 30.1% of patients tested positive for herpesviruses, whereas no Mpox cases were detected. Common symptoms include fever, skin rash, headache, and myalgia, which closely resemble Mpox symptoms, increasing the risk of misdiagnosis. The most affected group was children under 15 years of age (50% of herpesvirus cases), followed by adults over 30 years of age (30.8%). The male/female sex ratio among herpesvirus-positive patients was 2.1, indicating a higher prevalence in males. Phylogenetic analysis of 14 newly characterized Varicella-Zoster virus genomes from metagenomic sequencing revealed that the strains circulating in Senegal were closely related to those from Guinea-Bissau, suggesting possible regional transmission. In addition, viral and bacterial coinfections were identified in Mpox-negative patients, which may have contributed to some skin lesions initially suspected to be Mpox. Our data highlight the importance of differential diagnostic testing to distinguish between Mpox and other infections, such as Chickenpox. The unexpectedly high prevalence of herpesviruses among suspected Mpox cases underscores the need for improved laboratory diagnostics, enhanced epidemiological surveillance, and targeted public health interventions to prevent misdiagnosis and improve patient management.}, }
@article {pmid41813906, year = {2026}, author = {Vass, M and Abramova, A and Bengtsson-Palme, J}, title = {Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41813906}, issn = {2399-3642}, support = {KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2024-05922//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Fresh Water/microbiology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Seawater/microbiology ; *Water Microbiology ; }, abstract = {Aquatic ecosystems are major reservoirs of antibiotic resistance genes (ARGs) and hubs for microbial interactions that can facilitate their spread through horizontal gene transfer (HGT). While mobile genetic elements (MGEs), including plasmids and viruses, are recognized as important drivers of ARG mobility, the extent to which water column stratification constrains their vertical dissemination remains unresolved. Here, we analysed depth-resolved metagenomic data from stratified freshwater and marine systems to assess the role of HGT in ARG spread. We found that ARG diversity is consistently lower in marine than freshwater environments and that only a small fraction of ARGs is mobilized by plasmids and viruses. Importantly, we detected no evidence for recent HGT-mediated dissemination of ARGs across depth layers, despite genetic compatibility among co-occurring bacteria. Instead, ARGs appear largely confined to lineage-specific inheritance and within-layer persistence. These findings suggest that stratification acts as a barrier, limiting vertical ARG transfer while promoting within-layer accumulation. Given projections of intensified and prolonged stratification under climate change, our results imply reduced vertical connectivity of ARGs in aquatic environments, with potential consequences of further mitigation in its dynamics by water stratification.}, }
@article {pmid41813975, year = {2026}, author = {Telles-de-Deus, J and Claro, IM and Bertanhe, M and Whittaker, C and Port-Carvalho, M and Rocha, EC and Coletti, TM and da Silva, CAM and Valença, IN and Lima-Camara, TN and Bicudo de Paula, M and Cunha, MS and de Jesus, JG and Dos Santos Andrade, P and Cox, V and de Azevedo, NCCF and Guerra, JM and Summa, JL and Teixeira, APP and Bergo, ES and Pereira, M and Moreira, FRR and Felix, AC and de Paula, AV and de Araujo Eliodoro, RH and da Silva Lima, M and de Oliveira, FM and de Souza, VR and Franco, LAM and Nardi, MS and Sanches, TC and da Silva, ETBC and Coimbra, AAC and Dos Santos, PR and Lima de Gouveia, K and Vilela, FESP and Hill, SC and Oliveira, DAG and Piedade, HM and Guimarães-Luiz, T and Abreu, CMG and Casoni da Rocha, G and Abade, L and de Souza, WM and Lambert, B and Pereira de Souza, R and Pinter, A and Sabino, EC and Mucci, LF and Faria, NR}, title = {Evolution and spillover dynamics of yellow fever at the forest-urban interface in Brazil.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41813975}, issn = {2058-5276}, support = {316633/Z/24/Z//Wellcome Trust (Wellcome)/ ; 226075/Z/22/Z//Wellcome Trust (Wellcome)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/X020258/1//RCUK | Medical Research Council (MRC)/ ; }, abstract = {Yellow fever virus (YFV) continues to threaten human and wildlife populations in the Americas, yet its transmission at the forest-urban interface remains unclear. Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018. Our analyses reveal that transmission was primarily driven by a single genetic cluster introduced during a period of high abundance of the main vector, Haemagogus leucocelaenus mosquitoes. A near-complete hepatitis A virus genome was detected in a YFV-infected howler monkey, suggesting potential co-infections at the human-wildlife interface. Phylogenetic and epidemiological modelling estimated a basic reproduction number, R0, for sylvatic yellow fever of 8.2 (95% CI 5.1-12.2), substantially higher than previous estimates for urban outbreaks. Our findings demonstrate that multisource surveillance could provide actionable early warnings in regions at risk for zoonotic spillover.}, }
@article {pmid41814006, year = {2026}, author = {Baldanzi, G and Larsson, A and Sayols-Baixeras, S and Dekkers, KF and Hammar, U and Nguyen, D and Graells, T and Ahmad, S and Gazolla Volpiano, C and Meric, G and Järhult, JD and Tängdén, T and Ludvigsson, JF and Lind, L and Sundström, J and Michaëlsson, K and Ärnlöv, J and Kennedy, B and Orho-Melander, M and Fall, T}, title = {Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41814006}, issn = {1546-170X}, support = {20230687//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2023-0380//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2025-02673//Vetenskapsrådet (Swedish Research Council)/ ; 2022-01460//Vetenskapsrådet (Swedish Research Council)/ ; 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784//Vetenskapsrådet (Swedish Research Council)/ ; Strategic Research Area Exodiab 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2020-00989//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; IRC-0067//Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; }, abstract = {Disruptions in gut microbiome are implicated in cardiometabolic disorders and other health outcomes. Antibiotics are known gut microbiome disruptors, but their long-term consequences remain underexplored. Here we combined individual-level data from the Swedish Prescribed Drug Register with fecal metagenomes of 14,979 adults to examine the association between oral antibiotic use over 8 years and gut microbiome. In multivariable confounder-adjusted regression models, antibiotic use <1 year before fecal sampling was associated with the greatest reduction in species diversity, but significant associations were also observed for use 1-4 and 4-8 years earlier. Clindamycin, fluoroquinolones and flucloxacillin accounted for most of the associations with the abundance of individual species. Use of these antibiotics 4-8 years earlier was associated with altered abundance of 10-15% of the species studied; penicillin V, extended-spectrum penicillins and nitrofurantoin were associated with only a few species. Similar results were found comparing one antibiotic course 4-8 years before sampling versus none in the past 8 years. These findings indicate that antibiotics may have long-lasting consequences for the gut microbiome.}, }
@article {pmid41814161, year = {2026}, author = {Platova, SE and Poliushkevich, LO and Starunova, ZI and Starunov, VV and Novikova, EL}, title = {Transcriptomic analysis of three annelid species: looking for markers of positional information.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12671-5}, pmid = {41814161}, issn = {1471-2164}, support = {21-14-00304//Russian Science Foundation/ ; }, }
@article {pmid41814421, year = {2026}, author = {Lee, CZ and Worsley, SF and Davies, CS and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS}, title = {Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41814421}, issn = {2049-2618}, mesh = {*Gastrointestinal Microbiome/genetics/immunology ; Animals ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Songbirds/microbiology/immunology/genetics ; *Major Histocompatibility Complex/genetics ; Animals, Wild/microbiology/immunology ; Immunogenetics ; }, abstract = {BACKGROUND: The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.
RESULTS: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts.
CONCLUSION: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve. Video Abstract.}, }
@article {pmid41814441, year = {2026}, author = {Stead, CE and Walker, L and Greco, C and Galloway, T and R Cousins, C and Nagel, F and Breitling, R and Takano, E and Björnsdóttir, SH and Nixon, SL}, title = {Exploring the biotechnological potential of terrestrial hot spring microbiomes for CO2 utilisation.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00875-x}, pmid = {41814441}, issn = {2524-6372}, support = {ST/W002337/1//UK Space Agency/ ; BB/V00560X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RGS\R2\222350//Royal Society/ ; }, abstract = {BACKGROUND: Terrestrial hot springs are extreme environments shaped by geothermal heat, geogenic gases and extremes of pH and temperatures. Their gas fluxes, which include CO2, CO, H2S and SO2, mirror the chemical composition of CO2-rich waste streams. Microbial communities inhabiting these environments are typically thermotolerant or thermophilic and sustained by CO2 fixation and chemolithotrophic metabolism. Such communities may therefore provide a natural starting point for developing ex-situ, consortium-based biotechnologies capable of operating under elevated temperatures and chemically harsh conditions. Here, we assess the metabolic capabilities of hot spring microbiomes systematically through a biotechnological lens.
RESULTS: We conducted comparative analysis of 73 worldwide hot spring metagenomes, spanning a wide range of environmental conditions (pH 1.5-10.0, temperatures 25-98 °C). By taking a gene-centric approach to whole communities, we show that hot spring microbiomes ubiquitously encoded carbon fixation pathways and biosynthetic genes (and gene clusters) for the synthesis of value-added products, regardless of geographical location and pH-temperature conditions. Candidate value-added products include platform chemicals such as acetone, lactic acid, and 1,2-propanediol, as well as high-value biomolecules including B vitamins and alginate.
CONCLUSIONS: This first biotechnology-focused assessment of hot spring microbiomes demonstrates that these communities encode the genomic potential to support novel, ex situ microbial platforms for upgrading CO2 and transforming chemically complex gas mixtures.
SIGNIFICANCE: Industrial CO2 waste streams pose both an environmental challenge and an unutilised resource. Harnessing microbial consortia to valorise CO2, through a circular bioeconomy, remains underexplored and could offer an alternative to energy-intensive chemical methods. By reanalysing predominantly publicly available metagenomic data, we demonstrate how hot spring microbiomes can be mined for traits pre-adapted to CO2-rich, high-temperature, and chemically extreme conditions. In doing so, we provide proof-of-concept for their future biotechnological application and establish a blueprint for other microbiome-scale bioprospecting surveys.}, }
@article {pmid41814651, year = {2026}, author = {Tao, D and Xu, B and Li, S and Liu, H and Wei, Y and Cao, X and Shi, S and Wang, Y and Jiang, R and Zhang, Y and Zhao, C and Ruan, J and Fu, L and Huang, X and Li, X and Zhao, S and Xie, S}, title = {Structural mining and engineering of metagenome-derived Cas12a orthologs expands the CRISPR genome editing and multiplex diagnostics toolkit.}, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ymthe.2026.03.011}, pmid = {41814651}, issn = {1525-0024}, abstract = {CRISPR-Cas12a is a compact, RNA-guided nuclease widely deployed in genome editing and molecular diagnostics, yet its broader utility is limited by suboptimal cis-cleavage efficiency and incompletely defined trans-cleavage behavior. To overcome these constraints, we developed an artificial intelligence-guided structural discovery pipeline powered by AlphaFold2, which identified 1,261 previously uncharacterized Cas12a orthologs. From this set, 21 structurally conserved but sequence-divergent candidates were selected for biochemical characterization. Using structure-informed engineering, we generated PcuCas12a MAX, a high-fidelity variant that achieves genome-editing efficiencies in human cells comparable to the benchmark AsCas12a Ultra while retaining robust activity in murine and porcine systems. In addition, four orthologs (LcoCas12a, FcaCas12a, EsoCas12a, and Mac2Cas12a), when paired with specifically engineered CRISPR RNAs, exhibited distinct single-stranded DNA trans-cleavage signatures. These properties enabled construction of a multiplex CRISPR sensor capable of simultaneously detecting multiple nucleic acid targets. Together, these findings expand the Cas12a endonuclease repertoire and enhance its utility in genome engineering and next-generation diagnostics.}, }
@article {pmid41814700, year = {2025}, author = {Wu, D and Niu, JJ and Hu, JP and Wang, H and Kuang, HX}, title = {[Mechanism study on anti-hyperuricemic effects of Zhejiang Plantaginis Semen glycosides based on metabolomics and metagenomics].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {50}, number = {24}, pages = {6919-6927}, doi = {10.19540/j.cnki.cjcmm.20250725.705}, pmid = {41814700}, issn = {1001-5302}, mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism/microbiology/genetics ; Rats, Sprague-Dawley ; Rats ; Male ; Metagenomics ; Metabolomics ; *Drugs, Chinese Herbal/administration & dosage ; *Glycosides/administration & dosage ; Uric Acid/blood/metabolism ; Humans ; Kidney/drug effects/metabolism ; Liver/drug effects/metabolism ; }, abstract = {A rat model of hyperuricemia was established using potassium oxonate, hypoxanthine, and adenine. The anti-hyperuricemic mechanisms of Zhejiang Plantaginis Semen glycosides(ZPG) were subsequently explored utilizing metabolomics and metagenomics approaches. Forty SD rats were randomly divided into five groups: control, model, benzbromarone(20 mg·kg~(-1)), low-dose ZPG(100 mg·kg~(-1)), and high-dose ZPG(400 mg·kg~(-1)), with 8 rats in each group. Hyperuricemia was induced by continuous intragastric administration of potassium oxonate(200 mg·kg~(-1)), hypoxanthine(500 mg·kg~(-1)), and adenine(50 mg·kg~(-1)) for 21 days, while drug treatment was administered simultaneously. Serum and liver tissues were collected to measure the levels of uric acid(UA), creatinine(Cr), blood urea nitrogen(BUN), and xanthine oxidase(XOD). Renal tissues were subjected to histopathological examination. Additionally, untargeted metabolomics analysis was performed on serum samples, and fecal metagenomics sequencing was conducted to analyze the composition of the gut microbiota. The results showed that ZPG effectively reduced the levels of serum UA, Cr, and BUN in hyperuricemic rats, inhibited XOD activity in both serum and liver, alleviated renal pathological damage, and mitigated inflammatory responses. Metabolomics analysis identified 16 differential metabolites, mainly involved in lipid metabolism, purine metabolism, and amino acid metabolism pathways. The results of fecal metagenomics analysis revealed that ZPG restored the Firmicutes-to-Bacteroidetes ratio and increased the relative abundance of probiotics such as Lactobacillus＿johnsonii, Limosilactobacillus＿reuteri, and Ligilactobacillus＿murinus. In summary, ZPG effectively reduces serum UA levels, improves renal injury, and attenuates inflammatory symptoms in hyperuricemic rats. These effects may be attributed to its inhibition of XOD activity, correction of inflammatory lipid metabolism abnormalities, regulation of disordered purine metabolism, and modulation of gut microbiota structure.}, }
@article {pmid41815497, year = {2026}, author = {Pan, J and Jiang, H and Luo, S and Zhang, L and Wu, G and Li, W and Cai, S and Mei, Y and Chen, X and Chen, B and Zhang, W and Tong, P and Xie, J}, title = {Identification of a novel Ungulate copiparvovirus 10 in sheep of Hami, East Xinjiang, China.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1678726}, pmid = {41815497}, issn = {2297-1769}, abstract = {Parvovirinae viruses are a subfamily of the Parvoviridae family that can infect various vertebrate hosts and cause infections ranging from asymptomatic to severe disease. This study performed a metagenomic assessment of the sheep sera virome to evaluate emerging and exotic viruses in border zones, and identified a novel copiparvovirus. The DNA of Ovine copiparvovirus (OVPV) was only observed in the serum of sheep in Dahe Town of Hami City. Furthermore, the region-dependent prevalence was 10.4% (96/807) from 2022 to 2024. The OVPV genome was 5,219 nucleotides (nt) long and shared 99.3% nt identity with two bovine parvovirus 2 SXO335parvoV2 and SXO338parvoV (GenBank accession numbers: MZ244302 and MZ244302), reported in the ticks collected from China. Comparison of NS1 protein showed that two OVPVs obtained in this study had 99.8%-99.9% amino acid homology with the tick-derived bovine parvoviruses, which had not been classified within the genus Copiparvovirus and then provisionally designated "Ungulate copiparvovirus 10," because they are far distant from other 10 species in Copiparvovirus genus with 48.5%-72.8% homology identified. Phylogenetic analysis further confirmed the classification of the OVPVs as a new species in the genus Copiparvovirus.}, }
@article {pmid41816570, year = {2026}, author = {Zou, T and Zheng, J and Xie, Z and Hu, Y and Yang, X and Xue, X and Lu, L and Chen, X and Mao, S and Niu, M}, title = {Colon cancer cachexia remodels gut microbiota and metabolite profiles in a murine model.}, journal = {Journal of gastrointestinal oncology}, volume = {17}, number = {1}, pages = {13}, pmid = {41816570}, issn = {2078-6891}, abstract = {BACKGROUND: Cancer cachexia is a multifactorial syndrome involving involuntary weight loss, muscle atrophy, and systemic inflammation, contributing significantly to mortality in advanced cancers. Although gut microbiota dysbiosis has been implicated in metabolic and inflammatory disturbances relevant to cachexia, the functional metabolic consequences remain poorly understood. Using a murine model of colon carcinoma 26 (C26)-induced cachexia, we integrated metagenomic sequencing and non-targeted metabolomics to delineate cachexia-specific microbial and metabolic alterations compared to non-cachexia tumor-bearing and healthy controls.
METHODS: To investigate colon cancer cachexia-induced remodeling of the gut ecosystem, we established mouse models using cachexia-inducing and non-cachexia-inducing colon carcinoma 26 cells. Food intake, body weight, muscle and fat weight were monitored. Cecal content was collected for metagenomic sequencing and non-targeted metabolome analysis.
RESULTS: Colon cancer cachexia models were successfully established as evidenced by reduced food intake, decreased body weight, and loss of muscle and fat mass. Metagenomic sequencing revealed decreased microbial diversity and distinct structural separation in colon cancer cachexia mice, with enriched genera including Bacteroides, Phocaeicola, Escherichia, Enterobacter, Helicobacter, and Proteus, and depletion of butyrate- and bile acid-producing taxa including Alistipes, Eubacterium, Roseburia, Clostridium, and Hungatella. Functional analysis indicated significant alterations in metabolic pathways. Metabolomic profiling identified reduced levels of ursodeoxycholic acid (UDCA), hyodeoxycholic acid (HDCA), branched-chain amino acids, and bacterial amino acid metabolites (bAAms), alongside enrichment in nucleotide and steroid hormone metabolism. Correlation analyses demonstrated significant associations between specific microbial genera and altered metabolites.
CONCLUSIONS: Colon cancer cachexia remodeled the gut microbiota and metabolite landscape in a murine model. These findings suggested specific bacterial taxa and metabolites as potential biomarkers and therapeutic targets, offering new directions for the prevention and treatment of cancer cachexia. This study reveals distinct taxonomic and functional shifts in the gut microbiota alongside associated metabolic disruptions, offering new insights into cachexia pathophysiology and potential therapeutic targets.}, }
@article {pmid41816693, year = {2026}, author = {Xiao, X and Niu, Q and Zhou, K and Ma, L and Zhao, Z and Zhang, J and Chu, X and Shan, G}, title = {The invasion of Euphorbia jolkinii is mediated through the regulation of nitrogen transformation by functional microbial abundance in rhizosphere soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1757844}, pmid = {41816693}, issn = {1664-302X}, abstract = {INTRODUCTION: Euphorbia jolkinii Boiss. is a native invasive weed. Its invasion altered microbial composition, total nitrogen (TN) and available nitrogen (AN). However, the mechanisms influencing N transformation remain unclear. Particularly, the roles of the microbiome and genes in mediating N transformations to facilitate E. jolkinii invasion remain poorly understood. Therefore, the primary objectives of this study were to evaluate how E. jolkinii invasion affects N transformation, microbial interactions, and key genes associated with AN accumulation.
METHODS: We compared three patches (non-invaded, lightly, and heavily invaded patches of E. jolkinii) by analyzing rhizosphere soils of E. jolkinii and Poa crymophila Keng. Integrating soil physicochemical indices with metagenomic sequencing, we investigated the relationships among microbial communities, gene abundance, and N transformation.
RESULTS: With E. jolkinii increasing invasion intensity, N accumulation and transformation rates were significantly reduced in the rhizosphere of P. crymophila but enhanced in that of E. jolkinii, particularly for AN. Metagenomic analysis revealed that the invasion and expansion of E. jolkinii promoted functional adaptation of the microbial community, particularly by enriching the N cycling-related genes and increasing their relative abundance in the rhizosphere soil of E. jolkinii. Moreover, it inhibited the accumulation of N transformation functional genes in the rhizosphere soil of the companion plant, P. crymophila. Structural equation modeling identified Nitrospirota, Edaphobacter, Anaeromyxobacter, and soil N transformation rates as key drivers of AN accumulation.
DISCUSSION: E. jolkinii facilitated N accumulation in its rhizosphere by modulating N-transforming microbes and key functional genes, underscoring one of its invasive advantages.}, }
@article {pmid41816706, year = {2026}, author = {Tu, Y and Chen, Z and Jing, M and Tan, W and Huang, D and Xu, J and Wang, M and Li, H and Yang, Y and Liu, X and Hu, X and Pan, Y and Niu, C and Huang, Z}, title = {Supragingival Actinomyces naeslundii aggravates metabolic dysfunction-associated fatty liver disease via the oral-gut axis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2639208}, pmid = {41816706}, issn = {2000-2297}, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is the most prevalent chronic liver disease but lacks effective therapies. Oral microbial dysbiosis is closely associated with metabolic dysfunction.
OBJECTIVE: This study aimed to delineate MAFLD-specific oral microbiota signatures and identify diagnostic biomarkers.
DESIGN: Supragingival plaque samples from 21 patients with MAFLD and 20 healthy individuals were subjected to metagenomic sequencing. Potential oral biomarkers were identified bioinformatically and further validated using a MAFLD mouse model.
RESULTS: Patients with MAFLD exhibited significantly reduced supragingival microbial diversity, altered composition, and enhanced consortial interactions compared to healthy individuals. Seven resident oral species were identified as candidate biomarkers. Among these, Actinomyces naeslundii was notably enriched in the oral cavity of patients with MAFLD and strongly correlated with clinical indices. In vivo experiments further demonstrated that the oral administration of A. naeslundii significantly aggravated MAFLD phenotypes and induced gut dysbiosis in mice fed a high-fat diet.
CONCLUSION: This study reveals a potential link between the oral microbiota and MAFLD. Specifically, the excessive enrichment of the oral resident bacterium A. naeslundii is associated with the MAFLD progression in mice.}, }
@article {pmid41816992, year = {2026}, author = {Rao, B and Jiang, J and Zhang, R and Zhang, D and Zhang, C and Li, A and Lu, H and Zhang, H and Zhou, L and Guo, W and Wen, P and Xue, J and Pan, J and Aji, T and Lan, Z and Jiang, X and Zheng, S and Yu, Z and Ren, Z}, title = {Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17658}, doi = {10.1002/advs.202517658}, pmid = {41816992}, issn = {2198-3844}, support = {82470654//National Natural Science Foundation of China/ ; 232300421124//Natural Science Foundation Key Project of Henan Province/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; ZYYC202301ZD//Henan Zhongyuan Medical Science and Technology Innovation and Development Foundation/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, abstract = {Growing evidence suggests a role for the gut microbiome in progression of cholangiocarcinoma (CCA), however, its diagnostic and therapeutic potential remains incompletely characterized. Here, metagenomic sequencing was performed on fecal samples (n = 785) from individuals across East, Central, and Northwestern China. Gut microbial dysbiosis in CCA was characterized by depletion of short-chain fatty acids-producing species and enrichment of potential pathobionts (Klebsiella aerogenes, Clostridium symbiosum). Diagnostic models built using species-level markers demonstrated superior performance, compared to pathway-based models, achieving area under the curve (AUC) values of 98.63% and 99.42% in the discovery cohort, with robust cross-regional validation (AUC = 80.89% and 80.43%). The model effectively distinguished CCA from hepatocellular carcinoma (AUC = 97.86%) and liver fibrosis (AUC = 98.73%) and nonalcoholic fatty liver disease (mean AUC = 96.86%). Analysis of public datasets encompassing 6847 samples across 31 studies and 11 disease states revealed moderate disease specificity influenced by biomarker overlap across conditions. Mechanistically, depleted Bifidobacterium pseudocatenulatum suppressed CCA progression, associated with inhibition of the PI3K-AKT-mTOR pathway. Collectively, this study supports the potential of fecal metagenomic signatures as a complementary noninvasive aid for CCA detection, and provides functional evidence for a candidate protective microbe.}, }
@article {pmid41816995, year = {2026}, author = {Zhao, F and Zhang, R and Wei, R and Fan, H and Hu, Y and Shi, W and Wang, J}, title = {Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e16916}, doi = {10.1002/advs.202516916}, pmid = {41816995}, issn = {2198-3844}, support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; 32370053//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; }, abstract = {Phages dominate the human gut virome and are known for their ability to prey on bacteria and shape microbiota. However, their response to diet has only been elucidated using small-scale studies. By integrating a massive meta-analysis of 6932 diet-associated metagenomes with a time-resolved mouse model of a high-fat diet and polysaccharide intake, the impact of diet on the gut virome and phage-bacterial interactions was systematically characterized. Diet types, particularly high-fat and polysaccharide-rich diets, exert the strongest shaping force on the gut virome, enhancing the crosstalk between phages and bacteria. High-fat diets promote changes in phage abundance across a broad taxonomic range, from 34.21% to 50.00%, drive phages of diet-associated bacteria toward a lytic lifestyle, and remarkably enrich auxiliary metabolic genes related to amino acid metabolism. Conversely, fucoidan reversed HFD-induced dysbiosis and enhanced phage-mediated horizontal gene transfer by 8.5-fold relative to the baseline. crAssphages and Parabacteroides phages may be important contributors, broadly supporting horizontal gene transfer and auxiliary metabolism or strengthening phage-host interactions in polysaccharide interventions, including fucoidan supplementation. These findings provide a comprehensive landscape of diet-driven cross-kingdom interactions and phage-mediated gene exchange in the gut, offering new insights into potential strategies for precise nutritional interventions targeting the intestinal microbiota.}, }
@article {pmid41817311, year = {2026}, author = {Zhang, Q and Hu, L and Rono, JK and Li, B and Wang, S and Lyu, Y and Feng, Z}, title = {Discovery of a Novel Cellulase ZF580 From Mount Everest Metagenome Featuring a Catalytically Active DUF5916 Domain.}, journal = {Biotechnology journal}, volume = {21}, number = {3}, pages = {e70210}, doi = {10.1002/biot.70210}, pmid = {41817311}, issn = {1860-7314}, support = {32370089//National Natural Science Foundation of China/ ; MMLKF21-07//State Key Laboratory of Microbial Metabolism/ ; ALAQ202401011//Anhui Vocational College of Grain Engineering/ ; }, mesh = {*Metagenome/genetics ; *Cellulase/genetics/metabolism/chemistry ; Catalytic Domain ; Cellulose/metabolism ; Substrate Specificity ; Phylogeny ; Mutagenesis, Site-Directed ; Models, Molecular ; Hydrolysis ; Carboxymethylcellulose Sodium/metabolism ; }, abstract = {Cellulases are crucial biocatalysts with extensive industrial applications, yet their study has been constrained by cultivation limitations of native microorganisms. Here, we report the discovery and characterization of a novel multifunctional cellulase (ZF580) from the extreme environment of Mount Everest using metagenomic approaches. Functional screening revealed ZF580's unique capacity to hydrolyze diverse substrates, including 4-nitrophenyl-β-D-glucopyranoside (pNPG), chitin, microcrystalline cellulose, and carboxymethyl cellulose sodium (CMC-Na). Phylogenetically, ZF580 forms an independent clade distinct from characterized β-glucosidases and known glycoside hydrolase (GH) families, suggesting its classification as a progenitor of a novel GH lineage. Structural modeling revealed a distinctive (β/α)8 TIM-barrel fold, diverging from canonical GH family architectures. Crucially, truncation analysis and site-directed mutagenesis identified the previously uncharacterized Domain of Unknown Function 5916 (DUF5916) as a catalytic functional region, with residue E373 serving as its essential proton donor. This study provides the first experimental evidence of DUF5916's enzymatic activity, redefining it as a novel catalytic domain. Overall, these findings suggest that ZF580 is a cellulolytic enzyme with β-glucosidase activity and that DUF5916 forms its catalytic core, offering insights that may be valuable for future studies on enzyme function and engineering.}, }
@article {pmid41817429, year = {2026}, author = {Zhang, L and Yang, K and Zhang, X}, title = {Draft metagenome-assembled genome sequence of a Dehalogenimonas species from an enriched consortium for complete trichloroethylene reductive dechlorination.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0131625}, doi = {10.1128/mra.01316-25}, pmid = {41817429}, issn = {2576-098X}, abstract = {A draft metagenome-assembled genome was recovered from an anaerobic consortium capable of complete reductive dechlorination of trichloroethene to ethene. The draft genome, assigned to a Dehalogenimonas species, is 1.84 Mb in size with a G + C content of 54.53% and encodes 33 reductive dehalogenase homologs.}, }
@article {pmid41817433, year = {2026}, author = {Mounchili-Njifon, A and Heang, V and Pum, L and E Messanga, LL and Moumbeket-Yifomnjou, MH and Modiyinji, AF and Tsafack, DTT and Nzi Mbouo-Njoya, L and Lissock, SF and Mbouyap, PR and Assam Assam, JP and Karlsson, EA and Nouhin, J and Njouom, R}, title = {Characterization of near-complete human Pegivirus 2 (HPgV-2) genomes in individuals co-infected with hepatitis C virus (HCV) in Cameroon.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0006926}, doi = {10.1128/mra.00069-26}, pmid = {41817433}, issn = {2576-098X}, abstract = {Human pegivirus (HPgV) genomes were detected in HCV-infected plasma via nanopore metagenomics. Six nearly complete HPgV-2 genomes were identified. Phylogenetic analysis confirmed HPgV-2 genotype. This study reveals co-infection dynamics, highlights viral diversity, and supports improved diagnostics.}, }
@article {pmid41818685, year = {2026}, author = {Qu, Q and Jia, Y and Wang, S and Hu, K and Liu, C and Hu, X and Mu, L}, title = {Responses of Microbial Communities in River to Atmospheric Deposition.}, journal = {Environmental science & technology}, volume = {60}, number = {11}, pages = {8583-8592}, doi = {10.1021/acs.est.6c01648}, pmid = {41818685}, issn = {1520-5851}, mesh = {*Rivers/microbiology ; Atmosphere ; Bacteria ; Fungi ; Nitrogen ; China ; Microbiota ; Air Pollutants ; }, abstract = {Atmospheric deposition threatens aquatic ecosystems, yet its effects on the microbial diversity, composition, and function in rivers remain unclear. Here, we examined the responses of microbial communities to atmospheric pollutants across 105 Chinese rivers. We found that PM2.5 and PM10 were associated with reduced bacterial and fungal diversity and richness. Structural equation modeling revealed that atmospheric deposition (e.g., PM2.5, SO2, NO2, and organic matter aerosol) was directly and indirectly associated with bacterial and fungal community composition through cascading pathways mediated by dissolved oxygen, pH, Mn, inorganic nitrogen, nitrate nitrogen, ammonium nitrogen, and chlorophyll-a. Compared with fungal communities, bacterial communities exhibited broader environmental thresholds and greater sensitivity to atmospheric pollutants. Ecological network analysis further revealed that deposition preferentially disrupted mutualistic motifs in bacterial networks but intensified competitive interactions in fungal networks. Metagenomic analysis revealed that atmospheric pollution is significantly associated with key microbial functional genes involved in carbon degradation (e.g., glucoamylase, pullulanase, and β-glucosidase), nitrogen assimilation and reduction (e.g., nifD, narB, and nirS), and sulfur reduction (e.g., sat, aprA, and dsrA) in rivers. Our findings underscore the importance of air quality mitigation in terms of protecting river ecosystem health.}, }
@article {pmid41818964, year = {2026}, author = {Sun, B and Kuang, P and Cui, Y and Yang, Y and Zheng, C}, title = {Simultaneous nitrification and denitrification microbial fuel cells (SND-MFC) for nitrogen removal and bioelectricity recovery: a review of performances, mechanisms, microorganisms, and applications.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129278}, doi = {10.1016/j.jenvman.2026.129278}, pmid = {41818964}, issn = {1095-8630}, abstract = {Complex nitrogen pollution in wastewater and the rising energy consumption are calling for the development of coupled advanced technologies to simultaneously remove pollutants and recover energy. Simultaneous nitrification and denitrification microbial fuel cells (SND-MFCs) enable efficient removal of nitrogen and recovery of energy. This review systematically discusses the latest developments of SND-MFC system under different system designs, including reactor configurations, electrode materials, and critical operating parameters that govern the efficiency of the removal of nitrogen and the generation of power. Meanwhile, mechanisms are firstly analyzed from the points of reacting substances, functional zoning and distribution of electrons. This review also describes microbial synergy among nitrifiers, denitrifiers and electroactive taxa from the points of biofilm's stratification, microbial community, strain screening with metagenomic detection and electron-transfer pathways. Furthermore, characteristics of real wastewater of SND-MFC in coking, pharmaceutical, and livestock wastewater are also summarized, exhibiting comprehensive elimination of nitrogen and recovery of bioelectricity under carbon- and aeration-free conditions. Subsequent research should further optimize the performance of the system by developing intelligent strategies based upon machine learning (ML) and digital twin technologies, electrobiological communication circuits, combination of strain screening and gene editing to unlock the full-scale potential of SND-MFC technology. In addition, the transition from laboratory-scale to practical applications also faces multiple technical challenges that require attention.}, }
@article {pmid41819166, year = {2026}, author = {Zhao, X and Zhang, J and Li, Y and Wang, Q and Li, J and Xia, Y and Zha, M and Chen, Y}, title = {Elucidating the microbiota-metabolite interplay in Hurood and Chula: An integrated multiomics investigation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28134}, pmid = {41819166}, issn = {1525-3198}, abstract = {Hurood and Chula, traditional fermented dairy products from Xilingol, China, show flavor and quality differences due to variations in production processes. Therefore, how heating and kneading affect their microbial, nonvolatile metabolite, and volatile organic compound (VOC) composition warrants exploration. In this study, shotgun metagenomic sequencing revealed the differential micro-organisms between Hurood and Chula. Ultra-performance liquid chromatography-tandem MS identified 47 differential metabolites. Among these, organic acids and their derivatives, benzene and substituted derivatives, free fatty acids (FFA), and lysophosphatidylcholines showed the highest content in Chula, whereas lactose, melibiose, and histamine were significantly enriched in Hurood, suggesting that the heating and kneading process affected galactose and histidine metabolic pathways. In contrast, headspace solid-phase microextraction GC-MS identified 4 differential VOC with elevated levels in Hurood. These compounds functioned as key aroma contributors, imparting richer and more complex aroma characteristics that included creamy, oily, fatty, caramel, coconut, woody, spice, and maple notes. Correlation analysis indicated that the differential micro-organisms were involved in metabolite dynamics and VOC accumulation and further revealed that they drove the directed accumulation of VOC through regulating FFA release and transformation and by regulating the Maillard reaction of small peptides, thereby underpinning their distinct flavor profiles. This study provides important insights into the heating- and kneading-induced formation of flavor and quality in traditional fermented dairy products from Xilingol, China, thereby facilitating the precise control of traditional processes and subsequent product quality improvement.}, }
@article {pmid41819185, year = {2026}, author = {Yoshida, S and Matsumoto, Y and Kajihara, A and Funato, M and Tsuyuguchi, K and Mitarai, S and Takemoto, K and Nakamura, S}, title = {Fomite transmission of Mycobacterium abscessus between severely disabled patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.02.029}, pmid = {41819185}, issn = {1469-0691}, abstract = {OBJECTIVES: We aimed to investigate a nosocomial outbreak of Mycobacterium abscessus subspecies massiliense (MAM) and to track its transmission route via genomic analyses and environmental surveys at a hospital in Osaka, Japan. The outbreak was initially detected in two patients (M1 and M2) with severe disability in 2020 and then expanded to five other patients (M3‒M7).
METHODS: The 34-month observation period was divided into three phases separated by two interventions. Mycobacterial culture screening was performed for 294 clinical and environmental samples. We confirmed that five patients (M1‒M5) had infections in phase 1 (March 2020 to July 2021) and implemented an initial intervention. In phase 2 (November 2021 to May 2022), new patients (M6 and M7) were identified, wherein an environmental survey identified MAM strains, prompting a second intervention. No patients were identified in phase 3 (September to December 2022). However, MAM was isolated from the environment during follow-up surveys. A total of 52 MAM isolates were analysed, including 11 clinical isolates (one from M1 and M2 in each phase and one each from M3-M7) and 41 environmental isolates obtained from care gloves, medical devices, and room equipment surrounding patients. We sequenced the isolate genomes and identified 15 subclone clusters with a threshold of 24.5 single-nucleotide variants (SNVs).
RESULTS: The overall SNV distribution of the clinical and environmental strains was within 61 SNVs, showing near-identical genomes. Clinical strains from patient M2 with persistent positivity were classified as the same subclone, with 0-6 SNVs. The isolate from a wagon brought into patient rooms showed the lowest number of SNVs (3-8) compared with isolates from M2. This subclone cluster, involving M2 and wagon isolates, formed the hub of the intercluster connection of 11 clusters comprising other clinical and environmental strains.
CONCLUSIONS: M. abscessus could persist in dry environments and might be indirectly transmitted via fomites.}, }
@article {pmid41819201, year = {2026}, author = {Jiang, J and Wei, J and Zhang, B and Chen, Y and Wang, J and Zhang, Y and Hu, J and Dai, Q}, title = {Integrating metabolomics and metagenomics reveals potential mechanism of rice root exudates in inhibiting nitrification in coastal saline soils.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124265}, doi = {10.1016/j.envres.2026.124265}, pmid = {41819201}, issn = {1096-0953}, abstract = {Rice root exudates are known to suppress nitrification and mitigate nitrogen losses in agricultural soils; however, their specific roles in coastal saline soils remain poorly understood. Here, root exudates were collected at 6 and 10 weeks after transplanting from two genotypes (Oryza sativa L. 'Nanjing 9108' and 'Yangjing 5118') using a hydroponic system, and their effects on nitrification in coastal saline soils were investigated through microcosm experiments integrating metabolomic and metagenomic analyses. Root exudates inhibited net nitrification rate (NNR) and potential nitrification activity (PNA), with the inhibitory effect primarily dependent on genotype. The abundance of nitrification genes was not significantly altered by root exudates and was negatively correlated with PNA, suggesting that root exudates mainly inhibited heterotrophic rather than autotrophic nitrification. Root exudates at 10 weeks after transplanting significantly increased the abundance of nitrate reduction genes. Integrated analyses revealed that differential metabolites dominated by terpenoids and lipids, as well as several exudates (e.g., L-isoleucine, L-valine, and pyridoxine) that generated reducing electrons during metabolism, particularly in treatments with root exudates from Nanjing 9108, showed a negative correlation with PNA and positively correlated with the abundance of nitrate reduction genes. Furthermore, the mechanisms of NNR inhibition varied with genotype. Specifically, root exudates from Nanjing 9108 inhibit NNR synergistically by reducing heterotrophic nitrification and promoting nitrate reduction, whereas those from Yangjing 5118 inhibit NNR mainly by reducing heterotrophic nitrification. Overall, root exudates primarily enhance nitrate reduction and/or reduce PNA by creating microhabitats and generating reducing agents, which inhibit nitrate accumulation in coastal saline soils. These findings provide a scientific basis for the formulation of nitrogen management measures in coastal saline paddy fields.}, }
@article {pmid41819204, year = {2026}, author = {Qi, Y and Zheng, X and He, X and Huang, K and Wang, D and Zhang, XX}, title = {Linkages between core microbiome and functional convergence during artificially selecting microbial communities for benzotriazole degradation.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124241}, doi = {10.1016/j.envres.2026.124241}, pmid = {41819204}, issn = {1096-0953}, abstract = {The escalating prevalence of benzotriazole (BTR), an emerging refractory organic pollutant, has drawn significant attention for the development of efficient bioremediation solutions. Although the construction of microbial consortia represents a promising strategy, the intrinsic relationship between community succession and functional features during artificial selection remains poorly understood. To address this, this study engineered two distinct microbial consortia from activated sludge using a top-down selection strategy in sequencing batch reactors fed with increasing BTR concentrations. While the two consortia evolved along divergent taxonomic pathways, they exhibited remarkable functional convergence, maintaining consistently high BTR transformation (>96%) and chemical oxygen demand (>75%) removal efficiencies. This robust performance under the stringent condition of BTR as the sole carbon source highlighted their significant adaptive potential. Metagenomic analysis further attributed this functional stability to the principle of functional redundancy, wherein taxonomically distinct keystone species (e.g., Nocardioides and Methylobacterium) harbored functionally analogous gene clusters. Additionally, multiple congeneric species (e.g., MAG.480 and MAG.17) within the Bacteroidota phylum exhibited significant divergence in their degradation gene repertoires. These findings not only advance ecological understanding of microbiome-mediated BTR biodegradation but also provide a foundation for the rational design and optimization of high-performance bioremediation consortia.}, }
@article {pmid41819291, year = {2026}, author = {Kalimuthu, S and Muthusamy, A}, title = {MobiRes: An integrative pipeline for resistome risk prediction through mobilome profiling.}, journal = {Journal of microbiological methods}, volume = {244}, number = {}, pages = {107448}, doi = {10.1016/j.mimet.2026.107448}, pmid = {41819291}, issn = {1872-8359}, abstract = {Antimicrobial resistance (AMR) poses a significant global health challenge, with the environment serving as a crucial reservoir and conduit for resistance determinants. Although antibiotic resistance genes (ARGs) have been extensively studied in environmental contexts, systematic approaches for assessing and prioritizing the risks associated with mobile genetic elements (MGEs), such as plasmids, phages, transposons, and integrative elements (IEs), remain unclear. To address this gap, we present MobiRes, an open-source computational framework designed to predict resistome risk by integrating information from the mobilome and microbiome. The pipeline was evaluated using a wide range of publicly available metagenomic datasets spanning diverse environments, including wastewater, poultry, soil, sediments, and human fecal samples. To validate the framework, statistical analyses and machine learning models were applied to evaluate the role of MGEs in driving ARG dissemination. The pipeline identified transposons as the dominant MGE class while capturing environment-specific variation in plasmid, phage, and IE -associated ARGs. Transposon-associated ARGs showed the most consistent environmental differentiation (ANOVA p = 0.0017; Kruskal-Wallis p = 0.018), whereas plasmid and phage-associated ARGs varied moderately (p = 0.015-0.040) and IE-associated ARGs remained comparatively stable across environments (p > 0.05). The Random Forest (RF) model achieved an AUC of 0.82, and subsequent feature importance and SHapley Additive exPlanations (SHAP) analyses revealed that transposon abundance is the primary factor driving ARG dissemination across diverse environments. By integrating host, mobility, and ecological factors, MobiRes provides a scalable and One Health-oriented framework for comprehensive AMR risk assessment. This pipeline is publicly available at https://github.com/santhiyakc17/MobiRes_Pipeline.}, }
@article {pmid41819657, year = {2026}, author = {Li, E and Xie, X and Zhang, Y and Yan, L and Wang, Y}, title = {Biogeochemical cycling of sulfur and iron constrains arsenic enrichment in groundwater: Microbial functionality and organic matter composition.}, journal = {Water research}, volume = {297}, number = {}, pages = {125724}, doi = {10.1016/j.watres.2026.125724}, pmid = {41819657}, issn = {1879-2448}, abstract = {Groundwater arsenic contamination is governed by the coupled iron-sulfur-arsenic biogeochemical cycle, where microbial functional genes and organic matter transformation play central roles, though regional-scale mechanisms remain unclear. This study integrates hydrogeochemistry, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), metagenomic sequencing, and metagenome-assembled genomes (MAGs) to reveal microbially driven mechanisms of arsenic migration and transformation in the Datong Basin. The results indicate distinct zonation of arsenic, sulfur, and iron speciation along the groundwater flow path. Furthermore, dissolved organic matter (DOM) dominated by carboxyl-rich alicyclic molecules (CRAM) and aromatic compounds promotes arsenic release through chelation and electron transfer. Microbial community and functional gene analyses further reveal key zonation characteristics. In the recharge zone, genera such as Acinetobacter and Hydrogenophaga were predominant, with functional genes related to arsenite oxidation (aioA, aoxB) contributing to arsenic retention. In the transition zone, sulfate-reducing bacteria including Desulfovibrio became abundant, and sulfate reduction genes (CysND, CysH, CysJI) facilitated the formation of thioarsenates, leading to arsenic release. In the discharge zone, methylotrophic genera such as Methylocystis together with methanogens were enriched. The co-occurrence of the methane metabolism gene ackA and the arsenic reduction gene arsC suggested a potential coupling between methane-related metabolism and arsenic transformation under reducing conditions. This study elucidates iron-sulfur-arsenic coupling as a key mechanism governing arsenic biogeochemical cycling, providing a theoretical biogeochemical framework for understanding regional arsenic spatial heterogeneity.}, }
@article {pmid41819697, year = {2026}, author = {Ciaralli, L and Valente, T and Monfardini, E and Berto, D and Rampazzo, F and Libralato, G and Manfra, L and Piermarini, R and Silvestri, C and Radicioli, M and Gioacchini, G and Chemello, G and Trotta, E and Capó, JD and Tomassetti, P and Matiddi, M}, title = {Callinectes sapidus - coast to coast: Integrating stable isotope analysis and shotgun metagenomics to unravel trophic dynamics and microlitter ingestion across two Mediterranean sites.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119532}, doi = {10.1016/j.marpolbul.2026.119532}, pmid = {41819697}, issn = {1879-3363}, abstract = {The increasing presence of microlitter in the marine environment poses a growing threat to aquatic organisms. This study investigates microlitter ingestion and trophic ecology of Callinectes sapidus from two populations of the Mediterranean basin: the Adriatic and Tyrrhenian Seas. To disentangle potential differences in feeding strategies between the populations, we adopted an integrated framework combining stable isotope analysis with shotgun metagenomic analysis of gastrointestinal contents, thus providing a complementary view of long-term trophic position and short-term dietary composition. Gastrointestinal analysis revealed microlitter ingestion in 39% of Adriatic and 50% of Tyrrhenian individuals, with 123 particles retrieved. Fibres dominated (94.3%), though composition varied regionally: Adriatic individuals ingested mainly cellulose-based microlitter (62.5%), whereas Tyrrhenian ones mostly synthetic polymers (61.4%). Eight chemical types were identified, with cellulose, polyethylene terephthalate, and resin-based polymers most abundant. Stable isotope analysis (δ[15]N and δ[13]C) indicated distinct trophic patterns: Adriatic population had higher δ[15]N (mean ± sd: 11.50 ± 2.27‰) and less depleted δ[13]C (-16.20 ± 1.52‰) compared to the Tyrrhenian one (δ[15]N: 9.01 ± 2.27‰; δ[13]C: -18.57 ± 0.88‰), suggesting region-specific feeding strategies. Shotgun metagenomics provided complementary information on prey composition, helping to characterise the opportunistic diet of C. sapidus. Overall, these findings highlight spatial differences in microlitter exposure and trophic dynamics, likely shaped by environmental availability and feeding behaviour. By integrating microlitter ingestion, stable isotope analysis, and metagenomics, this study provides insight into how C. sapidus interacts with anthropogenic and natural resources, emphasizing the feeding flexibility underlying its invasive success in Mediterranean Sea.}, }
@article {pmid41819887, year = {2026}, author = {Onohuean, H and Igere, BE and Apollo, E and Idris, SO and Olutona, GO}, title = {Meta-synthesis of research advances on drug residues associated with antihelmintic, antibiotics in livestock and poultry: Implications for public health.}, journal = {Food research international (Ottawa, Ont.)}, volume = {231}, number = {Pt 2}, pages = {118757}, doi = {10.1016/j.foodres.2026.118757}, pmid = {41819887}, issn = {1873-7145}, mesh = {Animals ; *Anthelmintics/analysis ; *Anti-Bacterial Agents/analysis ; *Poultry ; *Livestock ; *Drug Residues/analysis ; *Public Health ; *Food Contamination/analysis ; Meat/analysis ; Humans ; }, abstract = {INTRODUCTION: This meta-synthesis summarizes research advances on drug residues associated with using antihelmintic/antibiotics in poultry and livestock farming to highlight their implications on public health.
METHODS: The study applied the Preferred Reporting Items guidelines for the Systematic Reviews and Meta-Analyses (PRISMA) on diverse core databases (PubMed, Scopus, Medline and Web of Science) using the title-specific search keywords/terms.
RESULTS: Among the 176 included and eligible articles on drug residues associated with the use of antihelminthic/antibiotics in livestock and poultry farms, only 77 were meta-synthesized which revealed a poor growth rate of 1.95% within the periods. The meta-synthesis depicts the most reported pharmaceuticals, residue/metabolite to include Monensin (MON), unchanged Nicarbazin (NCZ), Doxycycline (DOX), Thiabendazole, Dimetridazole (DMZ), concentrated in meat, chicken, eggs, muscle, and liver of livestock with a concentration detected ranging from 0.01 μg/kg to 4840 μg/kg. It is important to note that the residual concentration observed was higher than major countries maximum residual limits (MRLs) for such farm products which reveals the risk of such observed values to consumers. Also, most reported method of residue detection was HPLC-MS/MS and LC-MS/MS, usually, this is due to the disease and infection threat of coccidiosis and histomoniasis in livestock production.
CONCLUSION: The relatively low annual growth rate of 1.95%indicates poor study between 2000 and 2024 which further emphasizes that the mainstream research in this regard may be neglected gradually if the trend continues, leaving the concern of drug residue unattended while the implications on public health systems remain unengaged. It also revealed high residue and risk associated with the use of antihelminthic/antibiotics in poultry/livestock farming which necessitates intentional and adroit surveillance especially in low- and middle-income nations.}, }
@article {pmid41820042, year = {2026}, author = {Zhou, F and Liu, ZP and Cao, B}, title = {[Annual review of community-acquired pneumonia (CAP) 2025].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {3}, pages = {339-344}, doi = {10.3760/cma.j.cn112147-20251124-00741}, pmid = {41820042}, issn = {1001-0939}, support = {2024ZD0522500//Major Project of the Ministry of Science and Technology of China/ ; }, mesh = {Humans ; *Community-Acquired Infections/drug therapy/epidemiology/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; Mycoplasma pneumoniae/drug effects ; Pneumonia, Mycoplasma/drug therapy/epidemiology ; *Pneumonia/drug therapy/epidemiology/diagnosis ; China/epidemiology ; Macrolides/therapeutic use ; Metapneumovirus ; Respiratory Syncytial Virus Infections ; High-Throughput Nucleotide Sequencing ; Community-Acquired Pneumonia ; }, abstract = {Community-acquired pneumonia (CAP) remains a significant global health challenge. This review summarizes the major advances in clinical research or CAP between October 1, 2024, and September 30, 2025. Given the high prevalence of macrolide-resistant Mycoplasma pneumoniae (MRMP) in China, PCR test for MRMP was recommended in pediatric patients to guide appropriate antibiotic selection. Increased attention is warranted for respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) due to their increasing prevalence and poor prognosis. PSI and CURB-65 scores remain the reliable tools for assessing the severity of CAP, while the SOFA-2 score may offer a promising approach for identifying patients requiring intensive care unit (ICU) admission. Although multiplex PCR (mPCR), targeted next-generation sequencing (tNGS), and metagenomic next-generation sequencing (mNGS) have been widely adopted in clinical practice, current evidence does not demonstrate sufficient benefits in improving patient survival or optimizing antibiotic stewardship. A rational, empirical antibiotic strategy should be individualized according to local pathogen epidemiology, risk of antimicrobial resistance and aspiration, and patient's clinical presentation. Short-course antibiotic therapy guided by "clinical stability" criteria is reliable, yet achieving stability requires more time in elderly patients and cases with comorbidities. Cefpirome and lefamulin are new antimicrobial agents on the market, but further clinical data are needed to support their use in severe cases and elderly patients. Suraxavir marboxil (GP681), a newly antiviral agent drug targeting the polymerase acidic protein of the influenza virus RNA polymerase, has recently been approved in China. Extending the administration of steroids to severe CAP without septic shock should be approached with extreme caution. High level of C-reactive protein may serve as a potential indicator for identifying cases who could benefit from steroids. In addition, RSV vaccines and monoclonal antibodies will emerge as important strategies for preventing RSV pneumonia in high-risk populations.}, }
@article {pmid41820832, year = {2026}, author = {Vela-Chauvin, MG and Ramirez-Villacis, DX and Armijos, CE and Narvaez, M and Quelal-Madrid, F and Bustamante, G and Torres-Sobrevilla, C and Debut, A and Corredor, F and Calero-Cáceres, W and Machado, A and Zapata-Mena, S}, title = {Characterization and evaluation of a phage cocktail targeting Salmonella enterica in a Turkey farm.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04849-4}, pmid = {41820832}, issn = {1471-2180}, support = {FSPI grant (Project ID 17827)//French Embassy in Ecuador/ ; Collaboration Grant (Project ID 23185)//Universidad San Francisco de Quito/ ; }, }
@article {pmid41821123, year = {2026}, author = {Thygesen, VFDF and Farahani, MF and Nielsen, SH and Constancias, F and Givskov, M and Abranches, J and Scorrano, G and Jørkov, MLS and Ebrahimi, G and Bendezu-Sarmiento, JC and Demeter, F and Kristiansen, K and Belstrøm, D and Sikora, M}, title = {The genomic history of Streptococcus mutans from the Mesolithic until modern times.}, journal = {Genome biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13059-026-04018-w}, pmid = {41821123}, issn = {1474-760X}, support = {R302-2018-2155, R155-2013-16338//Lundbeck Foundation/ ; NNF18SA0035006//Novo Nordisk Foundation/ ; UNS69906/WT_/Wellcome Trust/United Kingdom ; CF18-0024//Carlsberg Foundation/ ; DNRF94, DNRF174//Danish National Research Foundation/ ; KU2016 programme//University of Copenhagen/ ; }, abstract = {BACKGROUND: Streptococcus mutans is a member of the human oral microbiota and is considered one of the most important cariogenic organisms. Previous studies have suggested an expansion of S. mutans populations about 10,000 years ago with the onset of agriculture, yet direct molecular evidence of its presence from ancient DNA remains sparse.
RESULTS: Here, we present population genomic analyses of 25 ancient S. mutans genomes (average read depth 0.1X - 387X) recovered from archaeological remains across Eurasia spanning ~ 8,000 years of human evolution. Recombination-corrected phylogenomic analyses using Gubbins show a star-like phylogeny indicative of an early radiation, with the ancient genomes falling within the genomic diversity of modern isolates but restricted to one of the major clades of the phylogeny (D). Analyses of genes encoding present day virulence factors reveals that the presence of the mutanobactin operon involved in oxygen tolerance is restricted to specific subclades (A & B) and absent among the ancient samples. Using the MEGAHIT assembler followed by binning of contigs with CONCOCT, we recover metagenome-assembled genomes (MAG) of 7 high-coverage ancient S. mutans strains, including a 7,500-year-old sample from an early European Neolithic farmer. Pangenome analysis with modern isolates using the anvi'o's suite revealed the presence of specific functional genes in the ancient isolates, which were lost through time.
CONCLUSIONS: Our study demonstrates that Streptococcus mutans DNA is well preserved in tooth samples from archaeological remains and show that it formed part of the human oral microbiota already before the onset of agriculture, consistent with a radiation and population expansion well before 8,000 years ago.}, }
@article {pmid41821330, year = {2026}, author = {Yi, XH and Zhu, HX and He, MY and Gao, S and Li, M}, title = {Decoding Links between Gut Microbiota and Metabolic-associated Fatty Liver Disease: Meta-analysis and Mediation Study Uncover Species-specific Taxa and a Novel Bile Acid Mediator.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {2}, pages = {202-214}, doi = {10.3967/bes2025.162}, pmid = {41821330}, issn = {2214-0190}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bile Acids and Salts/metabolism ; Mendelian Randomization Analysis ; Species Specificity ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Fatty Liver/microbiology ; Bacteria/classification/genetics ; }, abstract = {OBJECTIVE: Previous Mendelian randomization (MR) studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease (MAFLD). However, the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights. To address this, we conducted a de novo MR analysis using species-level shotgun metagenomic data, combined it with a meta-analysis to consolidate the existing evidence, and explored metabolite-mediated pathways.
METHODS: Bidirectional MR analyses were performed between 883 gut microbiota taxa (derived from shotgun metagenomic genome-wide association study) and MAFLD. Published MR studies (up to December 1, 2024) were identified using PubMed, Embase, Web of Science, and the Cochrane Library for meta-analysis. Multivariable MR (MVMR) and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.
RESULTS: The de novo MR identified 25 MAFLD-associated microbial taxa. Integration with 7 published studies revealed 34 causal taxa, including 10 at the species level. Among the 1,400 metabolites, 53 showed causal links with MAFLD. MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk (22.06% mediation proportion).
CONCLUSION: This study elucidated the connections between species-level gut microbiota and MAFLD, highlighting the interplay between microbiota, metabolites, and disease pathogenesis. These findings provide novel insights into the potential therapeutic targets for MAFLD.}, }
@article {pmid41821545, year = {2025}, author = {Yun, S and Seo, Y and Yoon, Y}, title = {Prevalence of Microorganisms and Suggestion for Potential Contribution of Microorganisms to Volatile Basic Nitrogen Production in Beef at Current Purchase Stages.}, journal = {Food science of animal resources}, volume = {45}, number = {6}, pages = {1710-1723}, pmid = {41821545}, issn = {2636-0780}, abstract = {This study investigated the prevalence of microorganisms related to meat quality and analyzed volatile basic nitrogen (VBN) levels in beef samples to suggest potential bacteria that might contribute to VBN production at current purchase stages using metagenomic analysis. Seventy beef samples were analyzed for coliform, Escherichia coli, enterohemorrhagic E. coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, total aerobic bacteria (TAB), Enterobacteriaceae, lactic acid bacteria (LAB), Pseudomonas spp., yeast and molds (YM), and psychrotrophic bacteria (PB). VBN levels ranged from 0.69 to 22.51 mg%. Microbiota from three samples with the highest and three with the lowest VBN levels were analyzed. S. aureus was detected in only one sample at 1.2 Log CFU/g. The cell counts for TAB, coliform, Enterobacteriaceae, LAB, Pseudomonas spp., YM, and PB were 5.1, 1.7, 2.6, 4.2, 1.9, 2.9, and 5.4 Log CFU/g, respectively. Microbiota analysis revealed that samples with high VBN levels had high relative abundances of Lactobacillus and Leuconostoc. This study showed that these relatively abundant LAB were potential bacteria that might contribute to producing more VBN in beef at current purchase stages. However, the potential bacteria were suggested only by metagenomic analysis with a limited sample size without considering the endogenous meat enzymes. Therefore, further research is necessary to identify and isolate these bacteria with a larger sample size while excluding VBN produced by endogenous enzymes. Additionally, environmental factors not included due to the limited objective of this study could also be considered in further research with the different objectives from this study.}, }
@article {pmid41821969, year = {2026}, author = {Lim, JJL and Chin, NL and Chong, CW and Ripen, AM and How, S and Teoh, SQ}, title = {Review on kefir beverages from milk and water: health benefits, processing and applications.}, journal = {Food science of animal resources}, volume = {46}, number = {1}, pages = {31}, pmid = {41821969}, issn = {2636-0780}, abstract = {Kefir is a trending and highly valued fermented beverage known for its beneficial microbes and giving a wide spectrum of health benefits. It includes milk kefir and water kefir which have gained separate attention. Although milk kefir is more heard of than water kefir, it is essential to understand both in greater details in terms of similarities and differences. The key health benefits such as probiotics, protection in the gastrointestinal tract, control of glucose level, antioxidant, antimutagenic, anticarcinogenic, regulating cholesterol, antimicrobial and improving lactose digestion are discussed and supported with recent in-vivo or in-vitro scientific evidences. This review addresses the gap of individual focus of each kefir by direct comparison of its microbial diversity, processing and physicochemical qualities. It provides updated information on lactic acid bacteria by species from advanced techniques of metagenomic analysis and also highlights the potential of kefiran, exopolysaccharides of milk kefir grains in food, biopharmaceutical and packaging industries.}, }
@article {pmid41822155, year = {2026}, author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S}, title = {Learning functional groups in complex microbiomes.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {41822155}, issn = {2331-8422}, abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.}, }
@article {pmid41822221, year = {2026}, author = {Donbraye, E and McLeod, L and Chai, Z and Lacoste, SR and McCarthy, EL and Hill, JE and Erickson, NEN and Links, MG and Otto, SJG and Huang, Y and Waldner, CL}, title = {Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1704414}, pmid = {41822221}, issn = {2297-1769}, abstract = {INTRODUCTION: Very few studies have examined the diagnostic sensitivity and specificity of currently available laboratory tests for detecting respiratory pathogens in cattle, and even fewer have examined test performance on samples from animals before the onset of clinical disease.
METHODS: In this study, Bayesian latent class modeling (BLCM) was used to assess diagnostic test performance in the absence of a gold standard on nasal swabs collected from 19 western Canadian feedlots. Viruses associated with bovine respiratory disease (BRD) were identified using qPCR from a commercial diagnostic laboratory from 760 nasal swabs collected from fall-placed calves (FPC) and yearlings (YRL) at and shortly after feedlot arrival. Using BLCM, the qPCR results were compared to previously reported matching nanopore metagenomic sequencing data for these same samples. Based on BLCM, test sensitivities and specificities were estimated for the detection of bovine coronavirus (BCoV), bovine herpesvirus type 1 (BoHV-1), bovine parainfluenza virus type 3 (BPIV-3), bovine respiratory syncytial virus (BRSV), and influenza D virus (IDV). Estimates informed by BLCM were not available for the detection of bovine viral diarrheal virus (BVDV) because qPCR did not detect this virus in any samples.
RESULTS: Diagnostic sensitivity of qPCR was higher than metagenomic sequencing for detecting BCoV (qPCR 0.90, 95% CrI 0.81-0.99; sequencing 0.35, 95% CrI 0.25-0.46) and BoHV-1 (qPCR 0.39, 95% CrI 0.19-0.99; sequencing 0.04, 95% CrI 0.01-0.15). However, the estimated diagnostic sensitivity of metagenomic sequencing was higher than qPCR for identifying BRSV (qPCR 0.32, 95% CrI 0.22-0.43; sequencing 0.60, 95% CrI 0.44-0.77). No significant difference among sensitivities was noted for the detection of BPIV-3 (qPCR 0.42, 95% CrI 0.21-0.66; sequencing 0.52, 95% CrI 0.19-0.87) and IDV (qPCR 0.65, 95% CrI 0.53-0.79; sequencing 0.60, 95% CrI 0.48-0.73). Diagnostic specificity was comparable for most viruses, except for BCoV, where metagenomic sequencing (BCoV 0.91, 95% CrI 0.88-0.95) outperformed qPCR (BCoV 0.59, 95% CrI 0.51-0.68). The specificity and sensitivity for detection of BRD-associated bacteria from the same metagenomic data were also similar to those estimated for culture and qPCR results for the same samples.
DISCUSSION: Estimated test sensitivities of both nanopore metagenomic sequencing and qPCR for the detection of BRD viruses of interest in nasal swab samples were moderate to very low for most viruses. While the tests varied in their ability to detect individual viruses, data from this study suggest nanopore metagenomic sequencing offers a potential alternative for diagnostic laboratories to identify three of six important BRD viruses as well as bacteria associated with BRD.}, }
@article {pmid41822328, year = {2026}, author = {Hu, H and Cai, D and Li, J and Wang, K}, title = {Pulmonary infection by Nocardia saintgeorgesii mimicking lung cancer with concurrent pulmonary embolism in an immunocompetent host: a case highlighting the diagnostic role of mNGS.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765925}, pmid = {41822328}, issn = {2235-2988}, mesh = {Humans ; *Nocardia Infections/diagnosis/drug therapy/microbiology/complications ; *Pulmonary Embolism/diagnosis/complications ; *Nocardia/genetics/isolation & purification/classification ; *Lung Neoplasms/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Diagnosis, Differential ; Male ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Tomography, X-Ray Computed ; Middle Aged ; }, abstract = {BACKGROUND: Pulmonary nocardiosis presents a diagnostic challenge due to its frequent mimicry of lung cancer on imaging and the low sensitivity of conventional cultures. We report a case initially misdiagnosed as malignancy in an immunocompetent host, where metagenomic next-generation sequencing (mNGS) provided a definitive diagnosis and revealed a concurrent pulmonary embolism, suggesting a potential underrecognized association.
CASE PRESENTATION: This report describes a case of PN in an immunocompetent patient who was initially misdiagnosed with lung cancer based on imaging findings but later confirmed as pulmonary nocardiosis via mNGS. Notably, the patient also developed pulmonary embolism (PE). Empirical antibiotic therapy with piperacillin-tazobactam was initiated initially, supplemented with inhaled ipratropium bromide and expectorants to alleviate symptoms. Based on imaging findings suggestive of lung cancer, an invasive procedure was scheduled. mNGS was subsequently performed for further diagnosis. The subsequent results, along with CT scans, indicated no evidence of malignancy, leading to a consideration of Nocardia infection. The treatment regimen was then adjusted to ceftriaxone sodium combined with compound sulfamethoxazole, and the surgical schedule was canceled. The patient's condition showed significant improvement, and he was discharged without fever or dyspnea. Some literature suggests that many PN patients present with concurrent deep vein thrombosis (DVT), suggesting a potential yet underrecognized association between Nocardia infection and thrombotic events. However, this correlation has not been fully reported before.}, }
@article {pmid41822329, year = {2026}, author = {Tee, KK and Xia, X}, title = {Strengthening preparedness and response to emerging henipavirus diversity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1761347}, pmid = {41822329}, issn = {2235-2988}, mesh = {*Henipavirus Infections/epidemiology/prevention & control/diagnosis/virology/transmission ; Humans ; Animals ; *Henipavirus/classification/genetics/isolation & purification ; Zoonoses/epidemiology/virology/prevention & control ; *Communicable Diseases, Emerging/prevention & control/epidemiology/virology/diagnosis ; Chiroptera/virology ; Disease Reservoirs/virology ; Hendra Virus/genetics ; Animals, Wild/virology ; }, abstract = {Henipaviruses, including the highly pathogenic Nipah virus and Hendra virus, represent a major zoonotic threat with high mortality rates and potential for human-to-human transmission. Recent discoveries of novel henipaviruses in China, Europe and other regions highlight the urgent need for enhanced surveillance in both wildlife reservoirs such as bats, shrews, rodents, and human populations, particularly in high-risk areas. Despite advancements in metagenomic sequencing, gaps in integrated surveillance, fragmented One Health implementation, and insufficient diagnostic infrastructure in large parts of the world hinder global preparedness. This paper identifies key challenges in henipavirus detection and control and proposes an operational roadmap for surveillance, diagnostics, and cross-sectoral collaboration. With the known animal hosts of henipaviruses and related henipa-like orthoparamyxoviruses now documented across more than 130 countries and territories, strengthening these capabilities is critical to preventing future epidemics and addressing the evolving threat of emerging henipavirus diversity.}, }
@article {pmid41822332, year = {2026}, author = {Xu, Y and Wu, W and Dong, D and Liu, N and Liu, J and Qi, B and Gu, Q}, title = {The value of metagenomic next-generation sequencing in lower respiratory tract infections among critically ill patients in the ICU.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1746117}, pmid = {41822332}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Respiratory Tract Infections/microbiology/virology/diagnosis ; Intensive Care Units ; *Metagenomics/methods ; Critical Illness ; Female ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Adult ; }, abstract = {Lower respiratory tract infections (LRTIs) frequently occur as a severe complication in intensive care unit (ICU) patients, substantially raising patient mortality rates and extending hospitalization periods. In this study, a retrospective cohort study of 261 suspected LRTI patients in the ICU of Nanjing Drum Tower Hospital between April 2021 and February 2024 was conducted. The results showed that metagenomic next-generation sequencing (mNGS) had a sensitivity of 80.1%, a specificity of 35%, and an accuracy of 66.3% across all samples. For pathogen detection, mNGS outperformed conventional microbiological testing (CMT) in detecting bacteria and DNA viruses, while CMT had a slight advantage in RNA virus detection, though the difference was not statistically significant (p = 0.305). When comparing microbial profiles between survival and death groups, survivors had a more diverse pathogen spectrum, particularly in bacteria and RNA viruses. There were 262 species detected in both groups, with Corynebacterium striatum being the dominant species in the survival group and Pseudomonas aeruginosa in the death group. In the 128 patients whose treatment plans were adjusted based on mNGS results, 59.4% underwent escalation, 25.8% had their medications changed, and 1.6% initiated new treatment regimens. Further follow-up revealed that mNGS - guided treatment adjustments were effective in improving clinical symptoms in 58.6% of ICU patients. A predictive model for patient outcomes was developed utilizing the random forest algorithm, achieving an area under the receiver operating characteristic curve (AUC) of 0.722.}, }
@article {pmid41823069, year = {2026}, author = {Savini, F and Indio, V and Prandini, L and Tomasello, F and De Cesare, A and Oliveri, C and Seguino, A and Zanato, E and Serraino, A}, title = {Outside in: assessment of microbial composition of the crust of dry-aged beef and its relevance in relation to food business operator practices.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.14620}, pmid = {41823069}, issn = {2239-7132}, abstract = {Dry aging of beef has recently been defined in Delegated Regulation 1141/2023, amending Regulation 853/2005. The delegated regulation lists specific measures to be applied when processing such a product. Specifically, a point is dedicated to the crust trimming that should be carried out in a hygienic manner, since the interventions performed at the end of the process might determine contamination of the edible parts. Nevertheless, despite the punctual application of good hygiene practices (GHP) and good manufacturing practices (GMP), a certain degree of contamination with pathogenic and spoilage microorganisms of the cut portions cannot be avoided, as demonstrated by some authors reporting contamination of the inner parts of dry-aged meat. In order to investigate the level of contamination occurring in field conditions during trimming and portioning, we performed two different trials: the sterility trial with the aim of evaluating the sterility of the inner parts of beef during aging and the contamination trial to assess the transfer of microbial populations from the outer to the inner part of the dry-aged beef. All tests were performed by means of cultural and non-cultural methods. Results of the sterility trial show that a very limited percentage of non-host DNA is present in the inner parts of the meat starting from the beginning of the test and that the detectable DNA increases slightly during the time of aging. Besides, the contamination trial results showed that the contamination of the trimmed meat is qualitatively and quantitatively related to the contamination of the crust. As a consequence, adherence to GHP and GMP during trimming and handling of dry-aged meat according to scientific literature is crucial to avoid/minimize cross-contamination since our data clearly demonstrate that processing practices are fully reflected in the final product quality.}, }
@article {pmid41823302, year = {2026}, author = {Al, KF and Jia, S and Silverman, M and Reid, G and Burton, JP and Parvathy, S}, title = {Prebiotic Modulation of FMT Donor Microbiota Enhances MASLD-Relevant Taxa and Functions in an In Vitro Gut Model.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag074}, pmid = {41823302}, issn = {1365-2672}, abstract = {AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly non-alcoholic fatty liver disease) is a prevalent and progressive condition closely linked to gut microbiota composition. Fecal microbiota transplantation (FMT) may help restore a health-associated microbiome, but its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may selectively support keystone microbes associated with reduced MASLD risk. This study evaluated two prebiotics, inulin and xylooligosaccharides (XOS), for their ability to modulate the microbiota of healthy FMT donors in an in vitro gut model, focusing on enriching beneficial taxa and functions associated with MASLD resilience.
METHODS AND RESULTS: Stool from eight clinically qualified FMT donors was cultured anaerobically for 24 hours with or without prebiotics. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid (SCFA) concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis. Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides-genera associated with SCFA production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional pathways relevant to MASLD pathophysiology were enriched, including carbohydrate metabolism, vitamin biosynthesis, fatty acid metabolism, and tryptophan degradation. Both prebiotics significantly increased acetate levels, while butyrate showed a donor-dependent increasing trend.
CONCLUSIONS: These findings suggest that prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting their potential as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.}, }
@article {pmid41823408, year = {2026}, author = {Thorn, AV and Brinch, C and Aarestrup, FM and Munk, P}, title = {Urban sewage resistomes partially reflect clinical resistomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0003126}, doi = {10.1128/msystems.00031-26}, pmid = {41823408}, issn = {2379-5077}, abstract = {Antimicrobial resistance (AMR) poses a major global public health threat, and ongoing surveillance of antimicrobial resistance genes (ARGs) is critical to mitigate current and future risks. Sewage-based ARG surveillance is gaining traction, but insight into how it compares to surveillance by clinical bacterial isolates is limited, especially when it comes to ARG mutational variants. We compared ARGs identified in clinical bacterial isolates (n = 2,989) with those detected in sewage metagenomes (n = 468) across 33 countries. ARG variant detection data from clinical isolates and sewage metagenomes shared some regional patterns in detection, but many ARG variants were detected exclusively in either sewage metagenomes or clinical isolates. We found that across all samples, only 69% of ARG clusters detected in clinical isolates were also detected via read mapping in sewage. Some ARGs highly prevalent in clinical isolates were not detected in sewage. Among clinically widespread ARGs, prevalence varied across bacterial species and clinical isolate types depending on whether the ARGs were also detected in sewage. This could indicate that sewage surveillance is better suited for detection of clinically relevant ARGs prevalent in certain bacterial species and infection sites than others. Spearman correlation between ARG abundance in sewage and the proportion of clinical isolates from the same country with detection was 0.28 overall, with stronger correlations for certain ARGs. The results demonstrate that sewage ARG profiles correlate, to some extent, to the clinical AMR landscape, but do not capture the full spectrum of clinically relevant ARGs at currently realistic sequencing depths.IMPORTANCEAntimicrobial resistance (AMR) is a major public health threat. Surveillance of AMR is important and can be conducted via the detection of antimicrobial resistance genes (ARGs). Sewage can be used as a medium for surveillance as an alternative to analyzing individual bacterial isolates from health clinics. We compared detection in large global data collections of sewage metagenomes and clinical isolates. We found that while there were significant positive correlations between findings in sewage and clinical isolates, some widespread clinical ARGs were not detectable in sewage. This should be considered if establishing sewage surveillance systems.}, }
@article {pmid41823694, year = {2026}, author = {Pessi, IS and Eronen-Rasimus, E and Näkki, P and Thomas, DN and Kaartokallio, H}, title = {Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag052}, pmid = {41823694}, issn = {1751-7370}, abstract = {Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterised the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss to CO2 after four weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term bioplastisphere to denote the distinctive microbial communities associated with biodegradable plastics.}, }
@article {pmid41824008, year = {2026}, author = {Wen, M and Wang, X}, title = {Diagnostic value of metagenomic next-generation sequencing on bronchoalveolar lavage fluid via radial endobronchial ultrasound for peripheral pulmonary infectious lesions: A retrospective cohort study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02865}, pmid = {41824008}, issn = {1588-2640}, abstract = {The etiological diagnosis of peripheral pulmonary infectious lesions (PPILs) is challenging due to the limitations of conventional microbiological methods (CMMs). This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) performed on bronchoalveolar lavage fluid (BALF) obtained via radial endobronchial ultrasound (r-EBUS) for PPILs. This single-center, retrospective diagnostic accuracy study enrolled 110 patients with PPILs who underwent r-EBUS-guided BALF between January 2023 and December 2024. BALF samples were subjected to both mNGS and CMMs. The final diagnosis was established by two senior pulmonologists based on a comprehensive review of all clinical data. The diagnostic performance of mNGS and CMMs was compared against this final diagnosis. A definitive diagnosis was established in all 110 patients, with 68 cases identified as infectious lesions and 42 as non-infectious. The sensitivity of mNGS for detecting pathogens in infectious lesions was significantly higher than that of CMMs (89.7% vs. 47.1%, P < 0.001). The overall diagnostic accuracy of mNGS was also superior to CMMs (90.9% vs. 66.4%, P < 0.001). Among patients with positive mNGS results, clinical management was altered in 73.8% of cases based on the findings. mNGS uniquely identified pathogens in 31 cases that were missed by CMMs. For patients with PPILs, mNGS analysis of BALF samples obtained via r-EBUS demonstrates significantly greater diagnostic sensitivity and accuracy than conventional methods. This approach has a substantial impact on clinical decision-making, facilitating targeted antimicrobial therapy and representing a powerful tool in the diagnostic workflow for peripheral pulmonary infections.}, }
@article {pmid41824271, year = {2026}, author = {Singh, K and Sambyal, D and Julka, JM}, title = {Metagenomic exploration of bacterial community shifts before, during, and after passage through earthworm Eutyphoeus waltoni.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {41824271}, issn = {2676-8607}, }
@article {pmid41824493, year = {2026}, author = {De Anda, V and Appler, KE and Aguilar-Pine, E and Aitolo, GL and Halverson, GP and Baker, BJ}, title = {The archaeal roots of eukaryotic life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2516062123}, doi = {10.1073/pnas.2516062123}, pmid = {41824493}, issn = {1091-6490}, support = {73592LPI//Simons Foundation (SF)/ ; LI-SIAME-00002001//Simons Foundation (SF)/ ; }, mesh = {*Archaea/genetics/classification ; Phylogeny ; *Eukaryota/genetics ; *Biological Evolution ; *Eukaryotic Cells ; Genome, Archaeal ; }, abstract = {Resolving the biological and geological events that led to the origin of eukaryotes is an ongoing challenge in biology. A major step in the evolution of complex cellular life was the merger between an ancestral host cell and a bacterium (that became the mitochondrion) some two billion years ago. Recently, metagenomics has enabled the reconstruction of a broad diversity of genomes, referred to as the Asgard Archaea. The Asgards are monophyletic with eukaryotes on the tree of life. Asgards have an array of genes, previously thought exclusive to eukaryotes, involved in cellular trafficking, the ubiquitin system, endosomal sorting, and cytoskeleton formation, with growing evidence demonstrating the functions of these proteins mirror those in eukaryotes. This gene repertoire suggests that these Archaea are descendants of the archaeal host from which eukaryotes evolved. Increased sampling has revealed that Asgard lineages are metabolically versatile and play key roles in various ecosystems and uncovered evolutionary transitions between Archaea and eukaryotes, such as innovations in eukaryotic defense systems. The positioning of eukaryotes in the Asgards is debated, but eukaryotes appear to branch within the Heimdallarchaeia. Lineages within this group, particularly Hodarchaeales and Kariarchaeaceae, contain a broad repertoire of eukaryote-like traits, including high-energy yielding metabolisms. Observing and studying Asgard interactions with bacterial descendants of mitochondria in a modern setting will transform our understanding of the origin of complex cellular life.}, }
@article {pmid41825203, year = {2026}, author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T}, title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106607}, doi = {10.1016/j.clnu.2026.106607}, pmid = {41825203}, issn = {1532-1983}, mesh = {Humans ; *Obesity/metabolism/microbiology/blood ; Male ; Female ; Adult ; Postprandial Period/physiology ; *Nutrients ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Metabolomics/methods ; *Diet ; Proteomics ; Feeding Behavior ; Overweight ; Body Mass Index ; Multiomics ; }, abstract = {BACKGROUND& AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.
METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.
RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 ± 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).
CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.}, }
@article {pmid41825216, year = {2026}, author = {Li, S and Gao, Z and Da, Y and Zhang, Y and Huang, Z and Yuan, G and Wu, C and Huang, T and Sun, Q and Zhou, G}, title = {ESKAPE pathogens contribute largely to antibiotic resistance spread via horizontal gene transfer in aquatic environments.}, journal = {Journal of contaminant hydrology}, volume = {279}, number = {}, pages = {104922}, doi = {10.1016/j.jconhyd.2026.104922}, pmid = {41825216}, issn = {1873-6009}, abstract = {The overuse of antibiotics in human healthcare, livestock, and aquaculture has led to the accumulation of antibiotic residues in aquatic environments. It promotes the dissemination of antibiotic-resistant bacteria (ARB) that pose a threat to public health. However, the mechanisms that shape antibiotic resistance gene (ARG) profiles in different water types remain poorly understood. In this study, three water types, including hospital wastewater, breeding wastewater, and natural waters, were employed. Using a combination of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), 16S rRNA gene sequencing, and metagenomic analysis, we found that ofloxacin in hospital wastewater posed the highest ecological risk, whereas norfloxacin and tetracycline in natural waters posed elevated health risks. Among 101 detected ARG subtypes, hospital effluents carried the highest abundances of high-risk ARGs and their host bacteria compared to breeding wastewater and natural waters. Interestingly, mobile genetic elements (MGEs) were the primary direct driver of ARG enrichment (PLS-PM path coefficient = 0.725), in contrast to the negligible contributions from typical antibiotic residues, physicochemical parameters, and microbial community structure. Furthermore, genera associated with ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) dominated the co-hosts of both ARGs and MGEs across all water types. Among these, Enterobacter spp. and Klebsiella pneumoniae were found to co-harbor the most diverse MGEs and multidrug-resistant ARGs. Consequently, this study underscores the critical role of ESKAPE pathogens in the environmental dissemination of ARGs and provides a scientific foundation for targeted antibiotic resistance control and sustainable water resource management.}, }
@article {pmid41825251, year = {2026}, author = {Chang, L and Su, X and Hu, W and Fang, Y and Liu, J and Li, J and Huang, L and Shu, W}, title = {Genomic insights into adaptation and microevolution of two novel non-AOA Nitrososphaeria, Acidarchaeum fankouense and Thermosulfuris yongpingense, in acid mine drainage ecosystems.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126711}, doi = {10.1016/j.syapm.2026.126711}, pmid = {41825251}, issn = {1618-0984}, abstract = {The class Nitrososphaeria is best known for ammonia-oxidizing archaea (AOA), yet deeply branching non-AOA lineages remain poorly characterized, leaving a critical gap in our understanding of the group's early evolution and ecological diversification. Herein, we recovered 44 non-AOA Nitrososphaeria metagenome-assembled genomes (MAGs) from acid mine drainage (AMD) sediments in diverse metal mines, representing two novel genera within the family Thermosulfuridaceae, Acidarchaeum and Thermosulfuris. A meta-analysis of 251 AMD-associated metagenomes worldwide showed that these potentially thermophilic lineages were detected only in China and were typically rare, with localized blooms (up to ∼7.65%) at a few sites, particularly Fankou lead-zinc mine. Metabolic reconstruction suggested a facultatively anaerobic, mixotrophic lifestyle capable of CO oxidation and sulfur reduction, and extensive acid- and heavy-metal resistance mediated primarily by ether-linked archaeal lipids, ion efflux systems, and enzymatic reduction. Genus-specific traits include dissimilatory sulfate reduction in Thermosulfuris and urea utilization in Acidarchaeum, illuminating distinct ecological niches. Population-genomic analyses reveal low homologous recombination and pervasive purifying selection in these non-AOA populations, together with local relaxation of selection and elevated diversity, the former being correlated with geochemical stressors (notably copper), pointing to long-term, geochemically driven adaptation. Overall, these findings provide insights into the biodiversity, ecophysiology, and evolutionary dynamics of non-AOA Nitrososphaeria.}, }
@article {pmid41825425, year = {2026}, author = {Wu, B and Zhai, Y and Li, S and Yang, Y and Cao, D and Wu, W and Yang, J and Huang, T and Zhuang, J}, title = {Oligo-cyanobacterial microalgae-bacteria granular sludge for mitigating cyanotoxin risk: Cultivation, characteristics, and formation mechanism.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129300}, doi = {10.1016/j.jenvman.2026.129300}, pmid = {41825425}, issn = {1095-8630}, abstract = {Microalgae-bacteria granular sludge (MBGS) is a promising technology for wastewater treatment, due to its advantage of superior nutrient removal and potential for carbon-neutrality. However, cyanobacteria, which produce cyanotoxins and raise environmental concerns, was prevalent in previously cultivated MBGS. In this study, Oocystis borgei (O.borgei), which could inhibit cyanobacteria in microalgae-bacterial mixed culture (MBMC), was added in inoculum for the oligo-cyanobacterial MBGS cultivation. Flow cytometry and 16S/18S rRNA gene sequencing showed that the abundance of cyanobacteria was maintained at consistently low levels during the cultivation of MBGS. Moreover, the cyanotoxin concentration was only 0.15 μg/g-VSS, which was significantly lower than that in MBGS cultivated with other inoculums. Using autofluorescence-based cell sorting technology (AFCS), we found that the extracellular protein (PN) content of bacteria increased remarkably in the mixed culture with O.borgei, leading to the significant increase of extracellular polymeric substances (EPS) in MBMC. In addition, metagenomic analysis revealed that the abundance of lipoprotein (LPP) directed transport ATPase gene (lolD) and lipopolysaccharide (LPS) transport gene (lptB), key genes associated with EPS secretion, was increased from 493 to 343 fragments per kilobase of transcript per million mapped reads (FPKM) in inoculum to 775 and 548 FPKM in rapid granulation period. Genomic-annotation found that the Proteobacteria, encoded the EPS-producing genes, was dominated in oligo-cyanobacterial MBGS. These results suggested that microalgae could stimulate Proteobacteria to secrete PN, promoting MBGS formation. This work provides an effective approach for oligo-cyanobacterial MBGS cultivation and deep insight into the granulation mechanism, which provides theoretical support for the engineering application of MBGS technology.}, }
@article {pmid41825544, year = {2026}, author = {Li, D and Kim, S and Tang, T and Wu, S and Ma, H and Liu, Y}, title = {Thermophilic keystone taxa drive humification in coal gangue co-composting via shikimate-pathway carbon flux.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124250}, doi = {10.1016/j.envres.2026.124250}, pmid = {41825544}, issn = {1096-0953}, abstract = {Co-composting of coal gangue and organic solid waste is an effective resource utilization method, but systematic understanding of the humification process in co-composting systems remains limited. The study systematically investigated the evolution of humic substances in a coal gangue co-composting system and identified the roles of thermophilic keystone taxa by machine learning models combined with metagenomic analysis in the humification process. The results indicate that maintaining the thermophilic phase is crucial for humification in the coal gangue co-composting system. Experimental groups that maintained a stable thermophilic phase achieved complete humification and produced compost that effectively promoted wheatgrass growth on sandy soil. The key thermophiles (Thermobifida, Thermopolyspora, and Planifilum) are significantly associated with humic substances and the shikimate pathway. These bacteria support the humification process by enhancing the synthetic potential of the shikimate pathway, thereby providing the necessary supply of aromatic precursor substances. This study elucidates the humification process in the coal gangue co-composting and identifies the role of key thermophiles, providing theoretical and practical guidance for the bioutilization of coal gangue and the improvement of desertified soils.}, }
@article {pmid41825562, year = {2026}, author = {Li, D and Ravindran, B and Liang, J and Xu, Q and Zhang, J and Yan, X and Yuan, L and Wong, JWC}, title = {Enhancing nitrogen retention in low C/N food waste digestate composting: synergistic effects of biochar and nitrifying inoculation.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134412}, doi = {10.1016/j.biortech.2026.134412}, pmid = {41825562}, issn = {1873-2976}, abstract = {Food waste digestate (FWD) composting at low C/N ratios is increasingly applied to enhance treatment capacity, but it is often limited by severe nitrogen (N) loss caused by excessive ammonia (NH3) volatilization, nitrous oxide (N2O) emissions, and delayed nitrification. This study evaluated the individual and combined effects of biochar and a nitrifying bacterial inoculant on N transformation, gaseous emissions, microbial community succession, and functional gene dynamics during FWD composting at an initial C/N ratio of around 15. Results showed that biochar alone reduced total N loss by 33% relative to the control, primarily by suppressing NH3 and N2O emissions through physicochemical adsorption and a higher N2O-reduction potential (e.g., increased nosZ abundance). In contrast, nitrifying inoculation alone accelerated nitrification and compost maturity, but increased N2O emissions due to enhanced nitrifier-denitrification. The combined application of biochar and nitrifiers exhibited a synergistic effect, maintaining high nitrification efficiency while mitigating N2O emissions associated with nitrifier addition. This strategy reduced NH3 emissions by 41%, reduced total N loss by 27% relative to the control, and shortened the composting period required to reach maturity by 14 days. Metagenomic and qPCR analyses revealed that nitrifying inoculation significantly increased amoA and hao abundances, whereas biochar amendment was consistently associated with higher nosZ abundance, suggesting an increased N2O reduction potential. Overall, integrating biochar with nitrifying inoculants offers a promising strategy to enhance nitrogen retention, reduce gaseous emissions, and accelerate maturity during low C/N FWD composting.}, }
@article {pmid41825563, year = {2026}, author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G}, title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134417}, doi = {10.1016/j.biortech.2026.134417}, pmid = {41825563}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Microbial Consortia/physiology ; Methane/metabolism/biosynthesis ; Bioreactors/microbiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.}, }
@article {pmid41825740, year = {2026}, author = {Alvarado, DA and Holthaus, TA and Martell, S and Southey, NL and Atallah, M and Sarma, R and Revilla, D and Brown, M and Mehta, T and Khan, NA and Holscher, HD}, title = {Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101473}, doi = {10.1016/j.tjnut.2026.101473}, pmid = {41825740}, issn = {1541-6100}, abstract = {BACKGROUND: Dietary fiber may support cognition through gastrointestinal-microbiota mechanisms, but clinical evidence is limited.
OBJECTIVES: We aimed to determine whether soluble corn fiber (SCF) improved cognition and altered fecal microbiota and fermentation end products in adults.
METHODS: In a randomized, double-blind, crossover trial, 42 healthy adults (45-75 y) consumed SCF (18 g/d) or a maltodextrin placebo control (CON: 22 g/d) for 4 wk, separated by a washout. Cognitive outcomes included executive function with event-related potentials, relational memory, neuropsychological performance, and mood. Secondary outcomes included fecal microbiota, metabolomics, and gastrointestinal tolerance. Tertiary analyses related microbial and metabolite changes to cognitive improvements using correlation, mediation, and moderation models, and explored SCF fermentation pathways with 16S-predicted functional profiling, shotgun metagenomics, and in vitro culturing.
RESULTS: SCF improved reaction times (RT) during congruent (β = -9.8 ms, 95% confidence interval (CI): -18.4, -1.2, false discovery rate (FDR) P = 0.01) and incongruent (β = -14.2 ms, 95% CI: -22.8, -5.6, FDR P = 0.003) flanker trials and increased Parabacteroides (∼4-fold, β = 1.44 log, 95% CI: 1.01, 1.88, FDR P < 0.001). At the SCF endpoint, congruent RT tended to be inversely associated with fecal acetate (ρ = -0.33) and propionate (ρ = -0.36), whereas Parabacteroides was marginally positively associated with acetate (ρ = 0.34) (all FDR P < 0.1). Moderation analyses indicated that SCF-RT relation varied by Parabacteroides magnitude change. At endpoint, SCF increased the predicted functional potential of carbohydrate-related KEGG Orthologs and pathways (FDR P < 0.05). In vitro culturing confirmed Parabacteroides distasonis ferments SCF.
CONCLUSIONS: SCF consumption improved attentional inhibition, altered the gut microbiota, and selectively enriched Parabacteroides. Although mediation analyses did not support a direct microbiota-to-cognition pathway, moderation analyses suggested that SCF-related cognitive effects may depend in part on Parabacteroides abundance. Collectively, these findings suggest that certain cognitive benefits of SCF consumption may be partly underpinned by the gut microbiota. This study was registered at clinicaltrials.gov as NCT05066425 (https://clinicaltrials.gov/study/NCT05066425).}, }
@article {pmid41826827, year = {2026}, author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E}, title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04915-x}, pmid = {41826827}, issn = {1471-2180}, support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; }, }
@article {pmid41826873, year = {2026}, author = {Wang, X and Tian, W and Tian, X and Qin, X and Ma, Y and Yang, T and Cao, S and Wu, L and Feng, H and Ma, B}, title = {Metagenomic analysis of wolfberry branch substrates under tomato cultivation without additional nitrogen fertilization.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08573-z}, pmid = {41826873}, issn = {1471-2229}, support = {32160706//National Natural Science Foundation of China/ ; 2023GKLRLX09//Science and Technology Innovation Leading Talent Program of Ningxia Hui Autonomous Region/ ; }, }
@article {pmid41826874, year = {2026}, author = {Wang, H and Fu, Y and Xu, H and Song, X and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W}, title = {Viromic profiling of amniotic fluid reveals distinct viral communities associated with maternal health status.}, journal = {BMC pregnancy and childbirth}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12884-026-08933-5}, pmid = {41826874}, issn = {1471-2393}, support = {No. 2023YFD1801300//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; JSYGY-1-2023-03(03)//Hospital Management Innovation Research Project of Jiangsu Provincial Hospital Association/ ; Nos. SH2023058, SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; }, }
@article {pmid41826937, year = {2026}, author = {Ma, X and Zhang, R and Zuo, L and Liang, X and Geng, J and Xia, Y}, title = {When cough leads to infarction: systemic arterial embolism as a sentinel complication of insidious pulmonary mucormycosis in an immunocompetent patient.}, journal = {BMC pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12890-026-04230-1}, pmid = {41826937}, issn = {1471-2466}, support = {2024YFC2309202//National Key Research and Development Program of China/ ; 202402AA310055//Yunnan Provincial Department of Science and Technology Major Science and Technology Special Program/ ; }, }
@article {pmid41827056, year = {2026}, author = {Chen, X and Xu, X and Lin, Y and Shi, X and Wang, D and Zhang, T}, title = {Pilea: profiling bacterial growth dynamics from metagenomes with sketching.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02374-0}, pmid = {41827056}, issn = {2049-2618}, support = {T21-705/20-N//University Grants Committee/ ; }, abstract = {BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.
RESULTS: We introduce Pilea (https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.
CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.}, }
@article {pmid41827072, year = {2026}, author = {Takkar, B and Maddheshiya, A and Adhikary, P and Reddy, VA and Majumder, PP and Mukherjee, S and Das, T and , }, title = {Gut microbiome changes in people with diabetic retinopathy in India. DRMS-India report # 1: operational protocol and trends from first 100 participants.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00821-9}, pmid = {41827072}, issn = {1757-4749}, abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM), and the leading cause of vision impairment and blindness. India is among the top three countries in DM prevalence, and both DM and DR are projected to rise sharply in the future. There is no accepted strategy for the prevention of DR other than DM control. Recent studies suggest that DM is associated with alterations in a core group of gut microbiota, and progression to DR may be influenced by changes within this core group, highlighting a potential link between DR and gut microbiome. We studied these changes in a protocol-driven large case-control study, the Diabetic Retinopathy Microbiome Study-India (DRMS-India: CTRI/2024/02/062511), analysed the results of the first 100 individuals, and evaluated variations in gut microbiome in DR.
METHODS: The DRMS is designed to recruit 462 people aged ≥ 30 years into three cohorts: healthy controls (HCs), DM, and DR, at 17 independent sites in India. Shotgun metagenomic sequencing of first-pass morning fecal samples is performed at a centralized laboratory and correlated with disease status, lifestyle, dietary, and systemic factors.
RESULTS: The first 100 participants included 26 HC, 33 DM, and 41 DR. The trends showed the DR group had 1, 6, and 10 unique core phyla, genera, and species, respectively. Alpha diversity was highest in the DR group; Beta diversity plots showed separate clusters of HCs and DR, with DM overlapping both. Firmicutes (highest in DR), Proteobacteria (highest in DM), Bacteroidetes, and Actinobacteria (highest in HC) were common phyla. Segatella was the most common genus, and Segatella copri was the most common species across all groups to date. Most microbial gene families were annotated to Molecular Functions (MF), and the pathways attributed to carbohydrate, amino acid, lipid, and nucleotide metabolism, indicating distinct functional adaptations in their gut microbiome.
CONCLUSION: Trends from the first 100 individuals indicate that the gut microbiome of Indians with DR exhibits discriminatory features in microbial diversity and abundance, as well as in gene families and pathways that impact host gut metabolism. Data trends from DRMS-India indicate a region-specific non-invasive biomarker that may guide preventive therapy for DR.}, }
@article {pmid41827905, year = {2026}, author = {Braile, A and Bani, A and Hosseininasab, SF and Regno, ND and Orabona, N and Bove, A and Braile, M}, title = {Profiling Osteoporosis via Integrated Multi-Omics Technologies.}, journal = {Cells}, volume = {15}, number = {5}, pages = {}, pmid = {41827905}, issn = {2073-4409}, mesh = {Humans ; *Osteoporosis/genetics/metabolism ; *Metabolomics/methods ; Proteomics/methods ; *Genomics/methods ; Biomarkers/metabolism ; Epigenomics ; Multiomics ; }, abstract = {BACKGROUND: Osteoporosis is a complex disorder involving bone loss and muscle degeneration. Multi-omics technologies provide novel insights into its molecular mechanisms and may support biomarker discovery, patient stratification, and therapeutic development.
OBJECTIVE: This scoping review aimed to synthesize current evidence on the application of multi-omics approaches in osteoporosis, focusing on molecular insights, methodological diversity, and translational potential.
METHODS: A literature search of PubMed, Embase, and Scopus retrieved 433 records using the keywords "osteoporosis," "osteosarcopenia," and "omics." After removing duplicates and screening titles, abstracts, and full texts, 30 studies met the inclusion criteria. Data on study populations, biological samples, multi-omics techniques, and integration methods were extracted.
RESULTS: Studies employed transcriptomics, proteomics, metabolomics, lipidomics, epigenomics, and metagenomics, often combined in multi-omics analyses with computational modeling. Key pathways included osteoclast differentiation, immune regulation, ferroptosis, and microbiome-metabolite interactions. Multi-omics integration enabled the identification of molecular subtypes, candidate biomarkers, and potential therapeutic targets. Limitations included small or single-center cohorts, heterogeneous designs, and limited validation, restricting generalizability and clinical translation.
CONCLUSIONS: Multi-omics approaches offer a powerful framework to uncover the molecular mechanisms underlying bone and muscle degeneration and to guide precision diagnostics and interventions. Future studies should prioritize large, multicenter, longitudinal designs integrating multi-omics data with clinical and functional validation to facilitate clinical application.}, }
@article {pmid41828538, year = {2026}, author = {Chen, J and Xu, Y and Liu, Z}, title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828538}, issn = {1422-0067}, mesh = {*Gastrointestinal Microbiome ; Animals ; Biotransformation ; Mice ; *Stress, Physiological ; Fermentation ; *Metabolic Networks and Pathways ; Lactiplantibacillus plantarum/metabolism ; Metabolomics/methods ; Male ; }, abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.}, }
@article {pmid41828642, year = {2026}, author = {Sadurski, J and Ostrowska, M and Staniszewski, A and Waśko, A}, title = {Genomic Plasticity and Functional Reweighting Facilitate Microbial Adaptation During the Ripening of Artisanal Goat Cheese.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828642}, issn = {1422-0067}, mesh = {*Cheese/microbiology ; Animals ; Goats ; *Genome, Bacterial ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Metagenome ; Food Microbiology ; Phylogeny ; }, abstract = {This study presents a genome-resolved shotgun metagenomic analysis of artisanal raw-milk goat cheese from the Masurian region of Poland, addressing the limited understanding of strain-level diversification and functional restructuring during traditional cheese ripening. While microbial succession in cheese has been widely described, comprehensive genome-resolved analyses integrating strain-level genomic heterogeneity, pathway reweighting, and mobile genetic elements in artisanal goat cheese remain scarce. By combining taxonomic profiling with metagenome-assembled genome (MAG) reconstruction and pathway-level functional analysis, we characterised microbial succession and genome plasticity across ripening stages. Genome reconstruction yielded 37 MAGs during early ripening and 141 MAGs in mature cheese, revealing increased genome recoverability and pronounced strain-level heterogeneity within dominant taxa, including Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, and Lactococcus lactis. Alpha diversity increased in mature samples, consistent with progressive community restructuring. Functional profiling demonstrated coordinated metabolic reweighting, particularly within carbohydrate metabolism, while amino acid and lipid metabolism remained proportionally stable. Genome-resolved analyses further identified tetracycline- and sulfonamide-associated resistance determinants and diverse bacteriophages targeting lactic acid bacteria, highlighting the role of mobile genetic elements in horizontal gene transfer and microevolutionary adaptation during ripening.}, }
@article {pmid41828944, year = {2026}, author = {Xu, S and Zhang, B and Liang, W and Jia, M and Guo, X and Su, B and Wang, R and Pan, Y and Lin, Y and Li, X and Hu, D and Yan, D}, title = {Comparative Analysis of Gut Microbiota and Metabolome of Captive Male Malayan Pangolins with Normal and Abnormal Reproduction.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41828944}, issn = {2076-2615}, support = {1(2024GXNSFBA010369);2(Forestry Science No. 202301);3(JA-23-03-01); 5(2024RT05)//1Guangxi Natural Science Foundation;2Basic Research Project of Guangxi Forestry Research Institute; 3Key Laboratory Project of Guangxi Characteristic Economic Forest Cultivation and Utilization;4Guangxi's first batch of Young Talents Support Program (Natu/ ; }, abstract = {Ex-situ conservation and captive breeding are important measures for protecting endangered species. However, captive conditions inhibit reproduction in some wild animals, especially males. Under captive conditions, which differentially expressed microbiota and metabolites significantly influence or are key to reproductive performance? This study aimed to investigate the effects of differentially expressed microbiota and metabolites on reproductive performance, including male Malayan pangolins with normal reproductive behavior (NR, with natural mating behavior) and those with abnormal reproductive behavior (AR, without natural mating behavior). Five male Malayan pangolins with normal reproductive behavior and eight with abnormal reproductive behavior were divided into NR and AR groups. Fresh fecal samples were collected for metagenomic and metabolomic analysis. The results showed that Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, and Fusobacteriota were the dominant phyla. Escherichia, Lactobacillus, Lactococcus, Limosilactobacillus, and Ligilactobacillus were the dominant genera. The abundance of Absiella, Butyribacter, and Candidatus Scatovivens in the gut of the NR group was significantly higher than in the AR group (p < 0.05), while the abundance of Clostridium, Mycoplasmopsis, and Facklamia in the gut of the AR group was significantly higher than in the NR group. A total of 94 differentially expressed metabolites were identified, with Argininosuccinic acid and Cortol significantly upregulated in the AR group, and gamma-Aminobutyric acid and gamma-Glutamylglutamic acid significantly downregulated. These microbiota and metabolites can be screened as potential key biomarkers that might influence the reproductive performance of male pangolins. These findings provide important insights into the husbandry and management of captive pangolins and other endangered wild animals.}, }
@article {pmid41829143, year = {2026}, author = {Song, D and Song, L and Luo, Y and Chen, J and Zhang, C and Yang, L}, title = {Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829143}, issn = {2304-8158}, support = {NSFC 32460269//National Natural Science Foundation of China/ ; QianKeHeJiChu- ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; MTXYTD202501//The Science and Technology Innovation Team of Maotai Institute/ ; mygccrc[2022]011//Research Foundation for Scientific Scholars of Moutai Institute/ ; mygccrc [2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; mygccrc [2022]026//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Group Co., Ltd./ ; }, abstract = {The production of Chinese Baijiu relies on the synergistic metabolism of multi-species microbial communities in an open environment. Its intricate microbial succession and flavor formation mechanisms have long been considered complex systems that are difficult to fully deconstruct. Traditional culture-dependent techniques inherently fail to comprehensively capture the actual functional roles and dynamic regulation of "viable but non-culturable" (VBNC) microorganisms within this complex system. In recent years, the rapid advancement of multi-omics technologies has offered a novel perspective for elucidating the underlying fermentation mechanisms of Baijiu. This paper systematically reviews the recent progress in the application of metagenomics, metatranscriptomics, metaproteomics, and metabolomics in Baijiu research. Specific focus is placed on the unique contributions of these tools to resolving microbial community structural diversity, mining key functional genes and enzymes, uncovering microbial stress response mechanisms under environmental fluctuations, identifying phages and spoilage microorganisms, and tracing the metabolic pathways of flavor substances. Furthermore, the pivotal role of multi-omics integration strategies in constructing "microbe-metabolite" regulatory networks is highlighted. Finally, current challenges regarding standardization and data integration are discussed, with an outlook on leveraging omics big data to promote digital monitoring and intelligent brewing in the Baijiu industry.}, }
@article {pmid41829938, year = {2026}, author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW}, title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829938}, issn = {2072-6643}, support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Dietary Supplements ; Male ; Whey Proteins/administration & dosage ; Young Adult ; Adult ; Pea Proteins/administration & dosage ; *Plant Proteins/administration & dosage ; Oryza ; Resistance Training ; *Soccer ; RNA, Ribosomal, 16S/genetics ; Athletes ; *Animal Proteins, Dietary/administration & dosage ; Animals ; }, abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.
METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.
RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.
CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.}, }
@article {pmid41830297, year = {2026}, author = {Chen, W and Zhang, L and Zhang, W}, title = {Integrated multi-omics elucidates the microbial-metabolite interplay governing antioxidant capacity in mung bean sour liquid.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70579}, pmid = {41830297}, issn = {1097-0010}, support = {262102111058//Department of Science and Technology of Henan Province, P.R. China/ ; }, abstract = {BACKGROUND: Mung bean sour liquid (MBSL) is a traditional fermented food, yet the microbial-metabolic basis of its antioxidant capacity is unclear. This study employed integrated metagenomics and metabolomics to elucidate the dynamic formation of antioxidant biomarkers during fermentation.
RESULTS: The mid-fermentation stage (6-12 h) was critical for antioxidant development, marked by peak accumulation of key biomarkers such as phenyllactic acid, epigallocatechin and catechin. Antioxidant activity [2,2-diphenyl-1-picrylhydrazyl/2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)] (DPPH/ABTS) significantly increased during this period, reaching 77.4% and 74.5% by 24 h. These changes were directly correlated with specific Lactobacillus spp. (e.g. Lactobacillus curvatus and Lactobacillus mudanjiangensis). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed stage-specific metabolic reprogramming, from early activation of amino acid/lipid metabolism to late-phase downregulation of central carbon metabolism. Correlation networks further linked these Lactobacilli to key carbohydrate-active enzymes (CAZy), such as glycoside hydrolases.
CONCLUSION: This study decipheedr the microbial-driven metabolomic remodeling that governs antioxidant capacity in MBSL, demonstrating a clear temporal alignment between key metabolite accumulation and functional enhancement. This work decodes the scientific basis of its traditional value and establishes a robust foundation for its targeted optimization and development as a health-promoting functional beverage. © 2026 Society of Chemical Industry.}, }
@article {pmid41830759, year = {2026}, author = {Nasir, MM and Qayyum, H and Shuhui, S and Ali, A and Kayani, MUR}, title = {MetaBolt: A computationally efficient pipeline for the rapid recovery of metagenome-assembled genomes.}, journal = {Computational biology and chemistry}, volume = {123}, number = {}, pages = {109006}, doi = {10.1016/j.compbiolchem.2026.109006}, pmid = {41830759}, issn = {1476-928X}, abstract = {Metagenome-resolved metagenomics refers to the recovery of metagenome-assembled genomes from the metagenomic datasets. It is a multi-step and laborious process that requires substantial computational resources and technical expertise. Though various semi-automated pipelines have been developed to automate the recovery process, high computational requirements remain a major bottleneck. Since de novo assembly is the key step that consumes higher computational time and resources, optimizing this step can address the underlying challenges. Hence, to address these limitations, we introduce MetaBolt, an automated Nextflow-based pipeline designed for the rapid recovery of metagenome-assembled genomes from short-read metagenomic datasets. Based on an empirically optimized set of k-mers for MEGAHIT-based assembly, this pipeline offers a unique solution. When tested on both real and simulated metagenomic datasets, it consistently exhibited efficient performance within reduced computational time. From gut metagenomes, MetaBolt recovered MAGs at a 2.3 and 3.8-times faster rate than nf-core/mag and MetaWRAP, respectively, while recovering ∼5% more high-quality MAGs compared to the other two pipelines. Whereas, in the case of real metagenome samples, it reduced the computational times to 2-4%, particularly for low-biomass samples. By integrating optimized assembly parameters with automated workflow management, MetaBolt lowers computational barriers to genome-resolved metagenomics without compromising output quality. MetaBolt is available on the web at https://github.com/muneebdev7/metabolt.}, }
@article {pmid41830810, year = {2026}, author = {Martins, IB and Silva, JM and Almeida, JR}, title = {A systematic review and benchmarking of modern metagenomic tools for taxonomic classification.}, journal = {Computers in biology and medicine}, volume = {206}, number = {}, pages = {111600}, doi = {10.1016/j.compbiomed.2026.111600}, pmid = {41830810}, issn = {1879-0534}, mesh = {*Metagenomics/methods ; *Software ; Benchmarking ; Computational Biology/methods ; Databases, Genetic ; Humans ; }, abstract = {Advancements in metagenomics have been driven by the continuous development of bioinformatic tools, particularly taxonomic classification software, which are central to the accurate characterization of microbial communities. However, establishing direct comparisons between these tools remains challenging due to variations in evaluation metrics, reference databases, and input data types. In this study, we present a systematic review of recently developed metagenomic taxonomic classification tools. Of the 31 identified tools, nine satisfied all functional and methodological criteria for the benchmark analysis. We evaluated their accuracy and computational performance using a standardized dataset derived from the NCBI RefSeq database. Our analysis revealed that most of these tools are domain-specific, each excelling in particular areas. Tools like TAMA, CAMITAX and PhyloFlash achieved higher accuracy for prokaryotic organisms, while ViWrap and PhaBOX achieved higher accuracy for viral classifications. SqueezeMeta achieved high F1 scores across most domains, though its assembly-based architecture limits effectiveness on highly diverse samples. MegaPath-Nano was least affected by increased mutation rates. The execution time varied widely among the tools, with domain-specific and machine learning-based tools generally being faster, while tools like BASTA had longer runtimes and lower accuracy. This review synthesizes performance results for current tools, providing an overview of their strengths and computational methodologies.}, }
@article {pmid41831184, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Venkataraman, P and Arunachalam, R and Pramanik, R and Dharne, M and Gopal, D}, title = {Integrated omics analyses reveal insights into microbial dark matter associated with deep-sea water in Central Indian Ocean.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41831184}, issn = {1573-0972}, support = {DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; }, }
@article {pmid41831290, year = {2026}, author = {Tang, Z and Li, Y and Zhang, L and Xi, B and Tan, W and Yuan, Y}, title = {Space-for-time substitution reveals mechanisms driving heavy metal induced dynamics of antibiotic resistance genes of varying risk levels in landfill leachate.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141740}, doi = {10.1016/j.jhazmat.2026.141740}, pmid = {41831290}, issn = {1873-3336}, abstract = {Landfills are recognized as persistent reservoirs of antibiotic resistance genes (ARGs); however, the temporal dynamics of their risk profiles after closure remain poorly understood. Because long-term monitoring of ARG risks in landfill leachate is challenging, a "space-for-time" substitution was employed to characterize ARGs, metal resistance genes (MRGs), mobile genetic elements (MGEs), and microbial hosts in landfill leachate at three stages: unclosed landfills (UL), landfills closed for 1-5 years (CF), and landfills closed for more than 6 years (CS). Metagenomic analyses identified 518 ARG subtypes across 22 classes. ARG abundance peaked in the CF stage (1.28 copies/cell), significantly higher than in UL (0.292 copies/cell) and CS (0.597 copies/cell) stages (p < 0.05). Elevated concentrations of nickel, copper, and arsenic during the CF stage promoted ARG enrichment via co-selection, primarily driven by efflux pump-mediated cross-resistance and co-resistance within ARG-MRG clusters. IntI1 was strongly linked to high-risk ARGs, indicating horizontal gene transfer as a major dissemination pathway. Key bacterial hosts, including Pseudomonas spp. and Escherichia coli, harbored both ARGs and MRGs. These findings highlight the early post-closure period (1-5 years) as a critical surveillance window and support targeted monitoring of high-risk ARGs, MGEs, indicator taxa, and heavy metals to mitigate environmental dissemination of antibiotic resistance.}, }
@article {pmid41831647, year = {2026}, author = {Tashiguano, VM and Sierra, K and Black, MT and Sirmon, M and Leeds, P and Jones, J and Doster, J and Smith, C and Jia, Z and Garner, L and Cho, S and Hanna, J and Trout, K and Almasri, M and Li, H and Morey, A}, title = {A Multidisciplinary Approach for Predicting the Microbiological Spoilage of Chicken Breast Fillets due to Cold-Chain Disruption.}, journal = {Journal of food protection}, volume = {89}, number = {5}, pages = {100754}, doi = {10.1016/j.jfp.2026.100754}, pmid = {41831647}, issn = {1944-9097}, abstract = {Cold-chain disruptions during the storage and distribution of raw poultry can significantly reduce product shelf-life and safety. This study evaluated the effects of short-term cyclic temperature abuse (TA) on the retail shelf-life of fresh chicken breast, using a multidisciplinary approach that combined food microbiology, machine learning (ML), metagenomics, and volatile compound (VC) analysis. Boneless, skinless chicken breast trays (n = 450) were obtained from a commercial poultry processor and transported under refrigeration (4 °C) to Auburn University. In three independent trials, trays were randomly assigned to one of three treatments: (1) Control at 4 °C for 24 h; (2) TA Cycle 1: alternating 30 min at 4 °C and 1 h at 30 °C; and (3) TA Cycle 2: alternating 30 min at 4 °C and 1 h at 37 °C. TA cycles lasted 7.5 h, after which all trays were stored at 4 °C. Samples were analyzed on days 0, 2, 4, 6, and 8 for aerobic, facultative anaerobic, and lactic acid bacteria (LAB) counts, and for VCs using an electronic nose. Rinsates from Trial 3 were stored at -80 °C for metagenomic analysis. TA Cycle 2 resulted in the highest spoilage rates, followed by TA Cycle 1. A neural network model moderately predicted bacterial growth (R[2] = 0.65-0.75 for aerobic and facultative anaerobic microorganisms; lower for LAB). Metagenomics demonstrated a shift toward Pseudomonas spp. dominance under TA conditions, while control samples retained microbial diversity. These findings underscore that even short-term TA significantly alters the microbiome and accelerates spoilage in raw poultry, emphasizing the importance of cold-chain integrity. Practical Relevance. This study shows that short, high-temperature abuse events from refrigeration failure, handling delays, or other supply chain disruptions can accelerate spoilage in raw chicken. By combining rapid spoilage-detection tools with predictive models, poultry producers and retailers may better monitor these events, helping to maintain cold-chain integrity and reduce losses.}, }
@article {pmid41831799, year = {2026}, author = {Qi, H and Wu, R and Liao, J and Alvarez, PJJ and Yu, P}, title = {Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134410}, doi = {10.1016/j.biortech.2026.134410}, pmid = {41831799}, issn = {1873-2976}, mesh = {*Sewage/microbiology/virology ; *Bacteria/genetics/virology ; Symbiosis ; Metagenome ; Microbiota ; Bacteriophages/genetics ; Multiomics ; }, abstract = {Virus-prokaryote interactions within microbial aggregates critically influence microbiome function and stability, yet the interactive dynamics during microbial aggregation remain largely unexplored. Here, longitudinal multi-omics revealed that prokaryotic host community diversity underwent decline and subsequent recovery during algal-bacterial granular sludge (ABGS) formation from activated sludge. Declined host diversity in the collapse phase enriched for lysogenic viruses and facilitated virus-host mutualistic symbiosis, during which the proportion of lysogenic metagenome-assembled genomes (MAGs) peaked at 84% (841,649 TPM), with auxiliary metabolic genes (AMGs) primarily involved in genetic information processing and amino acid metabolism. Moreover, low host diversity increased viral microdiversity by 1.97-fold and selected for virion structure genes that were conducive to viral fitness and replication. As host diversity recovered during the recovery phase, viruses and hosts engaged in an evolutionary arms race, with both host defense systems (DS) (Spearman's Rho = 0.68, P < 0.05) and viral anti-defense systems (ADS) (Spearman's Rho = 0.51, P < 0.05) enriched along with granule maturation. Furthermore, active lysogenic infections were accompanied by the dissemination of AMGs predominantly associated with the metabolism of cofactors, vitamins, terpenoids, and polyketides. Despite their phase-dependent functional profiles, lysogenic phages with AMGs putatively enhanced the structural and functional stability of the microbiome during ABGS formation. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and prokaryotic hosts during ABGS formation, providing insights into virus-mediated microbial structural and functional resilience in engineered ecosystems.}, }
@article {pmid41831800, year = {2026}, author = {Xie, J and Zhu, W and Wang, W and Min, B and Xu, J and Xie, L}, title = {Optimizing anaerobic digestion for antibiotic degradation and antimicrobial resistance mitigation.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134409}, doi = {10.1016/j.biortech.2026.134409}, pmid = {41831800}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is widely applied to treat antibiotic pharmaceutical wastewater for antimicrobial resistance mitigation and synchronous bio-energy recovery. However, process efficiency and risk control depend critically on operational strategies. Here, we systematically evaluated the roles of feedstock composition and digestive temperature in optimizing lincomycin-containing AD. Glucose-rich mesophilic digestion achieved superior lincomycin degradation and methane recovery compared to thermophilic and protein-rich systems. Transformation product analysis suggested that glucose-rich feedstock might facilitate the furan ring-opening step during lincomycin degradation, possibly owing to structural and metabolic similarities between glucose and lincomycin. The enrichment of lincomycin-degrading Clostridium and Methanobacterium in response to glucose-rich mesophilic condition, together with their potential syntrophic interaction, further supported the accelerated lincomycin degradation and methanation. Metagenome-assembled genome analysis revealed that protein-rich and thermophilic operation intensified the proliferation of host consortia harboring gene clusters with antibiotic resistance gene-mobile genetic element (ARG-MGE) co-occurrence, and induced putative horizontal transfer of ARG, resulting in the increased ARG abundance. ARG proliferation in thermophilic systems was associated with enrichment of lincomycin-resistant consortia (JAAYZQ01 sp034428935 and Tenuifilum sp018056955) after antibiotic exposure, which preferentially enriched under higher-temperature conditions. In contrast, glucose-rich digesters exhibited a reduced potential for horizontal gene transfer mediated by MGEs and natural conjugation. Overall, feedstock composition exerted a greater influence on antimicrobial resistance dissemination compared to temperature. Collectively, our findings provide an operational framework for sustainable treatment and valorization of antibiotic-containing wastewater.}, }
@article {pmid41831863, year = {2026}, author = {Patel, SS and Shree, T and Kumar, A}, title = {Microbial consortia interactions and bioremediation of pesticides: A review on designing, mechanism and efficacy.}, journal = {Pesticide biochemistry and physiology}, volume = {219}, number = {}, pages = {106993}, doi = {10.1016/j.pestbp.2026.106993}, pmid = {41831863}, issn = {1095-9939}, mesh = {*Pesticides/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {Ecosystems and human health are at serious risk due to the extensive application of pesticides in the agricultural system for controlling pests and diseases. The use of microbial consortia (MicroCons) has emerged as a promising solution for the remediation of pesticide-contaminated soil, offering a sustainable and eco-friendly alternative to physical and chemical methods; however, a systematic review on this aspect is still lacking. This comprehensive review provides an in-depth analysis of the current knowledge on microbial consortia-based remediation of pesticides in agricultural soil. Efficacy of single-strain vs multiple strains in MicroCons have been discussed to unravel the workload distribution between microbial strains in pesticide degradation. We also discuss the design and optimization of microbial consortia for remediation, highlighting the role of advanced tools and the mechanisms of MicroCons action. Furthermore, emerging trends and future directions in the field, including the potential of synthetic biology, machine learning (ML), and artificial intelligence (AI) are also covered. This review aims to critically expand the mechanistic understanding of how microbe-mediated remediation strategies might reduce pesticide phytotoxicity, enhance crop production in pesticide-stressed soils, and inspire future research and practices in MicroCons-based remediation to achieve the Sustainable Development Goals (SDGs).}, }
@article {pmid41831922, year = {2026}, author = {Kashyap, B and Jayaraj, H and Rajpal, S and Sidiq, Z and Arora, VK}, title = {Landscape of metagenomics: fight against tuberculosis and other infectious disease in India.}, journal = {The Indian journal of tuberculosis}, volume = {73}, number = {1}, pages = {13-16}, doi = {10.1016/j.ijtb.2026.02.012}, pmid = {41831922}, issn = {0019-5707}, mesh = {Humans ; *Metagenomics/methods ; India ; *Tuberculosis/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomics is an evolving diagnostic tool worldwide for studying microorganisms which cannot be cultured in routine laboratory settings. From Sanger sequencing to Next Generation Sequencing like Illumina, and now Oxford Nanopore sequencing has been a boon in detecting difficult-to-diagnose infectious disease conditions and delivering patient-tailored treatment. In developing countries like India, these advancements in diagnostics aid in decreasing disease burden, growing antimicrobial resistance and to study new microorganism.}, }
@article {pmid41832076, year = {2026}, author = {Gundra, SR and Jiang, W and Aouida, M and Wang, Q and Kazlak, AM and Elbehery, AHA and Saleh, A and Masood, M and Ghouneimy, A and Mahfouz, M}, title = {Characterization and engineering of highly efficient Cas12j genome editors.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2026.02.001}, pmid = {41832076}, issn = {1879-3096}, abstract = {The large size of widely used CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) enzymes limits their delivery for therapeutic applications. Cas12j nucleases offer a hypercompact alternative but show modest editing efficiency. To overcome this limitation, we identified eight novel Cas12j orthologs from viral metagenomes, which in their native form exhibit low editing activity in mammalian cells. We therefore engineered T5 exonuclease-Cas12j fusions, resulting in substantially enhanced genome-editing activity across multiple mammalian cell types, reaching levels comparable to established compact CRISPR-Cas editors. Intriguingly, robust cellular editing occurred in the presence of a previously unrecognized trinucleotide sequence context within the target DNA. Furthermore, we developed Cas12j-based adenine base editors by coupling catalytically inactive Cas12j orthologs with adenine deaminase, enabling efficient A-to-G base conversion in mammalian cells. This study expands the CRISPR toolbox by establishing engineering principles that convert compact Cas12j nucleases into efficient and modular genome-editing platforms well suited for delivery-constrained therapeutic applications.}, }
@article {pmid41832122, year = {2026}, author = {Van Etten, J and Johnson, MD}, title = {The ecology of horizontal gene transfer.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2026.02.002}, pmid = {41832122}, issn = {0168-9525}, abstract = {Horizontal gene transfer (HGT) generates genetic variation in populations across all domains of life; however, most studies focus on individual transfers and functional information derived therefrom. This is useful but does not consider DNA transfer more broadly, that is, nongene transfers, donor-recipient dynamics, or trends and background levels that may help infer ecological information. Here, we review the mechanistic underpinnings of DNA transfer, literature from diverse fields that addresses HGT on a community basis and the associated methodological challenges, and propose a framework for conceptualizing the process of DNA transfer, highlighting DNA mobility as a feature of community ecology and DNA itself as a public good. These ideas coalesce to support DNA transfer as a fundamental ecological phenomenon that remains largely unmeasured.}, }
@article {pmid41832496, year = {2026}, author = {Ali, S and Hassan, M and Essam, T and Abdelmalek, S and Al-Amry, KF}, title = {Antimicrobial resistance profiling in poultry industry: a culture-independent resistome analysis and risk factor assessment.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05334-w}, pmid = {41832496}, issn = {1746-6148}, }
@article {pmid41833387, year = {2026}, author = {Han, Z and Wang, Y and Yang, J}, title = {Physiological and Biochemical Changes and Microbial Community Succession During the Postharvest Rot Process of Stropharia rugosoannulata.}, journal = {The Journal of general and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2323/jgam.2026.03.001}, pmid = {41833387}, issn = {1349-8037}, abstract = {This study systematically elucidated the microbial community succession and functional gene dynamics during the postharvest spoilage process of Stropharia rugosoannulata by integrating physiological and biochemical indicators with metagenomic analysis. The experimental results demonstrated that as storage time extended, the activities of antioxidant enzymes (superoxide dismutase, peroxidase) in S. rugosoannulata significantly declined, while the content of membrane lipid peroxidation product malondialdehyde increased, leading to compromised cell membrane integrity and creating favorable conditions for microbial colonization. Metagenomic analysis revealed that during the spoilage phase (post-harvest day 14), the relative abundance of Pseudomonadota increased to 85.7%, with Pseudomonas replacing Ewingella as the absolutely dominant microbial population. Further functional gene analysis showed that the post-harvest day 14 exhibited significant enrichment of glycosyltransferases (GT0, GT1, GT2, GT4) and carbohydrate-binding modules (CBM10, CBM16, CBM50), along with pectinase (GH78), chitinase (GH19), and polysaccharide-modifying enzymes (CE4, CE11). This indicated a metabolic shift towards cell wall synthesis and substrate recognition. In contrast, the post-harvest day 7, prior to fruiting body softening, demonstrated high expression of glycoside hydrolases (GH1, GH2, GH4, GH94) and carbohydrate esterase CE8, focusing on the degradation of cellulose and starch. These findings, for the first time from a molecular ecology perspective, clarify that the essence of postharvest spoilage in S. rugosoannulata is a quality deterioration process driven by a Pseudomonas-dominated microbial community. The study provided a basis for the development of targeted antibacterial preservation strategies.}, }
@article {pmid41833574, year = {2026}, author = {Saibu, S and Obayori, OS and Diagboya, PN and Oso, SO and Shedrack, AE and Agbomeji, RO and Eletu, MO and Ajibike, OR and Ishola, FM and Adimabua, RN and Oyetibo, GO}, title = {Spatial variation in bacterial community structure and pollution response in river sediment.}, journal = {Journal of contaminant hydrology}, volume = {279}, number = {}, pages = {104923}, doi = {10.1016/j.jconhyd.2026.104923}, pmid = {41833574}, issn = {1873-6009}, abstract = {Rivers are unique ecosystems where pollution frequently occurs, altering the biogeochemical characteristics of both water bodies and sediments. However, little is known about the effects of human activities on the lower course of River Ogun. This study assessed the association between anthropogenic activities and sediment bacterial communities at the time of sampling by comparing sediment physicochemical properties and the bacterial community structures of samples. Samples were taken from four distinct sites along the lower course of the river. Bacterial community structure of these sites was investigated using the 16S rRNA gene PacBio sequencing. Total polycyclic aromatic hydrocarbons (PAHs) were lowest at Location B (6.95 mg/kg) and highest at Location A (15.6 mg/kg). The dominant bacterial phyla in the sediments were Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. A notable abundance of Thauera was observed across all the locations, particularly at Location A, and Psychrobacter known for plastic degradation was detected exclusively at this site. Among all the sites, Location A exhibited the lowest bacterial diversity, as indicated by both species' richness and evenness, where the Thauera selenatis group and Psychrobacter maritimus were dominant. Location B exhibited the highest bacterial diversity, Location C and D displayed intermediate diversity, sharing a 40% similarity index. Environmental variables that significantly explained beta diversity patterns included pH, anthracene and fluoranthene. This study provides insights into bacterial metagenomes of a freshwater inundated with plastics, heavy metals and consortium of persistent organic compounds. The findings highlight the value of integrating metagenomic and physicochemical analyses to identify correlations that help explain the key drivers shaping ecosystem dynamics.}, }
@article {pmid41833938, year = {2026}, author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L}, title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00964-2}, pmid = {41833938}, issn = {2055-5008}, support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.}, }
@article {pmid41834217, year = {2026}, author = {Yuan, X and Gong, H and Zhang, L and Liu, Y and Zhou, M and Liu, Y and Tang, J and Pan, S and Xu, X and Wang, Y and Zhang, X and Zhang, T and Song, J}, title = {T2DM-Induced Gut Dysbiosis Exacerbates Periodontitis Through Intestinal Barrier Disruption and Redox Imbalance.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70116}, pmid = {41834217}, issn = {1600-051X}, support = {U22A20314//National Natural Science Foundation of China/ ; 82170968//National Natural Science Foundation of China/ ; 82301082//National Natural Science Foundation of China/ ; 2022YFC2504200//National Key Research and Development Program of China/ ; 2025MD774176//China Postdoctoral Science Foundation/ ; YXQN202401//Chongqing Youth Talent Support Program/ ; }, abstract = {AIM: To investigate the potential role and underlying mechanisms of gut microbiota in type 2 diabetes mellitus (T2DM)-exacerbated periodontitis.
MATERIALS AND METHODS: A T2DM-associated periodontitis model was established in C57BL/6 mice and analysed using multi-omics sequencing (16S rRNA, metagenomics and metabolomics). Faecal microbiota transplantation (FMT) from T2DM donors was carried out in recipient mice to investigate the impact of gut dysbiosis on periodontitis. FMT from healthy donors, supplementation of intestinal barrier protectant or the metabolite oleic acid (OA) was administered to mice with T2DM-associated gut dysbiosis to examine their ameliorative effects on periodontal damage.
RESULTS: T2DM-associated gut dysbiosis, independent of hyperglycaemia, triggered intestinal barrier disruption, which disturbed systemic redox-related metabolisms and elevated oral oxidative stress, thereby aggravating periodontitis. Restoring gut microbiota via FMT from a healthy donor or protecting the intestinal barrier ameliorated periodontitis. Exogenous supplementary metabolite OA rescued periodontal damage by activating the SIRT1/FoxO1 pathway and enhancing antioxidant enzymes in mice with T2DM-associated gut dysbiosis.
CONCLUSIONS: T2DM-induced gut dysbiosis exacerbates periodontitis through intestinal barrier disruption and redox imbalance. These findings provide new adjunctive therapeutic perspectives including microbiota restoration, intestinal barrier protection and antioxidant supplementation for managing patients with T2DM-induced periodontitis.}, }
@article {pmid41834639, year = {2026}, author = {Soliman, MS and Abbas, AM and Algebaly, HF and El-Kholy, AA and Soliman, NS}, title = {Metagenomics profiling of the lower respiratory tract microbiome and relevant respiratory pathogens in pediatric intensive care unit patients: a pilot exploratory study in Egypt.}, journal = {Acute and critical care}, volume = {41}, number = {1}, pages = {136-147}, pmid = {41834639}, issn = {2586-6060}, abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of mortality in children. These infections disrupt the equilibrium of lower respiratory tract (LRT) microbiota, allowing respiratory pathogens to dominate. The conventional culture method has limitations in describing complex microbiomes and may fail in the detection of respiratory pathogens. In the present study, we sought to use the advanced technology of 16S metagenomics next-generation sequencing (16SmNGS) to characterize the LRT microbiome among children with LRTIs and to identify the underlying respiratory pathogens that commonly evade detection by traditional culture.
METHODS: Twenty LRT specimens from hospitalized children with LRTIs were analyzed using 16SmNGS, as well as standard microbiological culture.
RESULTS: The 16SmNGS taxonomical analysis revealed the highest relative abundances for Streptococcus (27.7%) and Escherichia (13.3%) genera, which belong to the phyla of Firmicutes (45.4%) and Proteobacteria (45.3%), respectively. Streptococcus pneumoniae (45%), Escherichia coli (45%), Pseudomonas aeruginosa (15%), Staphylococcus aureus (10%), Acinetobacter baumannii (5%), and Haemophilus influenzae (5%) were the primary respiratory pathogens. Conventional culture failed to detect growth in 100%, 77.7%, and 55.5% of 16SmNGS-positive specimens for H. influenza, S. pneumoniae, and E. coli, respectively.
CONCLUSIONS: The 16SmNGS technique revealed a predominance of Streptococcus and Escherichia genera belonging to the phyla of Firmicutes and Proteobacteria in pediatric LRTIs. In this exploratory study, 16SmNGS was able to enhance the identification of significant respiratory pathogens, particularly those difficult to isolate in culture. However, to rule out contamination by flora, it is advisable not to interpret metagenomics results independently from culture, clinical, and radiological data. In addition, further clinical correlations are desired to reach appropriate clinical decisions.}, }
@article {pmid41834860, year = {2026}, author = {Du, Y and Chen, L and Zhang, X and Zeng, J and Hu, C}, title = {Based on untargeted metabolomics and metagenomics: a study on the mechanism of Miao ethnomedicine Zingiber mioga (Thunb.) Rosc. in treating slow transit constipation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751739}, pmid = {41834860}, issn = {1664-302X}, abstract = {INTRODUCTION: Slow transit constipation (STC) is a prevalent gastrointestinal disorder characterized by impaired intestinal motility, metabolic dysregulation, and gut microbial dysbiosis. Zingiber mioga (Thunb.) Rosc. (RH), a traditional medicinal-edible plant, is empirically used to alleviate gastrointestinal dysfunction, but its therapeutic mechanisms in STC remain unclear. Herein, we investigated the laxative efficacy and mechanism of RH in a rat STC model via integrated untargeted metabolomic and metagenomic analyses, providing experimental evidence for its clinical use.
METHODS: A rat STC model was established by intragastric loperamide hydrochloride (5 mg/kg) for 35 consecutive days. Thirty-six SD rats were randomly divided into six groups (n = 6): normal control, STC model, mosapride-positive control (2 mg/kg), and low- (1350 mg/kg), medium- (2700 mg/kg), high-dose (3400 mg/kg) RH groups, with concurrent drug intervention. Serum concentrations of SP, MTL, and GAS (key gastrointestinal motility regulators) were quantified. Colonic pathological damage was histopathologically evaluated, and intestinal propulsive rate was measured. Untargeted serum metabolomics and fecalmetagenomics identified differential metabolites and gut microbiota alterations.
RESULTS: Compared with the STC model, RH significantly reduced serum SP (intestinal motility inhibitor) and increased MTL/GAS (motility promoters). It also dose-dependently ameliorated colonic lesions and improved intestinal propulsive rate. Serum metabolomics identified 15 differential metabolites, mainly enriched in nitrogen metabolism, neuroactive ligand-receptor interaction, and amino acid metabolism. Fecal metagenomics showed RH restored the Eubacteriales/Lachnospirales ratio (a STC dysbiosis marker) and increased beneficial genera (e.g., Ruminococcus sp., Eubacterium sp.).
DISCUSSION AND CONCLUSION: Our findings show RH effectively ameliorates colonic injury and gastrointestinal motility in STC rats, associated with regulating gastrointestinal hormone secretion. Its benefits are likely mediated by improving dysregulated amino acid/nitrogen metabolism and modulating gut microbiota composition. This study provides mechanistic evidence for RH as a natural functional agent for STC management, laying a foundation for exploring its active components and clinical translation.}, }
@article {pmid41834868, year = {2026}, author = {Niu, M and Pan, J and Guo, Y and Zhang, F and Guan, H and Yang, X and Li, H and Xiong, H and Zhang, Y and Chen, Y}, title = {Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761712}, pmid = {41834868}, issn = {1664-302X}, abstract = {BACKGROUND: Neonatal jaundice is a common condition, yet inter-individual variation in its onset and severity cannot be fully explained by traditional clinical risk factors. Emerging evidence suggests that the infant gut microbiome may modulate bilirubin metabolism, but its compositional and functional signatures in jaundiced neonates remain incompletely defined. This study aimed to characterize the taxonomic and functional features of the gut microbiome in neonatal pathologic jaundice and to explore potential causal links using Mendelian randomization (MR).
METHODS: We conducted a case-control study of term infants with pathologic jaundice and matched healthy controls. Stool samples were subjected to shotgun metagenomic sequencing to assess microbial diversity, taxonomic composition, functional gene repertoires, and carbohydrate-active enzyme families, and publicly available genome-wide association study summary statistics were used to perform bidirectional MR between microbiome-related traits and neonatal jaundice.
RESULTS: Alpha diversity indices did not differ significantly between groups, whereas beta diversity based on Bray-Curtis dissimilarity showed clear separation of jaundiced and control infants, indicating a restructured microbial community rather than a simple loss of richness. Jaundiced neonates exhibited increased relative abundance of Gram-negative taxa, including Escherichia coli, and reduced levels of putatively beneficial genera such as Bifidobacterium and Lactobacillus. Functionally, pathways involved in bile acid synthesis and metabolism, carbohydrate and energy metabolism, and cofactor and vitamin biosynthesis were enriched in the jaundiced group, accompanied by marked shifts in carbohydrate-active enzyme profiles. Forward MR suggested that several microbial metabolic pathways exert genetically predicted effects on jaundice risk, whereas reverse MR provided little evidence that genetic liability to jaundice substantially alters microbiome traits.
CONCLUSIONS: Neonatal pathologic jaundice is associated with distinctive compositional and functional alterations in the gut microbiome. Genetic evidence from MR supports a potential causal contribution of specific microbial pathways to jaundice risk, highlighting candidate targets for microbiome-based prevention or adjunctive therapy in early life.}, }
@article {pmid41834872, year = {2026}, author = {Han, Z and Wang, H and Liu, X and Tian, Z and Gong, Q and Zhang, X and Li, X and Du, R and Hu, X and Xu, C}, title = {Cross-species transmission alert: a novel canine-raccoon dog coronavirus infecting an Amur Tiger in China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1764349}, pmid = {41834872}, issn = {1664-302X}, abstract = {Canine coronavirus (CCoV) is an important enteric alphacoronavirus primarily affecting canids. Here, we detected canine coronavirus RNA in a captive 9-year-old Amur tiger (Panthera tigris altaica) in China. The complete viral genome was obtained using metagenomic next-generation sequencing. Phylogenetic and recombination analyses were then performed to investigate its evolutionary relationship with canine and feline coronaviruses. The identified CCoV strain clustered within established canine coronavirus lineages and showed sequence evidence of recombination involving coronavirus strains previously reported in other carnivore species. Although the detection of viral RNA alone does not establish a causal relationship between CCoV infection and disease outcome, this study provides molecular evidence that Amur tigers are susceptible to canine coronavirus infection. These findings expand the known host range of CCoV and contribute to understanding the evolution and cross-species transmission potential of coronaviruses among carnivores.}, }
@article {pmid41834952, year = {2026}, author = {Tu, Y and Niu, C and Huang, Z}, title = {[Analysis of the Characteristics of the Oral Virome in Metabolic Dysfunction-Associated Fatty Liver Disease].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {65-72}, pmid = {41834952}, issn = {1672-173X}, mesh = {Humans ; *Virome ; *Saliva/virology ; Male ; Female ; Middle Aged ; Adult ; *Fatty Liver/virology ; *Mouth/virology ; *Dental Plaque/virology ; }, abstract = {OBJECTIVE: To investigate the characteristics of salivary and supragingival plaque viromes in patients with metabolic dysfunction-associated fatty liver disease (MAFLD), and provide new insights for noninvasive oral screening and ecological intervention for MAFLD.
METHODS: This study included 21 MAFLD patients and 20 healthy controls. Saliva and supragingival plaque samples were collected, and metagenomic sequencing was used to analyze the characteristics of the oral virome.
RESULTS: The α-diversity and β-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the α-diversity (Shannon index) and β-diversity (Bray-Curtis distance) of the supragingival plaque virome showed significant differences (P = 0.0303, P = 0.001). For species with a relative abundance greater than 0.1%, 14 viral species in saliva and 5 in supragingival plaque differed significantly in relative abundance between the two groups (P < 0.05), with multiple Streptococcus phages enriched in the saliva of MAFLD patients. LEfSe and random forest analyses identified potential biomarkers in saliva and supragingival plaque. Receiver operating characteristic (ROC) curve analysis showed strong diagnostic performance for these biomarkers in both saliva (area under the curve [AUC] = 0.9548, 95% CI: 0.8898-1.0000) and supragingival plaque (AUC = 0.8952, 95% CI: 0.7774-1.0000). Spearman correlation analysis revealed associations between viral species in saliva or supragingival plaque and various disease indicators (P < 0.05). Compared with healthy individuals, MAFLD patients showed higher node counts, significant relationship numbers, and average node degrees in the co-occurrence networks of salivary and supragingival plaque viromes.
CONCLUSION: Differences in the species composition and structure of the oral virome between MAFLD patients and healthy individuals suggest that oral viral species could serve as potential biomarkers for diagnosing MAFLD.}, }
@article {pmid41835009, year = {2026}, author = {Kariithi, HM and Volkening, JD and Mueni, SN and Helmy, MA and Afonso, CL and Chaudhari, PP and Decanini, EL}, title = {Co-detection and genomic characterization of avian rotavirus A, avian orthoreovirus, and chicken megrivirus-C using nontargeted metagenomic surveillance in Indian broiler chickens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1690222}, pmid = {41835009}, issn = {2235-2988}, mesh = {Animals ; *Chickens/virology ; *Poultry Diseases/virology/epidemiology ; *Orthoreovirus, Avian/genetics/isolation & purification/classification ; Genome, Viral ; *Rotavirus/genetics/isolation & purification/classification ; Metagenomics ; *Reoviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; India/epidemiology ; *Rotavirus Infections/veterinary/virology/epidemiology ; Coinfection/virology/veterinary ; Genotype ; High-Throughput Nucleotide Sequencing ; Genomics ; *Orthoreovirus/genetics/isolation & purification/classification ; }, abstract = {Nontargeted metagenomic surveillance of the poultry enteric virome reveals underrecognized threats to poultry health and productivity in intensive production systems. In South Asia, avian rotavirus A (AvRV-A) and avian orthoreovirus (ARV) are frequently detected in broilers by conventional diagnostics, whereas chicken megrivirus genotype C (ChMeV-C) is often identified through metagenomic surveillance. Often present in both clinical disease and coinfections, these viruses may impair gut function, immune responses, and growth performance, yet their genomic diversity and evolutionary dynamics in poultry remain poorly characterized. Here, we report complete genomes of AvRV-A, ARV, and ChMeV-C strains co-detected via nontargeted metagenomic next-generation sequencing (ntNGS) in a pooled cloacal sample comprising 150 commercial broiler chickens (19 and 33 days old) collected from three commercial farms in Kamrup Rural District, Assam, Northeast India. Despite routine vaccination, all three flocks experienced > 10% mortality, poor weight gain, and postmortem lesions including pale kidneys and hepatomegaly. Phylogenetic analyses revealed segmental clustering in ARV and AvRV-A consistent with reassortment-driven divergence, though not supported by detectable recombination, while ChMeV-C clustered within a distinct C1 sublineage, suggesting intercontinental lineage connectivity and highlighting the need to expand regional genomic baseline data. We also identified nonsynonymous single nucleotide polymorphisms in several key viral proteins, including RNA-dependent RNA polymerases (VP1 of AvRV-A, λB of ARV, and 3D of ChMeV-C), capsid proteins (VP2 and VP7 of AvRV-A, λA and σB of ARV, and VP0 and VP1 of ChMeV-C), and replication-associated nonstructural proteins. These findings expand the genomic baseline for poultry enteric viruses in South Asia, reveal novel polymorphic signatures, and underscore the value of ntNGS-based metagenomic surveillance in virus detection, diversity monitoring, and informing vaccine and biosecurity strategies.}, }
@article {pmid41835092, year = {2026}, author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {130}, pmid = {41835092}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.}, }
@article {pmid41836173, year = {2026}, author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL}, title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20880}, pmid = {41836173}, issn = {2167-8359}, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; *Metagenomics ; *Culicidae/virology ; Brazil ; Phylogeny ; Female ; *Mosquito Vectors/virology ; Virome ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; }, abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.}, }
@article {pmid41836379, year = {2026}, author = {Wang, P and Pang, J and Xu, H and Wang, M and Lai, W and Hui, D and Cai, Q and Li, X and Zhu, J}, title = {Hemophagocytic lymphohistiocytosis directly triggered by peginterferon alfa-2b in a patient with chronic hepatitis B.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760610}, pmid = {41836379}, issn = {1664-3224}, mesh = {Humans ; Male ; Adult ; *Lymphohistiocytosis, Hemophagocytic/chemically induced/diagnosis/drug therapy/etiology ; Recombinant Proteins/adverse effects/therapeutic use ; *Polyethylene Glycols/adverse effects/therapeutic use ; *Hepatitis B, Chronic/drug therapy ; *Interferon alpha-2/adverse effects ; *Antiviral Agents/adverse effects/therapeutic use ; *Interferon-alpha/adverse effects ; }, abstract = {This case report describes a 42-year-old male with chronic hepatitis B (CHB) who developed hemophagocytic lymphohistiocytosis (HLH) following treatment with peginterferon alfa-2b (PegIFN-α-2b). The patient tolerated the initial injections well. After the 16th injection in February 2025, laboratory tests revealed cytopenia, prompting discontinuation of PegIFN-α-2b. The onset of a high-grade fever approximately three weeks after drug cessation coincided with the timeframe for the drug's clearance, suggesting a continued immunostimulatory effect. HLH was diagnosed based on hyperferritinemia (>50,000 ng/mL), elevated soluble interleukin-2 receptor (sCD25), and hemophagocytosis on bone marrow biopsy. He responded well to etoposide and dexamethasone. However, his course was complicated by sequential opportunistic infections: severe anemia due to parvovirus B19 (confirmed by plasma metagenomic next-generation sequencing, mNGS) and subsequent herpes simplex virus (HSV) encephalitis (diagnosed via CSF mNGS). Both complications were managed successfully with intravenous immunoglobulin and acyclovir, respectively. This case highlights PegIFN-α-2b as a rare direct trigger of HLH in CHB and underscores the critical risk of opportunistic infections during immunosuppressive therapy, demonstrating the pivotal role of mNGS in diagnosing elusive infections in immunocompromised hosts.}, }
@article {pmid41836788, year = {2026}, author = {Cha, JH and Jeong, SA and Ye, BS and Lee, I and Jung, BY}, title = {Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2643036}, pmid = {41836788}, issn = {2000-2297}, abstract = {INTRODUCTION: Dementia poses a growing burden in the aging population, prompting the search for noninvasive biomarkers for early detection.
MATERIALS AND METHODS: We performed shotgun metagenomic sequencing of tongue-coating samples from older adults with dementia (n = 30) and cognitively healthy controls (n = 28) to identify oral microbiome signatures.
RESULTS: The analysis revealed distinct microbial compositions associated with dementia, including an enrichment of Veillonella parvula in dementia patients, whereas Lautropia dentalis was more abundant in healthy controls. We also identified functional alterations in the microbiome in the dementia group, including increased abundance of the histidine degradation and biotin biosynthesis pathways, whereas ubiquinol biosynthesis was more abundant in the healthy control group. The abundance of several microbial taxa and metabolic pathways were correlated with scores on the Korean Mini-Mental State Examination 2nd edition (K-MMSE), a clinical assessment of dementia severity. Prevotella pleuritidis, Actinomyces sp., Leptotrichia buccalis, and Leptotrichia sp. were positively correlated, whereas Oribacterium parvum was negatively associated with K-MMSE scores. Among the metabolic pathways, glutamine/glutamate biosynthesis was positively correlated with cognitive performance.
CONCLUSIONS: These results suggest that specific oral taxa and their metabolic functions are associated with cognitive status and may reflect underlying neurodegenerative processes.}, }
@article {pmid41836789, year = {2026}, author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P}, title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2641915}, pmid = {41836789}, issn = {2000-2297}, abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.
OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).
METHODS: Participants (51 dentate and 56 edentulous) aged ≥64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.
RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.
CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.}, }
@article {pmid41837347, year = {2026}, author = {Arnold, MJ and Bergner, LM and Malik, H and Ten Doeschate, M and Davison, NJ and Brownlow, A and Mollentze, N and Babayan, SA and Streicker, DG}, title = {Drivers of Viral Diversity and Sharing in Marine Mammals.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70294}, pmid = {41837347}, issn = {1365-294X}, support = {217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 218518/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/V003798/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DEB 2011069/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PLP-2020-362//Leverhulme Trust/ ; NE/X01424X/1//Natural Environment Research Council/ ; INV-003079/GATES/Gates Foundation/United States ; INV-030025/GATES/Gates Foundation/United States ; MC_UU_00034/3/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Viruses/genetics/classification ; Scotland ; *Aquatic Organisms/virology ; *Cetacea/virology ; *Mammals/virology ; }, abstract = {Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.}, }
@article {pmid41837390, year = {2026}, author = {Abagnale, V and Palacin-Lizarbe, C and Paul, D and Kerttula, J and Ronkainen, J and Siljanen, HMP}, title = {Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70279}, pmid = {41837390}, issn = {1462-2920}, support = {342362//Academy of Finland/ ; 346516//Academy of Finland/ ; 361980//Academy of Finland/ ; 337550//Academy of Finland/ ; 357905//Academy of Finland/ ; 359343//Academy of Finland/ ; 202400252//Maj ja Tor Nesslingin Säätio/ ; 20231200//OLVI-Säätiö/ ; }, mesh = {*Picea/microbiology ; *Lichens/microbiology ; *Nitrous Oxide/metabolism ; Finland ; Oxidoreductases/genetics/metabolism ; Taiga ; *Bacteria/metabolism/genetics/isolation & purification/classification ; Forests ; Oxidation-Reduction ; Oxygen/metabolism ; }, abstract = {The nitrous oxide (N2O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N2O dynamics of the lichen Platismatia glauca in boreal forests near Kuopio, North Savo, Finland. At the study sites, P. glauca is the most abundant lichen colonising Norway spruce (Picea abies). Despite their abundance, the contribution of epiphytic lichens like P. glauca to N2O dynamics in boreal forests has received little attention. By incubating P. glauca, we assessed the effects of moisture, temperature, and oxygen availability on its N2O dynamics. We observed net N2O consumption potential, particularly at +5°C at aerobic condition. Quantitative real-time PCR analysis targeting the N2O reductase gene fragment (nosZ) revealed that it was present and active in both in situ and incubated lichens. nosZ transcription was higher at +5°C. Clade I nosZ was dominant, with most sequences affiliated with the order Rhizobiales. We confirmed the presence of nosZ gene with targeted metagenomics sequencing. Our results demonstrate that P. glauca acts as a net consumer of N2O, with potential ranging between 0.1 and 0.4 ng N2O-N g DW[-1] h[-1] under aerobic conditions.}, }
@article {pmid41837422, year = {2026}, author = {Mwasya, SK and Okanda, D and Odoyo, S and Katama, EN and Lewa, C and Lambisia, AW and Githinji, G and Agoti, CN}, title = {Eight coding-complete genomes of human metapneumovirus recovered by virus metagenomics in coastal Kenya, 2021-2024.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0006526}, doi = {10.1128/mra.00065-26}, pmid = {41837422}, issn = {2576-098X}, abstract = {Few human metapneumovirus coding-complete genomes are available from Africa despite significance in optimizing local molecular diagnostics and global phylogeographic analysis. We report eight genomes recovered following nanopore metagenomic sequencing of samples collected in coastal Kenya (2021-2024). These fell into sub-lineages A2b/A2.2.1 (n = 3), A2c-wt/A2.2.2 (n = 4), and B1 (n = 1).}, }
@article {pmid41837616, year = {2026}, author = {Fleres, G and Kline, EG and Squires, KM and Tate, T and Creager, HM and Shields, RK and Van Tyne, D}, title = {Within-patient evolution of Pseudomonas aeruginosa populations during antimicrobial treatment.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0065625}, doi = {10.1128/msphere.00656-25}, pmid = {41837616}, issn = {2379-5042}, abstract = {UNLABELLED: Multidrug-resistant (MDR) Pseudomonas aeruginosa infections pose a major challenge to effective treatment. Understanding genomic adaptations during antimicrobial therapy in patients infected with this pathogen is crucial for preventing therapeutic failure. Here, we investigated the population diversity and evolution of P. aeruginosa collected longitudinally from six patients who evolved multidrug-resistant infections. Serial clinical P. aeruginosa single-colony isolates (n = 63) and culture-enriched metagenomic population samples (n = 39) were collected and subjected to whole-genome sequencing. The resulting data were used to characterize and compare the species composition, multi-locus sequence types (STs), and resistance-associated mutations present within each sample type. Single-colony isolate sequencing showed that each patient was infected with a single P. aeruginosa strain that accumulated mutations and became increasingly more antibiotic-resistant over time. Mutations in genes associated with β-lactam resistance, including ampC, ftsI, and mexR, arose over time and corresponded with changes in antimicrobial susceptibility in single-colony isolates. Species profiling of culture-enriched metagenomic populations revealed that all samples contained P. aeruginosa, but also additional gram-negative pathogens. Metagenomic analysis of culture-enriched populations identified resistance-associated mutations at low frequency, many of which were not identified in single-colony isolates from the same sample. In some cases, resistance-associated mutations initially detected at low frequency rose to fixation after antimicrobial treatment. Overall, this study shows that population-based metagenomic sequencing effectively captures the within-patient genomic diversity of P. aeruginosa during antimicrobial therapy and could aid the detection and interpretation of resistance-associated mutations in this pathogen.
IMPORTANCE: Pseudomonas aeruginosa infections are notoriously difficult to treat and are associated with high rates of morbidity and mortality. While the genetic basis of resistance in P. aeruginosa is well documented in vitro, less is known about how resistance evolves within patients during antibiotic therapy. Standard approaches based on analysis of clonal isolates may miss within-patient diversity, potentially overlooking low-frequency mutations that contribute to treatment failure. In this study, we compared single-colony isolate whole-genome sequencing with culture-enriched metagenomic sequencing to monitor the evolution of P. aeruginosa populations in patients receiving antibiotic therapy. The culture-enriched metagenomic approach enabled the detection of emerging resistance mutations, such as low-frequency variants in ampC and ftsI, before these variants rose to fixation. It also revealed genetically resistant subpopulations missed by isolate sequencing alone. Overall, our findings highlight the value of population-based metagenomic sequencing in capturing bacterial adaptation during infection and underscore its potential to improve resistance surveillance and guide personalized antimicrobial therapy.}, }
@article {pmid41837716, year = {2026}, author = {Pantiukh, K and Krigul, KL and Aasmets, O and Org, E}, title = {Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011426}, doi = {10.1128/msystems.00114-26}, pmid = {41837716}, issn = {2379-5077}, abstract = {UNLABELLED: Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research.
IMPORTANCE: Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus, currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.}, }
@article {pmid41838353, year = {2026}, author = {Xu, Q and Wang, M and Wang, H and Wu, Z and Li, X and Sun, J and Yang, Z and He, N and Sun, Y and Zhang, H and Zhong, Y and Xiao, L and Li, S and Zou, Y}, title = {Lactobacillus gasseri TF08-1 Alleviates DSS-Induced Acute Colitis by Protecting Intestinal Epithelial Barrier.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41838353}, issn = {1867-1314}, support = {2025YFA1310200//Ministry of Science and Technology of the People's Republic of China/ ; U25A2015//National Natural Science Foundation of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; }, }
@article {pmid41838746, year = {2026}, author = {Adachi, K and Chikaraishi, Y and Nomura, S and Goto-Inoue, N and Zaima, N and Kuriya, Y and Araki, M and Morioka, K and Yanagimoto, T and Nakaya, M and Yamamoto, J}, title = {New insights into the feeding behaviour of the Japanese squid Todarodes pacificus paralarvae, and a combined analysis of metagenome and amino acid isotope ratios.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0340579}, pmid = {41838746}, issn = {1932-6203}, mesh = {Animals ; *Decapodiformes/physiology/microbiology/genetics ; *Feeding Behavior/physiology ; *Metagenome ; *Amino Acids/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Japanese flying squid Todarodes pacificus (Ommastrephidae) is a commercially and ecologically important species; however, there remains much room for investigation in its early life phase, especially its diet in wild environments. After excising the digestive gland (cecum sac) of wild paralarvae of T. pacificus using Laser Microdissection (LMD), the dietary species were estimated via metagenomic analysis. The 16S rRNA analysis predominantly detected Burkholderiales and Xanthomonadales, regardless of mantle length (ML) of T. pacificus and capture area. COI (Cytochrome c oxidase subunit I) analysis detected in various organisms including Discosea, Arthropoda, Nemertea, Porifera, golden algae, and fungi (Ascomycota and Basidiomycota), which were found irregularly. About half of the paralarval cecum sacs were found empty during the histological analysis. We also estimated the trophic position (TP) of wild paralarvae in the same sea region via stable isotope analysis of amino acids. The TP estimated was 3.0 for all larval groups regardless of ML, suggesting that the trophic tendency of paralarvae is carnivorous, likely feeding on herbivorous organisms. Taken together, our results suggest that the paralarvae feed mostly on various kinds of living herbivorous organisms and partly on detritus.}, }
@article {pmid41838875, year = {2026}, author = {Chen, Q and Zhang, B and Peng, C and Huang, J and Liu, Z and Shen, X and Jiang, C}, title = {Kun-peng enables scalable and accurate pan-domain metagenomic classification.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41838875}, issn = {1477-4054}, support = {82341109//National Natural Science Foundation of China/ ; 82173645//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Databases, Genetic ; *Software ; Computational Biology/methods ; Algorithms ; }, abstract = {Comprehensive pan-domain metagenomic classification is increasingly constrained by the memory and runtime costs of building and querying the rapidly expanding reference genome space. We introduce Kun-peng, a taxonomic classifier powered by an intelligent block-partitioned database structure and optimized search strategies, enabling ultra-scalable, memory-efficient pan-domain profiling. Using the Critical Assessment of Metagenome Interpretation II benchmark, Kun-peng substantially reduces the memory usage of database-building and querying by up to 24-fold, and accelerates sample classification by up to 4.73-fold compared with Kraken2. Kun-peng achieves competitive accuracy with fewer false positives than Kraken2, Centrifuger, and even KrakenUniq, while maintaining consistently high sensitivity across diverse datasets. In a real-world evaluation of 586 metagenomic samples spanning air, water, soil, and human-associated environments, we performed classification using a 4.3 TB pan-domain database comprising 204,477 genomes, which was built by Kun-peng with only 4.1 GB peak memory. Kun-peng processed each sample in 0.2-11.2 min with 4.0-35.4 GB peak memory, corresponding to a 54-473-fold reduction in memory usage relative to Kraken2. Compared with Sylph, Kun-peng achieved up to a 46-fold speedup while requiring 21-fold less memory. Kun-peng classified 69.8%-94.3% of reads, improving coverage by 20%-60% over the standard Kraken2 database with 62,026 genomes. This improvement reflects expanded reference coverage, although a small fraction of false positives is inherent to k-mer-based methods. Overall, Kun-peng effectively eliminates the long-standing memory bottleneck in pan-domain database building and classification, enabling rapid and scalable pan-domain taxonomic analysis of complex environmental, ecological, and exposomic sequencing datasets.}, }
@article {pmid41839407, year = {2026}, author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D}, title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134433}, doi = {10.1016/j.biortech.2026.134433}, pmid = {41839407}, issn = {1873-2976}, mesh = {*Composting/methods ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Lignin/metabolism ; Bacteria/metabolism/genetics ; Metabolic Reprogramming ; }, abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.}, }
@article {pmid41839411, year = {2026}, author = {Duan, Z and Kong, X and Yue, J and Han, X and Zhu, G and Yu, H}, title = {Integrated multi-barrier attenuation of antibiotic resistance genes by self-elevating ultra-high temperature composting: Phase-resolved evidence for within-process risk reduction.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134432}, doi = {10.1016/j.biortech.2026.134432}, pmid = {41839411}, issn = {1873-2976}, abstract = {The dissemination of antibiotic resistance genes (ARGs) from livestock manure poses risks to environmental and public health, while conventional composting often shows limited and inconsistent ARG attenuation. Here, we evaluated ARG and mobile genetic element (MGE) dynamics during self-elevating ultra-high temperature composting (sf-HTC) and examined phase-resolved associations among thermal conditions, microbial succession, MGE patterns, and humification indicators using metagenomics, network analysis, and structural equation modeling (SEM). Sf-HTC reduced the absolute abundance of total ARGs and MGEs by 98.86% within 28 days. High-risk ARG classes (tetracycline and sulfonamide-resistance genes) decreased by>94.3%, outperforming traditional composting (TC). The hyperthermophilic phase coincided with the largest decreases in ARGs and with enrichment of thermophilic genera (Calditerricola and Thermophilum) and increased microbial network complexity. SEM further suggested that the thermal regime, reductions in MGEs, and increased humification were major, interrelated pathways statistically associated with ARG reduction (standardized path coefficients: 0.97, -1.41, and 0.78, respectively). Sf-HTC also promoted humic acid accumulation (up to 58.9 g/kg) and more aromatic dissolved organic matter, which was consistent with enhanced immobilization potential for residual ARGs. Overall, our results support a phase-resolved "thermal-biological-chemical" multi-barrier conceptual model for ARG attenuation during sf-HTC and highlight its potential for reducing resistome burdens in agricultural organic wastes.}, }
@article {pmid41839668, year = {2026}, author = {Nadeem, SA and Ali, I and Hussain, H and Ullah, I and Ali, W and Alzahrani, KJ and Ali, H and Khan, ZI and Abass, KS and Rahman, RU}, title = {Metagenomic analysis of bacterial and viral communities of Aedes aegypti and Aedes albopictus.}, journal = {Journal, genetic engineering & biotechnology}, volume = {24}, number = {1}, pages = {100643}, pmid = {41839668}, issn = {2090-5920}, abstract = {BACKGROUND: The complicated relationship between the Aedes mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the Aedes microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in Aedes mosquitoes from Pakistan.
METHODS: Ae. aegypti and Ae. albopictus were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.
RESULTS: We found diverse bacterial and viral communities in both studied species. In Ae. aegypti, the most abundant bacterial species was Klebsiella pneumoniae followed by Acinetobacter baylyi. Ae. albopictus presented Pseudomonas putida as the most abundant bacterial species followed by Brevundimonas diminuta. Similarly in Ae. aegypti, we found that Escherichia phage HK639 was the most abundant viral species while in Ae. albopictus, it was Lactobacillus phage 2. It is important to mention that the prevalent viruses in both Aedes species belong to the Siphoviridae genus.}, }
@article {pmid41840004, year = {2026}, author = {Das, R and Tamang, B}, title = {Metagenomic insights reveal β-glucosidase-producing lactic acid bacteria from Miyamikhri with taxiphyllin degradation potential.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-43021-w}, pmid = {41840004}, issn = {2045-2322}, }
@article {pmid41840154, year = {2026}, author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A}, title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41840154}, issn = {1678-4405}, support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; }, abstract = {UNLABELLED: The gut microbiota of insects plays a crucial role in host health and is thought to have co-evolved with each species. In stingless bees, a general understanding of these associations has begun to emerge; however, several important knowledge gaps remain. In this study, we employed amplicon sequencing to compare the gut microbiota of individual specimens from two closely related and sympatric Neotropical stingless bee species from the Maya region, Melipona beecheii and Melipona yucatanica. Our results revealed that (i) most amplicon sequence variants (ASVs) in both species were transient; (ii) the core microbiota of these species was almost entirely distinct, sharing only one ASV out of a total of 31; and (iii) despite this divergence, all core ASVs identified in both species belonged to only four bacterial orders. This pattern suggests that, while their microbiota have differentiated at finer taxonomic scales, it likely originated from a shared ancestral community. We contextualize these findings within the current understanding of stingless bee microbiotas and highlight future directions for exploring their evolution and diversity.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01905-z.}, }
@article {pmid41840625, year = {2026}, author = {Zhang, Y and Zhang, Q and Luo, Y and Li, X and Zhao, R and Xu, Y and Zhang, S and Bai, X and Chen, H and Li, H and Hong, Y and Xie, Z}, title = {Bifidobacterium breve inhibits colorectal cancer via extracellular vesicles containing formate acetyltransferase.}, journal = {Journal of nanobiotechnology}, volume = {24}, number = {1}, pages = {}, pmid = {41840625}, issn = {1477-3155}, support = {82574649//National Natural Science Foundation of China/ ; JCYJ20250604175304006//Shenzhen Municipal Science and Technology Innovation Council/ ; 2023B03J1382//Guangzhou Science and Technology Program/ ; 2022ZD004//Nansha Science and Technology Program/ ; }, mesh = {*Colorectal Neoplasms/therapy/microbiology/pathology ; Animals ; Humans ; Mice ; *Bifidobacterium breve/enzymology/metabolism ; *Extracellular Vesicles/metabolism ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Probiotics/pharmacology ; *Acetyltransferases/metabolism ; Apoptosis/drug effects ; Female ; Feces/microbiology ; Male ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. The gut microbiota exerts unique therapeutic advantages against CRC, and the probiotic Bifidobacterium breve (B. breve) has been extensively documented to suppress CRC initiation in murine models. Although the role of B. breve in CRC has been established, whether its extracellular vesicles (EVs), as key mediators of bacteria-host crosstalk, exert a functional impact remains undefined. Here, we aim to explore the therapeutic potential of B. breve-derived EVs (B.breEVs) and their active cargo, formate acetyltransferase (pflB), in CRC.
RESULTS: Integrative analysis of the curated database of human gut metagenomes cohort (GMrepo) database and an MC38 subcutaneous tumor model revealed a significant reduction of B. breve abundance in faecal samples from CRC patients and tumor-bearing mice. Administration of live B. breve or its cell-free supernatant markedly inhibited tumor growth, whereas pasteurized bacteria or GW4869-mediated EVs blockade abolished this effect, indicating that EVs are the critical effector entities. Isolated B.breEVs selectively accumulated within tumor tissue, directly triggered apoptosis of colorectal cancer cells, and elevated the proportion of IFN-γ⁺ CD8⁺ cytotoxic T lymphocytes (CTLs) in tumor while concurrently ameliorating gut microbial structure and function. Mass-spectrometric profiling identified the pflB as an important active protein within B.breEVs. Recombinant pflB selectively inhibited MC38 cell viability in vitro and significantly reduced CRC burden in vivo. RNA sequencing of tumor issue demonstrated that pflB up-regulated granzyme B, perforin1 and CTL/NK-associated transcripts, and activated the intrinsic apoptotic pathway. Immuno-combination studies further revealed that pflB plus anti-PD1 therapy markedly increased the infiltration of CD8⁺ CTL and NK cells, and enhanced their cytotoxicity compared to either monotherapy.
CONCLUSIONS: B. breve secretes pflB-loaded EVs that reshape the intestinal micro-ecology, activate CD8⁺ CTL/NK anti-tumor immunity, directly induce mitochondrial apoptosis in malignant cells, and enhance the effects of immune checkpoint blockers to overcome drug resistance, offering a precision "probiotic-EVs-active protein" triadic intervention strategy for CRC.}, }
@article {pmid41840712, year = {2026}, author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z}, title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02388-8}, pmid = {41840712}, issn = {2049-2618}, support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; }, abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.
RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (γ-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.
CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.}, }
@article {pmid41840715, year = {2026}, author = {Liang, R and Liu, X and Chen, Q and Zhang, M and Xu, Y and Shi, H and Wang, S and Jing, W}, title = {Daikenchuto ameliorates dextran sulfate sodium-induced acute and chronic ulcerative colitis by regulating gut microbiota-derived indoles to activate AhR signaling.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {41840715}, issn = {1749-8546}, support = {82174059//National Natural Science Foundation of China/ ; 2022SF-123//Natural Science Foundation of Shaanxi Province/ ; 2023-ZQNY-004//Outstanding Young and Middle-Aged Scientific and Technological Talents of Shaanxi Administration of Traditional Chinese Medicine/ ; 2022-SLRH-YQ-001//Shaanxi Administration of Traditional Chinese Medicine/ ; JCYJ20250604184258076//Science and Technology Planning Project of Shenzen Municipality, China/ ; }, abstract = {BACKGROUND: Ulcerative colitis (UC), a chronic-relapsing inflammatory disease with rising prevalence worldwide, is primarily driven by intestinal epithelial barrier dysfunction resulting from gut microbial dysbiosis and metabolic disturbances. Daikenchuto (DKT), a traditional Chinese medicine formulation, is commonly used for digestive disorders. Although DKT has demonstrated therapeutic potential for gut inflammation by modulating gut microbiota, its therapeutic effects on chronic ulcerative colitis (CUC) and the related mechanisms remain elusive.
METHODS: The main components of DKT were tentatively identified using ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF-MS), and the therapeutic effects of DKT were evaluated in the mouse models of acute colitis (AC) and CUC induced using dextran sulfate sodium. The models were validated based on alterations in the disease activity index (DAI), colonic inflammatory status, and intestinal barrier integrity. The impact of DKT on the dysbiosis of gut microbiota was evaluated using the 16S rRNA gene and metagenomic sequencing. Targeted metabolomics was conducted to quantify shifts in short-chain fatty acids and tryptophan (Trp) metabolites. To further elucidate the underlying mechanisms of DKT, key pathways were analyzed using Western blotting, immunohistochemistry, and real-time quantitative polymerase chain reaction.
RESULTS: The principal constituents of DKT were tentatively identified. DKT administration significantly alleviated the symptoms of AC and CUC, reduced inflammation, and maintained intestinal barrier function. Furthermore, DKT modulated the structure and abundance of gut microbiota. Metagenomic sequencing analysis demonstrated that DKT significantly enriched the relative abundance of Ligilactobacillus murinus, Lactobacillus taiwanensis, and Lactobacillus johnsonii. Moreover, Trp metabolism and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathways might be the therapeutic mechanisms of DKT. Targeted metabolomics confirmed that Trp/indole was the major pathway during the therapeutic process of DKT on CUC. Further mechanistic studies demonstrated that activation of the aryl hydrocarbon receptor (AhR) signaling enhanced proliferation in the colonic crypts by stimulating IL-22 secretion and promoting STAT3 phosphorylation.
CONCLUSIONS: DKT alleviated AC and CUC in mouse models by modulating gut microbiota, restoring Trp metabolism, and activating the AhR/IL-22/STAT3 signaling pathway. These findings provide a basis for the clinical application of DKT in UC patients.}, }
@article {pmid41840729, year = {2026}, author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T}, title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02385-x}, pmid = {41840729}, issn = {2049-2618}, support = {JPMJND2206//Japan Science and Technology Agency/ ; }, abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.
RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.
CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.}, }
@article {pmid41841243, year = {2026}, author = {Sbampato, V and Khan, AA and Tsoupras, A and De Marco, G and Ceroni, D}, title = {From Culture to Sequencing: Evolving Strategies for the Diagnosis of Pediatric Spondylodiscitis.}, journal = {Orthopaedic surgery}, volume = {}, number = {}, pages = {}, doi = {10.1111/os.70283}, pmid = {41841243}, issn = {1757-7861}, abstract = {Pediatric spondylodiscitis is a rare but clinically significant infection affecting the intervertebral disc and adjacent vertebral bodies. Diagnostic delays are common due to its nonspecific presentation and the limited sensitivity of conventional microbiological methods. Early and accurate pathogen identification is essential to guide antimicrobial therapy, minimize unnecessary invasive procedures, and prevent long-term sequelae. Traditional diagnostic tools-including laboratory tests, imaging, blood cultures, biopsy, and histopathological evaluation-remain fundamental but are often insufficient, as they may yield nonspecific results or culture-negative cases, particularly after prior antibiotic exposure or infection with fastidious organisms. In recent years, molecular approaches, ranging from polymerase chain reaction assays to metagenomic next-generation sequencing, have markedly improved diagnostic accuracy. These techniques allow rapid and comprehensive pathogen detection, including atypical or previously uncultivable organisms, thereby overcoming many limitations of conventional methods. This narrative review synthesizes current evidence on pediatric spondylodiscitis, outlining its epidemiology, clinical features, and the evolving spectrum of diagnostic strategies-from conventional methods to advanced molecular and sequencing-based technologies-while discussing future directions in this challenging field.}, }
@article {pmid41841491, year = {2026}, author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A}, title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.}, journal = {Nucleic acids research}, volume = {54}, number = {5}, pages = {}, pmid = {41841491}, issn = {1362-4962}, support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette & Yersin PhD Grant/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Metagenome ; Algorithms ; }, abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.}, }
@article {pmid41841524, year = {2026}, author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y}, title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2645267}, pmid = {41841524}, issn = {1949-0984}, mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; }, abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.}, }
@article {pmid41841608, year = {2026}, author = {Farsi, DN and Cotillard, A and Wilson, B and So, D and Gibson, PS and Slater, R and Probert, C and Morris, S and Scott, SM and Quinquis, L and Pichaud, M and Shetty, S and Tap, J and Le Nevé, B and Rossi, M and Whelan, K}, title = {Gut Microbiome Composition and Function, Diet and Clinical Factors in Relation to Fermentable Carbohydrate-Induced Bloating: A Double-Blind, Randomized, Crossover Trial.}, journal = {The American journal of gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ajg.0000000000003997}, pmid = {41841608}, issn = {1572-0241}, abstract = {BACKGROUND: Specific foods are associated with abdominal bloating, which can significantly impact quality of life.
OBJECTIVE: To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses.
DESIGN: Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or α-galacto-oligosaccharides (α-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics) and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized prior to each challenge to identify factors predicting response, and after the challenge to elucidate mechanisms underpinning food-induced bloating.
RESULTS: Thirty-nine participants completed both challenges (39 fructan, 40 α-GOS). Overall, seven (7/39, 17.9%) participants were fructan responders and eight (8/40, 20%) were α-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and non-responders to both challenges, including greater abdominal girth (fructan, p = 0.009; α-GOS, p = 0.030). α-GOS responders had higher breath hydrogen (H2) pre-challenge than α-GOS non-responders (p = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (pre-challenge, adjusted p-value (padj) = 0.024; post-challenge, padj = 0.042), and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in α-GOS responders (padj = 0.041).
CONCLUSION: A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for α-GOS, higher repeated fasting breath H2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.ClinicalTrials.gov (Identifier: NCT04802798).}, }
@article {pmid41841712, year = {2026}, author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE}, title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.}, journal = {Biomeditsinskaia khimiia}, volume = {72}, number = {1}, pages = {62-74}, doi = {10.18097/PBMCR1644}, pmid = {41841712}, issn = {2310-6972}, mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation & purification ; Prevotella ; }, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.}, }
@article {pmid41841737, year = {2026}, author = {Cruz, MC and Ruhal, R and Lavin, J and Bridwell, S and Maghboli Balasjin, N and Raasch, B and Melton, R and Mayer, BK and Marshall, CW and Hristova, K}, title = {Acinetobacter spp. with lower susceptibility to quaternary ammonium compounds enriched in microbial communities of frequently used sinks.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0196825}, doi = {10.1128/aem.01968-25}, pmid = {41841737}, issn = {1098-5336}, abstract = {Sanitary environments that undergo frequent cleaning and disinfection may harbor microbial communities with potential health risks. While biofilms in healthcare settings are well studied, comparatively less is known about sink-drain microbiomes in public and educational buildings, where hundreds of people may interact with shared sink fixtures. This study characterized the spatial and temporal heterogeneity of sink-drain biofilm microbiomes in academic buildings. We sampled 16 sinks from two buildings (four floors each, with sinks closest and furthest to the bathroom entrance), which are cleaned daily with quaternary ammonium compound (QAC) disinfectants, during periods of low and high student traffic (during and after academic breaks, respectively) across winter, spring, and summer. We observed significant spatial and temporal variations in microbial assemblages. Individual sinks accounted for 43% (PERMANOVA, P < 0.0001) of the variation in microbial communities. Microbiomes in each building were dominated by two genera, which together accounted for 30% of the community composition: Acinetobacter and Enhydrobacter (also classified as Moraxella) in the newer building, and Sphingomonas and Mycobacterium in the older building. Acinetobacter abundance varied seasonally and showed higher relative abundance during periods of high traffic. Metagenomic analysis of selected sinks revealed a high prevalence of qac genes and metagenome-assembled genomes (MAGs) harboring antimicrobial resistance genes (ARGs), including A. parvus. Notably, 34%-53% of qac genes were co-localized on contigs associated with mobile genetic elements. These findings suggest that disinfected sink drains serve as persistent reservoirs of diverse microorganisms and potentially mobile resistance elements.IMPORTANCESink drains are recognized as environmental reservoirs for multidrug-resistant bacteria and have been linked to healthcare-associated outbreaks. In public and educational buildings, these microbiomes are shaped by frequent human activity, making them potential sources of exposure and contributors to the environmental dissemination of antibiotic resistance genes. Quaternary ammonium compound (QAC) disinfectants are widely used on surfaces; however, they can select for resistant taxa and co-select for antibiotic resistance. In this study, despite routine cleaning of sink surfaces with QACs, public restroom sink drains remain colonized by resilient biofilms, posing a potential risk to multiple users. Additionally, factors such as human traffic and seasonal variation may influence drain usage and microbial community composition. Elucidating how seasonal dynamics and human activity shape sink-drain biofilms is essential for understanding their role in the environmental transmission of antimicrobial resistance and informing mitigation strategies in nonclinical settings.}, }
@article {pmid41841761, year = {2026}, author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L}, title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0231325}, doi = {10.1128/spectrum.02313-25}, pmid = {41841761}, issn = {2165-0497}, abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.}, }
@article {pmid41842581, year = {2026}, author = {Wang, X and Chen, J and Xia, J and Ma, T and Yang, W and Shan, T and He, W and Zhang, G and Xia, Z and Wang, W and Liu, Z and Zheng, Y and Nong, K and Niu, P and Chen, T}, title = {Brain-Targeted RVG-Liposomal Melatonin Ameliorates Manganese Neurotoxicity by Enhancing Neurogenesis and Modulating Systemic Amino Acid Profiles.}, journal = {Journal of pineal research}, volume = {78}, number = {2}, pages = {e70137}, doi = {10.1111/jpi.70137}, pmid = {41842581}, issn = {1600-079X}, support = {82173489//National Natural Science Foundation of China/ ; 7232234//Beijing Natural Science Foundation/ ; }, mesh = {Animals ; *Melatonin/pharmacology/administration & dosage ; Mice ; *Manganese/toxicity ; Liposomes ; *Brain/metabolism/drug effects ; *Neurogenesis/drug effects ; *Glycoproteins/pharmacology ; *Amino Acids/metabolism ; Male ; Mice, Inbred C57BL ; *Neurotoxicity Syndromes/drug therapy/metabolism ; *Neuroprotective Agents/pharmacology ; Gastrointestinal Microbiome/drug effects ; Peptide Fragments ; Viral Proteins ; }, abstract = {Chronic manganese (Mn) exposure induces severe neurotoxicity, characterized by impaired neurogenesis and disrupted metabolic homeostasis. Although melatonin (MT) possesses established neuroprotective properties, its clinical utility is hindered by poor bioavailability and limited brain delivery. Here, we developed a brain-targeted, rabies virus glycoprotein (RVG)-modified liposomal delivery system encapsulating melatonin (MT@RVG-Lip) to enhance therapeutic efficacy. Multi-omics analyses including brain and intestinal transcriptomics, serum metabolomics, and gut metagenomics were conducted to elucidate the underlying mechanisms. MT@RVG-Lip significantly improved motor deficits and enhanced neurogenesis while reducing neuroinflammation in Mn-exposed mice. Compared with regular MT and CaNa2-EDTA, MT@RVG-Lip more effectively alleviated Mn-disrupted gene expression in neurogenesis regions, particularly genes involved in amino acid metabolism. Additionally, MT@RVG-Lip demonstrated a regulatory effect on serum amino acid profiles and intestinal transporter gene expression. Gut microbiota analysis further revealed that MT@RVG-Lip partially reversed Mn-associated dysbiosis and promoted the improvement of key amino acid-related microbiota-mediated metabolic pathways. The RVG-modified liposomal formulation conferred sustained release and improved brain-targeting capability, prolonging MT bioavailability and enhancing therapeutic outcomes. These findings provide a new mechanistic framework for MT-based interventions in neurodegenerative diseases and highlight the therapeutic potential of multifunctional delivery strategies.}, }
@article {pmid41842880, year = {2026}, author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G}, title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.}, journal = {Puerto Rico health sciences journal}, volume = {45}, number = {1}, pages = {3-10}, pmid = {41842880}, issn = {2373-6011}, support = {K23 NR020039/NR/NINR NIH HHS/United States ; R21 CA288925/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; Male ; Female ; Middle Aged ; Pilot Projects ; *Gastrointestinal Microbiome ; *Diet ; Cross-Sectional Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Neoadjuvant Therapy ; }, abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.
METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.
RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.
CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.}, }
@article {pmid41843187, year = {2026}, author = {Chu, T and Wang, Q and Hu, C and Yu, J and Chen, L and Yu, Y and Wang, Y}, title = {Microalga-virus-virophage coculture reveals co-infection of multi-virophages with a giant virus.}, journal = {Archives of virology}, volume = {171}, number = {4}, pages = {}, pmid = {41843187}, issn = {1432-8798}, support = {31570112//National Natural Science Foundation of China/ ; }, mesh = {*Chlorella/virology ; Coculture Techniques ; *Microalgae/virology ; *Giant Viruses/physiology/genetics ; *Virophages/genetics/physiology ; Coinfection ; Virus Replication ; }, abstract = {Virophages parasitize the replication of co-infecting giant viruses within eukaryotic cells, forming tripartite cell-virus-virophage (CVv) systems. Tripartite interactions are well-documented in protozoa, yet comparable systems in algae remain largely unexplored at the experimental level. Here, we report an experimentally validated CVv system involving the green, single-celled microalga Chlorella sp. DSL01, Dishui Lake large algal virus 1 (DSLLAV1), and multiple Dishui Lake virophages (DSLVs). Inoculation of Chlorella sp. DSL01 at low MOI established laboratory co-cultures in which time-series PCR detected DSLLAV1 early but not after Day 10, whereas all tested virophages persisted. Metagenomic profiling of the terminal supernatant (end-point sample) indicated a virophage-dominated assemblage with DSLV3 most represented. Droplet digital PCR at discrete time points (Days 5, 10, and 15) then provided absolute counts for DSLLAV1 and DSLV1/3/7, corroborating an early DSLLAV1 peak followed by collapse and/or a delayed rise of multiple virophages coincident with host growth recovery. Nested PCR on the algal pellet detected virophages DSLV1/3/7 but not DSLLAV1. Together, these results demonstrate that Chlorella sp. DSL01 supports co-infection by DSLLAV1 and multiple virophages, establishing an experimentally validated algal CVv system and revealing multi-virophage participation in freshwater algal virus-virophage-host dynamics.}, }
@article {pmid41843252, year = {2026}, author = {Xia, HL and Liang, PY and Yuan, WG and Cao, XD and Sun, Y and Jiang, JZ and Yuan, LH}, title = {PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {}, number = {}, pages = {}, pmid = {41843252}, issn = {1867-1462}, support = {No. 2022KCXTD017//Innovation Team Project of Guangdong Universities/ ; No. 324CXTD435//Natural Science Foundation of Hainan Province/ ; No. 2023TD44//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, abstract = {Viruses are the most abundant biological entities on Earth, playing essential roles in shaping microbial communities, driving evolution, and maintaining ecosystem functions. Metagenomic sequencing has unveiled a vast landscape of uncharacterized viral "dark matter", comprising highly divergent sequences that elude traditional taxonomic approaches. Here, we develop PhaGCN_Cluster, a next-generation viral classification tool built upon a graph convolutional neural network (GCN) framework. By integrating protein-level sequence similarity and contig-level genomic features, PhaGCN_Cluster establishes a scalable knowledge graph-based analytical system. The optimized algorithm yields significant gains in computational efficiency, supporting accurate taxonomic assignment of up to 300,000 contigs per run. Compared with existing methods, PhaGCN_Cluster demonstrates superior classification accuracy and F1-scores, particularly under conditions of low sequence similarity, and exhibits strong robustness in detecting evolutionarily distant viruses. Notably, PhaGCN_Cluster incorporates an updated logic for assigning "_like" taxa, which enhances its capacity to accommodate novel viral groups while preserving high precision-though at the cost of a slight reduction in recall. By generating high-fidelity network graphs, PhaGCN_Cluster uncovers previously unrecognized clades and bridges evolutionary gaps between reference viruses and novel sequences, thereby providing critical insights into viral diversity and evolution. PhaGCN_Cluster represents an interpretable, efficient, and scalable solution for automated virus classification. The source code of PhaGCN_Cluster is available via https://github.com/xiahaolong/PhaGCN_Cluster .}, }
@article {pmid41843710, year = {2026}, author = {Qian, C and Jeunen, GJ and Han, W and Chan, TY and Jiang, Y and Fu, W and Seymour, M}, title = {Developing and Evaluating Aquatic Passive Sampling of Environmental DNA for Microbial Community Profiling.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70121}, pmid = {41843710}, issn = {1755-0998}, support = {MCEF21003//Marine Conservation Enhancement Fund/ ; }, mesh = {*DNA, Environmental/isolation & purification/genetics ; Biodiversity ; *Specimen Handling/methods ; Bacteria/genetics/classification ; *Microbiota ; *Metagenomics/methods ; Phylogeny ; }, abstract = {Environmental DNA (eDNA) metabarcoding has transformed biodiversity monitoring across taxa from bacteria to mammals, yet sample collection remains a major bottleneck. Passive sampling via adsorption and entrapment has emerged as a promising alternative to overcome the limitations of conventional active filtration. However, the performance of passive sampling for microbial biodiversity monitoring remains unknown. Here, we developed passive sampling-based microbial community profiling by testing five submersion times and three common eDNA extraction methods in mesocosms, and comprehensively evaluated it by comparing results with active filtration in estuarine and coastal environments. We found that passive sampling for 24 h with enzymatic extraction yielded significantly more eDNA and higher biodiversity than shorter durations and mechanical extractions. Passive sampling consistently outperformed active filtration at every field site, with average increases of >100% in eDNA yields and >50% in taxonomic and phylogenetic diversities. Additionally, active filtration and passive sampling yielded significantly different prokaryotic and microeukaryotic community compositions, driven primarily by turnover rather than nestedness (on average 4-fold larger), implying that passive sampling is better suited for spatiotemporal detection than active filtration. Passive sampling showed greater sensitivity in identifying key environmental factors (3 vs. 2) and potential environmental bioindicators (40 vs. 20) compared with active filtration. Overall, this study establishes an efficient and practical passive sampling method for microbial biodiversity monitoring and environmental assessment in aquatic environments.}, }
@article {pmid41843957, year = {2026}, author = {Zhu, L and Huang, C and Tian, Y and Zuo, W and Shan, G}, title = {Targeted enhancement of ammonia assimilation and microbial community metabolic synergy in chicken manure aerobic composting mediated by tricarboxylic acid cycle modulators.}, journal = {Waste management (New York, N.Y.)}, volume = {216}, number = {}, pages = {115471}, doi = {10.1016/j.wasman.2026.115471}, pmid = {41843957}, issn = {1879-2456}, mesh = {*Ammonia/metabolism ; Animals ; *Composting/methods ; *Citric Acid Cycle ; *Manure/microbiology/analysis ; Chickens ; Nitrogen/metabolism ; Microbiota ; Citric Acid/metabolism ; }, abstract = {Reducing nitrogen loss during composting is essential. To investigate the effects of directly modulating the tricarboxylic acid (TCA) cycle on microbial ammonia assimilation during composting, this study employed paired stable isotope labeling combined with metagenomic analysis to assess the role of the TCA cycle regulator citric acid (CA) in enhancing ammonia assimilation efficiency and regulating carbon-nitrogen metabolism within the microbial community. CA markedly reduced NH3 emissions (0.5-2265 ppm) and increased organic nitrogen retention (4.2%-17.7%), primarily through improved ammonia assimilation efficiency (0.06-0.22 mg N·kg[-1]·d[-1]) rather than weakened mineralization. Mechanistically, CA upregulated IDH1 (5.4%-18.5%) and increased IDH enzyme activity (0.35-0.66 IU/g), combined with NH3 uptake, balancing oxoglutarate and ammonium supply. Moreover, CA strengthened the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway (3.4%-23.4%) and enzyme activity (0.08-0.74 IU/g), particularly in the initial and thermophilic phases. In addition, CA induced an upregulation (14.8%-28.4%) of genes encoding succinyl-CoA synthetase, providing sufficient energy to support the ammonia assimilation process. Furthermore, CA enhanced microbial diversity and metabolic cooperation while reducing competition, thereby promoting NH3 assimilation and glutamate synthesis. Inorganic and amino acid metabolism emerged as critical cooperative processes within core microbial populations.}, }
@article {pmid41844593, year = {2026}, author = {Ni, N and Ding, Q and Zhang, T and Liu, C and Guo, X and Zhu, C and Wang, Q and Zhu, D and Wang, N and Luo, Y}, title = {Fragmented Microplastics Synergize with Biological Treatment To Potentiate Antibiotic Resistance Dissemination during Sewage Treatment.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c18221}, pmid = {41844593}, issn = {1520-5851}, abstract = {Wastewater treatment plants (WWTPs) are important reservoirs for antibiotic resistance genes (ARGs) and microplastics (MPs), and serve as hotspots for antibiotic resistance spread. However, actual survey data on their combined pollution along the entire sewage treatment chain remain scarce. This study integrated metagenomic sequencing and high-throughput qPCR to analyze the correlation between ARGs and MPs. The results revealed that clinically relevant and rank I high-risk intracellular antibiotic resistance genes (iARGs) were significantly enriched in the plastisphere throughout the sewage treatment process, particularly on fragmented MPs. FEAST source-tracking analysis revealed that MP-bound iARGs and extracellular ARGs in the biologically treated sewage contributed to 13-43 and 25-39% of the corresponding iARGs and eARGs detected in the effluent, respectively. Fragmented MPs also colocalized ARGs, virulence factors, and mobile genetic elements, potentially facilitating plasmid-mediated gene transfer. Acinetobacter, the primary ARG host and detected across 75 WWTPs with high ARG load, may serve as an antibiotic resistance indicator. This study highlights MP-driven ARG dissemination in WWTPs and informs resistance control strategies.}, }
@article {pmid41844673, year = {2026}, author = {Singh, NK and Garg, P and Kumari, S and Banda, L and Patel, AM and Sindhuja, RH and Bhandari, Y and Khan, NA and Tandon, S and Jain, R and Rajesh, T and Qureshi, A and Vodapalli, A and Singha, B and Esari, D and Annan, MO and Nagabandi, T and Panda, A and Kapley, A and Nandicoori, VK and Mishra, RK and Sowpati, DT and Siva, AB and Tallapaka, KB}, title = {Metagenomic profiling of antimicrobial resistance in wastewater from metropolitan cities of India.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70702-x}, pmid = {41844673}, issn = {2041-1723}, support = {2021 HTH 018//Rockefeller Foundation/ ; }, abstract = {Wastewater-based surveillance has emerged as a powerful tool for monitoring microbial diversity, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). In this study, wastewater samples collected from March 2022 to March 2024 from 19 locations in four metropolitan cities of India were profiled using shotgun metagenomics. Taxonomic abundance and beta diversity analyses revealed significant differences in microbial community compositions, with city-specific clustering; suggesting distinct local environmental influences. However, such distinct clusters were not evident with the ARGs. A high proportion of potentially novel metagenome-assembled genomes (MAGs) (53-70%) were identified on reconstructing the microbial genomes from the metagenomic data. ARGs conferring resistance to antibiotics such as tetracyclines and beta-lactams showed higher association with MGEs in contrast to macrolide resistance genes. Microbial co-occurrence network analysis revealed a city-specific structure and higher contribution of ARGs from specific communities of microbes. These findings underscore the complex interplay between microbial diversity, ARG dissemination, and MGEs in wastewater environments, emphasizing the need for continued surveillance, for designing appropriate mitigation strategies towards curbing the spread of antimicrobial resistance.}, }
@article {pmid41845022, year = {2026}, author = {Selvatici, S and Jin, C and Zazula, G and Hall, E and Hewitson, S and Moots, HM and Sharif, B and Ersmark, E and Parducci, L and Dalén, L and Díez-Del-Molino, D and Oteo-García, G}, title = {Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41845022}, issn = {2045-2322}, mesh = {*Porcupines/genetics ; Animals ; *Genome, Mitochondrial ; Permafrost ; *Mummies ; Canada ; Fossils ; DNA, Mitochondrial/genetics ; Phylogeny ; Genomics/methods ; *Mitochondria/genetics ; }, abstract = {We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ondëk Hwëch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as "Ts'ey" in the Hän language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.}, }
@article {pmid41845390, year = {2026}, author = {Sung, H and Hyun, DW and Whon, TW and Kim, PS and Kim, HS and Lee, JY and Lee, SY and Choi, JW and Yoo, JH and Jung, MJ and Yun, JH and Lee, JY and Tak, EJ and Jeong, YS and Kim, SW and Baeg, M and Eun, YG and Lee, YC and Bae, JW}, title = {Unraveling the diagnostic and prognostic signatures of oral microbiota in head and neck cancer.}, journal = {BMC biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12915-026-02573-z}, pmid = {41845390}, issn = {1741-7007}, support = {RS-2020-NR049315//National Research Foundation of Korea/ ; 22213MFDS537//Ministry of Food and Drug Safety/ ; }, abstract = {BACKGROUND: Head and neck cancer, predominantly squamous cell carcinoma, has emerged as a significant global health concern. Growing evidence has established a strong association between dysbiosis of the oral microbiota and both oral and systemic diseases. However, the association between the oral microbiota and head and neck cancer has not yet been fully described. This study aimed to investigate the distinct profiles of the oral microbiota in patients with head and neck cancer and their potential as diagnostic and prognostic biomarkers for head and neck cancer.
RESULTS: Comparative analyses revealed that compared to controls, the oral microbiota of patients with head and neck squamous cell carcinoma (HNSCC) exhibited an increased abundance of anaerobic, biofilm-forming bacteria, and potential pathogens. A machine learning model successfully differentiated HNSCC patients from controls with an area under the curve of 0.902. Key features of this model, such as Peptostreptococcus and Capnocytophaga, were found to be candidate biomarkers for HNSCC, with certain taxa, such as Abiotrophia, serving as prognostic indicators. Although pronounced differences in oral microbiota among HNSCC patients primarily resulted from inter-individual variations, distinct community types were identified, with the type dominated by Proteobacteria being associated with the lowest probability of survival.
CONCLUSIONS: Our findings indicate that the oral microbiota may predict HNSCC and may act as a therapeutic target to improve the prognosis of HNSCC. This investigation underscores the crucial role of oral microbial dysbiosis in the etiopathogenesis and clinical prognosis of HNSCC, making a case for further integrative metagenomic and clinical research.}, }
@article {pmid41845399, year = {2026}, author = {Luo, J and Guo, W and Zou, S and Tan, Y and Liu, J and Song, S and Yang, H and Liang, K}, title = {Case report: thoracic syphilitic gumma masquerading as a malignant tumor in a patient with AIDS.}, journal = {AIDS research and therapy}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12981-026-00868-3}, pmid = {41845399}, issn = {1742-6405}, support = {2020-PT320-004//The Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, abstract = {Syphilis, a systemic infection caused by Treponema pallidum, can present with atypical and severe manifestations in people living with the human immunodeficiency virus (HIV), posing significant diagnostic challenges. We report the case of a patient with acquired immunodeficiency syndrome (AIDS) who presented with a chest wall mass. Imaging findings were initially suggestive of a malignancy. However, subsequent evaluation, guided by positive serum syphilis antibodies despite non-specific inflammatory changes on histology and a negative metagenomic next-generation sequencing (mNGS) result, led to the diagnosis of a syphilitic gumma, which was confirmed by immunohistochemical staining. The lesion entirely resolved following penicillin therapy. This case highlights a critical clinical insight: syphilis must be considered in the differential diagnosis of mass lesions in immunocompromised hosts, and immunohistochemical staining is imperative for definitive diagnosis.}, }
@article {pmid41845494, year = {2026}, author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P}, title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02363-3}, pmid = {41845494}, issn = {2049-2618}, support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.
RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.
CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.}, }
@article {pmid41845521, year = {2026}, author = {Hoepfner, C and Moreno-Perlin, T and Pérez-Llano, Y and Cardona, K and Rivera, DS and Minter, D and Guzmán, D and Batista-García, RA}, title = {Microbial diversity, metabolic specialization, and genomic novelty across polyextreme saline lakes of the Central Dry Andes.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00868-w}, pmid = {41845521}, issn = {2524-6372}, support = {ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; PT09CB001//Swedish International Development Cooperation Agency/ ; PT09CB001//Swedish International Development Cooperation Agency/ ; Grant 31-001//Darwin Initiative/ ; Grant 31-001//Darwin Initiative/ ; Grant 31-001//Darwin Initiative/ ; Grant 31-001//Darwin Initiative/ ; Postdoctoral fellowship grant//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; }, abstract = {The high-altitude saline lakes of the Central Dry Andes are polyextreme environments characterized by hypersalinity, high alkalinity, fluctuating redox conditions, and elevated levels of trace metals (e.g., Li, As, Mn, Mg). These conditions challenge microbial life yet select for highly specialized and functionally versatile communities. Through metagenomic analyses across four lakes (Colorada, Hedionda, Mama Khumu, and Loromayu), we identified taxonomic assemblages dominated by halophilic and halotolerant bacteria (e.g., Halomonas, Marinobacter, Rhodohalobacter), phototrophic cyanobacteria and algae (Dunaliella, Chlorella), archaeal Halobacteria (Halorubrum, Natrinema, Haloterrigena), and halotolerant fungi (Aspergillus, Penicillium). Notably, Laguna Mama Khumu exhibited the highest microbial and functional diversity, reflecting its heterogeneous salinity and richer chemical gradients, whereas the most extreme lakes (Colorada and Loromayu) harbored narrower specialized communities. Across all sites, oxidative phosphorylation dominated as the primary metabolic strategy. Additional pathways such as photosynthesis, sulfur and methane cycling were especially prominent at Mama Khumu. Patterns of carbohydrate-active enzyme (CAZyme) also diverged: Loromayu harbored abundant glycoside hydrolases, indicating strong polysaccharide degradation potential, while Mama Khumu displayed a boarder and more functionally redundant CAZyme repertoire. High-quality metagenome-assembled genomes (MAGs) uncovered novel lineages (< 95% ANI to known species) encoding key traits including energy metabolism (ATP synthase, anoxygenic photosynthesis), sulfur oxidation, arsenic resistance, and heavy-metal efflux systems. These features highlight the genomic innovation fostered by polyextreme conditions. Overall, our findings showed that within a shared scaffold of aerobic respiration and halophilic resilience, local geochemistry drives divergent taxonomic and metabolic adaptations. The Bolivian Andean saline lakes thus emerge as natural laboratories for studying microbial adaptation under multiple stressors and offer promising sources for biotechnological discovery.}, }
@article {pmid41845557, year = {2026}, author = {Dormiente, A and Mancabelli, L and Ventura, M and Longhi, G and Mergoni, G and Manfredi, M}, title = {Metagenomic Evaluation of Oral Microbiota in Patients Affected by Oral Lichen Planus: A Pilot Study.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70296}, pmid = {41845557}, issn = {1601-0825}, support = {//Bando di Ateneo per la Ricerca 2023- Azione B/ ; }, abstract = {OBJECTIVE: To characterize the oral bacterial and fungal microbiota of symptomatic oral lichen planus patients undergoing topical corticosteroid therapy and to explore microbial patterns potentially associated with subsequent oral candidiasis.
METHODS: Twelve patients with clinically and histologically confirmed OLP were enrolled. Unstimulated saliva and tongue dorsum swabs were collected at baseline and weekly for three weeks during betamethasone therapy. Bacterial communities were profiled using shallow shotgun metagenomics analyzed with METAnnotatorX2, and fungal communities through ITS sequencing and QIIME 2 workflows. Beta-diversity analyses assessed the effects of time, clinical variables, and later candidiasis development. Associations between bacterial taxa and Candida abundance were evaluated using Spearman correlations.
RESULTS: Oral candidiasis developed in three patients (25%). Microbiota composition showed marked inter-individual variability but high intra-subject stability, with no consistent shifts linked to corticosteroid therapy. Commensal taxa such as Streptococcus, Rothia, and Actinomyces were negatively associated with candidiasis and Candida abundance, whereas anaerobic species including Porphyromonas gingivalis, Prevotella multiformis, and Lachnoanaerobaculum gingivalis displayed positive correlations with fungal proliferation.
CONCLUSIONS: Despite overall stability of the oral microbiota during therapy, specific bacterial signatures were associated with subsequent Candida overgrowth. These findings suggest that cross-kingdom interactions may influence susceptibility to corticosteroid-associated candidiasis and warrant validation in larger cohorts.}, }
@article {pmid41845564, year = {2026}, author = {Zhang, Y and Wang, DD}, title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644682}, pmid = {41845564}, issn = {1949-0984}, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Proteomics ; Multiomics ; }, abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.}, }
@article {pmid41846023, year = {2026}, author = {Segovia-Cruz, JA and Zárate-Romero, A and Herrera-Hernández, MM and Loza-Tavera, H and Vargas-Suárez, M and Ayala, M and Paz-González, AD and Rivera, G and Magaña-Montiel, N and Schnabel, D and Sánchez-Reyes, A}, title = {Characterization and application of two novel environmental DyP-type peroxidases as sustainable biocatalysts for textile dye treatment.}, journal = {International journal of biological macromolecules}, volume = {355}, number = {}, pages = {151457}, doi = {10.1016/j.ijbiomac.2026.151457}, pmid = {41846023}, issn = {1879-0003}, abstract = {The environmental impact of synthetic textile dyes highlights the urgent need for sustainable wastewater treatment solutions. Here, we report the cloning, heterologous expression, purification, and characterization of two novel bacterial dye-decolorizing peroxidases (DyPs), named PbDyP and MbDyP, selected from the metagenome of the BP8 polyurethane-enriched microbial consortium, isolated from a landfill. Both enzymes showed an acidic pH optimum (4.0-4.5) and a moderate temperature preference (∼40 °C), but they differed in stability and sensitivity to hydrogen peroxide. Spectroscopic analyses confirmed their heme-binding nature, while dynamic light scattering revealed different oligomerization states. Both enzymes achieved efficient biotransformation (>80%) of representative anthraquinone, azo, phthalocyanine, sulfur, and triphenylmethane dyes, with particularly high activity toward anthraquinone Reactive Blue 19. Following enzymatic treatment, FT-IR spectroscopy revealed structural changes in diagnostic functional groups of several dyes, such as Vat Red 10, Disperse Orange 30, Direct Black 22, and Reactive Blue 19, while UPLC-MS analysis identified a lower-mass sodium 2-(3-aminobenzene-1-sulfonyl) ethyl sulfate derivative (m/z 318.31), indicating biotransformation of the parent compound. We also conducted in vitro transformation assays for bisphenols, benzenedithiols, and substituted phenols to thoroughly assess the oxidative capabilities of the DyP-type peroxidases. Toxicity tests using Artemia salina demonstrated that, although enzymatic treatment reduced toxicity in the supernatants, the precipitated fractions remained harmful, underscoring the need for integrated remediation strategies. Overall, these findings position PbDyP and MbDyP as promising candidates for eco-friendly dye degradation, providing a foundation for their potential application in industrial wastewater treatment.}, }
@article {pmid41846078, year = {2026}, author = {Li, Q and Yuan, J and Sun, Y and Wang, Y and Li, Y and Ni, A and Zong, Y and Yang, H and Li, X and Huang, X and Ma, H and Chen, J}, title = {Multi-omics analysis revealed that oxidative phosphorylation contributed to the heterosis for feed efficiency in laying chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106658}, pmid = {41846078}, issn = {1525-3171}, abstract = {Improving feed efficiency has been the top priority in animal husbandry. Host genetics and gut microbiota synergistically regulate feed efficiency in laying chicken. However, the role of gut microbiota in heterosis for feed efficiency was rarely investigated. Herein, we used multi-omics data to elucidate the regulatory mechanisms of heterosis for feed efficiency in White Leghorn, Beijing-You chicken, and their reciprocal crosses. We observed divergent heterosis for residual feed intake (RFI) between two crossbreds during the laying period from 43 to 46 weeks of age. Metagenomic analysis showed the significant difference in richness and function of cecal microbiota among crossbreds and purebreds (P < 0.05), and the differential functional pathways were mainly related to metabolism. Most microorganisms (>90 %) were non-additive in crossbreds. Weighted gene co-expression network analysis and LDA effect size analysis revealed seven non-additive RFI-associated microorganisms, such as Leyella, Paraprevotella, and Zongyangia. We also identified 544 RFI-associted metabolites, which were mainly overrepresented in glycerophospholipid metabolism and oxidative phosphorylation. Integrative analysis further revealed the interactions among non-additive microorganisms, genes, and metabolites. Specifically, the non-additive expression of Zongyangia was positively correlated with UQCR10 and Ubiquinone-1 levels within the oxidative phosphorylation pathway. These factors were negatively correlated with RFI, contributing to the RFI heterosis. Our study highlighted that key microorganisms, genes, and metabolites involved in oxidative phosphorylation interact to regulate negative heterosis for RFI in laying hens. The findings established a theoretical and practical foundation for further exploring the molecular mechanisms that drive heterosis for feed efficiency.}, }
@article {pmid41846103, year = {2026}, author = {Trzos, K and Hutsch, T and Koval, A and Śmierciak, D and Machaj, G and Molano, LG and Rehner, J and Rahman, MM and Förster, MO and Bednarek, M and Yilmaz, B and Pilarczyk-Zurek, M and Surma, S and Koziel, J and Krawczyk, M and Keller, A and Becker, SL and Ylla, G and Jura, J and Kotlinowski, J}, title = {Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1872}, number = {5}, pages = {168216}, doi = {10.1016/j.bbadis.2026.168216}, pmid = {41846103}, issn = {1879-260X}, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by progressive biliary destruction and cholestasis. Current therapies, including ursodeoxycholic acid (UDCA), exhibit limited efficacy in advanced disease. In this study, we investigate the therapeutic potential of microbial intervention using Lactobacillus rhamnosus (Lbr) in the Mcpip1[fl/fl]Alb[Cre] knockout mouse model of PBC, which we described previously. Knockout mice develop human PBC-like features such as bile acid dysregulation, autoantibodies, cholangiocyte hyperplasia and fibrosis.
METHODS: Six-week-old Mcpip1[fl/fl] (wild-type) and Mcpip1[fl/fl]Alb[Cre] (knockout) mice were treated with Lactobacillus rhamnosus supplementation, UDCA (15 mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10 mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.
RESULTS: Treatment of Mcpip1[fl/fl]Alb[Cre] animals with Lbr decreased serum bile acids and reduced pathological cholangiocyte dysplasia in the liver, decreased leukocyte infiltration and fibrosis. RNAseq of liver tissue revealed enrichment of humoral immune responses and T cell activation pathways in knockouts, all of which were significantly attenuated by Lbr monotherapy. Gut pathology marked by increased intraepithelial lymphocyte infiltration and mucosal hypertrophy, was also normalized upon Lbr administration. Finally, probiotic treatment modulated the microbiome by increasing the Firmicutes/Bacteroidetes ratio and enriching butyrate-producing Lachnospiraceae. Administration of UDCA and UDCA+OCA had less pronounced effects: only decreased serum bile acids was detected in both groups.
CONCLUSIONS: Probiotic intervention with Lbr represents a feasible strategy to attenuate fibrotic progression in a mouse model of autoimmune cholestatic disease by modulation of the gut-microbiome-immune crosstalk.}, }
@article {pmid41846126, year = {2026}, author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE}, title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141760}, doi = {10.1016/j.jhazmat.2026.141760}, pmid = {41846126}, issn = {1873-3336}, abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.}, }
@article {pmid41846977, year = {2026}, author = {Sharaf, H and Bobay, LM}, title = {MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41846977}, issn = {2692-8205}, abstract = {SUMMARY: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging. We developed MetaStrainer, a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.
MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at https://www.github.com/lbobay/MetaStrainer and on Zenodo: https://doi.org/10.5281/zenodo.17872331.}, }
@article {pmid41847008, year = {2026}, author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR}, title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41847008}, issn = {2692-8205}, abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA) , which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.}, }
@article {pmid41847199, year = {2026}, author = {Ha, S and Kim, N and Song, CH}, title = {Age- and sex-dependent alterations of jejunal microbiota in Fischer 344 rats fed with a high-fructose, high-fat diet: depletion of Lactobacillus intestinalis in small bowel contents.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779112}, pmid = {41847199}, issn = {1664-302X}, abstract = {INTRODUCTION: Our previous research demonstrated that a high-fat diet (HFD) induced jejunal inflammation and hepatic steatosis, suggesting that small bowel microbiota contribute to these pathologies. This study investigated age- and sex-specific alterations in jejunal microbiota following a high-fructose, high-fat diet (HFHFD) in F344 rats.
METHODS: Six-week-old and two-year-old rats of both sexes were fed an HFHFD for 8 weeks, after which jejunal contents were collected for metagenomic analysis. Taxonomic profiling and linear discriminant analysis were performed, and Spearman's rank correlation analysis was used to evaluate associations with jejunal inflammation and hepatic steatosis. Beta-diversity analysis was conducted to assess group separation. In vitro, HIEC-6 human intestinal epithelial cells were used to test the protective effect of Lactobacillus intestinalis under palmitic acid-induced lipotoxic stress.
RESULTS: HFHFD reduced the Firmicutes/Bacteroidetes ratio in young females and in aged rats of both sexes. Notably, Lactobacillus intestinalis-which supports barrier function-decreased in young males and aged females. In contrast, Akkermansia muciniphila increased across all HFHFD groups, particularly in young females and aged rats. Bacteroides vulgatus increased in aged HFHFD-fed rats of both sexes, while Bacteroides caccae was elevated in females across both age groups. Furthermore, the Lactobacillus reuteri group decreased only in young HFHFD rats. L. intestinalis and L. reuteri groups negatively correlated with jejunal inflammation and hepatic steatosis, whereas B. caccae and A. muciniphila showed positive correlations with both pathogenic phenotypes. Beta-diversity revealed a pronounced diet- and sex-dependent separation in young rats, which was attenuated in aged groups. In HIEC-6 cells, L. intestinalis significantly restored viability under palmitic acid-induced lipotoxic stress, though its conditioned medium did not.
DISCUSSION: Collectively, HFHFD induces age- and sex-dependent dysbiosis in the jejunum, and L. intestinalis may serve as a potential probiotic for metabolic dysfunction-associated steatotic liver disease.}, }
@article {pmid41847396, year = {2026}, author = {Yan, J and Yang, H and Zhang, W and Li, Y and Yu, X and Xiong, Z and Shi, C and Hu, Y}, title = {A Case Report of Tuberculous Peritonitis with Negative GeneXpert and Positive Metagenomic Sequencing Results.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {560202}, pmid = {41847396}, issn = {1178-6973}, abstract = {A 65-year-old male patient undergoing peritoneal dialysis was diagnosed with Mycobacterium tuberculosis-related peritonitis. Initial diagnostic tests, including acid-fast smear of ascites, GeneXpert test, and Mycobacterium tuberculosis culture, yielded negative results. However, metagenomic capture sequencing (metaCAP) and metagenomic next-generation sequencing (mNGS) identified the presence of Mycobacterium tuberculosis. The patient was subsequently treated with standard anti-tuberculosis therapy, leading to clinical improvement. This case highlights the utility of advanced molecular diagnostics in identifying atypical pathogens in peritoneal dialysis-related infections.}, }
@article {pmid41847603, year = {2026}, author = {Zhang, Y and Zhang, Y and Zhang, K and Wang, L and Huang, D and Zhen, F and Wang, R and An, C}, title = {Parameter-Specific Effects of Low-Intensity Transcranial Focused Ultrasound Stimulation on Depression-Like Behaviors in a CUMS Mouse Model.}, journal = {Neuropsychiatric disease and treatment}, volume = {22}, number = {}, pages = {586583}, pmid = {41847603}, issn = {1176-6328}, abstract = {PURPOSE: Depression is a multifactorial disorder involving neurotransmitter dysregulation, gut microbiota imbalance, and metabolic disturbances. Low-intensity transcranial focused ultrasound stimulation (LIFUS) holds promise for treating depression. However, the effects of different LIFUS parameter settings on depression-like behaviors, and their potential associations with gut microbiota and fecal metabolite changes, remain largely unexplored. This study aims to investigate the parameter-specific effects of LIFUS on depression-like behaviors in a chronic unpredictable mild stress (CUMS) mouse model, and to explore potential associations with changes in gut microbiota and fecal metabolites.
METHODS: To establish a depression model, C57BL/6 mice were subjected to CUMS, while a separate cohort was kept as a control (CON) group. The CUMS-exposed mice were then randomly divided into four groups: CUMSpo, LIFUS1, LIFUS2 and SHAM. Depressive-like behaviors were evaluated using the sucrose preference test (SPT) and forced swim test (FST). The levels of neurotransmitters and Fecal concentrations of metabolites were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gut microbiota composition was analyzed by metagenomic sequencing, and α-diversity was assessed using the ACE, Chao1, and Shannon indices. Histopathology was assessed via HE staining.
RESULTS: LIFUS at 1.5 kHz PRF, but not 300 Hz, significantly attenuated CUMS-induced depressive-like behaviors, evidenced by increased sucrose preference and reduced immobility time, without affecting locomotor activity. This behavioral effect was accompanied by a significant increase in cortical glutamate. LIFUS2 protocol was associated with a significant increase in tryptamine, alongside a concurrent trend towards restoring the abundance of Clostridia and enhancing gut microbiota α-diversity. HE staining confirmed protocol safety.
CONCLUSION: The antidepressant-like effects of LIFUS appear to be associated with multi-systemic alterations, including changes in cortical glutamate, modulation of the gut microbiota, and specific changes in tryptophan metabolism.}, }
@article {pmid41848047, year = {2026}, author = {Xue, R and Zhang, Y and Li, H and Li, J and Ke, W and Hu, S and Li, C and Chan, FKS and Cui, L}, title = {Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag058}, pmid = {41848047}, issn = {1751-7370}, abstract = {Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman-D2O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42-65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a 2-to 3-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.}, }
@article {pmid41848058, year = {2026}, author = {Calusinska, M and Herold, M and Klimek, D and Bertucci, M and Lemaigre, S and Cambier, S and Zorzan, S and Leclercq, C and Dolfing, J and Westerholm, M and Müller, B and Nasirzadeh, L and Schnürer, A and Wilmes, P and Delfosse, P and Goux, X}, title = {Phylum-wide propionate degradation and its potential connection to poly-gamma-glutamate biosynthesis in Candidatus Cloacimonadota phylum.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag055}, pmid = {41848058}, issn = {1751-7370}, abstract = {The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota OTU. Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterised the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analysed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesise that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.}, }
@article {pmid41848770, year = {2026}, author = {Prabhu, A and Rinke, C}, title = {ICTV Virus Taxonomy Profile: Apasviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {3}, pages = {}, pmid = {41848770}, issn = {1465-2099}, mesh = {Genome, Viral ; *DNA Viruses/classification/genetics/isolation & purification/ultrastructure ; Phylogeny ; Virion/ultrastructure/genetics ; DNA, Viral/genetics ; *Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure ; Metagenomics ; *Archaea/virology ; }, abstract = {The family Apasviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. Members of this family have been identified using metagenomic analyses of brackish estuarine samples and are related to other 'magroviruses' infecting Poseidoniales archaea. The family belongs to the order Magrovirales and includes the genus Agnivirus and the species Agnivirus brisbanense. Viruses in the family possess a linear dsDNA genome of about 108 kbp and encode modules for DNA replication and virion morphogenesis, such as those relating to the formation of an icosahedral capsid and a helical tail, characteristic of members of the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Apasviridae, which is available at ictv.global/report/apasviridae.}, }
@article {pmid41849038, year = {2026}, author = {Biçer, Y and Sönmez, G and Turkal, G and Telli, AE and Akkurt, MY and Uçar, G}, title = {Potential use of whey in kefir production: evaluation of fermentation kinetics and microbiota.}, journal = {Food science of animal resources}, volume = {46}, number = {1}, pages = {}, pmid = {41849038}, issn = {2636-0780}, abstract = {This study was carried out on the effect of different amounts of whey on the kefir production process and the bacterial microbiota of the beverages. Fermentation was carried out by mixing commercial kefir grains with cow, sheep, and goat milk with their whey at concentrations of 0% (control group), 25%, 50%, and 75%. The bacterial microbiota in the produced beverages and the relative abundances of seven microorganisms (Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus delbrueckii, Lactococcus lactis, Streptococcus thermophilus, Leuconostoc mesenteroides, and acetic acid bacteria) were determined using metagenomic analysis targeting the V3-V4 region of 16 S rRNA gene, and quantitative polymerase chain reaction (qPCR), respectively. Lactococcus lactis and Leuconostoc mesenteroides were detected in higher abundance in whey-containing goat samples. While Lactobacillus was dominant in the cow milk samples containing 0%, 25%, and 50% whey, Enterococcus was dominant in the samples containing 75% whey. In sheep milk samples, Lactobacillus was dominant in samples with 75% and 50% whey, Lactococcus was dominant in samples with 25% whey, and Enterococcus was dominant in samples with no (0%) whey. Lactobacillus was dominant in all goat milk samples. In conclusion, high levels of lactic acid bacteria were shown to preserve their viability in the experimentally produced beverages with the addition of whey at different concentrations, and the whey could be used to produce kefir.}, }
@article {pmid41849467, year = {2026}, author = {Ferreira, LDS and Silva, JFBR and Vilhena, MPSP and Alegria, OC and Ramos, RTJ and Sousa, MPA}, title = {Bacterial diversity of lowland soils under cocoa cultivation in Amazon.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e295836}, doi = {10.1590/1519-6984.295836}, pmid = {41849467}, issn = {1678-4375}, mesh = {*Cacao/growth & development ; *Soil Microbiology ; Brazil ; *Biodiversity ; *Bacteria/classification/genetics ; }, abstract = {This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray-Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species-detected in five of the six samples-contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.}, }
@article {pmid41849523, year = {2026}, author = {Mardiyaningsih, A and Astuti, P and Widodo, W and Purwanto, P}, title = {Metagenomic analysis of Gatot, a cassava-based fermented food from Yogyakarta Indonesia: a potential source of Lactobacillaceae probiotic.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e298140}, doi = {10.1590/1519-6984.298140}, pmid = {41849523}, issn = {1678-4375}, mesh = {*Manihot/microbiology ; Indonesia ; *Fermented Foods/microbiology ; RNA, Ribosomal, 16S/genetics ; *Lactobacillaceae/genetics/classification/isolation & purification ; *Probiotics ; DNA, Bacterial/genetics ; Metagenomics ; Food Microbiology ; Fermentation ; }, abstract = {Gatot, a traditional Indonesian fermented food product made from cassava (Manihot utilissima), is valued for its potential health benefits and contribution towards local food security. As fermentation induces a rich microbial environment that could enhance nutritional properties and produce bioactive compounds, understanding the bacterial communities involved is fundamental for optimizing their health-promoting potential. However, the bacterial diversity of Gatot across different regions remains underexplored. This study aims to detect and identify the bacterial communities in Gatot samples, as well as to measure the differences in their abundance in Gatot from three different regions in Yogyakarta. Gatot samples were collected from Bantul, Gunungkidul, and Kulon Progo regions. Genomic DNA was extracted from the samples, and DNA concentration was measured using NanoDrop and Qubit. Libraries were then prepared with Oxford Nanopore Technology kits. For bacterial identification, the V1-V9 regions of the 16S ribosomal RNA gene were amplified using 27F and 1492R primers under specific polymerase chain reaction conditions. Sequencing was performed on a GridION platform using MinKNOW (version v24.02.16) and Dorado (version v7.3.11) for high-accuracy basecalling. Quality filtering and visualization of FASTQ files were performed using NanoPlot and NanoFilt, while taxonomic classification was referenced against the NCBI 16S RefSeq database. Data analysis was completed in Pavian and RStudio. The dominant bacterial family across all samples was the Lactobacillaceae family. However, each region exhibited unique microbial signatures at the genus level: Bantul samples were dominated by Weissella, Gunungkidul by Leuconostoc, and Kulon Progo by Lactiplantibacillus. Specific species were also predominant in each location, with Weissella confusa in Bantul, Liquorilactobacillus hordei in Gunungkidul, and Lactiplantibacillus plantarum in Kulon Progo. These regional variations highlight how location-specific bacterial communities influence the fermentation profile of Gatot, potentially affecting flavor, texture, and nutritional value. This study provides the first comprehensive metagenomic analysis of Gatot's bacterial communities across different regions, offering new insights into the influence of geographical environment on microbial composition in fermented cassava products. The findings support the potential for controlled fermentation processes tailored to local microbial ecosystems, to enhance Gatot's functionality as a health-promoting food and source of probiotic.}, }
@article {pmid41850876, year = {2026}, author = {Regmi, H and Dritsoulas, A and Kamali, S and Stelinski, LL and Diepenbrock, LM and Duncan, L}, title = {Edge effects, tree cover and soil properties linked to the distribution of Diaprepes abbreviatus in a Florida citrus orchard.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70723}, pmid = {41850876}, issn = {1526-4998}, support = {CRDF22-013//Citrus Research and Development Foundation, Inc./ ; }, abstract = {BACKGROUND: Diaprepes root weevil (DRW, Diaprepes abbreviatus) is a major economic pest of citrus trees in Florida and the Caribbean Basin. To identify potential drivers of local patterns of weevil abundance and tree condition, we measured relationships between DRW and edaphic properties in a Florida orchard in which half the trees were initially protected from herbivores by individual protective covers (IPCs) of fabric mesh. Weevils were monitored for 2 years in 94 plots arranged in a grid pattern. Soil samples were processed for physicochemical properties, and DNA from soil organisms was subjected to metabarcoding for ITS2 rDNA, 16S rDNA, and COI mtDNA.
RESULTS: Weevils aggregated each summer along plot boundaries adjacent to a natural area of alternate hosts, consistent with an edge-biased distribution reflecting seasonal weevil migration. Fourteen months after the covers were removed, 93% of 484 prokaryote species (dominated by Bacilli, Actinobacteria, Alphaproteobacteria, and Cyanobacteria) that were most closely associated with IPC use were less abundant beneath the trees that were formerly covered than under previously uncovered trees. Soil moisture, Paenibacillus spp. diversity, and IPCs were associated with DRW patterns and tree condition including mortality.
CONCLUSIONS: Early season, edge-biased distribution of DRW should be exploited for monitoring and management efficacy. The relationship here between tree mortality and microbiome species deficits associated with IPCs supports the need for research to resolve the role of tree covers in potential trophic cascades that affect plant health. © 2026 Society of Chemical Industry.}, }
@article {pmid41850962, year = {2026}, author = {Zhao, Y and Zheng, J and Liu, Q}, title = {The diversity of emerging tick-borne viruses globally.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.03.001}, pmid = {41850962}, issn = {1471-5007}, abstract = {Zhang et al. provide the first global synthesis of 230 emerging tick-borne viruses, introducing a genomic model that predicts zoonotic risk. Their approach identifies 25 very-high-risk viruses and clinically validates three novel human pathogens, shifting the paradigm from reactive discovery to proactive risk assessment for global health security.}, }
@article {pmid41851124, year = {2026}, author = {Luzmore, A and Grauer, J and Barber, D and Lau, P and Jorgensen, G and Jain, S and Perron, GG}, title = {Seasonal frost improves probiotic and nutrient availability in fermented vegetables.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00776-w}, pmid = {41851124}, issn = {2396-8370}, abstract = {Climate-driven shifts in seasonal frost patterns raise important questions about their impact on food quality and resilience. Here, we show that a single 12-h frost event at harvest can enhance both the microbial and nutritional properties of fermented cabbage and carrots, two cold-tolerant crops widely grown in the U.S. Northeast. Using microbial amplicon and metagenomic sequencing, we found that frost exposure led to subtle but consistent changes in microbial composition, including greater abundance of cold-adapted taxa such as Leuconostoc and Debaryomyces. These changes corresponded to increased abundance of genes involved in vitamin biosynthesis, particularly menaquinone (K2), cobalamin (B12), and threonine pathways. Nutritional assays confirmed higher concentrations of vitamins A and E in frost-conditioned carrot ferments and increased vitamin K1 in cabbage. Our findings suggest that exposure to seasonal frost can enhance the health-promoting and sensory qualities of fermented vegetables, offering a novel strategy for value-added, climate-resilient food production in temperate regions.}, }
@article {pmid41851530, year = {2026}, author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E}, title = {Advances and opportunities in measuring dietary intake: from omics to AI.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {41851530}, issn = {2522-5812}, abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.}, }
@article {pmid41851880, year = {2026}, author = {Sharma, AA and Martinou, AF and Cadar, D and Omirou, M and Neira, M and Christophides, GK}, title = {Integrated vector and arbovirus surveillance in Cyprus: first reports of Usutu virus and Culex pipiens bioform diversity highlight potential for zoonotic arbovirus transmission.}, journal = {Parasites & vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07350-z}, pmid = {41851880}, issn = {1756-3305}, support = {856612//Horizon 2020/ ; }, abstract = {BACKGROUND: Anthropogenic pressures, including urbanisation, globalisation and climate change, have facilitated an increased risk for emergence or re-emergence of mosquito-borne diseases into regions such as the Eastern Mediterranean and Middle East. Cyprus is a major stop-over site for migratory birds and has previously experienced outbreaks of West Nile virus (WNV). The island has native mosquito vector populations; however, it has also seen the recent establishment of invasive Aedes albopictus and Ae. aegypti mosquitoes. Given the dynamic climatic conditions and the shifting ecological and epidemiological landscapes in the region, the need for routine vector and pathogen surveillance has never been more critical.
METHODS: Herein, we present the results from localised adult mosquito surveillance that were conducted in two cities of Cyprus between 2019 and 2022. Mosquito taxa were identified through morphological analysis, and molecular techniques were used to further characterise the Culex pipiens bioforms. Engorged mosquito midguts were analysed to determine host blood meals. Metagenomic next-generation sequencing was employed to screen mosquito pools for arboviruses.
RESULTS: Our results provide the first report of Usutu virus in Cx. pipiens mosquitoes in Cyprus. Blood meal analysis identified multiple vertebrate hosts, including Cetti's warbler, a bird species previously reported to be seropositive for WNV on the island. Additionally, we report the presence of both Cx. pipiens pipiens and Cx. pipiens molestus, an ornithophilic and a mammophilic bioform, respectively, as well as their hybrids.
CONCLUSIONS: Our findings highlight the urgent need for enhanced mosquito surveillance strategies where mosquito populations will be regularly screened for pathogens to mitigate emerging risks of arbovirus transmission in Cyprus.}, }
@article {pmid41851941, year = {2026}, author = {Shrestha, E and Katuwal, N and Sitaula, RK and Gurung, H and Shrestha, A and Karki, P and Shrestha, R}, title = {Identification of the Causative Pathogen in the 2023 Conjunctivitis Outbreak of Nepal Using Unbiased Metagenomic Next Generation Sequencing.}, journal = {Journal of Nepal Health Research Council}, volume = {23}, number = {3}, pages = {527-532}, doi = {10.33314/jnhrc.v23i03.4749}, pmid = {41851941}, issn = {1999-6217}, mesh = {Humans ; Nepal/epidemiology ; *Disease Outbreaks ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Metagenomics/methods ; *Conjunctivitis/epidemiology/virology ; Adult ; Child, Preschool ; *Enterovirus C, Human/isolation & purification/genetics ; Adolescent ; Young Adult ; Middle Aged ; Infant ; }, abstract = {BACKGROUND: In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudden-onset redness, foreign body sensation, watery discharge, and occasional lid swelling. Most cases exhibited acute haemorrhagic conjunctivitis, with management involving ocular lubricants, personal hygiene, and topical antibiotics. This case series from Himalaya Eye Hospital in Pokhara details the genomic epidemiology and clinical characteristics of conjunctivitis cases during the outbreak.
METHODS: To understand the causative agents, conjunctival swabs from patients were subjected to unbiased metagenomic next-generation sequencing (mNGS) in Illumina iSeq100 at Dhulikhel Hospital Kathmandu University Hospital Results: This case series revealed the presence of Enterovirus C (coxsackievirus strain A24) as the major pathogen responsible for the outbreak.
CONCLUSIONS: This case series contributes valuable insights into the genomic diversity of conjunctivitis-associated viruses, highlighting the potential of mNGS in enhancing diagnostic capabilities and guiding public health responses.}, }
@article {pmid41852102, year = {2026}, author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X}, title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70268}, doi = {10.1111/1462-2920.70268}, pmid = {41852102}, issn = {1462-2920}, support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Fungi/genetics/classification/physiology ; China ; Phosphorus/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Biodiversity ; Bacteria/genetics/classification ; Ecosystem ; }, abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.}, }
@article {pmid41852114, year = {2026}, author = {Kaneko, Y and Hino, T and Taminishi, S and Matoba, Y and Motooka, D and Hoshino, A and Matoba, S}, title = {Inhibition of N-Terminal Acetyltransferase C Mitigates Endoplasmic Reticulum Stress-Mediated Muscle Atrophy in Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {2}, pages = {e70249}, doi = {10.1002/jcsm.70249}, pmid = {41852114}, issn = {2190-6009}, support = {22H03071//JSPS Grant-in-Aid Scientific Research/ ; 25K02651//JSPS Grant-in-Aid Scientific Research/ ; //Nakatomi Foundation/ ; }, mesh = {Animals ; *Cachexia/etiology/pathology ; *Endoplasmic Reticulum Stress ; *Muscular Atrophy/etiology/pathology/metabolism ; Mice ; Male ; *Neoplasms/complications ; Humans ; Unfolded Protein Response ; }, abstract = {BACKGROUND: Cancer cachexia is a complex syndrome marked by weight loss and muscle wasting, significantly impacting patient quality of life and survival. Mechanistically, it is characterized by suppressed protein synthesis and enhanced muscle catabolism, with the role of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) becoming increasingly evident. This study aimed to explore ER stress-tolerant factors in muscle wasting and evaluate their potential to prevent muscle loss in cancer cachexia.
METHODS: A genome-wide CRISPR screening was conducted in the context of ER stress-mediated growth inhibition of C2C12 myoblasts. The candidate genes resistant to ER stress were further evaluated in C2C12 myotubes treated with conditioned medium of Lewis lung adenocarcinoma (LLC) cells. Twelve-week-old male mice were administered LLC cells and shRNA against Naa35 via adeno-associated virus. Four weeks later, tibialis anterior (TA) muscles were analysed for muscle mass, grip strength and molecular changes with quantitative polymerase chain reaction, western blotting and histological analysis.
RESULTS: CRISPR screening identified Naa35, Naa38 and Naa30, all three components of N-terminal acetyltransferase C, as key molecules for resistance to ER stress. The atrophic muscles of mice bearing LLC demonstrated an elevation of UPR, as well as 1.64-fold upregulation of Naa35 protein (p = 0.0072). Among the three branches of the UPR, an ATF6 inhibitor, AEBSF, abolished upregulation of Naa35, Naa38 and Naa30, and an ATF6 activator, AA147, induced Naa35 expression in a dose-dependent manner (p < 0.001). In cells treated with LLC conditioned medium, Naa35 knockdown reduced the amount of cathepsin K (CTSK) protein, which subsequently resulted in the CTSK-mediated proteolysis of insulin receptor substrate 1. In LLC-bearing mice, Naa35 knockdown led to a 65.4% reduction in CTSK protein expression (p < 0.001) and preservation of the phosphorylation levels of protein kinase B (p < 0.0324) and anabolic-related S6 kinase (p < 0.0375). Concurrently, the expression of catabolism-related genes was repressed (MuRF1, p < 0.0015; MAFbx1, p < 0.0265). These alterations were associated with the restoration of TA muscle mass (2.52 ± 0.19 vs. 3.72 ± 0.45 mg/g, p = 0.0004), fibre area (1741 ± 992 vs. 2099 ± 1264 mm[2], p < 0.0001), grip strength in all four limbs (0.0328 ± 0.0076 vs. 0.0506 ± 0.0130 N/g, p = 0.0295) and wire mesh hanging time (496 ± 331 vs. 1038 ± 370 s, p = 0.0406).
CONCLUSIONS: Inhibition of N-terminal acetyltransferase C prevents ER stress-induced muscle wasting via the downregulation of CTSK and subsequent activation of the anabolic pathway. This suggests that N-terminal acetyltransferase C is a potential therapeutic target for combating muscle wasting in cancer cachexia.}, }
@article {pmid41852383, year = {2025}, author = {Urrutia-Angulo, L and Lavín, JL and Oporto, B and Aduriz, G and Hurtado, A and Ocejo, M}, title = {Resistome and microbiome profiling of bovine milk following antimicrobial dry cow therapy: insights from short- and long-read metagenomic sequencing.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1672438}, pmid = {41852383}, issn = {2813-4338}, abstract = {Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.}, }
@article {pmid41852393, year = {2025}, author = {Wadop, YN and Muhammad, J and Bernal, R and Satizabal, CL and Beiser, A and Vasan, RS and Xavier, R and Kautz, T and Seshadri, S and Himali, JJ and Fongang, B}, title = {Adherence to Life's Essential 8 enhances gut microbiota diversity and cognitive performance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1592023}, pmid = {41852393}, issn = {2813-4338}, abstract = {INTRODUCTION: Emerging evidence suggests a complex interplay among cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), developed by the American Heart Association, includes vital metrics of cardiovascular health, such as diet, physical activity, nicotine exposure, sleep health, body mass index (BMI), blood glucose, blood lipids, and blood pressure.
METHODS: In this study, we analyzed data from 781 participants in the Framingham Heart Study (FHS) to explore the relationship between LE8 adherence, gut microbiota, and cognitive performance. Multivariable linear regression models and mediation analysis were used to investigate this relationship.
RESULTS: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (α-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (β-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while a reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (α-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence both LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between LE8 adherence and cognitive performance. These taxa may serve as key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.
DISCUSSION: This study highlights the significance of comprehensive cardiovascular health metrics in shaping gut microbiota and enhancing cognitive resilience. Our findings underscore the therapeutic potential of targeting gut microbiota to mitigate cognitive decline, warranting further exploration through longitudinal and metagenomic studies.}, }
@article {pmid41852395, year = {2025}, author = {Ortega-Reyes, D and Takeuchi, T and Ogata, Y and Iwami, T and Suda, W and Kubota, T and Kubota, N and Kadowaki, T and Tomizuka, K and Ohno, H and Horikoshi, M and Terao, C}, title = {Interplay between host genetics and gut microbiome composition in the Japanese population.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1635907}, pmid = {41852395}, issn = {2813-4338}, abstract = {BACKGROUND: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.
METHODS: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.
RESULTS: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p ≤ 5×10[-8]). However, none of these associations surpassed the stringent significance threshold of p ≤ 2.75×10[-11]. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.
CONCLUSION: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.}, }
@article {pmid41852396, year = {2025}, author = {Zoruk, P and Morozov, M and Veselovsky, V and Strokach, A and Babenko, V and Klimina, K}, title = {Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1688681}, pmid = {41852396}, issn = {2813-4338}, abstract = {BACKGROUND: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.
RESULTS: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin[™] Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard[®] kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.
CONCLUSIONS: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.}, }
@article {pmid41852403, year = {2025}, author = {Helal, M and Bari, VK}, title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1549166}, pmid = {41852403}, issn = {2813-4338}, abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.}, }
@article {pmid41852404, year = {2025}, author = {Xuan, L and Sun, X and Wang, B and Chen, F and Yi, Y and Mao, H and Wang, Y and Zhao, G and Wang, J and Zhang, Y}, title = {Cold-water immersion alleviates intestinal damage induced by exertional heat stroke via modulation of gut microbiota in rats.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1531991}, pmid = {41852404}, issn = {2813-4338}, abstract = {OBJECTIVE: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.
METHODS: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.
RESULTS: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.
CONCLUSION: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.}, }
@article {pmid41852413, year = {2025}, author = {Guerrero-Toledo, FM and Espinosa-Solares, T and Hernández-Eugenio, G and Huber, DH}, title = {Community assembly following disturbance in batch anaerobic digesters displays highly reproducible secondary succession and a shifting stochastic-deterministic balance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1707779}, pmid = {41852413}, issn = {2813-4338}, abstract = {The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.}, }
@article {pmid41852418, year = {2025}, author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S}, title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1619859}, pmid = {41852418}, issn = {2813-4338}, abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.}, }
@article {pmid41852432, year = {2025}, author = {Mhuireach, GÁ and Collins, S and Dietz, L and Horve, PF and Laguerre, A and Northcutt, D and Stenson, J and Wymelenberg, KVD and Gall, E and Fretz, M}, title = {Effects of wetting events on mass timber surface microbial communities and VOC emissions: implications for building operation and occupant well-being.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1395519}, pmid = {41852432}, issn = {2813-4338}, abstract = {INTRODUCTION: Humans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.
METHODS: In this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.
RESULTS: VOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC-acetoin (3-hydroxy, 2-butanone)-was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.}, }
@article {pmid41852435, year = {2025}, author = {Trubl, G and Malard, L and Rahlff, J}, title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1604002}, doi = {10.3389/frmbi.2025.1604002}, pmid = {41852435}, issn = {2813-4338}, }
@article {pmid41852443, year = {2025}, author = {Palazzi, CM and Ciampaglia, G and Binato, B and Ragazzini, M and Bertuccioli, A and Cavecchia, I and Matera, M and Cazzaniga, M and Zonzini, GB and Zerbinati, N and Tanda, ML and Di Pierro, F}, title = {Position statement of the Microbiota International Clinical Society.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1657750}, pmid = {41852443}, issn = {2813-4338}, }
@article {pmid41852664, year = {2026}, author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H}, title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1748638}, pmid = {41852664}, issn = {2235-2988}, mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.}, }
@article {pmid41852665, year = {2026}, author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L}, title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1728182}, pmid = {41852665}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; }, abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.
METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.
RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.
CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.}, }
@article {pmid41852689, year = {2026}, author = {Anandan, S and Ali, A and Selvarajoo, A and Supramaniam, CV}, title = {Trichoderma combined with palm kernel shell biochar promotes root health and rhizosphere biodiversity in young oil palm seedlings infected with Ganoderma boninense.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1742803}, pmid = {41852689}, issn = {2813-4338}, abstract = {Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.}, }
@article {pmid41852814, year = {2022}, author = {Jagadeeshwari, U and Sasikala, C and Rai, A and Indu, B and Ipsita, S and Ramana, CV}, title = {Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1020341}, pmid = {41852814}, issn = {2813-4338}, abstract = {INTRODUCTION: Host-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept.
METHODS: We report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota.
RESULTS AND DISCUSSION: The phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated 'Candidatus' superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with 'Candidatus Heimdallarchaeota' were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb's pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea.}, }
@article {pmid41852815, year = {2022}, author = {van Belkum, A and Lisotto, P and Pirovano, W and Mongiat, S and Zorgani, A and Gempeler, M and Bongoni, R and Klaassens, E}, title = {Being friendly to the skin microbiome: Experimental assessment.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1077151}, pmid = {41852815}, issn = {2813-4338}, abstract = {Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically "microbiome friendly" while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.}, }
@article {pmid41852816, year = {2022}, author = {Tadmor, AD and Mahmoudabadi, G and Foley, HB and Phillips, R}, title = {Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1097124}, pmid = {41852816}, issn = {2813-4338}, abstract = {Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.}, }
@article {pmid41852852, year = {2026}, author = {Gusareva, ES and Vettath, VK and Gaultier, NE and Sadovoy, AV and Dacanay, JGA and Schuster, SC}, title = {Dermatophagoides pteronyssinus in ambient air bioaerosols.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {3}, pages = {100667}, pmid = {41852852}, issn = {2772-8293}, abstract = {BACKGROUND: House dust mite (HDM) sensitization is a leading cause of allergic rhinitis and asthma worldwide, with Dermatophagoides pteronyssinus, Dermatophagoides farinae, and Blomia tropicalis being the primary allergenic species typically associated with indoor environments. Even effective multicomponent interventions creating an HDM-free indoor environment are often insufficient to prevent allergy, as HDM exposure may also occur outdoors.
OBJECTIVE: To assess the potential for outdoor HDM exposure, we applied air biomass sequencing and metagenomic techniques to detect HDM DNA in both indoor and outdoor bioaerosols, offering an alternative to conventional dust sampling methods.
METHODS: We used 2 data sets in this study: (1) a global data set comprising 1,171 outdoor air samples collected across 33 countries in open air environments and (2) a data set of indoor (n = 161) and outdoor (n = 156) air samples collected across 156 apartments from 106 locations in Singapore. All air samples were collected by drawing 24,000 to 36,000 L of air using SASS3100 air samplers; all samples were processed identically. Species-level taxonomic classification was performed using Kaiju software aligned to the National Center for Biotechnology Information nonredundant database, with a minimum threshold of 40 reads per taxon.
RESULTS: Analysis of 1,171 global outdoor air samples revealed D pteronyssinus as the most prevalent HDM species; it was detected in 208 samples, with abundance increasing from temperate toward equatorial regions. In Singaporean households, D pteronyssinus was found in 58.4% of indoor samples and 21.2% of nearby outdoor samples, with high median DNA read counts outdoors suggesting that exposure to HDM is not limited to domestic environments. B tropicalis and D farinae were also detected in Singapore, albeit at lower frequencies.
CONCLUSION: Our findings highlight the need to expand environmental allergen surveillance beyond household dust to include ambient and outdoor air, particularly in tropical climates.}, }
@article {pmid41853108, year = {2026}, author = {Khan, A}, title = {Disseminated Mycobacterium intracellulare subsp. chimaera infection, undiagnosed for years, highlights the enduring clinical utility of "old school" microbiological testing and a robust differential.}, journal = {ASM case reports}, volume = {2}, number = {2}, pages = {}, pmid = {41853108}, issn = {2996-2684}, abstract = {Disseminated Mycobacterium intracellulare subsp. chimaera (MC) infections are rare, slow-progressing, and easily overlooked, particularly when a patient's history of prior cardiac surgery is not incorporated into the diagnostic evaluation. In a recent ASM Case Reports article (1:e00003-25, 2025, https://doi.org/10.1128/asmcr.00003-25), Ladines-Lim et al. describe a disseminated MC infection in a patient with prior aortic and mitral valve replacement that remained undiagnosed for over 4 years. Conventional microbiological testing was not pursued early in the course of illness because the history of cardiopulmonary bypass was not linked with the constellation of unexplained symptoms. This case urges clinicians to remain vigilant and suspect MC in patients with prior open-chest cardiac surgery who present with gradually worsening, systemic symptoms. Since 2013, global outbreaks of delayed-onset MC infections have been traced to contaminated heater cooler devices, yet many centers continue to face barriers to replacing or monitoring such equipment. A delayed diagnosis in this case was eventually established by cell-free metagenomic next-generation sequencing (cfmNGS). However, the result was not acted upon until weeks later, after central nervous system involvement. A more timely, cost-effective diagnosis might have been achieved using traditional, widely available, culture-based testing guided by a robust exposure-driven differential. Clinicians should suspect MC in patients with prior cardiac surgery-even years earlier-who develop unexplained, progressive systemic symptoms. Early suspicion and appropriate testing are critical to improved outcomes. This case shows that next-generation sequencing assays are only as useful as the clinical reasoning guiding their use. Traditional microbiological testing-when leveraged early and thoughtfully-remains an accessible cornerstone of diagnosing complex MC infections.}, }
@article {pmid41853337, year = {2023}, author = {Peter, H and Michoud, G and Busi, SB and Battin, TJ}, title = {The role of phages for microdiverse bacterial communities in proglacial stream biofilms.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1279550}, pmid = {41853337}, issn = {2813-4338}, abstract = {Viruses modulate the diversity and activity of microbial communities. However, little is known about their role for the structure of stream bacterial biofilm communities. Here, we present insights into the diversity and composition of viral communities in various streams draining three proglacial floodplains in Switzerland. Proglacial streams are characterized by extreme environmental conditions, including near-freezing temperatures and ultra-oligotrophy. These conditions select for few but well-adapted bacterial clades, which dominate biofilm communities and occupy niches via microdiversification. We used metagenomic sequencing to reveal a diverse biofilm viral assemblage in these streams. Across the different floodplains and streams, viral community composition was tightly coupled to that of the bacterial hosts, which was underscored by generally high host specificity. Combining predictions of phage-host interactions with auxiliary metabolic genes (AMGs), we identify specific AMGs shared by phages infecting microdiverse clade members. Our work provides a step towards a better understanding of the complex interactions among bacteria and phages in stream biofilm communities in general and streams influenced by glacier meltwaters and characterized by microdiversity in particular.}, }
@article {pmid41853339, year = {2023}, author = {Wong, MT and Nesbø, CL and Wang, W and Couturier, M and Lombard, V and Lapebie, P and Terrapon, N and Henrissat, B and Edwards, EA and Master, ER}, title = {Taxonomic composition and carbohydrate-active enzyme content in microbial enrichments from pulp mill anaerobic granules after cultivation on lignocellulosic substrates.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1094865}, pmid = {41853339}, issn = {2813-4338}, abstract = {Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pulp mill. Both 16S ribosomal DNA and metagenome sequences were obtained following anaerobic cultivation of the digester inoculum on cellulose and pretreated (steam exploded) poplar wood chips. The community composition and profile of predicted carbohydrate-active enzymes were then analyzed in detail. Recognized lignocellulose degraders were abundant in the resulting cultures, including populations belonging to Clostridiales and Bacteroidales orders. Poorly defined taxonomic lineages previously identified in other lignocellulose-degrading communities were also detected, including the uncultivated Firmicutes lineage OPB54 which represented nearly 10% of the cellulose-fed enrichment even though it was not detected in the bioreactor inoculum. In total, 3580 genes encoding carbohydrate-active enzymes were identified through metagenome sequencing. Similar to earlier enrichments of animal digestive systems, the profile encoded by the bioreactor inoculum following enrichment on pretreated wood was distinguished from the cellulose counterpart by a higher occurrence of enzymes predicted to act on pectin. The majority (> 93%) of carbohydrate-active enzymes predicted to act on plant polysaccharides were identified in the metagenome assembled genomes, permitting taxonomic assignment. The taxonomic assignment revealed that only a small selection of organisms directly participates in plant polysaccharide deconstruction and supports the rest of the community.}, }
@article {pmid41853340, year = {2023}, author = {Yang, Q and Wang, J and Zhang, D and Feng, H and Bozorov, TA and Yang, H and Zhang, D}, title = {Effects of multi-resistant ScALDH21 transgenic cotton on soil microbial communities.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1248384}, pmid = {41853340}, issn = {2813-4338}, abstract = {Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis, in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.}, }
@article {pmid41853343, year = {2023}, author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y}, title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1329925}, pmid = {41853343}, issn = {2813-4338}, abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.}, }
@article {pmid41853350, year = {2023}, author = {Oliveira, RS and Pinto, OHB and Quirino, BF and de Freitas, MAM and Thompson, FL and Thompson, C and Kruger, RH}, title = {Genome-resolved metagenomic analysis of Great Amazon Reef System sponge-associated Latescibacterota bacteria and their potential contributions to the host sponge and reef.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1206961}, pmid = {41853350}, issn = {2813-4338}, abstract = {The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge's microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group's abundance in GARS sponges. The workflow consisted of MAG's quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host's survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.}, }
@article {pmid41853380, year = {2023}, author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN}, title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1067019}, pmid = {41853380}, issn = {2813-4338}, abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.}, }
@article {pmid41853383, year = {2023}, author = {Ramirez Garcia, A and Greppi, A and Constancias, F and Ruscheweyh, HJ and Gasser, J and Hurley, K and Sturla, SJ and Schwab, C and Lacroix, C}, title = {Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1194516}, pmid = {41853383}, issn = {2813-4338}, abstract = {INTRODUCTION: Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function.
METHODS: In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase (gdh)-harboring taxa, the proportion of resident A. hallii, and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 10[6] cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized.
RESULTS AND DISCUSSION: Six microbiota were assigned to Bacteroides, nine to Prevotella, and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 10[10] bacterial cells ranged between 1.32 × 10[8] and 1.15 × 10[9]. Eighteen out of the 20 donors were dominated by A. hallii, representing between 33% and 94% of the total gdh relative abundance of the samples. The microbiota with low A. hallii abundance (i.e., with a relative abundance < 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance > 1%). Furthermore, supplementing the low-A. hallii-abundant microbiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in all microbiota with glycerol and with the combination of glycerol and A. hallii, for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure.}, }
@article {pmid41853385, year = {2023}, author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P}, title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1147082}, pmid = {41853385}, issn = {2813-4338}, abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.
OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).
METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.
RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.
CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.}, }
@article {pmid41853387, year = {2023}, author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC}, title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1199766}, pmid = {41853387}, issn = {2813-4338}, abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.}, }
@article {pmid41853501, year = {2024}, author = {Faber, Q and Davis, C and Christner, B}, title = {Metagenomic inference of microbial community composition and function in the weathering crust aquifer of a temperate glacier.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1488744}, pmid = {41853501}, issn = {2813-4338}, abstract = {Bacterial, fungal, and algal communities that colonize aquatic systems on glacial ice surfaces mediate biogeochemical reactions that alter meltwater composition and affect meltwater production and storage. In this study, we sought to improve understanding of microbial communities inhabiting the shallow aquifer that forms seasonally within the ice surface of a glacier's ablation zone (i.e., the weathering crust aquifer). Using a metagenomic approach, we compared gene contents of microbial assemblages in the weathering crust aquifer (WCA) of the Matanuska Glacier (Alaska, USA) to those recovered from supraglacial features and englacial ice. High abundances of Pseudomonadota, Cyanobacteriota, Actinomycetota, and Bacteroidota were observed across all samples, while taxa in class Gammaproteobacteria were found at significantly higher abundances in the weathering crust aquifer. The weathering crust aquifer samples also contained higher abundances of Dothideomycetes and Microbotryomyetes; fungal classes commonly observed in snow and other icy ecosystems. Phylogenetic analysis of 18S rRNA and rbcL gene sequences indicated high abundances of algae in the WCA that are closely related (> 98% and > 93% identity, respectively) to taxa of Ancylonema (Streptophyta) and Ochromonas (Ochrophyta) reported from glacial ice surfaces in Svalbard and Antarctic sea ice. Many functional gene categories (e.g., homeostasis, cellular regulation, and stress responses) were enriched in samples from the weathering crust aquifer compared to those from proximal englacial and supraglacial habitats, providing evidence for ecological specialization in the communities. The identification of phagotrophic phytoflagellate taxa and genes involved in mixotrophy implies that combined phototrophic and heterotrophic production may assist with persistence in the low light, low energy, and ephemeral conditions of the weathering crust environment. The compositional and functional differences we have documented indicate distinct microbial distributions and functional processes occur in the weathering crust aquifer environment, and we discuss how deciphering these nuances is essential for developing a more complete understanding of ecosystem biogeochemistry in supraglacial hydrological systems.}, }
@article {pmid41853503, year = {2024}, author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T}, title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1451735}, pmid = {41853503}, issn = {2813-4338}, abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.}, }
@article {pmid41853504, year = {2024}, author = {Muwonge, A and Gerber, PF and Wee, BA and Thomson, J and Wang, J and Halbur, PG and Opriessnig, T}, title = {Exploring the utility of bioaerosol metagenomics compared to PCRs for swine pathogen surveillance.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1439108}, pmid = {41853504}, issn = {2813-4338}, abstract = {INTRODUCTION: Pathogen introduction and transmission at the farm, regional, or national level are associated with reduced animal welfare and negative impacts on herd economics. Ongoing infectious disease surveillance, active or passive, is therefore of high importance. For optimal resolution, each pig is sampled individually, for example by collecting blood or nasal swabs. In recent years, oral fluids have become very useful for population surveillance at the pen level. Another alternative is sampling the air to capture pathogens circulating across the entire barn via bioaerosols.
OBJECTIVE: This study aimed to examine the potential utility of bioaerosol metagenomics for pathogen detection on pig farms.
METHODS: Bioaerosols via automated air sampler, and oral fluid via pen-based ropes, were collected from each of two Scottish indoor pig farms. All samples were subjected to conventional routine bacterial isolation. Total genomic nucleic acids were extracted for PCR screening for three pig DNA viruses, three bacterial Mycoplasma species and an RNA virus. Illumina shotgun metagenomic sequencing was also conducted.
RESULTS: Oral fluids contained more DNA compared to bioaerosol samples. DNA integrity exhibited limited impact on PCR or sequence yield. While Streptococcus suis could be cultured from a single oral fluid sample, reads mapped to S. suis were detectable in all metagenomic samples. Other bacterial pig pathogens, including Mycoplasma hyorhinis, M. hyopneumoniae and M. hyosynoviae, were detected in oral fluid and aerosols by PCR and metagenomics. One of the two farms was PRRSV positive, and the virus was detectable via PCR in oral fluids but not in bioaerosols. Antimicrobial resistance (AMR) gene profiles had less variation between bioaerosols and oral fluids. Some identified AMR genes had strikingly similar abundance overall.
CONCLUSION: Overall, these findings indicate that there is potential utility of bioaerosol metagenomics for pathogen surveillance on pig farms; however, more research is needed for technical and cost optimization to allow for routine pathogen detection on livestock farms.}, }
@article {pmid41853506, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1484878}, doi = {10.3389/frmbi.2024.1484878}, pmid = {41853506}, issn = {2813-4338}, abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].}, }
@article {pmid41853507, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1359580}, pmid = {41853507}, issn = {2813-4338}, abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.}, }
@article {pmid41853508, year = {2024}, author = {Molotzu, MR and Cabras, PA and Di Marcantonio, L and Atzeni, R and Macciotta, NPP and Canu, A}, title = {Metagenomic analysis of goat feces from Ogliastra (Sardinia, Italy).}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1474497}, pmid = {41853508}, issn = {2813-4338}, abstract = {With its constitutive and functional characteristics, the intestinal microbiota plays a crucial role in the health condition of the animals. Variations in the composition and gene expression of the intestinal microbiota are associated with the risk of the onset of various pathologies of the gastrointestinal tract and chronic inflammatory intestinal diseases. The objectives of this study were to evaluate the variability in the composition of the intestinal microbiota of goats of different breeds (Sarda, Maltese, and Alpine) farmed in different flocks of the region of Ogliastra (Sardegna, Italy) and to assess whether the type of feeding (natural pasture grazing-based versus intensive) could affect the intestinal bacterial composition. We also evaluated possible differences in the composition of the intestinal microbiota between healthy and Caprine arthritis encephalitis (CAE)-affected goats. The economic damage caused by this pathology is due to the reduction in milk production, with infected animals having greater susceptibility to contract diseases. The results of our study highlighted a statistically significant difference (P = 0.001-0.005) in the intestinal bacterial composition between the intensively managed flock and the other natural pasture-based flock.g In particular, a significantly greater abundance of Acidoaminococcaceae in the intensive flock was obgserved. Furthermore, a significantly greater abundance of Prevotellaceae was found in two localities in which, out of a total of 29 animals, only four tested negative for CAE. From these data, we deduced that the presence of Prevotellaceae can be an indication of the disease. This difference could be attributed to the farming system, the Cardedu farm being the only intensive one, and to the geographical distance of this location from the other sampling sites. Therefore, the results of the present study suggest that extensive or intensive farm management may affect the intestinal microbiota of goats.}, }
@article {pmid41853526, year = {2024}, author = {Liu, S and Zhao, J and Feng, WL and Zhang, ZJ and Gu, YF and Wang, YP}, title = {Microbial community succession of cow manure and tobacco straw composting.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1301156}, pmid = {41853526}, issn = {2813-4338}, abstract = {Composting livestock manure using microorganisms is a safe and resourceful practice. The continual fluctuations in physicochemical parameters during composting are intricately linked to the composition of microbial communities. This study investigated the dynamics of microbial communities during the composting of cow manure and tobacco straw using amplicon sequencing and shotgun metagenomics. The sequencing results revealed major genera such as Sphaerobacter, Actinomadura, Thermomonospora, Flavobacterium, Bacillus, Hydrogenophaga, Pseudomonas, Lysinibacillus, Aneurinibacillus, and Azotobacter. Metagenomic analysis highlighted that the phylum Proteobacteria constituted the largest proportion. Furthermore, the presence of the genus Rhodococcus, known to cause human and animal diseases, gradually decreased over time. These findings offer initial insights into the microbial community composition and function during cow manure and tobacco straw composting.}, }
@article {pmid41853529, year = {2024}, author = {Huttelmaier, S and Shuai, W and Sumner, JT and Hartmann, EM}, title = {Phage communities in household-related biofilms correlate with bacterial hosts.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1396560}, pmid = {41853529}, issn = {2813-4338}, abstract = {The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.}, }
@article {pmid41853533, year = {2024}, author = {Liu, Z and Shen, Y and Fu, Y and Sun, D and Li, L and Lv, Z}, title = {Association of resistome abundance with hyperuricaemia in elderly individuals: a metagenomics study.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1384703}, pmid = {41853533}, issn = {2813-4338}, abstract = {INTRODUCTION: Hyperuricaemia (HUA), one of chronic diseases, has an increased prevalence and is related to diseases such as gout, arthritis, infectious diseases, etc. Antimicrobial resistance (AMR) in the gut is considered as an atypical chronic disease, and poses risk to human health. The gut microbiome has been proved to be a reservoir for AMR and play an important role in HUA patients. The microbial characteristics of the gut in individuals with HUA have been previously explored, however, the characteristics of the resistome in individuals with HUA have remained largely unexplored.
METHODS: Thus, we investigated the landscape of the AMR in individuals with HUA and without HUA, and the potentially influential factors in a case-control study using metagenomics-based approaches.
RESULTS: We found that drinking juice and abnormal stool were risk factors associated with HUA. The taxonomic diversity of gut microbiota in individuals with HUA was lower than that in non-HUA individuals. Notably, a higher abundance and diversity of the resistome (entire antimicrobial resistance genes) was observed in individuals with HUA (median: 1.10 vs. 0.76, P = 0.039, U-test), especially in tetracycline resistance genes (median: 0.46 vs. 0.20, P < 0.001, U-test), which are associated with more complex mobile genetic elements (MGEs) in individuals with HUA. Furthermore, we found that a higher abundance of the resistome was positively correlated with uric acid (UA) levels and affected by several host-associated factors (mainly dietary habits). Specifically, pork consumption and the consumption of root and tuber vegetables were identified as contributing factors. We also found a higher abundance of virulence genes (VGs), mostly related to adherence, antimicrobial activity, competitive advantage, and exoenzymes, in the gut microbial community of individuals with HUA.
DISCUSSION: All findings revealed higher activity of the resistome and pathogenicity of the microbiota in individuals with HUA, indicating a higher health risk in the elderly HUA population.}, }
@article {pmid41853535, year = {2024}, author = {Alian, OM and Brazelton, WJ and Aquino, KA and Twing, KI and Pendleton, HL and Früh-Green, G and Lang, SQ and Schrenk, MO}, title = {Microbial community differentiation in vent chimneys of the Lost City Hydrothermal Field reflects habitat heterogeneity.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1401831}, pmid = {41853535}, issn = {2813-4338}, abstract = {Oceanic hydrothermal vent systems represent some of the oldest habitats on Earth and serve as analogs for extraterrestrial environments. The Lost City Hydrothermal Field (LCHF) near the Mid-Atlantic Ridge is one such environment, and its large chimneys are unique in hosting actively venting hydrothermal fluids that are primarily controlled by serpentinization reactions in the subseafloor. Microbial communities within LCHF have been studied for insights into their functional adaptations to the warm, alkaline, and dissolved inorganic carbon-limited environment. Metagenomic and mineralogical data collected during a recent expedition to Lost City were analyzed to delineate associations between microbial populations and physical, chemical and biological characteristics of the chimneys. Bacterial 16S rRNA gene sequences show a high degree of putative microdiversity within the relatively dominant genera Desulfotomaculum, Sulfurovum, Thiomicrorhabdus, and Serpentinicella, which represent a large core of the overall LCHF vent bacterial community. This microdiversity relates to the compositional fraction of aragonite, brucite, and calcite minerals within chimney samples rather than just the composition of nearby vent fluids. Although many species are found in both chimneys and venting fluids, the overall microbial community structures in chimney biofilms remain distinct from the hydrothermal fluids that flow through them. Shotgun metagenomic analyses reveal differences among genes predicted to be involved in carbon, methane, nitrogen and sulfur cycling with respect to their correlations to the abundances of specific minerals. These data hint at microenvironmental complexity lost within standard bulk analyses. The findings of this study underscore the need to more closely examine microbe-mineral interactions in natural environments, critically informing not just population-level distributions, but also the functional underpinnings of these extremophile microbial communities.}, }
@article {pmid41853539, year = {2024}, author = {Chandel, N and Gorremuchu, JP and Thakur, V}, title = {Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1432646}, pmid = {41853539}, issn = {2813-4338}, abstract = {INTRODUCTION: The human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the risk of commensals being enriched with resistant genes, which may get even transmitted to opportunistic pathogens often with the help of mobile genetic elements. There is limited information about the current burden of resistant genes in the healthy gut microbiome of the Indian population, the latter is not only the largest in the world but is also periodically monitored for the prevalence of antibiotic resistance in clinical samples.
METHODS: We analyzed publicly available fecal whole-metagenome shotgun sequencing data from 141 samples from three healthy Indian cohorts for antimicrobial-resistance burden, and their likely transmission modes.
RESULTS: The overall resistance profile showed a higher number of resistance genes against tetracycline, glycopeptide, and aminoglycoside. Out of a total of 188 antimicrobial resistance genes identified in all cohorts, moderately to highly prevalent ones could potentially target seven of the 'reserve' group antibiotics (colistin, fosfomycin, Polymyxin). We also observed that geographical location affected the prevalence/abundance of some of the resistance genes. The higher abundance of several tetracycline and vancomycin resistance genes in tribal cohorts compared to the other two urban locations was intriguing. Species E. coli had the highest number of resistant genes, and given its relatively modest abundance in gut microbiomes can pose a risk of becoming a hub for the horizontal transfer of resistance genes to others. Lastly, a subset of the resistance genes showed association with several types of mobile genetic elements, which potentially could facilitate their transmission within the gut community.
DISCUSSION: This is a first systematic report on AMR genes in healthy gut microbiome samples from multiple locations of India. While trends for several of the prevalent AMR genes showed similarity with global data, but a few population specific trends need further attention by policy-makers. The association of AMR genes with mobile elements may pose a risk for transmission to other gut bacteria.}, }
@article {pmid41853546, year = {2024}, author = {Bailey, A and Hogue, S and Pierce, CM and Paul, S and La Fuente, N and Thapa, R and Kim, Y and Robinson, LA}, title = {Metagenomic characterization of the tracheobronchial microbiome in lung cancer.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1457537}, pmid = {41853546}, issn = {2813-4338}, abstract = {BACKGROUND: The tracheobronchial and oral microbiome may be associated with lung cancer, potentially acting as predictive biomarkers. Therefore, we studied the lung and oral bacteriome and virome in non-small cell lung cancer (NSCLC) patients compared to melanoma controls to discover distinguishable features that may suggest lung cancer microbial biomarkers.
METHODS: In this pilot case-control study, we recruited ten patients with early-stage NSCLC (cases) and ten age-matched melanoma patients (controls) who both underwent tumor resection. Preoperative oral gargles were collected from both groups, who then underwent transbronchoscopic tracheal lavage after intubation. Lung tumor and adjacent non-neoplastic lung were sterilely collected after resection. Microbial DNA from all lung specimens underwent 16S rRNA gene sequencing. Lavage and gargle specimens underwent whole-genome shotgun sequencing. Microbiome metrics were calculated to compare both cohorts. T-tests and Wilcoxon rank sum tests were used to test for significant differences in alpha diversity between cohorts. PERMANOVA was used to compare beta diversity.
RESULTS: No clear differences were found in the microbial community structure of case and control gargles, but beta diversity of case and control lavages significantly differed. Two species, Granulicatella adiacens and Neisseria subflava, which are both common oral commensal organisms, appeared in much higher abundance in case versus control lavages. Case lavages also maintained higher relative abundances of other oral commensals compared to controls.
CONCLUSIONS: Lung lavages demonstrated oral microbiota enrichment in cases compared to controls, suggesting microaspiration and resultant inflammation. The oral commensals Granulicatella adiacens and Neisseria subflava were more abundant in the tracheobronchial lavages of lung cancer versus melanoma patients, implicating these microorganisms as potential lung cancer biomarkers, warranting further validation studies.}, }
@article {pmid41853549, year = {2024}, author = {Mahmoudabadi, G and Homyk, K and Catching, AB and Mahmoudabadi, A and Foley, HB and Tadmor, AD and Phillips, R}, title = {Machine learning models can identify individuals based on a resident oral bacteriophage family.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1408203}, pmid = {41853549}, issn = {2813-4338}, abstract = {Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a "phageprint'', defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.}, }
@article {pmid41853558, year = {2024}, author = {Pannoni, SB and Holben, WE}, title = {Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1274277}, pmid = {41853558}, issn = {2813-4338}, abstract = {Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA-simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.}, }
@article {pmid41853664, year = {2026}, author = {Donbraye, E and McLeod, L and Chai, Z and Lacoste, SR and McCarthy, EL and Links, MG and Waldner, CL}, title = {Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.}, journal = {Veterinary and animal science}, volume = {32}, number = {}, pages = {100609}, pmid = {41853664}, issn = {2451-943X}, abstract = {Short nasal swabs (SNS) have potential advantages of lower costs, collection time and training of personnel than deep nasopharyngeal swabs (DNPS) for detecting bovine respiratory disease (BRD) pathogens. This study examined differences between DNPS and SNS in BRD-associated pathogens detected using a nanopore metagenomic sequencing protocol, optimized for respiratory RNA viruses, collected from 150 calves in six feedlot pens. Short nasal swabs yielded higher viral read counts and prevalence than DNPS for BCoV (mean reads 75 versus 17; OR = 21.4, P = 0.001) and IDV (mean reads: 560 versus 192; OR = 2.60, P = 0.02). Agreement varied among viruses: IDV (κ=0.57), BRSV (κ=0.43), and BCoV at both ≥1 read (κ=0.35) and ≥30 reads (κ=0.10). No BoHV-1 and BAdV3 were detected. Mannheimia haemolytica was detected (≥14 reads) more frequently in SNS than DNPS (mean reads: 169 versus 57; OR = 5.73, P = 0.001), as was Pasteurella multocida (≥ 1 read) (mean reads: 4.0 versus 1.2; OR = 2.02, P = 0.02). Mesomycoplasma dispar was less prevalent in SNS (mean reads: 5.2 versus 29; OR = 0.27, P = 0.001). Detection of Histophilus somni, Bibersteinia trehalosi, and Mycoplasmopsis bovis did not differ between swab types. Agreement for detection of M. haemolytica (≥14 reads) was moderate (κ = 0.46, P = 0.001). For all other bacteria examined in this analysis, kappa values were very low. Short nasal swabs were a sensitive and practical alternative for BRD pathogen surveillance providing evidence of which viruses and bacteria are circulating, potentially informing vaccination and disease management.}, }
@article {pmid41853712, year = {2026}, author = {Yao, J and Wang, F and Li, H and Zhang, R and Ji, G and Liu, D}, title = {Comparative analysis of microbial diversity and clinical outcomes in critically ill patients with and without malignancies: a single-center retrospective cohort study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1777861}, pmid = {41853712}, issn = {1664-302X}, abstract = {BACKGROUND: Sepsis and septic shock are severe complications for surgical malignancy patients. Conventional diagnostics often fail to capture the complex infectome in these populations. This study aimed to characterize the distinct microbial and resistome landscapes in cancer versus non-cancer patients using multi-site metagenomic next-generation sequencing (mNGS) to support specific antimicrobial strategies.
METHODS: We conducted a single-center retrospective cohort study at the General Surgery ICU of Xuanwu Hospital, including 107 septic shock patients (52 cancer; 55 non-cancer). mNGS was performed on blood, bile, ascitic fluid, and bronchoalveolar lavage samples to identify pathogens and antibiotic resistance genes (ARGs). Findings were analyzed for their association with ICU length of stay and mortality.
RESULTS: Cancer patients were significantly older (median 68 vs. 51 years, p < 0.0001) with higher comorbidity scores (CCI: 7.0 vs. 4.0, p = 0.006). However, mNGS revealed a lower pathogen detection rate in cancer patients (53.85% vs. 85.45%, p = 0.0006) and a lower incidence of bacteremia (25.0% vs. 45.45%, p = 0.0426). Cancer patients had shorter ICU LOS (9 vs. 13 days, p = 0.0369) and antibiotic durations (7 vs. 11 days, p = 0.0368). Dominant pathogens included Klebsiella pneumoniae and Enterococcus faecium, harboring diverse ARGs across beta-lactam and aminoglycoside categories. Multivariate Cox regression identified IL-6 (p = 0.018) was significant prognostic indicators for cancer patients. We also examined the distribution of virulence factors, despite their low detection rates.
CONCLUSION: Septic shock in cancer patients exhibits a unique resistome signature and distinct prognostic drivers. The identification of microbial targets via mNGS was associated with the implementation of targeted antimicrobial strategies and inflammation monitoring. These findings suggest that mNGS provides valuable molecular insights that may support clinical management and prognostic stratification for cancer patients in the surgical ICU.}, }
@article {pmid41853717, year = {2026}, author = {Matturro, B and Tucci, M and Firrincieli, A and Niccolini, L and Peña-Álvarez, V and Resitano, M and Trinchillo, M and Peláez, AI and Rossetti, S and Petruccioli, M and Viggi, CC and Aulenta, F}, title = {Multi-guild microbial cooperation sustains long-term anaerobic toluene degradation through sulfur cycling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773863}, pmid = {41853717}, issn = {1664-302X}, abstract = {Anaerobic degradation of aromatic hydrocarbons such as toluene plays a critical role in the natural and engineered attenuation of contaminated environments. Here, we developed and characterized a microbial consortium enriched under strictly anoxic conditions, capable of sustained toluene degradation through sulfate reduction. By integrating biodegradation kinetics, long-read 16S rRNA profiling, and genome-resolved metagenomics, we elucidated the structure and function of a multi-guild community. The consortium was co-dominated by Desulfoprunum, a sulfate-reducing bacterium (SRB), and Sulfurovum-affiliated sulfur oxidizers (~34% each), with additional members including Stenotrophomonas, Achromobacter, and Stutzerimonas. Such co-dominance appears uncommon, as sulfate-reducing enrichments are often characterized by low diversity and the predominance of a single lineage, such as Desulfobacula or Desulfosarcina in marine systems. Genome-resolved analyses recovered seven metagenome-assembled genomes (MAGs) with distinct but complementary metabolic roles. Desulfoprunum encoded the fumarate-addition pathway (bss/bbs) for anaerobic toluene activation and dissimilatory sulfate reduction (aprAB, dsrAB). In contrast, Sulfurovum and several Gammaproteobacteria encoded sulfide:quinone oxidoreductase (sqr), coupling H2S detoxification to energy conservation, while a Moranbacterales MAG carried a putative sulfhydrogenase (hydAB) potentially catalyzing elemental sulfur (S°) reduction. Additional MAGs encoded assimilatory sulfate reduction (cys), suggesting integration of sulfur into biosynthetic pathways. Together, these features are consistent with the presence of a putative distributed sulfur redox loop, in which biogenic H2S may be recycled via oxidation and reduction reactions mediated by co-occurring taxa. This sulfur loop is hypothesized to contribute to buffering sulfide toxicity and stabilize redox dynamics, thereby potentially supporting long-term toluene degradation under sulfidic conditions. Our findings highlight anaerobic degradation as a community-driven process enabled by sulfur-cycling interactions. By revealing the role of cryptic sulfur cycling in stabilizing hydrocarbon degradation, this work offers a new framework for designing bioremediation strategies in contaminated anoxic environments.}, }
@article {pmid41853758, year = {2025}, author = {Song, W and Liu, S and Zang, D and Meng, W and Liu, C and Chen, J}, title = {Correlation between gut microbiota and their metabolites and the efficacy of chemotherapy combined with immunotherapy for extensive-stage small cell lung cancer.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1683347}, pmid = {41853758}, issn = {2234-943X}, abstract = {INTRODUCTION: Gut microbiota has been reported to be associated with the host's immune system and immunotherapy response, as well as immune-related adverse events (irAEs). Additionally, gut microbial metabolites have various immunomodulatory effects. Our study focused on the differences in gut microbiota and their metabolites between long progression-free survival (PFS) and short PFS in patients with small cell lung cancer before and after chemotherapy combined with immunotherapy.
METHODS: The enrolled patients collected in our department were divided into long PFS and short PFS groups according to whether the PFS was ≥6 months, and the stool samples before and after treatment were analyzed using metagenomics and metabolomics.
RESULTS: The results showed that Streptococcus (P = 0.00648), Actinomyces (P = 0.0124), and Roseburia (P = 0.0127) differed between the long and short PFS groups. In the analysis of differential metabolites, we found that indirubin-3'-monoxime (AUC 0.611), stearidonic acid (AUC 0.867), leukotriene B4 (AUC 0.844), trans-cinnamic acid (AUC 0.792), and L-tyrosine (AUC 0.751) could be used as potential biomarkers.
DISCUSSION: Gut microbiota and their metabolites hold broad prospects for translational applications in cancer clinical management, such as the development of microbial biomarkers and the modulation of microbiota to enhance the efficacy of chemotherapy and immunotherapy.}, }
@article {pmid41853994, year = {2026}, author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C}, title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70245}, doi = {10.1111/1758-2229.70245}, pmid = {41853994}, issn = {1758-2229}, support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; }, mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; }, abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.}, }
@article {pmid41854100, year = {2026}, author = {Hu, K and Qu, Q and Ban, Z and Hu, X and Wang, A and Dong, X and Liu, C and Deng, P and Wang, R}, title = {Risks of Microplastics Shaping Viral Communities and Functions in Real Marine Environments.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c17054}, pmid = {41854100}, issn = {1520-5851}, abstract = {Microplastic (MP) pollution has become a global issue, especially in the oceans. However, the extent of changes in the ecological states of viruses that coexist with MPs and their subsequent influence on the biogeochemical cycle remain unclear. We found that the subtropical Atlantic has emerged as a viral diversity hotspot, while the hotspots of increasing viral diversity are concentrated in the South China and Eastern Archipelagic Seas, with 87.57% of the area showing increasing trends. Ignoring the effects of MPs would result in more than 15% underestimation of viral diversity in the Mediterranean region and temperate zone of the Indian Ocean, which is notably higher than the global overall underestimation of 2.4% for viral diversity. Beyond a critical MP threshold (1 × 10[4] items·km[-2], accounting for 55.26% of marine zones during 2025), a distinct positive association with marine viral diversity was observed, especially in low-diversity regions. In regions with higher MP concentrations, viral community networks exhibited higher connectivity and lower modularity, coinciding with a stronger presence of lytic bacteriophages for lysogenization. MPs emerge as significant environmental indicators linked to marine viral ecological niches and host-virus interactions. This work addresses the non-negligible role of MPs in shaping marine ecosystems by viruses.}, }
@article {pmid41854101, year = {2026}, author = {Liu, Q and Wu, S and Gong, S and Su, H and Jin, Y and Chen, H and Fan, Y and Yin, R and Ren, X and Wang, J}, title = {Ecologically Informed Design of Synthetic Microbial Community Enables Robust Degradation and Engraftment for Antibiotic Removal in Wastewater.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01020}, pmid = {41854101}, issn = {1520-5851}, abstract = {Conventional biological wastewater treatment often fails to remove emerging contaminants (ECs) because specialized degraders are absent. We developed a function-ecology-integrated framework for designing synthetic microbial communities (SynComs) by combining metagenome-guided identification of degradation potential, quorum-sensing functionality screening, and keystone-based selection from genome-scale metabolic models (GSMMs). Applied to sulfamethoxazole (SMX) degradation, this approach identified five strains with stable catabolic potential and high ecological coherence. GSMM simulations predicted SynCom5 (three species) and SynCom11 (four species) would achieve the highest SMX uptake fluxes (30.7 and 31.7 mmol gDW[-1] h[-1], respectively), driven by complementary amino acid cross-feeding and a high ratio of metabolic interaction potential to resource overlap. Experimentally, both SynComs removed >90% of SMX within 72 h, with SynCom11 selected for bioaugmentation. In activated sludge microcosms, SynCom11 achieved 91.3% SMX removal over 7 days, compared to 25.8% in controls, and successfully engrafted 2 of its 4 members. This approach avoids high-concentration selective pressure, minimizing resistance risks, and demonstrates that embedding an ecologically informed design within catabolic function enables robust, scalable bioaugmentation for ECs.}, }
@article {pmid41854267, year = {2026}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0106225}, doi = {10.1128/msystems.01062-25}, pmid = {41854267}, issn = {2379-5077}, abstract = {Metagenomes often contain many reads derived from eukaryotes, but there is usually no reliable method for estimating their prevalence. This forces many analysis techniques to make the often-faulty assumption that all reads are prokaryotic. Here, we present SingleM prokaryotic_fraction (SPF), an algorithm that scalably and robustly estimates the number of bacterial and archaeal reads in a metagenome. It also estimates the average genome size of bacteria/archaea in a sample. SPF does not use eukaryotic reference genome data and can be applied to any modern Illumina metagenome. Based on SPF, we propose the domain-adjusted mapping rate (DAMR) as an improved metric to assess prokaryotic genome recovery from metagenomes. Applying SPF to 136,284 publicly available metagenomes, we report substantial variation in prokaryotic fractions and biome-specific patterns of prokaryotic abundance, providing insights into how microorganisms and eukaryotes are distributed across Earth. Finally, we show that substantial amounts of human host DNA sequence data have been deposited in public metagenome repositories, possibly counter to ethical directives that mandate screening of these reads prior to release. As the adoption of metagenomic sequencing continues to grow, we foresee SPF being a valuable tool for the appraisal of genome recovery efforts and for investigating global patterns of microorganism distribution.IMPORTANCEMetagenomics data sets capture DNA from all organisms in a sample, enabling the analysis of communities without relying on culture-based techniques. However, many samples include uncharacterized eukaryotic organisms and viral elements, meaning the proportion of bacterial and archaeal DNA is often unknown. This study presents SingleM prokaryotic_fraction (SPF), a robust and scalable method for estimating the prevalence of bacterial and archaeal DNA in metagenomes. Crucially, SPF is calculated independent of eukaryotic and viral reference genomes, which are often incomplete or unavailable. Applying SPF to over 136,000 public metagenomes uncovered substantial variability between microbial communities living in different environments. SPF also identified previously overlooked human genetic data contamination in public data sets, raising important ethical and privacy considerations. Building on SPF, we propose the domain-adjusted mapping rate (DAMR) metric, a new metric that improves genome recovery assessment by accounting for non-prokaryotic reads.}, }
@article {pmid41854352, year = {2026}, author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J}, title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.}, journal = {Lupus}, volume = {}, number = {}, pages = {9612033261432163}, doi = {10.1177/09612033261432163}, pmid = {41854352}, issn = {1477-0962}, abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.}, }
@article {pmid41854356, year = {2026}, author = {Khadivar, H and Bui, H and Huesemann, M and Gao, S and Gerlach, R}, title = {Metagenome-assembled genome of the alkaliphilic Cyanobacterium sp. PNNL-SSL1.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0139825}, doi = {10.1128/mra.01398-25}, pmid = {41854356}, issn = {2576-098X}, abstract = {Microalgae and cyanobacteria are promising sources of fuels, chemicals, and bioproducts, but CO2 supply increases production cost. We present the metagenome-assembled genome of the alkaliphilic Cyanobacterium sp. strain PNNL-SSL1 obtained from Soap Lake (Washington, USA). PNNL-SSL1 shows strong potential for biomass production using only atmospheric CO2, reducing cultivation expenses.}, }
@article {pmid41854421, year = {2026}, author = {Colina Prisco, C and Fourie, NH and Wang, Y and Steck, M and de Jesús Vega, M and Graves-Dixon, LY and Jaime-Lara, RB and Henderson, WA and Joseph, PV}, title = {Examining mRNA-miRNA Interactions and Gene Expression in Overweight and Obesity.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004261433237}, doi = {10.1177/10998004261433237}, pmid = {41854421}, issn = {1552-4175}, abstract = {Obesity is characterized by excess adipose tissue, metabolic imbalance, and persistent low-grade inflammation, all of which can affect brain centers and their communication with peripheral organs. The genetic basis of obesity is complex, involving genetics, metagenomics, and gene-environment interactions that impact gene expression. Micro-RNAs (miRNAs) are small, single-stranded, non-coding RNAs that post-transcriptionally regulate the translational rates of target messenger RNAs (mRNAs). Exploring miRNA-mRNA interactions in obesity offers insights into molecular processes, potential biomarkers, and therapeutic targets of this condition. The current study examined the interplay between miRNA and mRNA collected from individuals with overweight and obesity, and normal weight controls. To our knowledge, this is the first experimental attempt to construct a comprehensive dataset of miRNA-mRNA interactions in overweight and obesity. Total RNA, including miRNA, was isolated from venous blood samples collected from 95 participants. Subsequently, 100 ng of RNA from each sample was analyzed using the NanoString quantitative assay. Quantile normalization, the Bayesian-based method Combat, multi-variable linear regression, over-representation, weighted gene correlation network analyses, and functional analyses were conducted. We found an association between IQGAP1 and DAZAP2 genes and miRNA-20-a and miRNA-2113. IQGAP1 and DAZAP2 were associated with insulin signaling and energy metabolism and insulin sensitivity, respectively. We also identified a positive correlation between peripheral cortisol levels and miRNA-548 with alterations in metabolic processes and the immune system. This suggests that miRNA-mRNA interactions in overweight and obesity may impact insulin sensitivity, metabolism, and immunity, providing novel insight into miRNA-mRNA interactions in overweight and obesity. (ClinicalTrials.gov identifier #NCT00824941; https://clinicaltrials.gov/study/NCT00824941).}, }
@article {pmid41854491, year = {2026}, author = {Wang, HC and Zhang, Y and Feng, R and Cai, LT and Chen, X and Hsiang, T and Wang, F}, title = {Metagenomic Analysis of Potential Pathogens and Other Microorganisms in Tobacco Leaves.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS03250520RE}, doi = {10.1094/PDIS-03-25-0520-RE}, pmid = {41854491}, issn = {0191-2917}, abstract = {Tobacco leaf spot is a major challenge for tobacco leaf production, and the phyllosphere of tobacco is the main habitat for many pathogens. In this study, tobacco leaves with typical symptoms were sampled, and morphological and molecular biological methods were used to identify pathogens. Illumina high-throughput sequencing and Biolog-ECO were used to investigate the composition and carbon metabolic capacity of the microorganisms in the tobacco leaves. A total of 24 fungal isolates were obtained, including one taxon each of Diaporthe, Paramyrothecium, Botrytis, Phoma, and Mortierella; six each of Fusarium and Epicoccum; four of Trichoderma; and three of Alternaria. Six genera of bacteria were isolated: Bacillus, Pantoea, Enterobacter, Pseudomonas, Prolinoborus, and Atlantibacter. Pathogenicity tests revealed that four isolates of Epicoccum and three isolates of Alternaria were pathogenic, and the leaf spot symptoms induced by coinfection with members from these two groups were similar to those observed in the field. These pathogens were identified as Epicoccum latusicollum and Alternaria alternata through multigene analysis. High-throughput sequencing analysis showed that the dominant fungi in diseased tobacco tissues were Alternaria and Epicoccum, and the dominant bacteria were Pseudomonas, Paenibacillus, and Pantoea. In carbon source utilization tests, where various carbohydrates were the main carbon sources, the utilization capacity of phyllosphere microorganisms in diseased tobacco leaves was lower than that in healthy leaves. The combined application of culture-dependent and independent methods provided comprehensive insights into plant disease diagnosis and tobacco phyllosphere microorganism community composition and metabolic function.}, }
@article {pmid41854683, year = {2026}, author = {Wang, J and Shi, Y and Jia, Y and Peng, J}, title = {Effect of Diosmetin on Gut Microbiota and Serum Metabolites in Acute Pancreatitis Mice: A Metagenomic and Metabolomic Study.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71679}, doi = {10.1096/fj.202503650RRR}, pmid = {41854683}, issn = {1530-6860}, support = {2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 82170661//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Pancreatitis/drug therapy/metabolism/microbiology/blood/chemically induced ; Male ; Metabolomics/methods ; Metagenomics/methods ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Metabolome/drug effects ; }, abstract = {Diosmetin is a bioactive flavonoid that exhibits well-documented antioxidant, anti-inflammatory, and anti-tumor properties. However, its potential to attenuate acute pancreatitis (AP) progression through gut microbiota modulation has not yet been elucidated. In this study, mice were pretreated with varying oral doses of diosmetin for 1 week before AP induction via intraperitoneal (i.p.) caerulein injections. The therapeutic efficacy and optimal dosage were determined through histopathological analysis of pancreatic tissue and serological biomarker assessment. Additionally, transcriptomic profiling and western blot were employed to elucidate the underlying signaling pathways. Furthermore, based on integrated metagenomic and metabolomic analyses, a core gut microbiota-metabolite-gene interaction network modulated by diosmetin was constructed. Finally, fecal microbiota transplantation (FMT) experiments validated the critical role of gut microbiota in the effects of diosmetin against AP. The results showed that medium-dose diosmetin treatment significantly attenuated pancreatic histopathological damage and acinar cell apoptosis in AP mice, while suppressing the activation of the MAPK inflammatory signaling pathway. Notably, diosmetin treatment was associated with restored microbial diversity, altered bacterial community structure, and changes in key metabolic pathways, reversing gut microbiota dysbiosis. Specifically, a diosmetin-responsive interaction network was constructed, highlighting associations between core bacterial taxa (Butyricimonas faecalis, Enterocloster bolteae, Roseburia intestinalis), key metabolites (3-indoleacrylic acid, 2-methoxy-4-vinylphenol, nitrite), and MAPK pathway-related genes. Finally, the protective effect of diosmetin was further substantiated by FMT, suggesting a potential role of the gut microbiota in this process. In conclusion, diosmetin ameliorated pancreatic injury in a murine model of caerulein-induced AP by modulating gut microbiota composition and associated metabolic profiles. These findings suggested that diosmetin represented a promising therapeutic option for AP, offering a scientific foundation for its clinical application and the underlying mechanisms involved.}, }
@article {pmid41855720, year = {2026}, author = {Miao, H and Zeng, W and Hao, X and Gu, Y and Peng, Y}, title = {S[0]-S[2-] co-substrate system achieves efficient nitrite accumulation under high alkalinity and ultra-short HRT: Multidimensional responses and metabolic regulation mechanism.}, journal = {Water research}, volume = {297}, number = {}, pages = {125737}, doi = {10.1016/j.watres.2026.125737}, pmid = {41855720}, issn = {1879-2448}, abstract = {Sulfur autotrophic denitrification under highly alkaline conditions provides a novel strategy for nitrite supply, but low nitrate conversion flux often limits nitrite accumulation rate. This study proposes an element sulfur-sulfide (S[0]-S[2][-]) co-substrate enhancement strategy based on an alkaline environment. Under high pH (10) with an ultra-short hydraulic retention time (0.65 h) and low S[2][-] feeding (S[2-]/NO3[-]-N ratio of 0.17), the nitrate conversion efficiency (84.3%) was nearly 20% higher than that only at high pH conditions. Moreover, the strategy achieved an excellent nitrite accumulation efficiency of 60.6% and a rate of 1.54 kg N·m[-3]· d[-1]. Microbial physiological responses revealed that reactive oxygen species accumulation significantly inhibited microbial activity and disrupted nitrogen-sulfur metabolism at high pH. However, supplemental S[2-] promoted the ring-opening activation of S[0] to form high bioavailability polysulfide, and restored electron transfer system activity and energy metabolism. The abundance of sulfur-oxidizing genes Sox and fccAB increased by 15.7%-95.6%, ensuring robust electron flux. Under this strategy, the system exhibited an optimized metabolic trade-off that prioritized survival advantages over complete denitrification. This was achieved by prioritizing energy allocation to Na[+](K[+])/H[+] antiporters (Mrp/Pha/Kef/Trk) and glutamate synthesis to maintain cellular homeostasis. Concurrently, the increased narGHI/napAB abundance (14.6%-58.9%) and reduced nirS abundance (25.6%-41.3%) ensured a higher nitrite accumulation rate. Functional annotation further revealed that Thiobacillus (40.2%) and Pseudoxanthomonas (3.9%) served as key genera driving nitrite accumulation. This study not only proposes an efficient nitrite supply strategy for Anammox but also reveals the underlying microbial response mechanisms under high alkalinity.}, }
@article {pmid41855876, year = {2026}, author = {Lou, J and Zhu, Z and Zheng, Y and Chen, J and Su, Q and Zhu, J}, title = {Response mechanism of the DAMO-associated denitrification system to oxytetracycline stress.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129409}, doi = {10.1016/j.jenvman.2026.129409}, pmid = {41855876}, issn = {1095-8630}, abstract = {Antibiotics and denitrifying anaerobic methane oxidation (DAMO) processes frequently coexist in natural ecosystems and wastewater treatment systems. This study investigated the performance and microbial ecology of a denitrification system coupled with Nitrite-dependent anaerobic methane oxidation (N-DAMO) under oxytetracycline (OTC) stress. Specifically, 1 mg/L OTC enhanced nitrogen removal efficiency by 15% relative to the control, whereas 10 mg/L OTC exerted a significant inhibition of 58%. The Michaelis-Menten kinetic model predicted that the system could tolerate the maximum OTC concentration of 26.76 mg/L. Mechanistically, the secretion of protein-rich extracellular polymeric substances (EPS) served as a protective barrier against toxicity. The abundance of the DAMO bacterium Candidatus Methylomirabilis correlated negatively with OTC concentration. At 1 mg/L OTC, denitrification was enhanced through the enrichment of Thauera. However, 10 mg/L OTC damaged EPS structure and suppressed microbial activity, and led to a decrease in the abundance of related functional bacteria and an increase in the abundance of antibiotic resistant bacteria such as Hyphomicrobium and Thermomonas. Metagenomic analysis revealed that denitrification genes (e.g., norB, norC) were upregulated with 1 mg/L OTC, whereas high-concentration OTC induced pronounced enrichment of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), with frequently co-localization within the same hosts. This suggests an increased potential for horizontal gene transfer (HGT) occurred within the DAMO community, which may contribute to the dissemination of ARGs. These findings provide new insights into the adaptive mechanisms of N-DAMO systems under antibiotic stress and highlight their potential for nitrogen removal in contaminated environments.}, }
@article {pmid41855937, year = {2026}, author = {Jiang, L and Liang, Z and Williams, TA and Deng, Y and Yu, H and Hao, Q and Cao, J and Zhou, H and Lai, H and Chen, J and Chen, H and Zhang, C}, title = {Vertical stratification and metabolic versatility of methanogens in Haima cold seep sediments: Alkane-fueled acetoclastic methanogenesis revealed by metagenomics and experimental verification.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107972}, doi = {10.1016/j.marenvres.2026.107972}, pmid = {41855937}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Alkanes/metabolism ; Metagenomics ; *Methane/metabolism ; *Archaea/metabolism/genetics ; Oxidoreductases ; }, abstract = {Cold seeps are hot spots for studying the biogeochemical processes mediated by methyl-coenzyme M reductase (MCR) containing archaea, yet these processes remain poorly understood. Here, we investigated the microbial communities in a 5-m-long sediment core encompassing sulfate-methane transition zone (SMTZ), collected from the Haima cold seep. We focused on distinct biogeochemical characteristics and metagenomics to study the vertical patterns of mcrA-containing archaea and their role in alkane metabolism. Background alkane analysis showed that long chain alkanes were dominant in the sediment core. Metagenomic and quantitative PCR (qPCR) analysis revealed that the abundance of mcrA gene within and below the SMTZ were substantially higher than those above the SMTZ. We recovered 21 mcrA-containing MAGs, 11 affiliated with Methanosarcinaceae. One MAG (CG1-BIN56) encoded complete key genes for all three methanogenic pathways. Functional gene profiles suggested that acetoclastic methanogenesis is the dominant pathway. Furthermore, a 10-month anaerobic enrichment with n-alkanes (C10/C16) using SMTZ (CG15: 350 cmbsf) inocula exhibited high degradation rate (C10: 94.2% ± 2.5%, C16: 66.8% ± 2.8%) accompanied by acetate accumulation. These findings suggest that acetate, as a likely intermediate associated with alkane degradation process, potentially fuels acetoclastic methanogenesis. This indicates a likely syntrophic interaction between alkane-degrading and methane-cycling microorganisms in cold seep sediments.}, }
@article {pmid41855981, year = {2026}, author = {Ye, T and Li, P and Zhou, Z and Xiong, B and Zhao, Y and Zhao, J and Qi, J and Ma, B and Chen, Y}, title = {Enhanced pollutant removal in multi-pollutants contaminated water by bioaugmented slow filtration.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141806}, doi = {10.1016/j.jhazmat.2026.141806}, pmid = {41855981}, issn = {1873-3336}, abstract = {Slow filtration is a low-cost and low-carbon water treatment approach, yet its broad application is limited by long start-up times and insufficient understanding of multi-pollutant removal. Here, we evaluate whether bioaugmentation with manganese-oxidizing bacteria enhances pollutant removal in water contaminated with NH4[+] -N, Mn[2+], readily biodegradable emerging contaminants (ECs, atenolol and trimethoprim), and relatively non-biodegradable ECs (carbamazepine and sulfamethoxazole). Bioaugmented filtration increased the removal rates of NH4[+]-N and Mn[2+] by 32.2% and 33.9%, respectively, during the first 10 days of the experiment. The proposed approach also demonstrated superior average removal rates (30.1%-99.6%) of four ECs compared to the filter column without QJX-1 inoculation (16.7%-99.3%). Furthermore, bioaugmented filtration effectively reduced the relative abundances of antibiotic resistance genes (ARGs) subtypes such as macB, tetA(58), and bcrA in the influent. The composition of ARGs on the filter media in both process groups is highly similar, with the relative abundance of ARGs at the top and middle of the filter column slightly higher than at the bottom. The mechanism study revealed that Mn[2+] was effectively oxidized to biological manganese oxides, which was conducive to the adsorption and oxidation of Mn[2+] and ECs. The metagenomic results confirmed the pmoC-amoC gene in Nitrospira promoted the removal of NH4[+]-N. Toxicity prediction indicated that the toxicity of most ECs intermediates was significantly lower than that of their parent compounds. The findings of this study verify the viability of employing cost-effective and few-chemical water treatment technologies to treat muti-pollutant contaminated water and guarantee the quality of drinking water.}, }
@article {pmid41855987, year = {2026}, author = {Demaria, F and Suleiman, M and Bargiela, R and Ferrer, M and Hernández, SB and Núñez, AE and Petchey, OL and Corvini, PF and Junier, P}, title = {Micropollutant-driven bacterial adaptation enables resilient pharmaceuticals biodegradation at trace concentrations in biologically treated wastewater.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141801}, doi = {10.1016/j.jhazmat.2026.141801}, pmid = {41855987}, issn = {1873-3336}, abstract = {Pharmaceutical residues are persistent contaminants that resist conventional wastewater treatment and can disrupt ecosystems; however, microorganisms provide a promising biobased solution to transform or mineralize these complex xenobiotics. Whether pollutant-adapted communities maintain their degradative capacity under realistic environmental conditions remains a long-standing debate in environmental biotechnology. Here, microbial consortia enriched in six membrane bioreactors under high pharmaceutical concentration (100 mg/L) retained full biodegradation capacity across a 5000-fold concentration range. After prolonged exposure to six model compounds (atenolol, caffeine, diclofenac, enalapril, ibuprofen, and paracetamol) complete removal occurred for all except diclofenac. Degradation remained efficient even at lower and environmentally relevant concentrations (1 mg/L-20 µg/L) and recovered rapidly upon re-exposure to higher loads (100 mg/L). Metagenomic profiling revealed enrichment of oxygenase-mediated catabolic pathways supporting this resilience. When transferred to a 7 liters bioreactor treating real wastewater, the adapted community removed targeted and untargeted pharmaceuticals, demonstrating robustness, scalability, and strong potential for sustainable micropollutant remediation.}, }
@article {pmid41856032, year = {2026}, author = {Caetta, A and Aasen, D and Adamcyzk, P and Yuan, H and Zhou, Y and Roberts, D and Grindle, C and Schoem, S and Hughes, A}, title = {Characterizing the microbiome of the middle ear using 16S RNA sequencing in pediatric patients with and without middle ear effusions requiring ventilation tubes.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {204}, number = {}, pages = {112798}, doi = {10.1016/j.ijporl.2026.112798}, pmid = {41856032}, issn = {1872-8464}, }
@article {pmid41856107, year = {2026}, author = {Potloane, D and Symul, L and Ngcapu, S and Lewis, L and France, M and Vermeren, L and Elsherbini, J and Chetty, C and Mafunda, NA and Polliah, AM and Mtshali, A and Kama, A and Magini, N and Mitchev, N and Mzobe, G and Khan, A and Demidkina, BC and Goldenberg, M and Xu, J and Rutt, L and Shirtliff, B and Cook, S and Murthy, M and Hussain, F and Passmore, JS and Jaspan, HB and Kullin, B and Happel, AU and Liebenberg, L and Relman, DA and Holmes, S and Kwon, DS and Ravel, J and Mitchell, CM}, title = {VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.02.016}, pmid = {41856107}, issn = {1934-6069}, abstract = {Bacterial vaginosis (BV) is characterized by high microbial diversity. High recurrence rates following antibiotics may stem from poor recolonization by protective Lactobacillus species. This phase 1 randomized trial in the United States and South Africa evaluated two vaginally delivered live biotherapeutic products (LBPs) containing multiple Lactobacillus crispatus strains. After metronidazole treatment for BV, participants received either a placebo or 3 or 7 days of active LBPs. LBP strains were detected by metagenomics in 66.1% (47/71) of participants in the active arms in the first 5 weeks. Among those, nearly half (49%, 23/47) remained colonized at 12 weeks despite the short initial treatment course. Participants were most often colonized by one of three component strains, with no geographic differences in strain colonization observed. LBPs were safe, acceptable, and well tolerated, with no serious adverse events (AEs) reported. These results provide a foundation for the development of transformational interventions aimed at optimizing the vaginal microbiome.}, }
@article {pmid41856148, year = {2026}, author = {Michels, EHA and Dequin, PF and Butler, JM and Guillon, A and Evrard, B and Paling, FP and Reijnders, TDY and Schuurman, AR and van Engelen, TSR and Brands, X and Haak, BW and Bos, LDJ and Leroux, C and Giamarellos-Bourboulis, EJ and Stoker, J and Prins, JM and Faber, DR and Douma, RA and Sweeney, TE and Malhotra-Kumar, S and Kluytmans, JAJW and Scicluna, BP and Cremer, OL and Matthay, M and Calfee, C and Wiersinga, WJ and Peters-Sengers, H and van der Poll, T}, title = {Quantifying immune dysregulation in pneumonia and sepsis with a parsimonious machine-learning model: a multicohort analysis across care settings and reanalysis of a hydrocortisone randomised controlled trial.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(25)00429-1}, pmid = {41856148}, issn = {2213-2619}, abstract = {BACKGROUND: Sepsis is a dysregulated host response to infection resulting in life-threatening organ failure. Although immune dysregulation is central to the sepsis definition, immunomodulation trials enrol participants based on clinical severity, not the extent of dysregulation, which could contribute to treatment heterogeneity. A pragmatic way to quantify immune dysregulation could improve prognostication, help to evaluate treatment responses, and identify individuals most likely to benefit from immunomodulation. We aimed to construct a parsimonious machine-learning tool that defines and quantifies immune dysregulation, thereby supporting biologically informed immunomodulation.
METHODS: In this multicohort analysis and reanalysis of a randomised controlled trial, the primary objective was to derive and validate a categorical and continuous immune dysregulation score that is independent of clinical presentation or outcome. We measured 35 plasma biomarkers reflecting key host response domains in individuals with community-acquired pneumonia (CAP) across different care settings (emergency department, general ward, and intensive care unit) and disease severities using data from three independent cohorts. We applied unsupervised trajectory inference analysis to identify an immune dysregulation gradient captured as discrete immune dysregulation stages (Dysregulated Immune Profile [DIP]) and a continuous score (cDIP; 0-1). We developed two parsimonious machine-learning models to predict the DIP stages and cDIP scores based on 35 biomarkers, and validated their ability to capture immune dysregulation and predict clinical outcomes in five independent cohorts. On the basis of our hypothesis that only individuals with severe immune dysregulation benefit from immunomodulation, we carried out a post-hoc analysis of a randomised trial evaluating hydrocortisone in severe CAP (CAPE COD trial, NCT02517489), assessing treatment effects across DIP stages and the cDIP continuum, and how hydrocortisone influenced dysregulation trajectories over time.
FINDINGS: We organised 398 participants with CAP along a continuum of immune dysregulation from mild to severe on the basis of 35 plasma biomarkers, yielding three dysregulation stages (DIP1-3) and a continuous score (cDIP). Clinical severity proved to be an inadequate proxy for immune dysregulation. A three-biomarker machine-learning framework (procalcitonin, soluble TREM-1, and IL-6) accurately predicted the degree of dysregulation derived from 35 biomarkers (DIP stage accuracy 91·2%; cDIP root mean square error 0·056). Although the framework was not designed for outcome prediction, increased immune dysregulation-reflected in DIP and cDIP-was associated with a gradual rise in mortality (cDIP odds ratio [OR] 1·26 [95% CI 1·13-1·40] per 10% increase, p<0·0001) and secondary infections (OR 1·50 [1·22-1·93] per 10% increase, p=0·0005), independent of clinical severity. The three-biomarker tool was validated in five external cohorts of varying infections, severities, and care settings (n=1191). Reanalysis of the CAPE COD trial showed that hydrocortisone conferred a survival benefit only in participants classified as severely dysregulated by our model (30-day mortality: DIP3 OR 0·25 [0·05-0·85], p=0·042; cDIP ≥0·63 OR 0·21 [0·10-0·72], p=0·011), accompanied by faster immune recovery (time × treatment interaction, p<0·0001). No such effect modification was observed when stratifying participants by clinical severity.
INTERPRETATION: We have provided a publicly available three-biomarker framework to determine the extent of host response dysregulation with potential value for precision-guided immunomodulatory therapy.
FUNDING: EU Horizon 2020.}, }
@article {pmid41856334, year = {2026}, author = {Ma, WJ and Zhang, HM and An, ZJ and Tian, Y}, title = {Biochar enhances nitrogen removal capacity in sulfur-driven autotrophic denitrification at low temperatures: Performance evaluation, microbial structure analysis, and metabolic pathway reconstruction.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134438}, doi = {10.1016/j.biortech.2026.134438}, pmid = {41856334}, issn = {1873-2976}, abstract = {Sulfur-driven autotrophic denitrification (SAD) is a low carbon-footprint wastewater treatment process, but its stable operation is hindered by low temperatures. This study found that biochar amendment enhanced the denitrification performance in the SAD process at low temperatures: at 15 °C, the biochar-amended reactor achieved 94.57% nitrogen removal efficiency (NRE); at 10 °C, the control reactor lost denitrification capacity, while the biochar reactor maintained 28.39% NRE. Mechanistic investigations revealed that biochar enhances microbial energy utilization and bioelectrochemical capacity, widens the ecological niche of sulfur-oxidizing bacteria, and enriches Thiobacillus at low temperatures. Metabolic pathway reconstruction reveals that Thiobacillus contains more genes related to nitrogen (nar, nir, nor, nos, nap, nrf, gln, glt, and gdh) and sulfur (dsr, sox, fcc, asr, soe, sat, apr) cycles. Therefore, Thiobacillus is more potent in nitrogen removal and sulfur utilization. However, Sulfurimonas possesses only one pathway for denitrification and sulfur oxidation mediated by sox enzymes. In carbon metabolism, Sulfurimonas contains genes for Calvin-Benson cycle, resulting in its potential for carbon fixation and low-temperature adaptability. Overall, this study proposes a low-carbon strategy to enhance denitrification performance at low temperatures.}, }
@article {pmid41856620, year = {2026}, author = {Lan, HY and Yang, XY and Zhang, YH and Lyu, YW and Bao, LL and Yu, YY}, title = {[Study on the characteristics and differences of intestinal microbiota in children with allergic diseases].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {3}, pages = {346-358}, doi = {10.3760/cma.j.cn112150-20251015-00988}, pmid = {41856620}, issn = {0253-9624}, support = {GSWS2024031//Research Project of the Gusu Talent Program of Suzhou City/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Child, Preschool ; *Hypersensitivity/microbiology ; Case-Control Studies ; Infant ; Dermatitis, Atopic/microbiology ; Female ; Food Hypersensitivity/microbiology ; Male ; Feces/microbiology ; Child ; Metagenomics ; }, abstract = {Objective: Based on metagenomic sequencing technology, this study aims to investigate the characteristics and differences of the intestinal microbiota in children with different allergic diseases, providing a theoretical basis for the early prevention and treatment of allergic diseases. Methods: The study adopted a case-control research method. 214 children with allergic diseases (Group A) who visited the Suzhou Hospital Affiliated to Nanjing Medical University from March 2023 to June 2024 were selected. According to age matching, 93 healthy controls (Group H) who participated in physical examinations during the same period were also included. Fecal samples and clinical data of the subjects were collected. The subjects were grouped according to age and type of allergic disease, and the fecal samples of the subjects were analyzed using metagenomic sequencing technology to study the characteristics and differences of the gut microbiota in different groups. The subjects were divided into 0-1 year old group (A1 and H1), 1-3 year old group (A2 and H2), and≥3 year old group (A3). According to the disease type, A1 was divided into food allergy without atopic dermatitis (F1) group and food allergy with atopic dermatitis (F2) group, A2 was divided into atopic dermatitis (AD) group, allergic rhinitis (AR) group and AD with AR group. A3 was divided into AR group, AD with AR group and AR with asthma (AS) group. Results: With age increase, the number of species annotated at the genus level in the microbiota showed a gradually increasing trend. There were significant differences in the diversity and composition of the intestinal microbiota between the allergic disease group and the control group. In the diversity analysis, it was found that there were differences in species richness between group A and group H (chao index, group A: 955.2±226.1, group H: 762.3±260.9, W=5 664, P<0.000 1), and significant differences in β-diversity between group A2 and group H2, and between group A3 and group AD-AR and group AR-AS (R=0.045, P=0.018, R=0.044, P=0.011). At the species level, the allergic disease group was mainly enriched with Bifidobacterium, Enterococcus, Escherichia, Mediterraneibacter and Blautia, while the control group was mainly enriched with Bifidobacterium. By age group analysis, the relative abundance of Mediterraneibacter and Blautia in group A1 (0-1 years old) was significantly higher than that in group H1 (Mediterraneibacter: A1: 5.2±9.4, H1: 0.9±2.1, W=718, P=0.000 8; Blautia: A1: 3.5±6.0, H1: 1.3±3.2, W=701, P= 0.000 5). In group A2 (1-3 years old), the relative abundance of Bacteroides and Faecalibacterium was significantly higher than that in group H2 (Bacteroides: A2: 5.6±8.7, H2: 3.1±5.8, W=456, P=0.020 8; Faecalibacterium: A2: 2.6±2.8, H2: 1.2±1.9, W=395, P=0.002 8). In the clinical subtype analysis, the relative abundance of Blautia and Fusicatenibacter was significantly increased in AR children (Blautia: AD: 8.0±7.9, AD-AR: 13.5±8.3, AR: 20.2±7.8, H=9.300 8, P=0.009 6; Fusicatenibacter: AD: 0.5±0.9, AD-AR: 1.2±1.6, AR: 2.2±2.4, H=7.878 3, P=0.019 5), and the relative abundance of Escherichia was significantly increased in AD children (AD: 3.3±4.3, AD-AR: 1.8±4.5, AR: 0.8±2.0, H=9.476 6, P=0.008 8). In group A3 (≥3 years old), Mediterraneibacter was significantly enriched (A3: 6.3±6.9, H3: 2.9±1.9, W=571, P=0.039 7), and the relative abundance of Anaerostipes was significantly increased in AR children (AD-AR: 2.9±2.9, AR: 5.2±4.9, AR-AS: 3.2±3.5, H=7.269, P=0.026 4). Conclusion: In infancy, the species of intestinal flora gradually increase with age. There are significant differences in the composition of intestinal flora among children with different allergic diseases. Bifidobacterium, as the main dominant species in infancy, has a lower relative abundance in the allergic disease group at different ages than in the healthy control group, suggesting that the lack of Bifidobacterium may be related to the occurrence and development of allergic diseases.}, }
@article {pmid41856866, year = {2026}, author = {Jelen, BI and Baker, BJ}, title = {Mapping environmental microbiomes across an entire country.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.02.013}, pmid = {41856866}, issn = {1878-4380}, abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.}, }
@article {pmid41857415, year = {2026}, author = {}, title = {Metagenomic surveillance of zoonotic yellow fever and spillover dynamics at a forest-urban interface.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41857415}, issn = {2058-5276}, }
@article {pmid41857851, year = {2026}, author = {Yu, X and Wen, Z and Zhou, W and Zheng, Y and Chen, J and Xiao, WJ and Lin, S and Liang, H and Duan, X and Wang, W and Wu, H and Chen, X}, title = {Respiratory syndromic disease study in Shanghai community population.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e103001}, pmid = {41857851}, issn = {2044-6055}, mesh = {Humans ; China/epidemiology ; Male ; Female ; *Respiratory Tract Infections/epidemiology/microbiology ; Adult ; Prospective Studies ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Child, Preschool ; Incidence ; Coinfection/epidemiology ; Urban Population ; Seasons ; }, abstract = {PURPOSE: This prospective community-based cohort study (Acute Respiratory Infection Epidemiological Characteristics Assessment Study (ARI-ECAS)) aims to systematically monitor acute respiratory infection (ARI) incidence, characterise multiple pathogen coinfection patterns and explore microbial landscape dynamics in Shanghai's general population. By integrating syndromic surveillance, molecular diagnostics and metagenomic sequencing, the study seeks to enhance understanding of ARI epidemiology, seasonal variation and host-pathogen interactions to inform predictive modelling and optimise public health interventions in high-density urban environments.
PARTICIPANTS: The study enrolled 15 199 permanent residents from all 16 districts of Shanghai, with baseline oropharyngeal swab samples across five representative districts (Xuhui, Jing'an, Jiading, Songjiang and Fengxian). Inclusion criteria required residency ≥6 months and consent for weekly follow-ups. Exclusion criteria addressed mobility limitations (planned relocation >6 months) and recent ARI history. Participants provided demographic, behavioural and clinical data via the Shanghai Health Cloud platform, with baseline and symptomatic-phase biological samples collected for analysis.
FINDINGS TO DATE: During the initial 8-month surveillance period (May 2024-January 2025), the ARI-ECAS cohort demonstrated critical insights into the epidemiology of acute respiratory infections in Shanghai's urban communities. Among 15 199 participants, 10.96% reported symptomatic episodes, of whom 21.43% experienced recurrent infections. Pathogen detection using targeted next-generation sequencing (tNGS) identified microbial aetiologies in 53.52% of symptomatic cases, revealing a high prevalence of coinfections: 27.96% involved dual pathogens, while 33.01% showed polymicrobial interactions (≥3 pathogens). Notably, 85.09% of symptomatic episodes were self-managed, underscoring a low healthcare-seeking rate (14.91%) consistent with patterns observed in urban China during postpandemic transitions.
FUTURE PLANS: The current phase of data collection will conclude in June 2025; however, syndromic surveillance and tNGS protocols will be sustained to capture multiyear seasonal transmission patterns. To enhance comparative rigour, future protocols will aim to collect samples from participants during asymptomatic periods in the subsequent year to serve as seasonal baseline controls. Building on this foundation, the study will integrate contact behaviour and mobility surveys to quantify parameters critical for understanding pathogen transmission dynamics (eg, household contacts and public transportation usage). Furthermore, pathogen detection and metagenomic data will be combined with transcriptomic and metabolomic profiling in selected cases to model multipathogen interaction networks and delineate host immune response pathways, thereby advancing mechanistic insights into polymicrobial cocirculation.}, }
@article {pmid41857857, year = {2026}, author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G}, title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e115290}, pmid = {41857857}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; }, abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.
METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.
ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.
TRIAL REGISTRATION NUMBER: DRKS00036475.}, }
@article {pmid41858204, year = {2026}, author = {Chen, X and Ji, M and Yan, D and Liu, Y and Chen, Y and Dong, R and Shen, L and Takeuchi, N and Kong, W}, title = {Metabolic capacities and potential microbial interactions in red and green snow of the Antarctic Peninsula.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71089}, pmid = {41858204}, issn = {1469-8137}, support = {32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 72574092//National Natural Science Foundation of China/ ; }, abstract = {Colored (red and green) snow is widespread in Antarctica due to climate warming. This phenomenon reduces snow albedo, accelerates snowmelt, alters microbial functions, and impacts regional geochemical cycles. Diverse microorganisms are associated with this phenomenon, yet their functions remain poorly understood. We employed metagenomic sequencing to reveal the metabolic interactions and functional specialization within microbial communities of colored snow, focusing on carbon, nitrogen, phosphorus, and sulfur metabolism. While broad metabolic profiles were similar between red and green snow, targeted analysis of specific pathways revealed significant enrichment of denitrification and organic-phosphorus mineralization genes in green snow and labile carbon degradation genes in red snow. Betaproteobacteria were dominant drivers of nitrogen, sulfur, and phosphorus transformation, while diverse eukaryotic algae and bacteria were responsible for carbon fixation. Additionally, we recovered 2257 bacteriophages, 529 algal viruses, and 2302 secondary metabolite gene clusters. Specifically, viruses encoded 126 auxiliary metabolic genes that may influence the elemental cycling of hosts, while secondary metabolites, such as pyoverdine, may assist algal iron acquisition. Our findings offer new insights into the metabolic potentials and interactions of microbial communities in Antarctic colored snow, highlighting their potential relevance to snow biogeochemical processes.}, }
@article {pmid41858247, year = {2026}, author = {Groninga, J and Wittig, L and Bouderka, F and Bornemann, TLV and Lipp, JS and Schubotz, F and Keden, S and Probst, AJ and Hinrichs, KU}, title = {Novel Extended Tetraether Lipids Found in a High-CO2 Geyser.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70286}, pmid = {41858247}, issn = {1462-2920}, support = {101118631/ERC_/European Research Council/International ; }, mesh = {*Carbon Dioxide/metabolism/analysis ; *Archaea/genetics/metabolism/chemistry ; Germany ; *Groundwater/microbiology ; *Lipids/chemistry ; *Ethers/chemistry ; Metagenome ; *Glyceryl Ethers/chemistry ; }, abstract = {The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.}, }
@article {pmid41858251, year = {2026}, author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L}, title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70131}, pmid = {41858251}, issn = {1755-0998}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; }, abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.}, }
@article {pmid41858257, year = {2026}, author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF}, title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70128}, pmid = {41858257}, issn = {1755-0998}, support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Programático FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; }, mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; }, abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.}, }
@article {pmid41858380, year = {2026}, author = {Beran, P and Rost, M and Beranová, K and Kváč, M and Stehlíková, D and Udoh, OE and Jozová, E and Čurn, V}, title = {genCRC32: collision-free CRC32-based hashing of DNA sequences.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbaf315}, pmid = {41858380}, issn = {2635-0041}, abstract = {MOTIVATION: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Traditional hashing methods often result in collisions, impacting the precision and/or performance of downstream analyses. Thus, it is highly advantageous to have hashing functions that guarantee collision-free mappings for DNA sequences, particularly for k-mers up to length 16, where practical limits for 32-bit hashing are reached. In this study, we evaluate genCRC32 as a hashing primitive, reporting collision behavior, bucket balance, sensitivity to single-base changes, and speed to inform its potential use in downstream tools. Evaluation within specific software tools is outside the scope of this paper and is planned as future work.
RESULTS: We present genCRC32, an innovative hashing method that integrates a straightforward preprocessing step (gen32) with CRC32 hashing, specifically identifying eight CRC32 polynomials that ensure collision-free hashing for all DNA k-mers up to 16 nucleotides in length. Through extensive empirical evaluations, genCRC32 demonstrated zero collisions for these k-mers, achieving a one-to-one mapping without auxiliary data structures. Benchmark tests confirmed minimal computational overhead introduced by preprocessing, maintaining hashing performance comparable to established methods such as MurmurHash3 and xxHash32.
The source code for genCRC32 is publicly available at: https://github.com/berybox/genCRC32. The implementation is provided in Go (version 1.24) and leverages only standard libraries, ensuring portability and ease of integration into existing bioinformatics workflows.}, }
@article {pmid41858392, year = {2026}, author = {Tu, W and Zeng, P and Wu, Z and Li, Z and Yu, T and Zhang, W and Chen, R and Liang, L}, title = {A case report of brain abscess caused by Nocardia cyriacigeorgica identified by metagenomic next-generation sequencing.}, journal = {World journal of emergency medicine}, volume = {17}, number = {2}, pages = {199-201}, pmid = {41858392}, issn = {1920-8642}, }
@article {pmid41858535, year = {2026}, author = {Zhang, L and Chen, S and Li, H and Li, L and Liu, H}, title = {Molecular epidemiology and genomic analysis of bulbul coronavirus in Guangdong, China.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1659863}, pmid = {41858535}, issn = {2297-1769}, abstract = {INTRODUCTION: Bulbul coronavirus (BuCoV), a delta coronavirus recently identified in passerine birds, remains poorly characterized regarding its ecology and evolutionary dynamics. This study aimed to determine the prevalence of BuCoV in wild avifauna, clarify its evolutionary relationship with other delta coronaviruses, and identify genetic signatures potentially relevant to host adaptation and cross-species transmission in southern China.
METHODS: From 2023 to 2024, we conducted molecular surveillance across 12 regions in Guangdong Province, China. A total of 2,145 avian fecal samples were collected and screened for BuCoV using real-time quantitative PCR. The complete genomes of representative strains were obtained using next-generation sequencing. Subsequent analyses included phylogenetic reconstruction using maximum likelihood methods, recombination detection using RDP4 and SimPlot, and comparative amino acid analysis.
RESULTS: BuCoV was detected exclusively in Shenzhen (3/168, 1.78%), with all positive samples originating from bulbuls (Pycnonotus spp.). The Shenzhen strain GD2411 exhibited the highest nucleotide identity with BuCoV strains HKU11-796 (97.26%) and HKU11-934 (96.79%), but far lower similarity (78.9%-82.4%) to other delta coronaviruses. Phylogenetic analysis placed GD2411 in a monophyletic clade with HKU11 strains. Recombination analyses revealed mosaic structures within the spike (S) gene, involving multiple coronavirus lineages. Thirty-one amino acid substitutions were detected in the S protein, together with mutations in RdRp, 3CLpro, and nucleocapsid.
DISCUSSION: These findings suggest that BuCoV GD2411 emerged through inter-lineage recombination and is undergoing adaptive evolution, particularly in the spike protein. The detection of BuCoV exclusively in Shenzhen, a critical node in the East Asian-Australasian Flyway, suggests that migratory birds may facilitate viral dissemination. The identified mutations may affect viral replication, host adaptation, or immune evasion. These findings provide essential baseline genomic and epidemiological data critical for understanding BuCoV diversity and assessing potential zoonotic risks in southern China.}, }
@article {pmid41858674, year = {2026}, author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z}, title = {Microbiome and plant relationship: a symbiosis against phytopathogens.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1722279}, pmid = {41858674}, issn = {1664-462X}, abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.}, }
@article {pmid41859061, year = {2026}, author = {Wang, Z and Yang, R and Xiao, Y and Huang, B and Yang, Z and Yang, L}, title = {Primary Cutaneous Aspergillosis Due to Aspergillus flavus in an Immunocompetent Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {565781}, pmid = {41859061}, issn = {1178-6973}, abstract = {Invasive aspergillosis is a life-threatening infection caused by Aspergillus species, affecting the lungs, central nervous system, nasal and orbital regions, and skin. Primary cutaneous aspergillosis (PCA) occurs through direct skin inoculation via trauma, burns, or surgical wounds, with Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger as common causative species, and is rare in immunocompetent individuals. We report a case of PCA in a 56-year-old immunocompetent patient with facial and right ankle ulcers, persisting for two years. The patient had no history of diabetes, corticosteroid use, or immunodeficiency. Fungal culture and metagenomic next-generation sequencing (mNGS) confirmed A. flavus infection. Voriconazole therapy, surgical debridement, and specialized wound care led to the gradual healing of the ulcers. This case highlights the importance of early diagnosis and intervention to prevent infection spread and progression to systemic aspergillosis or septic shock.}, }
@article {pmid41859064, year = {2026}, author = {Gu, P and An, X and Wei, Y and Xu, W and Han, Y and Gao, Q and Liu, S and Bi, Y}, title = {Elusive Diagnosis of Recurrent Subcutaneous Emphysema: Nocardia farcinica Infection in an Immunocompetent Female Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {556094}, pmid = {41859064}, issn = {1178-6973}, abstract = {This case report describes an immunocompetent female with recurrent subcutaneous emphysema and refractory soft tissue infections involving multiple non-contiguous sites-bilateral breasts, chest wall, and upper limb-over seven years, consistent with disseminated nocardiosis. Initial presentations mimicked bacterial mastitis, with localized swelling, erythema, crepitus, and elevated inflammatory markers. Despite repeated incision and drainage procedures, antibiotic therapies, and bilateral mastectomies, symptoms recurred persistently. Conventional microbial cultures repeatedly failed to identify a pathogen, while metagenomic next-generation sequencing (mNGS) of a late-stage chest wall lesion ultimately revealed Nocardia farcinica, an opportunistic actinomycete with a known propensity for systemic dissemination even in immunocompetent hosts. The patient's atypical clinical course-marked by multifocal gas-forming soft tissue necrosis, chronic recurrence, and resistance to empiric treatments-underscores the diagnostic challenges posed by fastidious pathogens like Nocardia. Key lessons include the utility of mNGS in identifying culture-elusive organisms, the importance of considering nocardiosis in refractory subcutaneous infections regardless of immune status, and the necessity of prolonged, targeted antimicrobial regimens (eg, sulfonamides) combined with surgical intervention. This case highlights evolving paradigms in managing complex disseminated infections through advanced genomic diagnostics and multidisciplinary approaches.}, }
@article {pmid41859067, year = {2026}, author = {Jiang, X and Wu, L and Duan, S and Bian, J and Lv, T and Zheng, L and Zhao, Y and Shen, P and He, J and Chen, Y}, title = {Long-Term Antibiotic-Driven Gut Microbiota Disruption Promotes Toxigenic Clostridioides difficile Proliferation: A Four-Year Retrospective Study of a Single ICU Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {562973}, pmid = {41859067}, issn = {1178-6973}, abstract = {OBJECTIVE: This four-year longitudinal study of a single critically ill patient leverages deep temporal profiling to unravel the dynamic interplay between antibiotic pressure, gut microbiota, and Clostridioides difficile (C. difficile) colonization, providing temporal insights unattainable through cross-sectional designs.
METHODS: We performed a retrospective analysis of one critically ill patient (2015-2019). Sixty-four fecal samples were subjected to toxigenic C. difficile culture and metagenomic sequencing. To isolate short-term effects, we implemented a 7-day retrospective window, categorizing each sample based on antibiotic exposure in the preceding week: no antibiotics, monotherapy, or polypharmacy.
RESULTS: Antibiotic exposure significantly reduced microbial diversity and promoted dysbiosis. Crucially, we identified a transitional C. difficile colonization state (Tcd±) that potentially determines progression to toxigenic (Tcd+) or non-toxigenic (Tcd-) outcomes. Analysis using the 7-day window revealed that intensive antibiotic pressure was strongly associated with successional progression towards toxigenic dominance. Conversely, brief antibiotic-free intervals were linked to partial restoration of microbial network complexity and a competitive landscape favoring non-toxigenic strains.
CONCLUSION: This deep temporal profiling of a single case provides novel, hypothesis-generating insights. The identification of a transitional colonization state and the association between short-term antibiotic pressure and colonization outcomes define critical dynamics for future validation. These findings highlight the potential of longitudinal data to inform precise antibiotic stewardship strategies in high-risk, critically ill populations.}, }
@article {pmid41859237, year = {2026}, author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H}, title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag011}, pmid = {41859237}, issn = {2730-6151}, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.}, }
@article {pmid41859321, year = {2026}, author = {Salama, RA and Abdel Kader, RG and Wadid, NA}, title = {Artificial intelligence in combating challenges in antimicrobial resistance: a narrative review.}, journal = {Infection prevention in practice}, volume = {8}, number = {2}, pages = {100522}, pmid = {41859321}, issn = {2590-0889}, abstract = {Antimicrobial resistance (AMR) is a major global health challenge that threatens the effective prevention and treatment of infections. It arises from increasing resistance rates, limited diagnostic capacity, inappropriate antimicrobial use, and a declining pipeline of new antibiotics. These challenges highlight the need for innovative approaches to complement existing AMR control strategies. Artificial intelligence (AI) has emerged as a valuable tool to address the complexity and scale of AMR. This narrative review examines how AI can be more effectively integrated into key components of AMR management. By analysing large clinical and laboratory datasets, AI-based surveillance and predictive models enable near real-time monitoring of resistance patterns and early outbreak detection. AI-powered diagnostic tools, including image analysis and genomic methods, improve rapid pathogen identification and prediction of antimicrobial susceptibility. In clinical practice, AI-driven decision support systems strengthen antimicrobial stewardship by optimizing prescribing and monitoring antibiotic use. In addition, deep learning approaches accelerate antimicrobial drug discovery and repurposing, reducing development timelines. AI also enhances the detection and surveillance of resistance genes through genomic and metagenomic analyses across human, animal, and environmental settings. Despite its potential, AI applications in AMR face challenges related to data quality, bias, interoperability, privacy, and clinician adoption. Therefore, AI should be seen as a tool that supports, rather than replaces, existing AMR strategies. When regulated well and integrated within One Health frameworks, AI can strengthen surveillance, improve treatment decisions, and support evidence-based interventions to curb AMR.}, }
@article {pmid41859442, year = {2026}, author = {Wang, Y and Zhang, L and Huang, W and Wang, N and Sun, M and Wu, L and Wang, W and Shi, C}, title = {Metagenomic analysis of the community structure and functional potential of Tamarix rhizosphere microbiomes along a soil salinity gradient.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1756020}, pmid = {41859442}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinization strongly shapes rhizosphere microbial communities and their functional potential in arid ecosystems. Tamarix is a key halophytic shrub in desert saline-alkali environments, yet how its rhizosphere microbiomes respond to natural salinity gradients remains insufficiently understood. Here, we compared community structure, functional potential, and potential salt-adaptation strategies across a soil salinity gradient.
METHODS: Rhizosphere soils of Tamarix were collected from four sites (S1-S4) in Xinjiang, China spanning increasing salinity. Soil physicochemical properties were measured, followed by shotgun metagenomic sequencing. Taxonomic profiles and functional annotations were generated from metagenomic data and compared among salinity groups.
RESULTS: Salinity was associated with clear shifts in community composition. Bacteria dominated at low-to-moderate salinity, whereas archaeal relative abundance increased at higher salinity, with Euryarchaeota becoming dominant in the high-salinity group. Functional profiling indicated that core metabolic pathways remained prevalent along the gradient, suggesting relative stability in overall metabolic capacity. However, higher salinity was accompanied by enrichment of functions linked to genetic information processing (e.g., translation and replication/repair) and ion transport, while lipid metabolism, cell motility, and signal transduction were reduced.
DISCUSSION: Together, these results support a salinity-driven transition in microbial functional strategy from "growth expansion" toward "homeostasis maintenance." Under high salinity, microbes appear to allocate more resources to maintaining cellular integrity and coping with stress, consistent with the observed enrichment of genetic information processing and repair-related functions. Mechanistically, the increased representation of Na[+]/H[+] antiporter systems and V/A-type ATPases in the very high salinity group suggests that energy-dependent ion homeostasis is a prominent adaptation, helping regulate intracellular ion balance and mitigate salt toxicity. In contrast, pathways for compatible solute synthesis (e.g., betaine and ectoine biosynthesis) were relatively reduced, indicating that osmoprotection may rely less on de novo solute production and more on ion regulation and maintenance processes along this gradient. Overall, the metagenomic evidence clarifies how Tamarix rhizosphere microbiomes restructure taxonomically and functionally with increasing salinity and highlights key candidate mechanisms underpinning salt-stress adaptation. These insights provide a microbial basis for understanding plant-microbe interactions in desert saline-alkali soils and may inform ecological restoration and management in salinized regions.}, }
@article {pmid41859445, year = {2026}, author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W}, title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783810}, pmid = {41859445}, issn = {1664-302X}, abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.}, }
@article {pmid41859451, year = {2026}, author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L}, title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1755652}, pmid = {41859451}, issn = {1664-302X}, abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.}, }
@article {pmid41860433, year = {2026}, author = {Boers, D and Chapleur, O and Andersson, AF and Schnürer, A}, title = {Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag029}, pmid = {41860433}, issn = {1574-6941}, abstract = {Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible; metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesising that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularised regression, which allowed filtering out irrelevant features even with limited sample sizes. Within studies, taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations. When applying trained models to other studies however, while performance was generally poor, functional models more often performed better compared to taxonomic models than the other way around. All in all, our hypothesis that functional metagenomics would outperform taxonomic metagenomics only found limited support.}, }
@article {pmid41860453, year = {2026}, author = {Shen, S and Zhao, S and He, Z and An, X and Dong, J and Wang, L and Ji, W and Li, A}, title = {The Efflux-Two-Component System (TCS)-Virulence Axis Drives Resistance-Virulence Convergence in Aquatic "Superhost Precursors" under Pollution Stress.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c09604}, pmid = {41860453}, issn = {1520-5851}, abstract = {The coexpression of antibiotic resistance and virulence traits in aquatic bacteria represents an emerging ecological and public health threat, yet the mechanisms underlying their coordinated regulation under complex environmental pressures remain unclear. In this work, we integrated metagenomic, proteomic, and metabolomic data sets from surface water samples across the Yangtze River Basin in Jiangsu Province to elucidate the drivers of resistance-virulence convergence under multipollutant stress. Among 392 multidrug-resistant (MDR; resistant to ≥3 antibiotic classes) isolates, approximately 5% were identified as "culturable superhost precursors" exhibiting pandrug-resistant (PDR; resistant to ≥10 antibiotic classes) phenotypes. Multiomics analyses indicated frequent colocalization and synchronous activation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in these environmental reservoirs. Functional assays under subinhibitory antibiotic exposure demonstrated enhanced cytotoxicity and efflux activity, accompanied by the upregulation of tolC and two-component regulators evgA/evgS. Together, these results characterize a putative redox-coupled efflux-two-component system (TCS)-virulence functional axis that synchronizes adaptive gene expression under pollution stress. Crucially, our findings challenge traditional antimicrobial resistance (AMR) surveillance approaches, which rely primarily on static gene abundance metrics, by demonstrating that the dynamic regulatory activation of this axis provides a more sensitive indicator of environmental health risks. Furthermore, tolC and evgA were identified as potential transcript-level biomarkers, providing a proof of concept for environmental antimicrobial resistance early warning tools within the One Health framework.}, }
@article {pmid41860568, year = {2026}, author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J}, title = {Klebsiella Enrichment Is Associated with Disease Severity in Ulcerative Colitis.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag079}, pmid = {41860568}, issn = {1365-2672}, abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.
METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥18 years) from First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.
RESULTS: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, p=0.005); mucosal diversity showed no difference (p=0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, p=0.14; mucosal: 3.40 vs. 3.72, p=0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g., allopurinol, histidine), enriching tyrosine and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g., quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.
CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.}, }
@article {pmid41860726, year = {2026}, author = {Stevens, KA and de Souza, JO and Li, H and Ouro-Djobo, A and Alabi, OJ and Al Rwahnih, M}, title = {Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave.}, journal = {Archives of virology}, volume = {171}, number = {4}, pages = {}, pmid = {41860726}, issn = {1432-8798}, abstract = {UNLABELLED: We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an Agave tequilana leaf sample during a routine metagenomic screening of Agave plants from California. The 16,161 bp genome contains the protein hallmarks of the family Closteroviridae, the HSP70h and the three coat protein homologs (CPh, CP, CPm), along with the open reading frames (ORFs) unique to criniviruses. Two ORFs downstream of the CPm are unique to AaCA. The monopartite nature of the genome was verified by PCR and Sanger sequencing. Phylogenetic analysis of the HSP70h gene clusters AaCA basally with existing criniviruses.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-026-06580-x.}, }
@article {pmid41860897, year = {2026}, author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S}, title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {3}, pages = {e0014118}, pmid = {41860897}, issn = {1935-2735}, mesh = {Humans ; Male ; Female ; Child ; Metagenomics ; *Microbiota/genetics ; *Noma/microbiology ; Child, Preschool ; *Saliva/microbiology ; Metagenome ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Nigeria ; *Bacteria/genetics/classification/isolation & purification ; Dysbiosis/microbiology ; Treponema/genetics/isolation & purification ; Adolescent ; }, abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.}, }
@article {pmid41861238, year = {2026}, author = {Yao, ML and Dai, Y and Zhang, W}, title = {Natural Products from the Oral Microbiome.}, journal = {Annual review of biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biochem-051024-050248}, pmid = {41861238}, issn = {1545-4509}, abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.}, }
@article {pmid41861543, year = {2026}, author = {Mohapatra, RK and Choi, Y}, title = {Exploring multi-omics approaches in anammox-based wastewater treatment processes: A review of recent applications and technological advances.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129342}, doi = {10.1016/j.jenvman.2026.129342}, pmid = {41861543}, issn = {1095-8630}, abstract = {Anaerobic ammonium oxidation (anammox) has arisen as a sustainable and energy-efficient approach for nitrogen removal in wastewater treatment. Recently, the utilization of multi-omics approaches, mainly metagenomics, metatranscriptomics, metaproteomics, and metabolomics has risen to reveal the complexity and functionality of anammox-based systems. These integrated approaches offer a comprehensive investigation of microbial community structure, gene expression, protein function, and metabolite dynamics across diverse operating contexts. Progress in high-throughput sequencing, mass spectrometry, and bioinformatics has facilitated the discovery of novel anammox bacteria, functional genes, and metabolic pathways, resulting in vital processes such as nitrogen cycling, microbial interactions, and system resilience. Metagenomics has shown the taxonomic and functional diversity within anammox consortia, whereas metatranscriptomics and metaproteomics have elucidated active metabolic pathways and functional responses to environmental alterations. Metabolomics has furnished direct evidence of metabolic states and biomarkers for enhancing reactor health and efficacy. Researchers have begun to elucidate the intricate physiological and biochemical mechanisms that govern the stability, recovery, and effectiveness of the anammox process through the integration of multi-omics datasets. This review explores recent technological breakthroughs and cutting-edge applications of multi-omics methods in anammox-based wastewater treatment. The article summarizes the principal research findings presented by numerous researchers, providing significant insights for the strategic design and management of robust and efficient water treatment systems aimed at future environmental sustainability.}, }
@article {pmid41861844, year = {2026}, author = {Tam, KK and Suster, CJE and Fong, W and Golubchik, T and Sivalingam, V and Jeoffreys, N and Tay, E and Ko, D and Wehrhahn, MC and Ginn, AN and Robson, J and Gardner, I and Papanicolas, LE and Kennedy, K and Graham, M and Tran, T and Speers, D and Cooley, L and Baird, RW and Meumann, EM and Harbidge, J and Campbell, S and Basile, K and Chen, SC and Sintchenko, V and Kok, J and Rockett, RJ}, title = {Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag163}, pmid = {41861844}, issn = {1537-6613}, abstract = {BACKGROUND: The resurgence of Mycoplasma pneumoniae (MP), first reported in China in 2023 was attributed to waning post-pandemic immunity with notable increases in macrolide-resistant MP (MRMP) (>80%). In Australia, infections peaked in early 2024, particularly among children under 15. While MRMP remains low in Europe, North America, and Australia (<5%), limited routine testing and surveillance restricts understanding of resistance dynamics. As macrolides are first-line therapy in many health settings, MRMP surveillance is essential for guiding empirical treatment and stewardship.
METHODS: We applied a novel capture-based targeted metagenomic sequencing (tNGS) to PCR-positive MP specimens (n=356) from across Australia. This approach enabled whole-genome recovery and MRMP detection directly from clinical specimens, without culture. MRMP detections were benchmarked against RT-PCR and clinical data were analysed to assess associations between resistance and healthcare utilisation.
RESULTS: This is the first genomics-informed national study of MP in Australia. We recovered 124 high-quality genomes, revealing a genetically diverse population with co-circulation of P1 Type 1 (69%) and Type 2 (31%). MRMP was identified in 13% of genomes, all belonging to clades prior to 2024 had only been reported in Asia (ST3 and ST14). MRMP cases were geographically widespread, suggesting importation and local transmission. Unlike reports from China, macrolide-susceptible clades (ST3, ST7, ST17 and ST20) predominated (87%) and were associated to significant lower healthcare utilisation compared to MRMP cases.
CONCLUSION: Our findings demonstrate the utility of tNGS for genomic epidemiology and highlight the need for MRMP surveillance. Although macrolides remain effective in Australia, emerging MRMP strains require close monitoring to inform treatment guidelines and antimicrobial stewardship.}, }
@article {pmid41861946, year = {2026}, author = {Wang, ST and Li, L and Yang, Q and Zhang, GF}, title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124314}, doi = {10.1016/j.envres.2026.124314}, pmid = {41861946}, issn = {1096-0953}, abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.}, }
@article {pmid41861947, year = {2026}, author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S}, title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124311}, doi = {10.1016/j.envres.2026.124311}, pmid = {41861947}, issn = {1096-0953}, abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71 ± 102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34 ± 4.27 nmol/(kg·h)). On average, both N2ODen (115.34 ± 143.60 nmol/(kg·h)) and N2ONif (5.29 ± 4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56 ± 62.52 and 3.88 ± 4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.}, }
@article {pmid41862052, year = {2026}, author = {Gunasekaran Rajalakshmi, S and K, RB and Viswanathan, P}, title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.}, journal = {Life sciences}, volume = {393}, number = {}, pages = {124336}, doi = {10.1016/j.lfs.2026.124336}, pmid = {41862052}, issn = {1879-0631}, abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.
METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.
KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p < 0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.
SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.}, }
@article {pmid41862850, year = {2026}, author = {Li, Z and Wu, C and Huang, D and Liang, Y and Zhai, Y and Mai, C and Han, Y and Tang, LA and Wang, W and Ning, C and Tan, W}, title = {Metagenomics reveals pathogenic diversity and temporal dynamics in severe pneumonia among patients in adult intensive care unit.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13107-x}, pmid = {41862850}, issn = {1471-2334}, support = {2021YFC2300101//the National Key Research and Development Program of China/ ; }, }
@article {pmid41863347, year = {2026}, author = {Lutfi, A and Holstein, T and Andreotti, S and Muth, T}, title = {MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag134}, pmid = {41863347}, issn = {1367-4811}, abstract = {MOTIVATION: A central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include in the protein reference database or to use tailored metagenome-derived databases, which are expensive and error-prone in their generation. A possible strategy to circumvent this database search issue is de novo sequencing, where peptide sequences are directly identified from mass spectra. However, these sequences must still be mapped back to potentially extensive databases. Here, alignment-based approaches enable robust and precise results, with the potential drawback of high memory usage and long run times.
RESULTS: We present MegaPX, a software for rapidly classifying de novo peptide sequences against large protein databases. MegaPX implemented as a C ++-based tool, uses an alignment-free, k-mer approach as a taxonomic classification method with the possibility of generating mutated reference databases for error-tolerant searching. It uses various algorithms, including interleaved Bloom filters, to efficiently compute approximate membership queries, ensuring fast processing times while querying and indexing large databases in a multi-indexing fashion. We demonstrate the potential of MegaPX by analyzing different samples, including metaproteomics, against extensive reference databases, highlighting its use as a fast screening tool.}, }
@article {pmid41863618, year = {2026}, author = {Majumder, D and Dash, S and Bhattacharya, D and Gill, HS and Raja, V and Dewi, JR and Roy, A and Rajeev, M and Pandit, S and Sharma, S and Dwivedi, SP and Nag, M and Lahiri, D}, title = {Genetically engineered lipases: advances in expression and upscaling for industrial applications.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41863618}, issn = {1432-072X}, }
@article {pmid41863619, year = {2026}, author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY}, title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41863619}, issn = {1432-072X}, support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Metagenomics/methods ; *Microbial Consortia ; Biodegradation, Environmental ; *Polyesters/metabolism ; Artificial Intelligence ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics ; }, abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.}, }
@article {pmid41863708, year = {2026}, author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H}, title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {41863708}, issn = {2509-2723}, abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.}, }
@article {pmid41863933, year = {2026}, author = {Dong, X and Zhu, L and He, Y and Li, C and Wu, R and Li, D}, title = {Microbial degradation of plastics in the environment: Mechanisms, enzymatic pathways, and constraints from laboratory studies to environmental reality.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129422}, doi = {10.1016/j.jenvman.2026.129422}, pmid = {41863933}, issn = {1095-8630}, abstract = {Microplastic (MP) pollution has become a persistent environmental challenge, raising increasing concern due to its global distribution and potential risks to human health. Biological degradation, including microbial and insect mediated processes, represents a promising and environmentally sustainable strategy for mitigating plastic and MP pollution; however, its effectiveness remains highly variable and strongly context dependent. This review systematically summarizes recent advances in microbial degradation of plastic, as well as emerging research on insect mediated plastic biodegradation, focusing on degrading microorganisms, key enzymes, metagenomic discovery, and enzyme engineering strategies. A wide range of bacterial and fungal taxa capable of degrading major plastic polymers, including polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS), polyvinyl chloride (PVC), polyurethane (PU), and polylactic acid (PLA), has been reported. In addition, several insect species capable of ingesting and transforming plastics have been identified as model systems for studying plastic degradation, where mechanical fragmentation, host digestive processes, and gut microbial metabolism jointly contribute to polymer transformation. Among these, PET degrading enzymes, particularly PETase, are the most extensively characterized, benefiting from detailed structural insights and intensive protein engineering efforts that have markedly enhanced catalytic efficiency and thermostability. In contrast, enzymatic mechanisms involved in the biodegradation of polyolefins such as PE and PP remain poorly understood, representing a major knowledge gap. Recent metagenomic approaches have substantially expanded the repertoire of candidate plastic degrading enzymes by accessing uncultured MP associated microbial communities and insect gut microbiomes. Nevertheless, functional validation and evaluation under environmentally relevant conditions remain critical bottlenecks. Moreover, most reported degradation efficiencies are derived from optimized laboratory settings and may substantially overestimate microbial performance under natural environmental constraints, including low temperature, high salinity, nutrient limitation, and mixed polymer substrates. Overall, this review highlights the gap between laboratory based biodegradation studies and real world applications and emphasizes the need for integrated strategies to advance scalable plastic and MP remediation solutions.}, }
@article {pmid41863937, year = {2026}, author = {Liu, X and Liu, X and Zhu, D and Wang, J and Wang, Z and Liu, W and Zhou, X and Zhou, H and Wu, L}, title = {Harvesting reshapes greenhouse gas exchange in reservoir drawdown soils via soil state control and context-dependent microbial functions.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129375}, doi = {10.1016/j.jenvman.2026.129375}, pmid = {41863937}, issn = {1095-8630}, abstract = {Reservoir drawdown zones, the seasonally exposed and re-flooded margins of reservoirs, are extensive pulsed wetlands that can act as hotspots of greenhouse gas (GHG) exchange. Vegetation harvesting is common in these zones, yet its net climate effect across CO2, CH4, and N2O, and the controls behind it, remain unclear. We compared harvested and unharvested plots across longitudinal river reaches and elevation bands in the drawdown zone of the Three Gorges Reservoir (China). We measured soil-atmosphere fluxes of CO2, CH4, and N2O, together with soil physicochemical properties and metagenome-derived functional markers. Harvesting increased CO2 flux and decreased CH4 flux, while N2O showed no detectable net treatment effect. Across analyses, soil hydrothermal and nutrient conditions were the dominant predictors of flux variation; microbial functional signals added information mainly through soil-dependent interactions. In CO2-equivalent terms, lower CH4 emissions only partly compensated for higher CO2, leaving a net positive effect under both 20- and 100-year horizons. These results underscore that harvest impacts in drawdown soils should be assessed as multi-gas trade-offs and interpreted through soil moisture-redox dynamics.}, }
@article {pmid41863981, year = {2026}, author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C}, title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106706}, pmid = {41863981}, issn = {1525-3171}, abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.}, }
@article {pmid41864025, year = {2026}, author = {Yu, H and Zhang, X and Liang, Y and Mu, Q and Shi, X and Deng, Z and Chen, J and Cao, J and Deng, Y and Han, Z and Chen, H and Zhang, C}, title = {Deciphering the environmental fate of halogenated organic compounds in cold seep sediments: Insights from non-targeted analysis and metagenomics across vertical redox gradients.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141804}, doi = {10.1016/j.jhazmat.2026.141804}, pmid = {41864025}, issn = {1873-3336}, abstract = {Halogenated organic compounds (HOCs) are pervasive in marine environments, yet their molecular diversity, vertical distribution, and fate in deep-sea ecosystems remain largely uncharted. Here, we integrated non-targeted analysis, geochemical profiling, and metagenomics to systematically analyze a 500-cm sediment core from the Haima deep-sea cold seep, deciphering these key aspects and their controlling factors. Non-targeted analysis identified 669 HOCs (at molecular formula level), predominantly of marine origin with saturated structures. The highest HOC diversity was found in the oxic/suboxic (OS) zone, where 73.4% of the frequently detected HOCs reached their peak abundance. Concurrently, a marked decrease in organochlorines was observed at the OS-suboxic/anoxic (SA) interface, followed by level stabilization below this transition, suggesting regulation by abrupt redox shifts. Correlation analyses revealed co-regulation of HOC distribution by geochemical (e.g., depth, pH, and SO4[2-]) and microbial (e.g., reductive and hydrolytic dehalogenases) factors. Metagenomics combined with redundancy analysis further demonstrated significant interactions between HOCs and dehalogenating microbial community along the vertical profile. In summary, this study provided an integrated perspective on the biogeochemical cycling of HOCs in the deep-sea cold seep, linking their removal at redox boundaries, long-term burial, and spatial organization to underlying microbial and geochemical drivers.}, }
@article {pmid41864266, year = {2026}, author = {Wang, X and Wang, Y and Yan, G and Chu, N and Huang, H and Nie, W}, title = {The Clinical Diagnostic Value of Metagenomic Next-Generation Sequencing for Patients with Suspected Nontuberculous Mycobacterial Osteoarticular Infection: A National Multicenter Clinical Cohort.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108578}, doi = {10.1016/j.ijid.2026.108578}, pmid = {41864266}, issn = {1878-3511}, abstract = {OBJECTIVE: This study aimed to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing non-tuberculous mycobacteria (NTM) osteoarticular infection (OAI) and compare it with mycobacteria growth indicator tube (MGIT) culture.
METHODS: This study was conducted on 193 patients with suspected NTM OAI treated from January 2019 to July 2022 at the Beijing Chest Hospital, Capital Medical University, Yantai Qishan Hospital or The Fourth People's Hospital of Nanning who had mNGS assay and MGIT culture results. Clinical comprehensive diagnosis was taken as the "gold standard". We investigated the diagnostic sensitivity, specificity, predictive value, and likelihood ratio of these tests.
RESULTS: Of the 193 patients, 26 (13.47%) were diagnosed with NTM OAI, and 167 (86.53%) had non-NTM OAI. Compared to the MGIT culture results, mNGS showed higher sensitivity (100.0% vs. 7.7%), specificity (99.4% vs. 80.2%), positive predictive value (96.3% vs. 5.7%), negative predictive value (100.0% vs. 84.8%), positive likelihood ratio (167.000 vs. 0.389) and negative likelihood ratio (0.000 vs. 1.150). The area under the curve of the mNGS assay was 0.997 (95% confidence interval, 0.990-1.000).
CONCLUSIONS: The mNGS assay had greater diagnostic accuracy than the MGIT culture in patients with suspected NTM OAI.}, }
@article {pmid41864408, year = {2026}, author = {Wang, Z and Chen, Z and Zhu, L and Liu, Y and Wen, Q}, title = {Substrate type determines the interplay between metabolic efficiency and microbial stress response in mixed culture PHA production under high salinity.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124330}, doi = {10.1016/j.envres.2026.124330}, pmid = {41864408}, issn = {1096-0953}, abstract = {Polyhydroxyalkanoates (PHAs) from mixed cultures offer a sustainable alternative to plastics, and high salinity presents a promising selective pressure for PHA producers. However, the osmotic stress imposed by high salinity perturbs carbon and energy metabolism, yet how different volatile fatty acid (VFA) substrates influence PHA synthesis efficiency under sustained saline conditions remains poorly understood, particularly regarding carbon flux partitioning and energy trade-offs. This study investigated the effects of single VFA (acetate, propionate, butyrate, and valerate) on the enrichment, PHA accumulation, and metabolic flux of PHA-producing mixed cultures under 1.8% salinity. Butyrate and valerate-fed systems achieved superior PHA accumulation (0.636 ± 0.015 and 0.698 ± 0.005 g PHA/g VSS, respectively) compared to acetate (0.541 ± 0.006 g PHA/g VSS) and propionate (0.382 ± 0.021 g PHA/g VSS). This was due to more direct precursor supply and lower energy demands. Carbon flux analysis confirmed butyrate and valerate directed over 85% of utilized carbon to PHA, whereas propionate diverted more to cell maintenance. Metagenomics revealed that Paracoccus was a versatile salt-tolerant PHA producer across all substrates. Cultures fed with butyrate and valerate also exhibited enhanced respiratory chain activity and higher ATP/NAD(P)H, enabling better salt stress while maximizing PHA synthesis. These findings highlight the critical interplay between VFA type, salt stress, and metabolic trade-offs, providing crucial insights for optimizing high-salinity waste to PHA bioprocesses.}, }
@article {pmid41864933, year = {2026}, author = {Dai, QB and Lai, LM and Zhu, Q and Yuan, L}, title = {Clinical efficacy of plasma cell-free dna metagenomic next-generation sequencing in diagnosing bloodstream infections.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13134-8}, pmid = {41864933}, issn = {1471-2334}, support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commissio/ ; }, }
@article {pmid41865546, year = {2026}, author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C}, title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129432}, doi = {10.1016/j.jenvman.2026.129432}, pmid = {41865546}, issn = {1095-8630}, abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.}, }
@article {pmid41865575, year = {2026}, author = {Xie, H and Zhou, J and Shi, Y}, title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141830}, doi = {10.1016/j.jhazmat.2026.141830}, pmid = {41865575}, issn = {1873-3336}, abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.}, }
@article {pmid41865593, year = {2026}, author = {Asokan, S and Banerjee, N and Saleem, M and Atiyah, HM and Pandey, RK and Abbas, RK and Yousif, SIA and Radhamanalan, G and Parashar, A and Gowtham, B and Balaji, VK and Jacob, T and Vijayan, S and Rajeswary, D and Atiyah, MM}, title = {Healthcare associated infections (HAI): Insights into epidemiology, microbiology, and diagnostics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {3}, pages = {117376}, doi = {10.1016/j.diagmicrobio.2026.117376}, pmid = {41865593}, issn = {1879-0070}, abstract = {Healthcare associated infections remain a major global health concern because they increase illness, mortality, hospital stay, and healthcare costs. This review provides an updated synthesis of recent evidence on the epidemiology, microbiology, diagnostics, and prevention of healthcare associated infections. These infections arise from patient susceptibility, invasive procedures, antibiotic overuse, contaminated equipment, and poor infection control practices. Device associated infections such as catheter associated urinary tract infection, central line associated bloodstream infection, ventilator associated pneumonia, and surgical site infection are common and often involve multidrug resistant pathogens. Biofilm formation on devices and hospital surfaces creates persistent reservoirs that promote resistance spread. Advances in automated culture systems, rapid molecular assays, metagenomics, and whole genome sequencing improve detection and surveillance. This article integrates evidence from 2020 to 2025 to provide a multidisciplinary framework for understanding and controlling HAIs.}, }
@article {pmid41865818, year = {2026}, author = {Wang, J and Sun, Y and Zhang, Y and Guo, Y and Liu, J and Wang, X and Yang, Y and Shi, L}, title = {Mechanisms underlying differences in nitrogen removal characteristics of anammox granular sludge immobilization filler with varying particle sizes: Performance, structure, and nitrogen removal pathways.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134471}, doi = {10.1016/j.biortech.2026.134471}, pmid = {41865818}, issn = {1873-2976}, abstract = {The anaerobic ammonium oxidation (anammox) process serves as a green, low-carbon, and sustainable wastewater nitrogen removal technology. However, anammox processes based on granular sludge systems face structural instability issues, resulting in the loss of anammox bacteria (AnAOB). In this study, an immobilized filler system for AnAOB based on hydrogel encapsulation was constructed using anammox granular sludge (AnGS) of varying particle sizes (G1: < 0.10 cm, G2: 0.10-0.20 cm, G3: 0.20-0.32 cm, and G4: > 0.32 cm). The differences in nitrogen removal characteristics, microstructures, and pathways of these AnGS immobilized fillers were thoroughly investigated. The large particles (G3 and G4) immobilized fillers showed the best nitrogen removal performance, with total nitrogen removal rates reaching 0.591 kgN·m[-3]·d[-1] and 0.615 kgN·m[-3]·d[-1], respectively. The G2 immobilized filler was more conducive to the self-growth and enrichment of AnAOB, and the absolute abundance and relative abundance of Candidatus Brocadia increased by 23-fold and 9.20-fold, respectively. Conversely, the G1 immobilized filler displayed the poorest nitrogen removal rate due to insufficient microbial growth. The G1-G3 immobilized fillers possessed uniform and dense small pores, whereas the G4 filler featured uniform large pores. Metagenomic analysis confirmed that the abundance of denitrification-related genes in G3 and G4 immobilized fillers was highest, indicating that anammox and denitrification synergistically achieve nitrogen removal, whereas G2 immobilized fillers mainly relied on anammox. This study provides a crucial theoretical basis and technical guidance for optimizing the application of anammox immobilized filler systems.}, }
@article {pmid41865820, year = {2026}, author = {Luo, Z and Li, W and Zhang, N and Lei, M and Chen, B and Li, Y and Liu, Q and Zhang, M and Lv, S and Cheng, F and Li, J}, title = {A novel continuous-flow three-stage tandem system based on partial nitrification/Anammox granular sludge and partial denitrification-Anammox biofilm (PN/A-PD-A) for advanced nitrogen removal from mature landfill leachate.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134474}, doi = {10.1016/j.biortech.2026.134474}, pmid = {41865820}, issn = {1873-2976}, abstract = {A novel continuous-flow system coupling partial nitrification/Anammox (PN/A), partial denitrification (PD), and Anammox (Amx) biofilm reactors was developed (PN/A-PD-A) to treat mature landfill leachate (MLL). To maximize synergy, the NH4[+]-N removal in the PN/A reactor was regulated based on the NO2[-]-N accumulation ratio (NAR) in the PD stage, ensuring optimal substrate stoichiometry for the final Amx polishing step. Over 174 days of operation, the system achieved a superior total nitrogen removal efficiency (TNRE) of 98.30 ± 0.14% (effluent TN: 21.80 ± 1.71 mg/L). The PN/A granular sludge, enriched with Candidatus_Kuenenia (5.87%) and Nitrosomonas (9.73%), demonstrated high adaptability to MLL characteristics and contributed to 83.51% of the TN removal. In the PD stage, the dominant genus Thauera (43.91%) facilitated efficient NAR (82.86 ± 1.61%) at a limited COD/NO3[-]-N ratio of 2.32 ± 0.02. The Anammox biofilm (Candidatus_Kuenenia, 27.80%) in the Amx reactor contributed to 13.10% of TN removal, ensuring to meet the MLL discharge standard. Kinetic and metagenomic analyses confirmed that distinct shifts from complete to partial nitrification (and denitrification) in enzymes activity and gene abundance under chronic MLL stress underpinned the robust NO2[-]-N accumulation in both PN/A and PD reactors. Notably, compared to conventional nitrification-denitrification process, the PN/A-PD-A system significantly reduced oxygen demand (60.18%), exogenous organic carbon consumption (91.61%), sludge yield (83.72%), and CO2 emission (94.66%), demonstrating a sustainable pathway for low-carbon nitrogen removal from high-strength wastewater.}, }
@article {pmid41865821, year = {2026}, author = {Wang, X and Liang, BJ and Wu, DN and Zhang, XM and Zhao, HP and Lai, CY}, title = {Efficient anaerobic metformin biodegradation driven by a Cross-Feeding Consortium: Novel Pathways, Enzymes, and toxicity dynamics.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134473}, doi = {10.1016/j.biortech.2026.134473}, pmid = {41865821}, issn = {1873-2976}, abstract = {Metformin is one of the most widely prescribed antidiabetic drugs worldwide and is now ubiquitously detected in aquatic environments, yet its anaerobic biodegradation remains largely unexplored and mechanistically unresolved. Here, an anaerobic membrane bioreactor (AnMBR) was operated and near-complete metformin removal (∼98%) at influent concentrations up to 5.3 mg/L was achieved, corresponding to a maximum degradation rate of 7.2 mg/L/d, approximately sixfold higher than previously reported anaerobic systems degrading metformin. High-resolution mass spectrometry identified three concurrent anaerobic metformin transformation pathways. Notably, a previously unreported biological -C-N bond cleavage route yielding dimethylguanidine was discovered, expanding the known anaerobic metabolic repertoire of metformin. In silico toxicity prediction revealed a non-monotonic toxicity trajectory during metformin transformation, with transiently elevated toxicity at intermediates (particularly 2,4-AMT) followed by an overall attenuation at the terminal product guanidine. Metagenomic and metatranscriptomic analyses uncovered a cooperative, cross-feeding microbial network dominated by Ignavibacterium album and Denitrolinea symbiosum, and identified HypAB (metformin-to-guanylurea), YafV and AmiA/B/C/E (guanylurea-to-guanidine), and, critically, SpeB as the key enzyme initiating the newly proposed -C-N bond cleavage pathway. Molecular dynamics simulations further suggested stable binding of metformin to SpeB with strong affinity, providing mechanistic support for SpeB-mediated initiation of the novel pathway. Overall, this study establishes the first mechanistic framework for anaerobic metformin biodegradation, reveals an unprecedented -C-N scission pathway, and demonstrates that high-rate, low-carbon pharmaceutical removal can be achieved through intrinsic microbial metabolism, offering new conceptual and practical foundations for energy-efficient treatment of emerging pharmaceutical contaminants.}, }
@article {pmid41865866, year = {2026}, author = {Wang, Y and Wang, D and Wang, H}, title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {316}, number = {}, pages = {111996}, doi = {10.1016/j.cbpa.2026.111996}, pmid = {41865866}, issn = {1531-4332}, abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.}, }
@article {pmid41865966, year = {2026}, author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J}, title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124325}, doi = {10.1016/j.envres.2026.124325}, pmid = {41865966}, issn = {1096-0953}, abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.}, }
@article {pmid41866421, year = {2026}, author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R}, title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866421}, issn = {1573-0972}, }
@article {pmid41866581, year = {2026}, author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW}, title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45459-4}, pmid = {41866581}, issn = {2045-2322}, support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; }, }
@article {pmid41867450, year = {2026}, author = {Jia, C and Liu, X and Liu, W and Yao, X and Chen, X and Zhao, J and Wang, P and Ge, W and Han, Y}, title = {Multi-Omics Reveal the Potential Associations of Streptococcus, 13'-Hydroxy-Alpha-Tocopherol and Glutathione Metabolism in Children with Chronic Rhinosinusitis with Nasal Polyps.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {567582}, pmid = {41867450}, issn = {1178-7031}, abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) in children is a clinically significant inflammatory disorder characterized by persistent symptoms and complex underlying mechanisms. This study used multi-omics approaches to investigate potential microbial and metabolic associations in pediatric CRSwNP.
METHODS: Nasal secretions from 20 children with CRSwNP and 19 healthy controls were analyzed using metagenomics, untargeted metabolomics, and proteomics.
RESULTS: CRSwNP patients showed higher microbial diversity and altered microbial communities, with increased Streptococcus abundance. Metabolomic sequencing revealed that 13'-Hydroxy-alpha-tocopherol was significantly upregulated in the CRSwNP group and exhibited a positive correlation with the abundance of Streptococcus. Proteomic sequencing revealed that proteins involved in glutathione metabolism were significantly downregulated in the CRSwNP group, with GCLM and GGCT showing a significant negative correlation with 13'-Hydroxy-alpha-tocopherol.
CONCLUSION: These associative findings suggest potential links among Streptococcus, 13'-Hydroxy-α-tocopherol, and glutathione metabolism, indicating that oxidative stress-related imbalance may contribute to pediatric CRSwNP. These results provide preliminary evidence that 13'-Hydroxy-α-tocopherol may serve as a potential biomarker for pediatric CRSwNP.}, }
@article {pmid41867493, year = {2025}, author = {Alali, M and Imani, M}, title = {Bayesian Topology Inference of Regulatory Networks under Partial Observability.}, journal = {Results in control and optimization}, volume = {19}, number = {}, pages = {}, pmid = {41867493}, issn = {2666-7207}, support = {R21 EB032480/EB/NIBIB NIH HHS/United States ; }, abstract = {Biological systems, such as microbial communities in metagenomics and gene regulatory networks (GRNs) in genomics, are composed of a vast number of interacting components observed through inherently noisy data. These systems play a critical role in understanding fundamental biological processes, including gene regulation, microbial interactions, and cellular dynamics. For example, microbial communities involve complex interactions between microbes, bacteria, genes, and small molecules observed through omics data, while GRNs consist of numerous interacting genes observed via various gene-expression technologies. However, reconstructing the topology of such networks poses significant challenges due to their large scale, high dimensionality, and the presence of noise. Existing inference techniques often struggle with scalability, interpretability, and overfitting, making them unsuitable for analyzing large and complex biological systems. To overcome these challenges, this paper proposes a Bayesian topology optimization framework for efficient and scalable inference of regulatory networks modeled as partially-observed Boolean dynamical systems (POBDS). The method combines the Boolean Kalman Filter (BKF) as an optimal estimator for POBDS, with Bayesian optimization, which employs Gaussian Process regression and a topology-inspired kernel function to model the log-likelihood function. Numerical experiments demonstrate the superior performance of our framework. In the p53-MDM2 network, our method accurately infers topology with 8 and 16 unknown regulations, achieving higher log-likelihood with 100 and 200 evaluations, respectively. For the mammalian cell cycle network with 10 unknown regulations, proposed method identifies the correct topology among 59,049 possibilities with lower error and faster convergence.}, }
@article {pmid41867523, year = {2026}, author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S}, title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.}, journal = {ACS omega}, volume = {11}, number = {10}, pages = {16913-16921}, pmid = {41867523}, issn = {2470-1343}, abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.}, }
@article {pmid41867691, year = {2026}, author = {Jiang, D and Wang, Y and Ling, Y and Eremin, SA and Mukhametova, LI and Du, J and Hu, H}, title = {Impacts of high-temperature and humidity transportation on rice quality: an integrated analysis of microbial community succession and flavor compound alterations.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1792369}, pmid = {41867691}, issn = {2296-861X}, abstract = {This study investigated the dynamic changes in rice quality, microbial communities, and volatile compound profiles during simulated summer transportation (35 °C, 70% RH, 15 days). Indica rice samples were systematically collected every 3 days and analyzed using HS-SPME-GC-MS/MS, HS-GC-IMS, and metagenomic sequencing. Prolonged transportation significantly altered the physicochemical properties of the rice. Moisture content plateaued on day 12, while germination rates declined significantly starting from day 6. Furthermore, fatty acid values increased continuously due to accelerated lipid hydrolysis and oxidation. Visible mold growth became evident on day 12, marking a critical tipping point for quality deterioration. The odor activity value (OAV) and relative odor activity value (ROAV) analyses revealed that the decline in unsaturated fatty aldehydes such as (E)-2-nonenal and the significant accumulation of alcohols, ketones, and short-chain esters, including 1-octen-3-ol and ethyl acetate, drove the transition from a "fresh and fatty" aroma to one characterized by moldy, fermented, and pungent notes. Metagenomic analysis demonstrated a profound ecosystem shift from bacterial dominance (Proteobacteria, Actinobacteria) to fungal dominance. Notably, Lichtheimia surged from <0.01% to 23.95%, becoming the dominant genus, while Aspergillus increased from 0.03% to 4.57%. Correlation analysis indicated that while Pseudomonas was associated with elevated fatty acid levels, the flavor shift was primarily linked to microbial succession. These findings provide insights into the synergistic mechanisms of rice spoilage and suggest that specific volatile markers could serve as early warning indicators for quality control in real-world grain logistics.}, }
@article {pmid41867766, year = {2026}, author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S}, title = {Learning functional groups in complex microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.03.709366}, pmid = {41867766}, issn = {2692-8205}, abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~ 4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.}, }
@article {pmid41867767, year = {2026}, author = {Nguyen, MH and Schatz, MC}, title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.06.710148}, pmid = {41867767}, issn = {2692-8205}, abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.
RESULTS: We present Perseus , a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.
Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus .
CONTACT: mnguye99@jh.edu , mschatz@cs.jhu.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available online.}, }
@article {pmid41868021, year = {2026}, author = {Zhan, M and Tu, S and Yang, S and Yin, Y and Wang, Z and Zhang, F and Zhang, Y and Wang, Q and Zhao, C and Wang, X and Wang, H and Chen, H}, title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Diagnosing Central Nervous System Infections in Hematopoietic Stem Cell Transplant Recipients: A Retrospective and Prospective Cohort Study.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {554425}, pmid = {41868021}, issn = {1178-6973}, abstract = {BACKGROUND: Diagnosing central nervous system infections (CNSI) in hematopoietic stem cell transplant (HSCT) recipients remains challenging due to nonspecific presentations and low sensitivity of conventional microbiological methods.
METHODS: This study evaluated the clinical utility of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in 127 HSCT recipients (87 retrospective, 40 prospective) from Peking University People's Hospital. Pathogens detected by mNGS and conventional methods were validated via Sanger sequencing.
RESULTS: mNGS identified 20 pathogen-positive samples (19 confirmed by sequencing), while conventional methods detected none. mNGS demonstrated 82.6% sensitivity and 99.0% specificity for CNSI diagnosis, with sensitivity rising to 100.0% when combined with conventional approaches. Notably, mNGS excelled in detecting viral pathogens, particularly in allogeneic HSCT recipients.
CONCLUSION: Our findings advocate for the integration of mNGS into the diagnostic algorithm for CNSI, especially in immunocompromised hosts. This approach enables earlier and more precise pathogen identification, which has the potential to streamline antimicrobial therapy and improve clinical management. To maximize its benefit and ensure reliable interpretation, mNGS results should be correlated with comprehensive clinical and paraclinical data. Further prospective studies are warranted to validate its impact on therapeutic decision-making and patient prognosis.}, }
@article {pmid41868024, year = {2026}, author = {Wang, QL and Teng, SN and Zhang, XJ and Guo, YX and Kong, Y and Tian, XH and Zhang, Y}, title = {Fatal Primary Amoebic Meningoencephalitis in Coastal Areas of North China in an Immunocompetent Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {559408}, pmid = {41868024}, issn = {1178-6973}, abstract = {PURPOSE: Primary amoebic meningoencephalitis (PAM) is a rapidly fatal infection caused by Naegleria fowleri (N. fowleri) with a mortality rate exceeding 95%. This study presented the clinical course, diagnosis, treatment, and outcome of a confirmed PAM case in an adult female. Additionally, we analyzed the epidemiology of PAM in China and review the therapeutic regimens of surviving cases worldwide, aiming to enhance disease awareness and improve clinical outcomes.
CASE PRESENTATION: The patient was a 50-year-old immunocompetent woman with a history of hot spring bathing before symptom onset, which was not initially disclosed. Moreover, her early infectious symptoms, particularly fever following a tick bite in an orchard, directed clinical suspicion toward tick-borne disease. Four days later, she was hospitalized with generalized convulsions and coma. Clinical examination suggested a bacterial intracranial infection, and treatment with meropenem and vancomycin was initiated. However, her condition deteriorated rapidly. The presence of N. fowleri was identified by cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and smear. The etiology was clarified only after retrospective confirmation of hot spring contact, which was later confirmed by blood mNGS. Despite intensive therapy with amphotericin B (AmB), the patient unfortunately died. To provide insights into PAM management in China, we also conducted a systematic analysis of 15 domestic cases and 18 global survivors.
CONCLUSION: PAM is characterized by rapid progression, underscoring the importance of early diagnosis. In cases of rapidly advancing meningoencephalitis, clinicians should maintain a high index of suspicion for rare pathogens such as N. fowleri, with thorough and repeated assessment of recent environmental exposures such as hot spring immersion or freshwater swimming. Early application of mNGS is essential for timely pathogen identification. While AmB remains the first-line therapy, its dosing and duration should be tailored to individual patient factors, and combination therapy should be considered to enhance efficacy. Overall, improved clinical vigilance, advanced pathogen diagnostics, and standardized anti-amoebic therapy form the cornerstone of enhancing outcomes in PAM. As the first documented PAM case in Shandong Province, China, this report highlights the need for heightened awareness in coastal regions while contributing valuable epidemiological insights into this devastating disease.}, }
@article {pmid41868028, year = {2026}, author = {Wang, Z and Ma, R and Ding, Z and Ma, L and Liu, X and Wang, Y}, title = {Brucellosis Complicated by Thyroid Abscess and Life-Threatening Hemophagocytic Syndrome: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {583365}, pmid = {41868028}, issn = {1178-6973}, abstract = {INTRODUCTION: Brucella infections can affect various systems in the body, such as the osteoarticular and genitourinary systems; however, cases involving the thyroid gland are rare. This case report describes the clinical management of a thyroid abscess associated with brucellosis in a farmer.
CASE PRESENTATION: A 67-year-old male farmer presented to Shanxi Bethune Hospital on 17 March 2024 with a chief complaint of "intermittent fever with fatigue for over 3 months and neck swelling and pain for 2 months". Upon admission, his serum Brucella tube agglutination test titre was 1:200, Rose Bengal plate agglutination test was positive, and blood culture was negative for Brucella. Neck computed tomography revealed a low-density nodular shadow in the right thyroid lobe measuring approximately 4.79×4.45 cm. Coffee-coloured pus was aspirated during thyroid puncture. Pathogenic metagenomic next-generation sequencing and pus culture confirmed Brucella infection as the cause of the thyroid abscess. During treatment, the patient developed hemophagocytic syndrome. The patient's condition was controlled with aggressive anti-infective therapy and glucocorticoid treatment. However, because of symptom recurrence, the patient ultimately underwent surgical intervention, comprising partial thyroidectomy, abscess incision and drainage, and thyroid injection, following which he recovered fully.
CONCLUSION: This article reports an extremely rare case of brucellosis leading to a thyroid abscess. Physicians should consider the possibility of brucellosis when encountering patients with thyroid abscesses and be vigilant of other potential complications.}, }
@article {pmid41868358, year = {2026}, author = {Ribeiro-Junior, MR and Cardwell, KF and Nascimento, D and Espindola, AS and Ramachandran, A and Gupta, SK and Tyungu, D}, title = {Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi[®]).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743643}, pmid = {41868358}, issn = {1664-302X}, abstract = {Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi[®]) software for detection of nine RNA viruses of human and veterinary clinical importance. Species specific signature sequences in the different pathogen genomes were identified, and specific electronic probe sets were curated using the MiFi[®] software. Analytical specificity and sensitivity were evaluated through simulated metagenomes and public sequence databases, respectively. Host-specific internal control probes were designed to ensure diagnostic reliability and quality control. Diagnostic performance was assessed using Oxford Nanopore sequence data from clinical nasal swab samples. In silico validation showed 100% specificity across 83 datasets and limits of detection as low as 0.0010% of total reads (10 reads per 10[6]) for some targets. Internal controls generated stable background signals without interfering with pathogen detection. In vivo testing of 44 clinical samples matched PCR performance for Human respiratory syncytial virus (HRSV), Influenza B virus (IBV), Influenza A virus (IAV), Bovine respiratory syncytial virus (BRSV), and Canine distemper virus (CDV). These findings demonstrate that the MiFi[®] software enables rapid, multiplex, and strain-specific detection of respiratory viruses in metagenomic sequence data without the need for advanced bioinformatics expertise. The approach supports scalable use in clinical laboratories, veterinary diagnostics for surveillance and triage, offering a valuable tool for improving respiratory pathogen detection across diverse settings.}, }
@article {pmid41869352, year = {2026}, author = {Zhou, YM and Cui, XQ and Zhao, P and Peng, ZG and Guo, N and Sun, HB and Liu, SL}, title = {The species, distribution, resistance of donor-derived pathogens and their impact on solid organ transplant recipients.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1777244}, pmid = {41869352}, issn = {1664-3224}, mesh = {Humans ; Middle Aged ; Male ; Female ; Retrospective Studies ; *Tissue Donors ; Adult ; *Transplant Recipients ; *Liver Transplantation/adverse effects ; *Kidney Transplantation/adverse effects ; Aged ; *Organ Transplantation/adverse effects ; Drug Resistance, Multiple, Bacterial ; Incidence ; Bacteria/isolation & purification/drug effects ; }, abstract = {BACKGROUND: Donor-derived infections (DDIs) have become a significant cause of infection in organ transplant recipients. Elaborating on the species, distribution, and resistance of donor-derived pathogens (DDPs) holds important implications.
METHODS: A retrospective cohort study included 302 deceased donors and their corresponding 464 kidney transplant recipients and 175 liver transplant recipients. We detected DDPs in preservation fluid (PF) using both conventional culture and mNGS, and subsequently analyzed the incidence of DDIs after transplantation.
RESULTS: 89.4% (270/302) of donors had positive cultures. Predominant multidrug-resistant organism included HLAR-Enterococcus, CRAB, CRKP, CRPA, MRS and ESBL-Escherichia coli. Compared with conventional culture, mNGS exhibited superior sensitivity for detecting bacteria and fungus in PF, with shorter turnaround time (p < 0.001). The incidences of DDIs in kidney and liver transplant recipients were 16.6% (77/464) and 19.4% (34/175) respectively. The recipients with DDIs were associated with elevated serum creatinine or total bilirubin levels, increased infection events, higher risks of graft loss, elevated mortality, and longer length of hospital stay (p < 0.05).
CONCLUSIONS: Multidrug-resistant organism are prevalent in deceased donors, with PF contamination primarily originating from donors. Integration of mNGS into donor screening protocols enables timely antimicrobial intervention, potentially improving transplant outcomes.}, }
@article {pmid41869502, year = {2026}, author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T}, title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.}, journal = {Environmental science and ecotechnology}, volume = {30}, number = {}, pages = {100683}, pmid = {41869502}, issn = {2666-4984}, abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.}, }
@article {pmid41869518, year = {2026}, author = {Liu, J and Wu, R}, title = {Intraoperative sampling for postoperative metagenomic next-generation sequencing to guide biofilm-targeted therapy for Cutibacterium acnes infective endocarditis complicated by ruptured sinus of Valsalva aneurysm: a case report.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1707117}, pmid = {41869518}, issn = {2297-055X}, abstract = {BACKGROUND: Cutibacterium acnes is an easily overlooked pathogen in infective endocarditis (IE) due to its slow growth, propensity for biofilm formation, and high rate of culture-negative results. When complicated by structural heart disease such as a ruptured sinus of Valsalva aneurysm (RSVA), its indolent course can lead to severe hemodynamic compromise.
CASE SUMMARY: A 35-year-old male with a known ventricular septal defect (VSD) and unruptured aortic sinus aneurysm presented with persistent fever and progressive heart failure (NYHA class IV). Echocardiography revealed a ruptured right coronary sinus of Valsalva aneurysm (RCSVA) into the right ventricular outflow tract (RVOT) with a large vegetation. Blood cultures were negative. After 6 days of ineffective empirical antibiotic therapy, emergency surgery was performed to resect the aneurysm and vegetation and repair the cardiac structures. Intraoperatively, a vegetation sample was collected for metagenomic next-generation sequencing (mNGS). Postoperatively, mNGS identified Cutibacterium acnes with high sequence reads (1,284) and coverage (47.62%), enabling a definitive diagnosis. Pathology confirmed microcolonies and necrotic inflammation. The antibiotic regimen was switched to a regimen with potential activity against biofilms with oral doxycycline and intravenous clindamycin for 6 weeks. The patient's inflammatory markers normalized, and cardiac function recovered to NYHA class I, with no recurrence at 12-month follow-up.
CONCLUSION: This case highlights the diagnostic synergy of intraoperative histopathology and mNGS for pathogen identification, underscores the rationale for biofilm-conscious adjuvant therapy, and reaffirms the crucial role of early surgical debridement and repair in achieving cure.}, }
@article {pmid41869816, year = {2026}, author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K}, title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0250325}, doi = {10.1128/spectrum.02503-25}, pmid = {41869816}, issn = {2165-0497}, abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.}, }
@article {pmid41869825, year = {2026}, author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G}, title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {15578666261428562}, doi = {10.1177/15578666261428562}, pmid = {41869825}, issn = {1557-8666}, abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.}, }
@article {pmid41869887, year = {2026}, author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J}, title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e20332}, doi = {10.1002/advs.202520332}, pmid = {41869887}, issn = {2198-3844}, support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; }, abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.}, }
@article {pmid41870053, year = {2026}, author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S}, title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0147625}, doi = {10.1128/mra.01476-25}, pmid = {41870053}, issn = {2576-098X}, abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.}, }
@article {pmid41870088, year = {2026}, author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S}, title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0010426}, doi = {10.1128/msystems.00104-26}, pmid = {41870088}, issn = {2379-5077}, abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.}, }
@article {pmid41870133, year = {2026}, author = {Ni, B and Chen, XP and Lin, D and Yao, Z and Xia, J and Zhang, TL and Zheng, J and Cai, TG and Wang, X and Vollertsen, J and Zhu, D and Zhu, DZ}, title = {Potential Viral Regulation of Sulfur Cycling in Urban Sewer Sediments.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15040}, pmid = {41870133}, issn = {1520-5851}, abstract = {Sewer sediments are microbial hotspots for sulfur cycling and sulfide generation, which is the leading cause of sewer corrosion and poses significant economic losses and public safety concerns. However, viruses in sewer sediments remain inadequately explored regarding their characteristics, interactions with their hosts, and ecological regulatory potential for sulfur cycling. In this study, we explored viral characteristics and virus-host interactions in sewer sediments from three distinct types of urban functional areas through metagenomics and viromics. Compared with single-function (commercial and residential) areas, sewer sediments in multifunctional areas contain higher nutrients and nutrient-induced acidification, which can promote host density and drive a shift from lytic to lysogenic infection. This shift may potentially enhance sulfide formation through the insertion of more auxiliary metabolic genes related to sulfate reduction into host genomes. Conversely, a higher viral lytic tendency in single-function area can lyse sulfate-reducing microorganisms, thereby mitigating sulfide formation. Phage transplantation experiments and the high prevalence of key viral hosts across global sewers (76 cities across six countries) demonstrated the high potential of viruses in alleviating sewer corrosion. Our findings reveal the dual role of viruses as metabolic "tuners" in sewer sulfur dynamics, suggesting that comprehensive urban sewer management requires consideration of exploiting viral lysis.}, }
@article {pmid41870192, year = {2026}, author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM}, title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261433762}, doi = {10.1177/15578100261433762}, pmid = {41870192}, issn = {1557-8100}, abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.}, }
@article {pmid41870201, year = {2026}, author = {Li, N-P and Gupta, S and Kollipara, SK and Hung, T-H and Rao, GP and Kuo, C-H}, title = {Draft genome sequence of "Candidatus Phytoplasma australasiaticum" strain TBB-AP associated with tomato big bud disease in India.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0003326}, doi = {10.1128/mra.00033-26}, pmid = {41870201}, issn = {2576-098X}, abstract = {We report the draft metagenome-assembled genome (MAG) of "Candidatus Phytoplasma australasiaticum" strain TBB-AP, obtained from a symptomatic tomato plant collected in Andhra Pradesh, India. This assembly provides a genomic resource for functional and evolutionary studies of phytoplasmas associated with tomato big bud disease.}, }
@article {pmid41870280, year = {2026}, author = {Werbowy, O and Håkansson, M and Dorawa, S and Stefańska-Kaźmierczak, A and Svensson, LA and Al-Karadaghi, S and Jurczak-Kurek, A and Kwiatkowska-Semrau, K and Plotka, M and Fridjonsson, OH and Hreggvidsson, GO and Aevarsson, A and Dąbrowski, S and Kaczorowska, AK and Kaczorowski, T}, title = {Structural and functional characterization of a hyperthermostable single-stranded DNA-binding protein from a hot spring metagenome.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {4}, pages = {e70538}, doi = {10.1002/pro.70538}, pmid = {41870280}, issn = {1469-896X}, support = {UMO-2019/34/H/NZ2/00584//National Science Centre (Poland)/ ; 685778//European Union Horizon 2020/ ; }, mesh = {*Hot Springs/microbiology ; *DNA-Binding Proteins/chemistry/genetics/metabolism ; *Metagenome ; Crystallography, X-Ray ; *DNA, Single-Stranded/metabolism/chemistry ; Models, Molecular ; Escherichia coli/genetics/metabolism ; *Bacterial Proteins/chemistry/genetics/metabolism ; Amino Acid Sequence ; Protein Multimerization ; }, abstract = {We present the structural and functional characterization of a single-stranded DNA-binding protein (SSB-M5) identified from a hot spring metagenome in Vatnajökull National Park, Iceland. This small protein (136 aa; 15,695 Da) shares 100% amino acid sequence identity with two previously uncharacterized SSBs from hyperthermophilic Fervidobacterium species. Functional complementation assay demonstrated that SSB-M5 can substitute for Escherichia coli SSB in an ssb[-] mutant strain, confirming its biological activity. A recombinant C-terminally His-tagged SSB-M5 was overproduced, purified to homogeneity, and subjected to structural, biochemical, and biophysical analysis. The crystal structure revealed that SSB-M5 forms a dimer through a crystallographic twofold axis, with each monomer contributing to a large antiparallel β-sheet. The flat surfaces of the β-sheets from the two dimers are packed together via a second crystallographic twofold axis, forming a tetramer that serves as the functional unit of the SSB-M5. Electrophoretic mobility shift assays showed that SSB-M5, after heat treatment up to 100°C, forms stable DNA-protein complexes with the (dT)40 oligo. Quantitative analyses revealed that SSB-M5 binds (dT)70 oligonucleotide with very high affinity (KD = 72 ± 6 pM). Hill analysis indicated cooperative binding, yielding an EC50 of 141 pM and a Hill coefficient of 2. Moreover, inclusion of SSB-M5 in PCR reactions significantly enhanced amplification by eliminating non-specific products. Together, these findings identify SSB-M5 as a hyperthermostable, high-affinity single-stranded DNA-binding protein with potential applications in molecular biology and biotechnology.}, }
@article {pmid41871361, year = {2026}, author = {Lipovac, J and Šikić, M and Vicedomini, R and Križanović, K}, title = {MADRe: Strain-level Metagenomic Classification Through Assembly-Driven Database Reduction.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag030}, pmid = {41871361}, issn = {2047-217X}, abstract = {Strain-level metagenomic classification is essential for understanding microbial diversity and functional potential, yet remains challenging, particularly when sample composition is unknown and reference databases are large and redundant. Here we present MADRe, a modular and scalable pipeline for long-read strain-level metagenomic classification based on Metagenome Assembly-Driven Database Reduction. Beyond system-level integration, MADRe introduces statistical strategies that leverage assembly-derived genomic context to guide database reduction and probabilistic read reassignment. Specifically, it combines long-read metagenome assembly, contig-to-reference reassignment using an expectation-maximization framework for reference reduction, and probabilistic read mapping reassignment on a reduced database to achieve sensitive and precise strain-level classification. We extensively evaluated MADRe on simulated datasets, mock communities, and a real anaerobic digester sludge metagenome. Across diverse similarity and coverage conditions, MADRe consistently improves precision by reducing false-positive strain detections. MADRe's design allows users to apply either the database reduction or read classification step individually. Using only the read classification step shows results on par with other tested tools. MADRe is open source and publicly available at https://github.com/lbcb-sci/MADRe.}, }
@article {pmid41871943, year = {2026}, author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB}, title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336675}, pmid = {41871943}, issn = {1468-3288}, abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.
OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.
DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.
RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.
CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.}, }
@article {pmid41871945, year = {2026}, author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT}, title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337436}, pmid = {41871945}, issn = {1468-3288}, abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.
OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.
DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.
RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.
CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.}, }
@article {pmid41872229, year = {2026}, author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q}, title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71095-7}, pmid = {41872229}, issn = {2041-1723}, abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.}, }
@article {pmid41872577, year = {2026}, author = {Shan, X and Cao, K and Jeckel, H and Alcalde, RE and Trindade, IB and Kwiecinski, JV and Newman, DK}, title = {Drought drives elevated antibiotic resistance across soils.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41872577}, issn = {2058-5276}, support = {2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2209379//National Science Foundation (NSF)/ ; ALTF 191-2023//European Molecular Biology Organization (EMBO)/ ; }, abstract = {Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.}, }
@article {pmid41872600, year = {2026}, author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E}, title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41872600}, issn = {1546-170X}, abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.}, }
@article {pmid41872963, year = {2026}, author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ}, title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00825-5}, pmid = {41872963}, issn = {1757-4749}, support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; }, }
@article {pmid41874180, year = {2026}, author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV}, title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0264825}, doi = {10.1128/spectrum.02648-25}, pmid = {41874180}, issn = {2165-0497}, abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.}, }
@article {pmid41874256, year = {2026}, author = {Lam, WKJ and Chan, KKP and Wang, G and Lai, CKC and Kang, G and Chan, C and Leung, ACY and Wong, NHL and Tso, CSN and Chow, KM and Ramakrishnan, S and Wong, KT and Lau, CHY and Ng, JKC and Lo, RLP and Yip, WH and Ngai, JCL and To, KW and Tse, IOL and Cheng, SH and Shang, H and Chan, KW and Lai, A and Chan, CML and Lee, VCT and Malki, Y and Choy, LYL and Ma, ML and Zhou, Q and Yu, SCY and Jiang, P and Ko, FWS and Chan, KCA and Hui, DSC and Lee, YCG and Lo, YMD}, title = {Sequencing of Pleural Fluid and Plasma for Tuberculous Pleuritis.}, journal = {NEJM evidence}, volume = {5}, number = {4}, pages = {EVIDoa2500237}, doi = {10.1056/EVIDoa2500237}, pmid = {41874256}, issn = {2766-5526}, mesh = {Humans ; *Tuberculosis, Pleural/diagnosis/microbiology/blood ; Male ; Female ; Middle Aged ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Pleural Effusion/microbiology ; *DNA, Bacterial/analysis ; Prospective Studies ; Sensitivity and Specificity ; Aged ; Adult ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The laboratory diagnosis of tuberculous pleuritis (TBP) is hindered by the paucibacillary nature of Mycobacterium tuberculosis in the pleural space, resulting in low sensitivity of microbiological culture and polymerase chain reaction-based analyses on pleural fluid. The use of metagenomic next-generation sequencing for diagnosing TBP may be limited by the background noise of DNA from nontuberculous mycobacteria.
METHODS: We performed targeted sequencing to analyze M. tuberculosis DNA in paired pleural fluid and plasma from prospectively enrolled consecutive patients with new-onset pleural effusion. We used a bioinformatics alignment algorithm to the M. tuberculosis genome that was masked for regions with high sequence similarity to nontuberculous mycobacteria. Our primary outcome was a comparison of diagnostic sensitivity between M. tuberculosis sequencing as described above and culture using McNemar's test.
RESULTS: Among the included 329 patients with pleural effusion, 34 patients with TBP were identified. Targeted sequencing detected M. tuberculosis DNA fragments in the pleural fluid of all TBP cases (median, 267.6 reads per 10 million [RP10M]; interquartile range [IQR], 30.8-2644.3) but absent in 288 out of 295 (97.6%) non-TBP samples (median, 0 RP10M; IQR, 0-0). Targeted sequencing of pleural fluid achieved a sensitivity of 97.1% for TBP detection at a cutoff of 2 RP10M, in contrast to 47.1% by M. tuberculosis culture (P<0.001, McNemar's test). Sequencing yielded an area-under-the-curve value of 0.9996 (95% confidence interval, 0.9988-1.0000) for differentiating TBP and non-TBP. Plasma analysis by targeted sequencing with the same alignment algorithm reported an area-under-the-curve value of 0.9475 (95% confidence interval, 0.8929-1.0000).
CONCLUSIONS: Targeted sequencing of pleural fluid with selectively masked M. tuberculosis genomic alignment accurately diagnosed TBP and outperformed conventional diagnostic tests. (Supported by InnoHK and the Hong Kong Tuberculosis, Chest and Heart Diseases Association; ClinicalTrials.gov number, NCT05397730.).}, }
@article {pmid41874416, year = {2026}, author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI}, title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.}, journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {}, number = {}, pages = {}, doi = {10.1093/ntr/ntag057}, pmid = {41874416}, issn = {1469-994X}, abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.
METHODS: We used osmotic minipumps as an application of chronic nicotine for 15 days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24 h and 1 week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.
RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24 h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.
CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.}, }
@article {pmid41874421, year = {2026}, author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X}, title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag066}, pmid = {41874421}, issn = {1751-7370}, abstract = {The biofilm colonizing plastic debris, termed 'the plastisphere', is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.}, }
@article {pmid41874457, year = {2026}, author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP}, title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00291.2025}, pmid = {41874457}, issn = {1522-1555}, support = {W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically-active men were randomized to receive 200mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ~2000 kcal/d SED. Multi-omic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.}, }
@article {pmid41874663, year = {2026}, author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C}, title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02742-1}, pmid = {41874663}, issn = {1432-184X}, support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; }, }
@article {pmid41874734, year = {2026}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM}, title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41874734}, issn = {1573-0972}, abstract = {UNLABELLED: This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04902-4.}, }
@article {pmid41874898, year = {2026}, author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM}, title = {Protective holobiome promotes strawberry tolerance of biotic stresses.}, journal = {Stress biology}, volume = {6}, number = {1}, pages = {}, pmid = {41874898}, issn = {2731-0450}, support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; }, abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.}, }
@article {pmid41874931, year = {2026}, author = {Gong, K and Xie, Z and Zhang, P and Xu, J and Huang, J and Li, X and Huang, L}, title = {Limosilactobacillus reuteri LR-99 Modulates Gut Microbiota and Core Symptoms in Children with Autism Spectrum Disorder: A Single-arm Pilot Study.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41874931}, issn = {1867-1314}, support = {3502Z202372073//Xiamen Natural Science Foundation of China/ ; }, }
@article {pmid41875072, year = {2026}, author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT}, title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70127}, pmid = {41875072}, issn = {1755-0998}, support = {LP190100555//Australia Research Council Linkage Project/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; }, abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.}, }
@article {pmid41875156, year = {2026}, author = {Shen, LQ and Wang, L and Yao, Z and Lin, D and Ye, YQ and Zhang, WR and Ye, M and Sun, MM and Du, S and Wu, D and O'Connor, P and Zhu, D}, title = {Phages drive the dissemination of antibiotic resistance genes by facilitating host adaptation to heavy metal stress.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2535653123}, doi = {10.1073/pnas.2535653123}, pmid = {41875156}, issn = {1091-6490}, support = {22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; }, mesh = {*Metals, Heavy/toxicity/metabolism ; *Bacteriophages/genetics/physiology ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Adaptation, Physiological/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/virology/drug effects ; Stress, Physiological ; Genes, Bacterial ; China ; Gene Transfer, Horizontal ; }, abstract = {Heavy metals are increasingly recognized as major drivers of antibiotic resistance gene (ARG) dissemination in soil ecosystems. However, the role of phages in heavy metal-driven ARG dissemination and the underlying mechanisms remain poorly understood. Here, through integrative metagenomic, viromics, and metabolomic analyses of paddy soils across China, we reveal that soil phages promote ARG dissemination under heavy metal stress, likely through two potential mechanisms. First, phage-encoded auxiliary metabolic genes (AMGs) reprogram host metabolism to enhance bacterial survival and adaptation, thereby facilitating the cotransfer of adjacent ARGs and indirectly promoting horizontal dissemination. Second, phage-encoded heavy metal detoxification genes (HDGs) directly mediate metal detoxification, driving the cotransfer of neighboring ARG fragments and inducing lipid peroxidation-associated increases in membrane permeability, which collectively enhance ARG mobilization. We further identify a significant enrichment of lysogenic phages coharboring ARGs with AMGs or HDGs (AMG-ARG and HDG-ARG fragments), underscoring their contribution to ARG dissemination. Phage transplantation experiments confirm that elevated heavy metal stress triggers lysogenic phage-mediated ARG transduction to bacterial hosts. Cumulatively, our experiments highlight the pivotal role of phages in mediating ARG transfer under heavy metal pressure and underscore the necessity of incorporating phage dynamics into ARG risk assessments.}, }
@article {pmid41875508, year = {2026}, author = {Estrada, CSD and de Oliveira, OA and Lopes, TAC and Maria, CRC and Avelino-Alves, D and Lima, M and Vidal, LM and de Siqueira Campos, L and Dias, GM and Thompson, C and Tschoeke, D and Thompson, F}, title = {Rhodolith metagenome diversity shifts across the Great Amazon System.}, journal = {The Science of the total environment}, volume = {1027}, number = {}, pages = {181652}, doi = {10.1016/j.scitotenv.2026.181652}, pmid = {41875508}, issn = {1879-1026}, abstract = {Rhodolith-forming coralline algae in the Great Amazon Reef System (GARS) occur under strong light and redox gradients imposed by the Amazon River plume. We tested whether a conserved microbial and metabolic core persists across sectors while functions reorganize with local conditions. We conducted shotgun metagenomics on rhodolith holobionts collected in the South, Central, and North sectors and profiled taxonomic composition and pathway markers (KEGG/SEED; METABOLIC). Bacteria dominated the holobiont, with Proteobacteria, Chloroflexi, and Bacteroidetes prevailing, and Thaumarchaeota as the main archaeal lineage. Functional profiles showed structured not random variation among sectors. In the South, high water transparency supported oxygenic phototrophy (psa/psb, rbcL/S; phycobiliproteins) and stronger coupling between carbon fixation and respiration. The Central sector displayed a transitional configuration combining oxygenic and anoxygenic phototrophy (pufL/M; bch genes) with co-occurring nitrification-denitrification (amoA, nxrAB, nirK, nosZ), indicating tight NS cycling. The North was enriched in sulfur redox pathways linked to suboxic microzones, with sulfate-reducing and sulfur-oxidizing lineages and contributions from methanogenic archaea. Across sectors, high diversity and functional redundancy likely underpin holobiont persistence in mesophotic settings. Our results indicate a resilient, sector-specific reorganization of rhodolith-associated microbiomes along plume-driven gradients, with implications for biogenic calcification and biogeochemical stability under climate change and ocean acidification scenarios.}, }
@article {pmid41875555, year = {2026}, author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S}, title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120059}, doi = {10.1016/j.ecoenv.2026.120059}, pmid = {41875555}, issn = {1090-2414}, abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.}, }
@article {pmid41875615, year = {2026}, author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J}, title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.}, journal = {Marine genomics}, volume = {86}, number = {}, pages = {101245}, doi = {10.1016/j.margen.2026.101245}, pmid = {41875615}, issn = {1876-7478}, abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.}, }
@article {pmid41875710, year = {2026}, author = {Gadoin, E and Massot, M and Callens, M and Arnout, P and Bedhomme, S and Rajkovic, A}, title = {Shotgun metagenomic profiling reveals a high diversity of taxa and genes within biofilms formed on microplastics incubated in urbanised aquatic ecosystems.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119569}, doi = {10.1016/j.marpolbul.2026.119569}, pmid = {41875710}, issn = {1879-3363}, abstract = {Microplastics (MPs) are ubiquitous in aquatic ecosystems, where they are colonized by microbial communities, called the plastisphere. Of great concern is the detection of potential pathogens and antimicrobial resistance genes (ARG) in the plastisphere, which might be transported across ecosystems through MPs drifting. We used shotgun metagenomic profiling to assess taxa diversity, ARG and virulence genes (VG), within biofilm formed on polypropylene (PP) particles incubated in situ in five locations, following an anthropic gradient around Ostend (Belgium). Our results demonstrated significant variability of the plastisphere across incubation sites, but not between PP and control glass beads. Potential pathogenic bacteria (PPB) represented about 7% of bacterial reads within biofilms and VG were mainly involved in nutrition and adherence. Using dqPCR results to normalize metagenomic reads, we demonstrated a selective enrichment of ARG and VG in biofilms, while these were less abundant but more diverse in surrounding water. These findings highlight the presence of PPB, ARG and VG across all sites, likely driven by anthropogenic pressures. Although no substrate-specific effect was detected, the ability of PP particles to act as microbial reservoirs, coupled with their high mobility, reinforces concerns about their potential role in the transport and dissemination of microbial hazards.}, }
@article {pmid41875745, year = {2026}, author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J}, title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.}, journal = {Water research}, volume = {297}, number = {}, pages = {125768}, doi = {10.1016/j.watres.2026.125768}, pmid = {41875745}, issn = {1879-2448}, abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.}, }
@article {pmid41875962, year = {2026}, author = {Rector, A and Karataş, M and Bloemen, M and De Coninck, L and Swinnen, J and Close, L and Thijssen, M and Pourkarim, MR and Matthijnssens, J and Desmet, S and Van Ranst, M and Johnson, MC and Wollants, E}, title = {Airplane wastewater as a gateway for pathogen surveillance.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {140}, number = {}, pages = {105930}, doi = {10.1016/j.meegid.2026.105930}, pmid = {41875962}, issn = {1567-7257}, abstract = {BACKGROUND: Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility of using wastewater surveillance from airplanes as a method for monitoring SARS-CoV-2 variants and other pathogens entering Belgium.
METHODS: From January to March 2023, in the wake of the COVID pandemic, 32 wastewater samples were collected at Brussels Airport from direct flights originating in Beijing, China. We applied various qPCR panels and sequencing methods, including hybrid-capture metagenomic sequencing (Twist Bioscience) targeting more than fifteen thousand strains of known human and animal viruses.
RESULTS: Nineteen out of 32 samples tested positive for SARS-CoV-2. Various other pathogens, including enterovirus/rhinovirus, adenovirus, norovirus, adenovirus 40/41, and multiple clinically relevant bacteria, were identified using respiratory and gastrointestinal qPCR panels. In 7 samples, SARS-CoV-2 variants could be determined, belonging to known lineages BA4/BA5, BA4.6/BF7, and XBB. Moreover, hybrid-capture approach allowed us to recover complete genomes of viruses from families Polyomaviridae, Papillomaviridae, Herpesviridae as well as Aichivirus A and Hepatitis B virus.
CONCLUSION: This pilot project demonstrates the feasibility of detecting SARS-CoV-2 and its variants in wastewater of commercial airplanes. This method offers a valuable means of obtaining information from regions with limited SARS-CoV-2 genomic surveillance data. Moreover, using a hybrid-capture approach, a broad range of viruses of concern can be detected. The implementation of this novel screening approach is promising for enhancing traveler-based surveillance.}, }
@article {pmid41876072, year = {2026}, author = {Shen, Q and Xiong, JQ and Wang, Q and Yang, L and Shen, Z and Lei, Z and Ru, S}, title = {Cyanobacteria-driven morphology and adaptive microbial succession: Resilience mechanisms in algal-bacterial granular sludge under tripartite stress.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134481}, doi = {10.1016/j.biortech.2026.134481}, pmid = {41876072}, issn = {1873-2976}, abstract = {Algal-bacterial granular sludge (ABGS) is a promising wastewater treatment technology, yet its practical application is constrained by its unknown stability under realistic multi-stressor conditions. This work demonstrated that ABGS could withstand combined low temperature (< 15°C), carbon scarcity, and sulfamethoxazole (SMX) exposure (0-100-1000 μg/L) through the defense strategy that integrated morphological, microbial and metabolic adaptations. Metagenomics revealed a metabolic trade-off, characterized by the downregulation of energy-intensive pathways (e.g., oxidative phosphorylation and TCA cycle), and the upregulation of biosynthetic and stress-responsive pathways (e.g., glyoxylate shunt and amino sugar metabolism), redirecting carbon towards extracellular polymeric substances (EPS) production. This was synergized by the protective cyanobacterial surface barrier and reconfigured protein-rich EPS for SMX sequestration. Microbial community restructuring enhanced functional resilience, as exemplified by the shift from Nitrospira to Candidatus Nitrotoga, which sustained stable nitrification. This coordinated adaptation not only enabled the robust removal of COD (> 90%) and NH4[+]-N (> 97%), but also suppressed the proliferation of antibiotic resistance genes (ARGs) under 100 μg/L SMX stress. These findings position ABGS as self-engineering ecosystems that actively modulate microbial community assembly and metabolic networks to remove nutrients and mitigate the dissemination of ARGs.}, }
@article {pmid41876074, year = {2026}, author = {Zhang, Y and Wu, J and Yue, C and Wang, X and Qu, Y and Zhang, X and Sun, Y and Liu, Z and Qu, J and Xu, X}, title = {Enhancing anaerobic digestion of agricultural waste via a stable Fe-Emodin-Biochar composite: Kinetic performance, energy recovery, and metabolic insights.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134463}, doi = {10.1016/j.biortech.2026.134463}, pmid = {41876074}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) efficiency is often constrained by energy transfer in interspecies electron transfer. To address this, a cost-effective electron mediator was engineered by immobilizing industrial-grade Emodin onto an Fe-biochar matrix via one-step hydrothermal synthesis. The optimal composite (Fe/Emodin molar ratio 1.5:1) achieved a 43.3 % increase in cumulative methane yield and shortened the lag phase by 38.1 %. According to biochemical tests, the composite reduced energy barriers on the breakdown of volatile fatty acids, as shown by a 2.2-fold rise in ATP levels and increased expression of Coenzyme F420. A community shift marked by the co-enrichment of Methanothrix and syntrophic bacteria was revealed by metagenomic analysis. A change from energetically constrained hydrogen transfer to pathways mediated by the composite was suggested by the abundance of Type IV pili genes and Cytochrome c genes, which suggested the possible activation of direct interspecies electron transfer (DIET). By utilizing low-cost precursors and overcoming the instability of free mediators, this study offers a scalable biotechnological method for agricultural residue valorization. Furthermore, this approach demonstrates economic viability and potential life-cycle sustainability.}, }
@article {pmid41876075, year = {2026}, author = {Wu, H and Wang, H and Man, S and Yan, Q}, title = {Biogenic FeS Reshapes microbial interactions to regulate acetogenesis in CO2-Fed microbial electrosynthesis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134480}, doi = {10.1016/j.biortech.2026.134480}, pmid = {41876075}, issn = {1873-2976}, abstract = {Inefficient electron transfer and poorly coordinated microbial communities often limit stable CO2-to-acetate conversion in microbial electrosynthesis (MES). Herein, Shewanella oneidensis MR-1 was introduced to induce in situ biogenic FeS formation at the cathode to regulate microbial interactions and enhance acetogenesis. Under the acetogenesis dominant condition (RAT: sludge to MR-1 ratio of 2:1, Fe/S = 5/10 mM, initial MR-1 inoculation), acetate production reached 1330.6 mg L[-1] with the carbon recovery efficiency of 62.9%. Community and metagenomic analyses showed that FeS selectively enriched acetogens and Fe/S transforming microorganisms while restructuring functional pathways related to redox metabolism and energy conservation. Co-occurrence network analysis further revealed that FeS promoted coordinated, function oriented microbial interactions rather than competitive associations. This study highlights the role of biogenic FeS in linking electron transfer with microbial cooperation, providing a mechanistic basis for improving MES performance through community level regulation.}, }
@article {pmid41876513, year = {2026}, author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE}, title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41876513}, issn = {2041-1723}, support = {1026-00159B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Phylogeny ; *Microbial Consortia/genetics ; Methane/metabolism ; Methanosarcina/metabolism/genetics ; Charcoal ; Cytochromes/metabolism/genetics ; Genome, Bacterial ; }, abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.}, }
@article {pmid41876637, year = {2026}, author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K}, title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.}, journal = {Npj mental health research}, volume = {5}, number = {1}, pages = {}, pmid = {41876637}, issn = {2731-4251}, support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; }, abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.}, }
@article {pmid41876857, year = {2026}, author = {Peñuelas, J and Zheng, B and Tariq, A and Sardans, J}, title = {Microbial phosphorus cycling in terrestrial ecosystems.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41876857}, issn = {1740-1534}, abstract = {Phosphorus is an essential yet often limiting macronutrient that shapes primary productivity and microbial activity in terrestrial ecosystems. Unlike carbon and nitrogen cycles, which have gaseous phases, the terrestrial phosphorus cycle is primarily governed by soil biogeochemistry, wherein microorganisms orchestrate key transformations. This Review synthesizes current knowledge of the microbial phosphorus cycle, emphasizing the diverse mechanisms used by bacteria, fungi and archaea to mobilize phosphorus (for example, via phosphatases such as PhoA and PhoD and organic acids such as citrate) and to directly enhance plant phosphorus uptake. We explore the ecological significance of these processes in maintaining soil health, supporting ecosystem productivity and influencing carbon sequestration. We propose the Microbial Phosphorus Adaptive Evolution Theory (MPAET): chronic phosphorus scarcity drives evolutionary and ecological shifts in microbial communities towards higher scavenging investment, polyphosphate handling and lipid remodelling. Furthermore, we examine how environmental factors, land use and climate modulate these shifts (for example, phoD expression increases under phosphorus stress), with cascading effects on ecosystem function and global phosphorus availability. New technologies such as metagenomics, [18]O-phosphate tracing and nanoscale secondary ion mass spectrometry are now revolutionizing our understanding of these dynamics. This Review underscores the critical need to integrate microbial phosphorus cycling into ecosystem models and to develop sustainable strategies for phosphorus smart management. Such approaches are essential for addressing global challenges related to soil degradation, food security and environmental change.}, }
@article {pmid41877267, year = {2026}, author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR}, title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00553-w}, pmid = {41877267}, issn = {2524-4671}, support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; }, abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.}, }
@article {pmid41877288, year = {2026}, author = {Wei, G and Liu, M and Huang, L and Chen, C}, title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00551-y}, pmid = {41877288}, issn = {2524-4671}, support = {32272831//National Natural Science Foundation of China/ ; }, }
@article {pmid41877461, year = {2026}, author = {Tagliabue, A and Furfaro, G and Pallavicini, A and Martino, F and Zane, L and Sattin, E and Valle, G and Piraino, S and Turon, X}, title = {Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70126}, pmid = {41877461}, issn = {1755-0998}, support = {MCIU/AEI/10.13039/501100011033//BlueDNA PID2023-146307OB/ ; CCI 2014IT16M2OP005//Programma Operativo Nazionale Ricerca e Innovazione 2014-2020/ ; ECS00000043//Interconnected Nord-Est Innovation Ecosystem/ ; //European Regional Development Fund/ ; 2020J3W3WC//Italian Ministry of Education, Universities and Research/ ; D33C22000960007//National Recovery and Resilience Plan/ ; C93C22002810006//National Recovery and Resilience Plan/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Animals ; *Geologic Sediments ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; *Seawater ; }, abstract = {This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.}, }
@article {pmid41877907, year = {2026}, author = {Xie, S and Zhang, H and Xie, Y and Liu, F and Ye, S and Liu, X and Lai, Z}, title = {Analysis of the Clinical Features of HSV-2 Encephalitis Confirmed by the mNGS Technique: Insights Derived from Seven Patient Studies.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {567731}, pmid = {41877907}, issn = {1178-6973}, abstract = {BACKGROUND: Herpes simplex virus type 2 (HSV-2) encephalitis is rare in immunocompetent adults. Diagnosis typically depends on cerebrospinal fluid (CSF) polymerase chain reaction (PCR), which has limited sensitivity and potential for false negatives. Metagenomic next-generation sequencing (mNGS) provides unbiased pathogen detection, facilitating rapid HSV-2 identification in CSF and minimizing misdiagnosis risks, especially in atypical cases or immunocompetent individuals. This study examines the diagnostic value of mNGS in a cohort of patients with HSV-2 encephalitis presenting atypically.
METHODS: A retrospective analysis was performed on patients diagnosed with HSV-2 encephalitis using mNGS at our institution between January 2022 and January 2025. Clinical characteristics, ancillary test results, and patient outcomes were analyzed to evaluate the diagnostic value of mNGS.
RESULTS: Seven patients (2 males, 28.57%; 5 females, 71.43%) with a mean age of 33.57 years were included; one had pre-existing immunodeficiency (14.28%). Most presented atypical symptoms; six treated within three days fully recovered, while one with delayed treatment died. Mean follow-up was 14.71 ± 5.82 months. Higher viral sequence counts correlated with worse outcomes. Initial CSF analysis showed normal cell counts in one patient; all exhibited lymphocytic pleocytosis and elevated protein levels.
CONCLUSION: This study contributes to the limited clinical data on adult HSV-2 encephalitis by summarizing clinical manifestations and treatment outcomes, thereby informing improved diagnostic and management strategies. It also highlights the prognostic importance of early diagnosis and immune status assessment through the application of mNGS.}, }
@article {pmid41877920, year = {2026}, author = {Zeng, F and Zhu, T and Chen, X and Huang, K and Liu, L and Wang, G and Mai, J and Zhang, S}, title = {Gut microbiota and metabolic status during pregnancy in captive Asian elephants.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1749490}, pmid = {41877920}, issn = {2297-1769}, abstract = {BACKGROUND: The gut microbiota is regarded as one of the key factors regulating host health. The gut microbiota and its connection to fecal metabolites are crucial for supporting fetal development and ensuring maternal health during reproductive stages. Although studies have examined Asian elephants, the composition and function of the gut microbiota in pregnant and non-pregnant captive Asian elephants have not been reported.
METHODS: We compared the fecal microbiota and fecal metabolites of pregnant (G1), non-pregnant (never gotten pregnant after reaching sexual maturity, G2), and subadult (G3) captive Asian elephants using metagenomic sequencing and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics.
RESULTS: We found significant differences in the gut microbiota among the G1, G2, and G3 groups. The phylum Bacteroidetes showed notable differences between G1 and G2. The analysis of fecal metabolomics revealed significant differences in 49 metabolites between G1 and G2, of which 25 were upregulated and 24 were downregulated. These results suggested significant differences in the composition of gut microbiota and fecal metabolites during reproductive stages, while gut microbial diversity remained stable. These findings inform our ongoing research on the potential health conditions of captive Asian elephants, with the aim of better understanding the role of the gut microbiota in reproductive regulation.}, }
@article {pmid41877937, year = {2025}, author = {Zhang, M and Pak, H and King, SD and Zuniga, AA and Hassan, YA and King, MD}, title = {Mitigating airborne pathogen risks in a full-scale meat processing facility.}, journal = {Total environment microbiology}, volume = {1}, number = {3}, pages = {}, pmid = {41877937}, issn = {3050-6417}, support = {R21 AI169046/AI/NIAID NIH HHS/United States ; }, abstract = {Foodborne illnesses caused by Shiga toxin-producing Escherichia coli (STEC) and Salmonella represent a major public health concern, particularly in meat processing facilities where bioaerosols generated during processes like carcass spraying and dehiding can lead to contamination. In this study, we assessed airborne concentrations of STEC and Salmonella at multiple locations within a full-scale meat processing facility using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Additionally, we utilized computational fluid dynamics (CFD) simulations to model airflow within the facility and evaluated the effectiveness of air curtains in mitigating the transfer of bioaerosols between high-risk (dehiding and tripe) and low-risk (chiller and fabrication) areas. qPCR results showed that pathogen concentrations in the dehiding rooms were 126 GCN/m[3] for STEC and 105 GCN/m[3] for Salmonella during spring, with levels rising significantly in summer (2198 GCN/m[3] for STEC and 1799 GCN/m[3] for Salmonella). Simulated airflow patterns revealed that entrained bioaerosols could be transported from unclean to clean areas, increasing the risk of cross-contamination. The use of air curtains effectively reduced this spread by creating barriers between high- and low-risk areas. Our findings suggest that bacterial survivability and aerosolization was enhanced in summer, highlighting the critical role of environmental factors and airflow management in controlling contamination risks. This study demonstrates the value of integrating experimental data with CFD simulations to assess pathogen spread and identify effective mitigation strategies in meat processing facilities.}, }
@article {pmid41878086, year = {2026}, author = {Luo, D and Jia, S and He, W and Fan, Z and Yin, W}, title = {Periplaneta americana Powder Alleviates Neuropathic Pain and is Associated with Gut Microbiota Changes in Rats.}, journal = {Journal of pain research}, volume = {19}, number = {}, pages = {564911}, pmid = {41878086}, issn = {1178-7090}, abstract = {BACKGROUND: This study aims to evaluate the therapeutic potential of Periplaneta americana powder (PAP) in alleviating neuropathic pain in a rat model of sciatic nerve injury induced by chronic constriction injury (CCI), and to systematically analyze its effects on the composition and structure of the gut microbiota during the intervention process, with the goal of elucidating the mechanisms underlying the analgesic effects of PAP.
METHODS: A rat model of CCI was established (n = 12 per group), and PAP was administered for intervention. The analgesic effects were evaluated using mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL). Pathological changes in the spinal cord and colon tissues were examined via hematoxylin-eosin (HE) staining, and the expression of the astrocyte marker glial fibrillary acidic protein (GFAP) in the spinal cord was detected by immunohistochemistry. The expression levels of pro-inflammatory cytokines TNF-α and IL-1β in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were collected at the endpoint of treatment for metagenomic sequencing and analysis.
RESULTS: After PAP treatment, behavioral tests in CCI rats showed a significant increase in MWT and TWL (P < 0.05). Histological analysis revealed marked alleviation of spinal cord and colon tissue damage as well as reduced inflammatory cell infiltration (P < 0.05). Immunohistochemistry further demonstrated a significant decrease in GFAP expression in the spinal cord (P < 0.05). ELISA results showed that the expression levels of TNF-α and IL-1β in spinal cord tissues were significantly decreased (P < 0.05).Metagenomic analysis indicated that PAP reshaped the gut microbiota structure, increased the abundance of SCFA-producing bacteria, and was associated with the butyrate metabolism pathway.
CONCLUSION: This study indicates that PAP can significantly alleviate neuropathic pain in a rat model of sciatic nerve chronic constriction injury (CCI) and suppress the central inflammatory response.Notably, this effect is accompanied by changes in the gut microbiota, particularly characterized by a significant alteration in the abundance of short-chain fatty acid-producing bacteria. These results suggest that PAP not only possesses substantial analgesic effects but may also mediate the intervention of CCI-induced neuropathic pain by regulating the structure of the gut microbiota.}, }
@article {pmid41878266, year = {2026}, author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B}, title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1598786}, pmid = {41878266}, issn = {2235-2988}, mesh = {Humans ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Metagenomics ; *Virome ; *Bacteriophages/genetics/isolation & purification/classification ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Feces/microbiology/virology ; Enterococcus faecalis ; Gastrointestinal Tract/microbiology ; }, abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.
METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.
RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).
DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.}, }
@article {pmid41878461, year = {2026}, author = {Li, Z and Zhang, Y and Xu, D and Huang, B}, title = {Diagnostic and therapeutic journey of infantile endobronchial tuberculosis: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1778717}, pmid = {41878461}, issn = {2296-2360}, abstract = {BACKGROUND: Endobronchial tuberculosis (EBTB) in infants is rare and is often overlooked because of nonspecific clinical manifestations. Coexisting primary immunodeficiency and opportunistic infections further increased diagnostic and therapeutic complexity.
CASE PRESENTATION: We reported a male infant aged 40 days who presented with fever and mild cough. Chest imaging showed progressive bilateral nodular and granulomatous lesions despite broad-spectrum antibacterial therapy. Microbiological evaluation revealed positive T-SPOT.TB and GeneXpert MTB/RIF results from bronchoalveolar lavage fluid (BALF), while metagenomic next-generation sequencing identified Pneumocystis jirovecii. Genetic testing demonstrated a heterozygous IKZF1 mutation, consistent with underlying immunodeficiency. Serial bronchoscopies confirmed necrotizing endobronchial tuberculosis with airway stenosis. The patient received standard anti-tuberculosis therapy, systemic corticosteroids, trimethoprim-sulfamethoxazole, intravenous immunoglobulin, and repeated bronchoscopic intraluminal drug delivery. Clinical and radiological remission was achieved, with no airway sequelae during 18-month follow-up.
CONCLUSIONS: This case highlighted the unique coexistence of infantile EBTB, IKZF1-related immunodeficiency, and P. jirovecii coinfection. Early bronchoscopy played a pivotal diagnostic and therapeutic role. Repeated intraluminal bronchoscopic therapy combined with systemic treatment might prevent irreversible airway damage in severe pediatric EBTB.}, }
@article {pmid41878469, year = {2026}, author = {de Azevedo, PS and Vedovatto, MM and de Freitas, PCG and Luz, RBS and Streit, RSA and Persinoti, GF}, title = {parsomics: a data-driven framework for metagenomics data integration powered by a local relational database.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag049}, pmid = {41878469}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomics enables the analysis of complex microbial communities directly from environmental samples, resulting in massive datasets that are processed using multiple tools and workflows. Data integration is key for metagenomics research, however, challenges in data organization and management locally remain open in existing workflows.
RESULTS: We present parsomics, a lightweight and extensible data management tool designed for efficient local storage, organization, and integration of metagenomic analysis results. Built upon PostgreSQL and implemented in Python, parsomics leverages a user-defined configuration file to automatically construct a relational database tailored to metagenomics-based data. It is user-friendly, easy to deploy, and implements modular plugin-based extensions to support diverse data types and outputs. parsomics can be installed in every major GNU/Linux environment and currently focuses on prokaryotic metagenomics analysis.
parsomics is an open-source project and its source code is available at https://gitlab.com/parsomics under the GPLv3 license. Comprehensive documentation can be found at https://parsomics.org and https://api.parsomics.org.}, }
@article {pmid41878742, year = {2026}, author = {Armijo-Godoy, G and Cottet, L and Rupayan, A and Carrasco, M and Levicoy, D and Salvo-Garrido, H}, title = {Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1759558}, pmid = {41878742}, issn = {1664-302X}, abstract = {BACKGROUND: Members of the genus Labrys are widely distributed in soil and plant-associated environments, yet their ecological roles and functional contributions within plant-associated microbiomes remain poorly understood. Labrys methylaminiphilus strain La1 was isolated from nodules of Lupinus luteus growing in acidic soils of southern Chile, providing an opportunity to investigate strain-level traits relevant to plant-microbe interactions under environmental stress.
METHODS: Strain La1 was characterized using physiological and biochemical, chemotaxonomic, and genomic approaches, including whole-genome sequencing and comparative genomics. Functional traits related to plant interaction were assessed through in vitro assays for indole-3-acetic acid (IAA) production, antifungal activity against lupine pathogens, and in planta experiments evaluating plant growth under salinity and osmotic stress. The ecological distribution of closely related taxa was inferred from screening of publicly available environmental microbiomes using protologger pipeline.
RESULTS: Although strain La1 showed high genomic similarity to L. methylaminiphilus JLW10[T], it exhibited distinct phenotypic, metabolic, and ecological features. These included tolerance to acidic and moderately saline conditions, utilization of rhizosphere-associated carbon sources, and a fatty acid profile consistent with adaptation to terrestrial environments. Genomic analyses revealed genes related to stress tolerance, exopolysaccharide biosynthesis, carbohydrate-active enzymes, siderophore production, IAA synthesis, and non-ribosomal peptide synthetases. Consistent with these traits, La1 inhibited the growth of Colletotrichum lupini and Pleiochaeta setosa and significantly enhanced L. luteus biomass under osmotic and salinity stress. Metagenomic screening indicated that sequences closely related to La1 are predominantly associated with soil, rhizosphere, and plant-associated habitats.
CONCLUSION: This study demonstrates that strain La1 represents a functionally versatile and ecologically specialized lineage within L. methylaminiphilus, contributing traits relevant to plant-associated microbiomes in acidic soils. This integrated functional and ecological evidence supports the designation of Labrys methylaminiphilus subsp. lupini subsp. nov. and highlights the relevance of strain-level analyses for understanding plant-microbe interactions.}, }
@article {pmid41878750, year = {2026}, author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J}, title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.}, journal = {Journal of asthma and allergy}, volume = {19}, number = {}, pages = {464532}, pmid = {41878750}, issn = {1178-6965}, abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.
METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24 healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.
RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.
CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.}, }
@article {pmid41878990, year = {2026}, author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B}, title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17444}, doi = {10.1002/advs.202517444}, pmid = {41878990}, issn = {2198-3844}, support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; }, abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.}, }
@article {pmid41879294, year = {2026}, author = {Liu, Y and Zhao, X and Gao, J and Xu, K}, title = {Therapeutic Evolution and Outcomes in EGPA Complicated by Diffuse Alveolar Hemorrhage: case-based review.}, journal = {Modern rheumatology case reports}, volume = {}, number = {}, pages = {}, doi = {10.1093/mrcr/rxag028}, pmid = {41879294}, issn = {2472-5625}, abstract = {BACKGROUND: Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare systemic vasculitis characterized by asthma, eosinophilia, and multi-organ involvement. Diffuse alveolar hemorrhage (DAH) is an uncommon but life-threatening pulmonary complication in EGPA.
CASE PRESENTATION: We report a 49-year-old previously healthy woman who presented initially with asthma-like symptoms and later developed fever, hemoptysis, cutaneous purpura, and periorbital edema. Laboratory evaluation revealed marked eosinophilia, anemia, elevated inflammatory markers, and strongly positive MPO-ANCA. Bronchoalveolar lavage fluid (BALF) was hemorrhagic and contained hemosiderin-laden macrophages, indicating DAH. Broad-spectrum antibiotics were empirically initiated but discontinued after metagenomic next-generation sequencing (mNGS) of BALF excluded infection. Bone marrow biopsy showed eosinophilic hyperplasia without clonal mutations. A diagnosis of MPO-ANCA positive EGPA with DAH was established. The patient received pulse methylprednisolone, prednisone, intravenous immunoglobulin, mepolizumab, and rituximab. Clinical symptoms improved rapidly, and radiological signs of alveolar hemorrhage nearly resolved within days.
CONCLUSION: Our case illustrates that integration of rituximab and mepolizumab with corticosteroids can achieve rapid remission and steroid sparing in EGPA-DAH. While evidence remains limited to case reports and small series, targeted biologics may fundamentally improve outcomes in this high-risk subset. Prospective studies are warranted to define optimal treatment strategies.}, }
@article {pmid41879323, year = {2026}, author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM}, title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0315525}, doi = {10.1128/spectrum.03155-25}, pmid = {41879323}, issn = {2165-0497}, abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.}, }
@article {pmid41879886, year = {2026}, author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F}, title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {41879886}, issn = {1869-1889}, abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.}, }
@article {pmid41880538, year = {2026}, author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, Á}, title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.}, journal = {Medical mycology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mmy/myag026}, pmid = {41880538}, issn = {1460-2709}, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, Gardnerella swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed greater abundance of Lactobacillus crispatus and Lactobacillus gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system (PTS), fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.}, }
@article {pmid41880703, year = {2026}, author = {Liang, H and Liu, J and Huang, Y and Wang, Z and Wang, J and Liu, H and Zhang, L and Peng, Y}, title = {Engineering the anammox pathway in a full-scale AOA process for industrial wastewater treatment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125793}, doi = {10.1016/j.watres.2026.125793}, pmid = {41880703}, issn = {1879-2448}, abstract = {The anammox process holds significant potential for municipal wastewater treatment, yet its full-scale application in industrial wastewater treatment plants (IWTP), particularly within endogenous denitrification-based processes, remains challenging. This study demonstrates the successful establishment of the anammox pathway in a full-scale (16,000 m[3]/d) anaerobic-aerobic-anoxic (AOA) process IWTP by implementing a synergistic control strategy that integrates low dissolved oxygen (DO: 0.5 - 1.4 mg/L) with residual ammonia (1.6 - 2.9 mg/L) at the aerobic outlet. During 450 days of operation, the system achieved stable and advanced nitrogen removal, with effluent NH4[+]-N and total nitrogen (TN) averaging only 0.2 mg/L and 5.7 mg/L, respectively. Metagenomic and isotope tracing analyses identified that the anoxic zone biofilm as a functional hotspot for anammox, where the relative abundance of anammox bacteria (AnAOB), predominantly Candidatus Brocadia, was significantly enriched to 0.074%. This community contributed to 36.7% of the TN removal via dual pathways coupling anammox with endogenous and exogenous partial denitrification. Economically, the incorporation of anammox reduced aerobic zone aeration energy consumption by 18.2% and decreased external carbon dosage by 44.4%. This work provides a pioneering demonstration of anammox under complex water quality conditions and offers a viable technological route toward low-carbon wastewater treatment.}, }
@article {pmid41881056, year = {2026}, author = {Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Fakhruddin, KS and Samaranayake, L and Shotelersuk, V and Porntaveetus, T}, title = {Metagenome and Metabolic Pathways in Plaque Biofilms of Thai ELANE-Associated Neutropenic Patients: An Original Study and Scoping Review.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0046-1818559}, pmid = {41881056}, issn = {1305-7456}, abstract = {Congenital neutropenia, particularly ELANE-associated forms, is associated with recurrent oral infections and aggressive periodontitis. While ELANE deficiency compromises oral health, its relationship to plaque biofilm ecology and metabolic function remains unclear. The oral microbiome-metabolome interplay in this condition remains largely uncharacterized globally. Here, we address this gap by characterizing the dental plaque metagenome and inferred metabolic pathways in a defined cohort of Thai neutropenia patients.In this exploratory study, we sequenced dental plaque samples from a defined cohort of nine individuals: three patients with severe congenital neutropenia or cyclic neutropenia (CyN) with confirmed ELANE variants, and six from age- and gender-matched healthy controls. Shotgun metagenomics was used for genomic analysis, followed by comprehensive microbiota examination. Subsequently, MetaCyc, a curated database, was used for in silico analysis and comparisons of the predicted functional pathways between the test and control plaque biofilms.The principal coordinate analysis plot and heat map revealed distinct segregation of microbial profiles between the patients and control groups. A significant variation in the proportions of the five core phyla was noted in patients and controls. Two commensal species, Aggregatibacter sp oral taxon 458 and Leptotrichia sp oral taxon 212, were enriched in the controls. Conversely, four species were significantly enriched in the patients, Selenomonas flueggei, Streptococcus milleri, Kingella oralis, and Actinobaculum sp oral taxon 183; the latter being notably elevated across all patients. The MetaCyc in silico analyses suggested predicted enrichment of functional pathways associated with inflammation and oxidative stress in patients, including L-methionine biosynthesis IV, formaldehyde assimilation III, L-rhamnose degradation, and the superpathway of (R,R)-butanediol biosynthesis pathways.Our study advances the understanding of ELANE-associated periodontitis by moving beyond descriptive microbiota analysis to suggest potential associations between host immune deficiency, microbial dysbiosis, and the microbiota-associated metabolic pathway alterations. These findings provide preliminary insights into targeted periodontal care in neutropenic patients, though further validation in larger cohorts is required.}, }
@article {pmid41881128, year = {2026}, author = {Song, Z and Yang, J and Zhang, L and Peng, Y}, title = {Photocatalytic Fe3O4@CDs Drives Nitrite-Independent extracellular respiration of anammox via efficient bidirectional electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134489}, doi = {10.1016/j.biortech.2026.134489}, pmid = {41881128}, issn = {1873-2976}, abstract = {Anaerobic ammonium oxidation (Anammox) process relying on extracellular electron transfer (EET) overcomes nitrite scarcity in practical wastewater, but inefficient EET rate constrains nitrogen removal. Herein, Fe3O4 with carbon dot shell (Fe3O4@CDs) was self-assembled with anammox bacterial as a photocatalytic hybrid. Building on bacteria inward uptake of photogenerated electrons from CDs and outward transfer of respiratory electrons to Fe3O4, a bidirectional electron pathway was established firstly. This novel route achieved efficient nitrite-independent Anammox, enabling direct and rapid removal of 80 mg/L NH4[+]-N. To elucidate efficient nitrogen removal essence, metagenomics was employed to reveal photogenerated electrons fate and their mediated nitrogen metabolism mechanism. Results showed that, following assembly via -P-O bonds, bacteria internalized CDs photogenerated electrons (0.82 µA/cm) into menaquinone (MQ) pool. This influx activated energy-generation route constructed by bc1 and Rnf enzymes, increasing intracellular ATP level by 3.36---6.51-fold. Consequently, energy drove electrons pumping from MQ pool to cytochrome c, followed by transport outward via CDs, pili and flavin, amplifying electrons eflux by 1.77-fold. Such efflux generated MQ pool electron vacancies, which were efficiently replenished by electrons from hydrazine synthase- and hydrazine dehydrogenase-catalyzed NH4[+]-N oxidation to N2 without nitrite. Underpinned by the photogenerated electron-driven EET process, Anammox bacteria was enriched from 25.26% to 48.02%, thus sustaining a total nitrogen removal efficiency of > 97% for over 80 days-far exceeding the performance of existing system. This technology provides an efficient and sustainable theoretical framework for the application of anammox in practical wastewater treatment.}, }
@article {pmid41881328, year = {2026}, author = {Zhang, N and Wang, J and Yang, S and Liu, F}, title = {Biogeochemical and genomic drivers of groundwater DNRA: predictability of ammonium accumulation risk.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {397}, number = {}, pages = {128006}, doi = {10.1016/j.envpol.2026.128006}, pmid = {41881328}, issn = {1873-6424}, abstract = {Widespread ammonium (NH4[+]-N) contamination in groundwater, with local concentrations exceeding 20 mg/L, challenges traditional nitrogen removal, which is dominated by denitrification. Dissimilatory nitrate reduction to ammonium (DNRA), a nitrogen-retaining pathway, competes with denitrification. However, the environmental conditions that promote DNRA in aquifers and its quantitative contribution to NH4[+]-N loading remain critical knowledge gaps in groundwater nitrogen cycling research. We investigated how C/N ratios, Fe[2+] concentrations, initial NO3[-]-N, hydrochemical types, total dissolved solids (TDS), and pH influenced DNRA efficiency and its competition with denitrification. We found that DNRA efficiency peaked in organic-rich aquifers (15.70-26.69%) and was minimum in industrially and agriculturally contaminated groundwater (0.71%). High Fe[2][+], high initial NO3[-]-N, and HCO3[-]-type environments markedly promoted DNRA, whereas Cl[-]-type water inhibited it. Competition analysis revealed that elevated C/N ratios, Fe[2+], and TDS increased the relative contribution of DNRA to nitrate reduction. Metagenomic analysis further demonstrated that high C/N ratios and Fe[2+]-rich conditions promoted DNRA dominance via selective enrichment of Enterobacteriaceae carrying the abundant nrfA gene. Conversely, high mineralization and Na-Cl water types drastically reduced DNRA efficiency by suppressing the expression of key functional genes. Furthermore, under intermittent nitrate input, NH4[+]-N accumulated even with low DNRA efficiency, posing long-term water quality risks. We developed a DNRA efficiency prediction model using the Extreme Gradient Boosting algorithm (R[2] = 0.92), thereby enabling accurate assessment across diverse groundwater conditions. This work advances mechanistic understanding and provides an innovative predictive methodology for assessing DNRA-driven NH4[+]-N enrichment risks in groundwater.}, }
@article {pmid41881444, year = {2026}, author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML}, title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003864}, pmid = {41881444}, issn = {2052-4439}, mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.
METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.
RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95% CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics ≤3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).
CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.}, }
@article {pmid41881804, year = {2026}, author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C}, title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70315}, doi = {10.1111/mec.70315}, pmid = {41881804}, issn = {1365-294X}, support = {FONDECYT N°1191769//Agencia Nacional de Investigación y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigación y Desarrollo/ ; Doctoral scholarship N°21201700//Agencia Nacional de Investigación y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. & The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; }, abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.}, }
@article {pmid41881873, year = {2026}, author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N}, title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120044}, doi = {10.1016/j.ecoenv.2026.120044}, pmid = {41881873}, issn = {1090-2414}, abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.}, }
@article {pmid41881888, year = {2026}, author = {Tuveng, TR and Hagen, LH and Rese, M and Eijsink, VGH and Arntzen, MØ}, title = {Meta-omics profiling of denitrifying bacterial communities with lignin as carbon source.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128503}, doi = {10.1016/j.micres.2026.128503}, pmid = {41881888}, issn = {1618-0623}, abstract = {Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. In this study, we established long-term bacterial enrichment cultures supplied with diverse lignin preparations as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis of eight enrichments involving five lignins recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed multiple oxidoreductases and uncharacterised proteins that are potential candidates for involvement in lignin modification. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompts intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of bacterial processing of lignin-associated carbon in anaerobic environments and suggests enzymatic targets for further exploration of lignin depolymerization under oxygen-limited conditions.}, }
@article {pmid41882035, year = {2026}, author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK}, title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36646-4}, pmid = {41882035}, issn = {2045-2322}, support = {2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; }, abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.}, }
@article {pmid41882344, year = {2026}, author = {Muammar, A and Retnaningrum, E and Daryono, BS and Prijambada, ID and Yashima, Y and Peterbauer, C}, title = {A fast workflow to explore active enzymes from environmental samples through functional metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41882344}, issn = {1432-0614}, mesh = {*Metagenomics/methods ; Feces/microbiology ; Workflow ; Animals ; *Cellulases/genetics/metabolism ; Indonesia ; Multiplex Polymerase Chain Reaction ; Gene Library ; Metagenome ; }, abstract = {Functional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool samples from Axis kuhlii, an endemic deer species from Indonesia, to identify active cellulases. We created an efficient workflow for expression of metagenomic sequences directly in Komagatella phaffii by combining metagenomic sequencing to investigate enzyme diversity, multiplex PCR to build a genes library, and rolling circle amplification (RCA) to streamline the cloning process, eliminating the need for intermediate Escherichia coli transformation and propagation steps. Furthermore, a semi-high-throughput screening method was used to evaluate multiple samples at once, allowing for the rapid identification of active enzymes. Using this approach, we discovered five endoglucanases and three β-glucosidases with confirmed enzyme activity. This study shows that functional metagenomics can bridge the gap between computational predictions and experimental validation, providing a reliable platform for enzyme discovery and characterization from complex environmental microbiomes. KEY POINTS: • We established K. phaffii expression of metagenomic sequences via multiplex PCR and RCA. • This approach links metagenomic and activity screening to enable enzyme discovery. • Eight active cellulases were obtained from environmental samples through this approach.}, }
@article {pmid41882399, year = {2026}, author = {Çilkiz, M}, title = {Microbial Biotechnology in Agriculture.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {251-306}, pmid = {41882399}, issn = {0079-6484}, mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Metagenomics/methods ; Crops, Agricultural/growth & development/microbiology ; Metabolomics/methods ; Fertilizers ; }, abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.}, }
@article {pmid41882401, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M}, title = {Microbial Omics.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {333-366}, pmid = {41882401}, issn = {0079-6484}, mesh = {*Metabolomics/methods ; *Proteomics/methods ; *Genomics/methods ; Metagenomics/methods ; *Computational Biology/methods ; Transcriptome ; Microbiota ; *Bacteria/genetics/metabolism ; }, abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.}, }
@article {pmid41882608, year = {2026}, author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J}, title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-08114-y}, pmid = {41882608}, issn = {1472-6831}, }
@article {pmid41882673, year = {2026}, author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C}, title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08013-4}, pmid = {41882673}, issn = {1479-5876}, abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.
METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.
RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.
CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.
TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.}, }
@article {pmid41882801, year = {2026}, author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM}, title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00554-9}, pmid = {41882801}, issn = {2524-4671}, }
@article {pmid41883029, year = {2026}, author = {Dip, SA and Mallick, D and Acharjee Shuvo, U and Barua Soumma, S and Rafsani, F and Kumar Paul, B and Ahmed Moumi, N and Ahmed, S and Zhang, L}, title = {Large language model agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41883029}, issn = {1477-4054}, support = {2125798//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2344169//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2319522//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; }, mesh = {*Genomics/methods ; *Proteomics/methods ; Humans ; *Computational Biology/methods ; *Artificial Intelligence ; Large Language Models ; }, abstract = {Large language models (LLMs) are evolving from passive predictors into agentic systems capable of planning, tool-use, and multimodal reasoning. This shift is especially consequential for biology, where complex, noisy, and multi-scale data require adaptive and integrative computational strategies. In this review, we provide the first systematic synthesis of LLM-based agents across genomics, molecular biology, imaging, biomedical analysis, and automated bioinformatics workflows. We analyze >60 emerging systems and organize them within a unifying framework that characterizes agentic traits, such as autonomous decision-making, external tool invocation, memory, and self-correction. Across domains, agentic LLMs show early promise in enabling multi-step analysis, linking heterogeneous evidence, and supporting exploratory scientific tasks. At the same time, our comparative assessment highlights consistent challenges, including unstable reasoning, limited biological grounding, retrieval misalignment, and barriers to reproducibility and biosafety. We conclude by outlining opportunities for trustworthy and collaborative biological agents, including multimodal integration, closed-loop experimental design, and robust evaluation practices. This survey aims to clarify the emerging landscape and chart a path toward reliable agentic systems for biological discovery.}, }
@article {pmid41883089, year = {2026}, author = {Duchêne, C and Jaubert, M and Falciatore, A}, title = {Beyond red/far-red sensing: phytochrome perception of the marine light field by microalgae.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71128}, pmid = {41883089}, issn = {1469-8137}, support = {ANR-25-CE20-4776//Agence Nationale de la Recherche/ ; ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; ANR-25-CE20-1717//Agence Nationale de la Recherche/ ; ANR-11-LABX-0011-01//Agence Nationale de la Recherche/ ; 101082304//Fourth Framework Programme/ ; }, abstract = {Phytochromes (PHYs) are a major group of photoreceptors, described as red and far-red light sensors in land plants. Recent genomic and metagenomic explorations have revealed the presence of PHYs also in various eukaryotic microalgae originating from distinct endosymbiotic events. Growing evidence indicates that these PHYs are spectrally and functionally tuned to shorter wavelengths, which are prevalent in the aquatic environments as depth increases. Investigations using emerging phytoplankton model species, along with environmental surveys, are uncovering new PHY-mediated responses that likely influence their growth and distribution in marine environments. This Tansley Insight explores the implications of these discoveries for understanding the evolution and functional significance of this major photoreceptor class in the upper ocean, where light drives both energy and information flow.}, }
@article {pmid41883376, year = {2026}, author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W}, title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {3}, pages = {420-433}, pmid = {41883376}, issn = {2833-8278}, abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.}, }
@article {pmid41883694, year = {2026}, author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A}, title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {50}, number = {}, pages = {e00956}, pmid = {41883694}, issn = {2215-017X}, abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.}, }
@article {pmid41883790, year = {2026}, author = {Way, J and Sherman, T and Leleika, S and Crippen, K and Wilson, R and Fida, TT}, title = {Enrichment and comparative metagenomics of microbes involved in biocorrosion of gas transport or storage steel infrastructure.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771929}, pmid = {41883790}, issn = {1664-302X}, abstract = {Biocorrosion, also known as microbiologically influenced corrosion (MIC), is the deterioration of metals caused by microbial activities that compromise the structural integrity, reliability, and safety of steel infrastructure. To identify the genetic determinants that MIC-causing microorganisms may use to attack steel infrastructure, field samples from natural gas infrastructure with a potential history of MIC were collected, enriched for different MIC categories, and subjected to whole-genome shotgun sequencing for metagenomic analysis. Biofilms were grown on carbon steel coupons or glass slides as attachment substrates to assess differences in microbial community composition and metabolic activities. The highest corrosion activities were observed in enrichments dominated by acid-producing bacteria (APB) and hydrogen-utilizing bacteria. APB enrichments resulted in the highest accumulation of organic acids and a severe decrease in culture fluid pH. A total of 57 metagenome-assembled genomes were recovered from the biofilms, some of which differed between carbon steel coupons and glass slide substrates. The metagenomes contained most of the known genes implicated in MIC and sulfide production, with substantial variation in estimated gene copy numbers among metagenomes and attachment substrates. Overall, comparative analysis of these biofilm metagenomes enriched from natural gas production and processing infrastructure highlights similarities to microbial communities commonly observed in oil production and processing systems and provides an overview of candidate genes that may be used as molecular probes for MIC.}, }
@article {pmid41883806, year = {2026}, author = {Peng, L and Zhang, Y and Li, X and Hu, Z}, title = {Integrated multi-omics analysis reveals gut microbiota and metabolic characteristics in coronary heart disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743914}, pmid = {41883806}, issn = {1664-302X}, abstract = {BACKGROUND: Coronary heart disease (CHD) is a leading cause of morbidity and mortality worldwide. Increasing evidence indicates that gut microbiota dysbiosis contributes to CHD pathogenesis through metabolic, inflammatory, and coagulation-related mechanisms. However, comprehensive multi-omics investigations of individuals with CHD remain limited. In this study, we aimed to characterize the multi-omics features of CHD and to identify potential diagnostic biomarkers.
METHODS: The study included 10 patients with clinically diagnosed CHD and 10 healthy controls. Blood and fecal samples were collected for further analysis. The gut microbiota composition was assessed using 16S ribosomal RNA high-throughput sequencing, and shotgun metagenomic sequencing was further performed to evaluate microbial functional potential through the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and differential pathway analysis. Non-targeted metabolomic profiling was performed using ultra-high-performance liquid chromatography coupled with Orbitrap mass spectrometry, and quantitative proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry. Functional interaction networks between differentially expressed metabolites and proteins were constructed using Spearman correlation analysis, and the diagnostic potential of candidate biomarkers was evaluated using receiver operating characteristic (ROC) curve analysis.
RESULTS: At the phylum level, the CHD group exhibited an increased abundance of Pseudomonadota and a decreased abundance of Bacillota and Actinomycetota. At the genus level, Escherichia-Shigella, Bacteroides, and Klebsiella were significantly enriched, whereas Bifidobacterium and Faecalibacterium were decreased in abundance. Shotgun metagenomic analysis revealed functional remodeling of gut microbiota in CHD, with upregulation of KEGG pathways related to energy metabolism, inflammatory signaling, and host-microbe interactions. Serum metabolomics and proteomic analyses identified 32 differentially expressed metabolites and 38 differentially expressed proteins, respectively. Correlation analysis revealed significant associations between phospholipid metabolites and apolipoproteins, inflammatory mediators and the complement system, asymmetric dimethylarginine and endothelial function-related proteins, and oxidative stress metabolites and antioxidant proteins. ROC analysis identified several potential biomarkers with high diagnostic value.
CONCLUSION: We demonstrate that individuals with CHD exhibit significant gut microbiota dysbiosis, distinct metabolic pathway alterations, and aberrant expression of coagulation- and inflammatory-related proteins. These findings provide novel insights into potential targets for CHD prevention and treatment strategies.}, }
@article {pmid41884347, year = {2026}, author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T}, title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2647511}, pmid = {41884347}, issn = {2000-2297}, abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.
OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.
DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.
RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.
CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.}, }
@article {pmid41885442, year = {2026}, author = {Rysava, M and Stredanska, K and Schwarzerova, J and Jakubickova, M and Cejkova, D and Aytan-Aktug, D and Otani, S and Dolejska, M and Palkovicova, J}, title = {Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0407425}, doi = {10.1128/spectrum.04074-25}, pmid = {41885442}, issn = {2165-0497}, abstract = {The expansion of intensive poultry farming has led to a substantial increase in antibiotic use, which, in turn, has promoted the accumulation of antibiotic resistance genes (ARGs). The chicken gut serves as a reservoir for these genes and provides favorable conditions for their horizontal transfer via mobile genetic elements, such as plasmids. Through this process, commensal bacteria can transfer ARGs to pathogens, facilitating their spread and increasing the risk of transmission to humans. In this study, long-read sequencing was used to characterize the plasmidome and resistome in 12 fecal samples from 3 houses of a commercial broiler chicken farm. All chickens received enrofloxacin in the first days of life, with one house additionally treated with sulfamethoxazole/trimethoprim combination. For comparison, metagenomic analysis using short-read sequencing was performed on the same samples. This study revealed the presence of various ARGs associated with resistance to 25 antibiotic classes. A strong genetic association between MOBP-type plasmids and fluoroquinolone resistance was observed within broiler chicken farms. Temporal trends indicated progressive mobilization of these ARGs, suggesting an increasing potential for horizontal gene transfer. While fluoroquinolone resistance expanded over time, diaminopyrimidine resistance remained stable despite the antibiotic treatment. Most ARGs were carried on small plasmids, and complete plasmid reconstructions ranged from 2.6 to 47.6 kb. Our findings demonstrate that plasmidome sequencing enables high-resolution detection of resistance-associated plasmids that may be overlooked by conventional metagenomic approaches. The observed patterns are consistent with an association between fluoroquinolone use in poultry farms and the presence of plasmid-mediated resistance genes with potential for horizontal dissemination.IMPORTANCEDespite the crucial role of plasmids in antimicrobial resistance (AMR) dissemination, studies focusing on plasmidomes, defined as the complete set of plasmids, remain limited. This study is the evidence that chicken farms, where fluoroquinolone treatment is a standard practice, act as an important reservoir of plasmid-mediated antibiotic resistance which may not be revealed by commonly used approaches. Combining a metagenomic approach with a focus on plasmids enhances our ability to understand the genetic context and mechanisms underlying AMR transmission. The findings emphasize the importance of targeted plasmid analysis to improve surveillance and risk assessment of AMR transmission in microbial ecosystems.}, }
@article {pmid41885716, year = {2026}, author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q}, title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70499}, pmid = {41885716}, issn = {1365-3040}, support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; }, abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.}, }
@article {pmid41885787, year = {2026}, author = {Ayed, M and Cadavez, V and Gonzales-Barron, U}, title = {Current research trends towards the control of protozoans in foods.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.15114}, pmid = {41885787}, issn = {2239-7132}, abstract = {Protozoan parasites such as Cryptosporidium spp., Giardia duodenalis, Toxoplasma gondii and Cyclospora cayetanensis remain difficult-to-control hazards in food due to environmental persistence, low infectious doses, and the interpretability gap between nucleic acid detection and infectivity. This review synthesizes 4-year research trends shaping protozoan control in food systems, focusing on three critical pillars: matrix-adapted front-end processing (concentration, lysis, inhibitor management); inhibitor-resilient quantification; and sequencing-based attribution for outbreak investigation and source tracking. Recent benchmarking across wastewater, the water-soil-produce nexus, and food-relevant matrices repeatedly indicates - depending on matrix and study design - that upstream workflow steps often dominate analytical sensitivity and reproducibility. Accordingly, tiered analytical strategies are emerging in which the quantitative polymerase chain reaction (PCR) technique supports scalable screening, droplet digital PCR is used for decision-grade confirmation/quantification under inhibition and low-template conditions, and targeted sequencing or metagenomics is deployed selectively for traceback and contextual investigation. We integrate these developments into an actionable control framework that links prevention at the water-soil-plant interface with tiered analytics and viability-aware interpretation of post-intervention results. Research priorities ahead include harmonized performance reporting (recovery, inhibition controls, limit of detection/quantification), transparent endpoint hierarchy for intervention claims (detectability versus viability/infectivity), and interoperable sequence databases to enable cross-laboratory attribution and program-level learning. The field is moving from "can we detect?" towards "can we decide? - requiring reproducible front-end processing, inhibitor-resilient quantification, interoperable attribution resources, and endpoint discipline for intervention efficacy claims.}, }
@article {pmid41886617, year = {2026}, author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Yu, H and Chen, L}, title = {Exogenous Elemental Sulfur Promoting Methane Production and Simultaneous Ammonia Nitrogen Removal in Anaerobic Digestion of Food Waste: Experimental Verification and Mechanism Analysis.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c18148}, pmid = {41886617}, issn = {1520-5851}, abstract = {The treatment of food waste (FW) via anaerobic digestion (AD) is frequently plagued by a low methane yield and ammonia (NH4[+]) inhibition. This study demonstrates that the addition of elemental sulfur (S[0]) effectively mitigates both of these issues. Through batch and continuous experiments, it was found that the specific methane yield was enhanced by up to 48.1% and the NH4[+] concentration decreased by 26.9% at the optimal S[0] dosages of 20 mg/L. Metagenomic analysis revealed a dual mechanism underlying this enhancement: at low dosages, S[0] provides a sulfur-containing functional group for the biosynthesis of methyl-coenzyme M, thereby accelerating the rate-limiting "methyl-transfer" step in methanogenesis; at high dosages, it promotes the biosynthesis of coenzyme A, which markedly enhances acidogenesis. Furthermore, S[0] alleviates NH4[+] inhibition by fostering a synergistic interaction between sulfate-reducing bacteria and anammox bacteria, which convert NH4[+] to N2. Continuous operation over 140 days confirmed the long-term stability and effectiveness of this S[0] addition strategy. This study provides mechanistic insights into S[0]-driven methanogenesis in complex organic waste (FW) and offers a cost-effective, sustainable approach to enhancing AD efficiency and stability.}, }
@article {pmid41886785, year = {2026}, author = {Tian, M and Li, J and Dai, S and Ma, L}, title = {Clinical Characteristics and Management of Four Cases of Visceral Leishmaniasis-Associated Hemophagocytic Lymphohistiocytosis.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.25-0530}, pmid = {41886785}, issn = {1476-1645}, abstract = {The aim for the present study was to analyze clinical features, diagnostic approaches, and therapeutic strategies for visceral leishmaniasis (VL)-associated hemophagocytic lymphohistiocytosis (HLH) in pediatric patients. The clinical characteristics and test results of the children were summarized. Among the four patients, three resided in VL-endemic regions, and one had traveled to a VL-endemic region. All patients presented with recurrent fever (>38.5°C), hepatosplenomegaly, and decreased hemoglobin (HGB) levels ([78.75 ± 8.50] g/L) and platelet (PLT) counts ([59.50 ± 17.48] × 109/L). Before a definitive diagnosis could be made, patients exhibited progressive declines in white blood cell counts, HGB levels, and PLT counts, along with elevated triglyceride, serum cytokine (interleukin [IL]-6, IL-10, IL-2R, and tumor necrosis factor α) levels. Bone marrow aspirate smears revealed hemophagocytosis and Leishmania donovani (LD) bodies in all cases: two were diagnosed via direct identification of LD bodies, one was diagnosed through re-examination of bone marrow smears after confirming a travel history, and one was diagnosed via re-examination prompted by metagenomic next-generation sequencing, which revealed leishmaniasis. All the patients were initially diagnosed with HLH and received HLH-directed immunochemotherapy before VL diagnosis, with suboptimal response. After confirmation of VL, sodium stibogluconate therapy was initiated, resulting in a partial response in all cases. Etiological investigation is critical for HLH diagnosis. For VL-associated HLH, sodium stibogluconate as targeted therapy rapidly controls HLH, facilitates immunosuppression withdrawal, and significantly improves patient outcomes. White blood cell count, HGB level, PLT count, and lactate dehydrogenase level may serve as critical prognostic biomarkers for VL-associated HLH.}, }
@article {pmid41886955, year = {2026}, author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ}, title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158089}, doi = {10.1016/j.phymed.2026.158089}, pmid = {41886955}, issn = {1618-095X}, abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.
OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.
METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.
RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.
CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.}, }
@article {pmid41887041, year = {2026}, author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z}, title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {59}, number = {}, pages = {101810}, doi = {10.1016/j.cbd.2026.101810}, pmid = {41887041}, issn = {1878-0407}, abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.}, }
@article {pmid41887065, year = {2026}, author = {Song, J and Hou, YN and Li, R and Feng, Z and Wang, AJ and Ren, N and Wei, W and Ni, BJ and Huang, C}, title = {Ectoine modulates mixotrophic denitrification pathway partitioning to sustain stable nitrogen and phenol removal under hypersaline stress.}, journal = {Water research}, volume = {298}, number = {}, pages = {125764}, doi = {10.1016/j.watres.2026.125764}, pmid = {41887065}, issn = {1879-2448}, abstract = {Hypersaline wastewater containing phenolic compounds imposes coupled osmotic and cytotoxic stresses that severely disrupts biological treatment processes. While compatible solutes are known to enhance cellular osmoprotection, their capacity to regulate microbial metabolic, particularly the balance between autotrophic and heterotrophic denitrification pathways under combined salinity stress remain poorly understood. This study reveals that the compatible solute ectoine modulates pathway partitioning in mixotrophic denitrification systems, enabling efficient nitrogen and phenol removal under 4% salinity. The ectoine amended reactor maintained nitrogen removal above 95% and phenol degradation above 80%, whereas the unprotected control collapsed to 34% and 33% respectively. Multi-scale mechanistic investigations revealed a coordinated protection cascade. First, ectoine enhanced cellular resilience by suppressing reactive oxygen species (ROS) by 88.2%, maintaining ATP level and electron transport activity, thereby preserving bioenergetic integrity. Second, structural fortification was achieved through intensified extracellular polymeric substance (EPS) production. The protein-to-polysaccharide ratio increased from 0.70 to 1.51 creating a protective matrix that stabilized membrane permeability and preserved catalytic enzymes, with nitrate reductase and nitrite reductase activities increasing 2.16- and 2.93-fold. Third, metagenomic profiling revealed community reconfiguration, with selective enrichment of halotolerant heterotrophs (Halomonas, Marinobacter) to 49% relative abundance. Aromatic‑degradation genes (catA, benB) rose by 7‑ and 48‑fold, while nitrogen‑metabolism genes (nasA, norC) remained high representation. This restructuring reversed pathway contributions from 81% sulfur-autotrophic dominance to 82% heterotrophic dominance. Ectoine thus functions as a metabolic modulator that links cellular stress alleviation and community-level functional potential to pathway repartitioning, offering a feasible strategy for the biotreatment of saline phenolic wastewater.}, }
@article {pmid41887066, year = {2026}, author = {Wang, H and Wu, Y and Weng, H and Zhang, L and Peng, Y}, title = {Denitrification mode management selects resource-conserving consortia for low-carbon municipal wastewater treatment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125775}, doi = {10.1016/j.watres.2026.125775}, pmid = {41887066}, issn = {1879-2448}, abstract = {Low-carbon municipal wastewater treatment increasingly relies on carbon-limited denitrification, yet how carbon limitation reorganizes denitrifying communities and their greenhouse-gas footprint remains poorly resolved. We implemented denitrification mode management in a municipal wastewater sequencing batch reactor by switching from anaerobic-aerobic (AO) to anaerobic-aerobic-anoxic (AOA) operation. This shift moved denitrification from an pre-anaerobic stage with higher carbon availability to a post-anoxic stage where readily available carbon was limited. We combined metagenomics and metatranscriptomics to link process performance with microbial traits and gene expression. The mode switch improved nitrogen removal from 67.1 ± 1.8% to 88.5 ± 3.9% and reduced carbon requirement from 4.9 ± 0.5 to 3.3 ± 0.4 mg COD per mg N removed, while decreasing the N2O emission factor from 0.024 to 0.005 mg N2O-N per mg NO3[-]-N and lowering CO2 and CH4 emissions by 20-30%. Carbon-limited post-denitrification selected taxa with smaller genomes, reduced metabolic redundancy and a pronounced shift from broad extracellular carbon catabolism and complete denitrification towards intracellular carbon storage and truncated denitrification. Intracellular carbon pools insulated organics at the single-cell level and buffered electron delivery across denitrification steps, enabling a division-of-labour network that prevents electron imbalance and suppresses N2O build-up. Together, these findings link denitrification mode management to trait-based community restructuring and offer a process-level framework for understanding low-carbon, low-emission nitrogen removal under carbon-limited conditions.}, }
@article {pmid41887069, year = {2026}, author = {Qiang, H and Xu, X and Liu, Z and Heo, S and Yue, X and Zhou, A and Makinia, J}, title = {New insights into the interplay between chain elongation and homoacetogenesis in microbial electrosynthesis: Chloroform-enhanced medium-chain carboxylate production.}, journal = {Water research}, volume = {298}, number = {}, pages = {125790}, doi = {10.1016/j.watres.2026.125790}, pmid = {41887069}, issn = {1879-2448}, abstract = {Microbial electrosynthesis (MES)-assisted chain elongation (CE) is a promising strategy for sustainable medium-chain carboxylic acid (MCCA) production from waste streams. However, MES induces inevitable H2 evolution, and the understudied interaction between H2-driven homoacetogenesis and CE creates a critical knowledge gap. To resolve this metabolic conflict, chloroform (CHCl3) at 0.0075%-0.045% was used to inhibit homoacetogenesis, with systematic investigations on carbon flux distribution, functional microbial communities, and key metabolic pathways. Results showed 0.03% CHCl3 optimized MCCA production to 2902.8 ± 116.1 mg COD/L (103.0% increase), with electron efficiency (40.8%) and acetate utilization efficiency (94.3%) significantly higher than the Control (21.8% and 43.5%, respectively). Homoacetogenesis inhibition conserved reducing power (moderated H2, lowered NAD[+]/NADH) and redirected acetyl-CoA to drive CE. Microbial community analysis revealed enriched chain-elongating bacteria with more modular, cooperative interaction networks. Metagenomic analysis confirmed elevated abundances of reverse β-oxidation genes (e.g., ACAT, crt) and reduced homoacetogenesis genes (e.g., cooF, cooS) after treatment. Taxon-function contribution analysis identified Clostridium_kluyveri as the dominant functional agent for CE-related key genes. Economic and life-cycle assessments demonstrated a net economic gain of $1.61-4.22/m[3] and mitigated key environmental impacts due to improved product yield. This study elucidates how regulating the competition between homo-acetogens and chain-elongating bacteria directionally enhances CE, providing a novel ecological perspective and strategy for optimizing electricity-driven biomanufacturing processes.}, }
@article {pmid41887245, year = {2026}, author = {Reddy, K and Sinha, P and Antcliffe, DB and McDowell, C and Bradley, PA and Black, L and Murphy, L and Barbaras, J and Conlon, J and Camporota, L and Ostermann, M and Hopkins, P and Szakmany, T and Cherian, S and Welters, I and Brealey, D and Parekh, D and Rostron, AJ and Bos, LDJ and Nichol, A and Shankar-Hari, M and Gordon, AC and Delucchi, K and O'Kane, CM and Matthay, MA and Calfee, CS and McAuley, DF and , }, title = {Bedside identification of subphenotypes in acute respiratory failure (PHIND): a multicentre, observational cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(26)00040-8}, pmid = {41887245}, issn = {2213-2619}, abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) is a clinically defined, biologically heterogeneous condition with no proven disease-modifying therapies. Retrospective analyses have identified two biologically distinct subphenotypes (hyperinflammatory and hypoinflammatory) of ARDS, with differing outcomes and responses to therapy. Rapid identification of these subphenotypes in an actionable timeframe has previously not been possible. The PHIND study aimed to prospectively identify these subphenotypes and to demonstrate differing 60-day mortality.
METHODS: The PHIND study was a prospective, multicentre, observational cohort study conducted in intensive care units (ICUs) within the National Health Service in the UK and the Health Service Executive in Ireland. Adult patients aged 18 years and older with ARDS or acute hypoxaemic respiratory failure (AHRF) were enrolled within 72 h of onset of the syndrome. Eligible patients were required to be receiving invasive mechanical ventilation, non-invasive ventilation, or high-flow nasal oxygen. Plasma interleukin (IL-6) and soluble TNF receptor-1 (TNFR1) were quantified at enrolment using a near-patient benchtop immunoanalyser (Randox multiSTAT) with a run time of approximately 1 h. Together with plasma bicarbonate measured from an arterial blood sample, these values were used to prospectively determine subphenotypes on an individual patient basis using a validated parsimonious logistic regression model. The primary outcome was 60-day mortality. The study was registered on ClinicalTrials.gov, NCT04009330.
FINDINGS: Between Nov 22, 2019, and Sept 28, 2023, 1853 patients from 30 centres were screened for eligibility. Of these, 1328 were excluded and 525 were recruited into the study, with 512 individuals included. 308 (60%) patients were male, 204 (40%) were female, and mean age was 57·0 years (SD 15·1). 443 (87%) patients were white, 18 (4%) were Black, and 16 (3%) were Asian. 490 were subphenotyped using the near-patient assay: 89 (18%) were classified as hyperinflammatory and 401 (82%) as hypoinflammatory. The primary outcome of 60-day mortality was measured in 486 patients after four patients withdrew consent for confirmation of vital status. 60-day mortality was significantly higher in the hyperinflammatory group (45 [51%] of 88) than in the hypoinflammatory group (111 [28%] of 398; risk ratio 1·8 [95% CI 1·4-2·4], p<0·0001). After adjustment, hyperinflammatory patients had increased odds of 60-day mortality (adjusted odds ratio 2·7 [95% CI 1·6-4·4], p=0·0002).
INTERPRETATION: Rapid identification of ARDS inflammatory subphenotypes using a near-patient assay was feasible and associated with many clinical characteristics and outcomes consistent with those described in earlier retrospective studies, including mortality, prevalence of sepsis, and incidence of metabolic acidosis. These findings support the implementation of precision medicine approaches in ARDS and the urgent need for prospective, subphenotype-stratified interventional trials.
FUNDING: Innovate UK, Randox Laboratories, and Belfast Health & Social Care Trust.}, }
@article {pmid41887297, year = {2026}, author = {Lin, X and Yang, J and Kong, H and Pu, L and Ma, P and Mu, W and Sheng, H and He, J and Zou, Y and Wang, Y and Guo, X and Zhang, S and Wang, S}, title = {Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108461}, doi = {10.1016/j.micpath.2026.108461}, pmid = {41887297}, issn = {1096-1208}, abstract = {Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.}, }
@article {pmid41887416, year = {2026}, author = {Zhang, L and Xie, J and Lu, Y and Kong, L and Zhou, L and Wu, S and Wang, W and Huang, J and Li, J and Cheng, S}, title = {Enhanced nitrogen removal and mitigated greenhouse gas emissions in bioelectrochemical system-modular moving bed wetland at low temperature: Functional zonation and multi-pathway electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134493}, doi = {10.1016/j.biortech.2026.134493}, pmid = {41887416}, issn = {1873-2976}, abstract = {This study integrated bioelectrochemical systems (BESs) into modular moving bed constructed wetlands (MMBCWs) to mitigate low temperature constraints on nitrogen removal and greenhouse gas emissions. Conventional MMBCW, microbial fuel cell-MMBCW (MFC-MMBCW), and microbial electrolysis cell-MMBCW (MEC-MMBCW) were constructed to assess feasibility. Results showed that MEC-MMBCW achieved superior nitrogen removal and the lowest global warming potential under cold conditions. Biofilm characteristics and metagenomic analyses revealed that MEC-MMBCW established spatially stratified functional zones. Specifically, the anode promoted organic matter and ammonia oxidation, while enhanced denitrification outcompeted compensatory anammox in the cathode. Furthermore, a multi-pathway extracellular electron transfer (EET) network mediated by extracellular polymeric substances (EPS), cytochrome c, and conductive pili accelerated electron transfer rates. These mechanisms synergistically boosted metabolic potential and activated latent degradation pathways, enhancing treatment resilience. Consequently, MEC-MMBCW represents a viable strategy for sustainable wastewater treatment in cold regions.}, }
@article {pmid41887490, year = {2026}, author = {Li, Z and Fu, J and Hu, J and Li, T and Xu, Y}, title = {Sediment-water interface reoxygenation by NO3-LDH promotes tetracycline degradation in sediments and modulates antibiotic resistance gene dynamics.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124357}, doi = {10.1016/j.envres.2026.124357}, pmid = {41887490}, issn = {1096-0953}, abstract = {The widespread presence of antibiotics in aquatic sediments, together with hypoxic conditions, constrains oxygen-driven natural degradation, thereby prolonging their environmental persistence. In this work, nitrate-intercalated layered double hydroxide (NO3-LDH) was employed as a controlled-release nitrate amendment to alleviate interfacial oxygen limitation while minimizing the secondary environmental risks associated with the high release peaks of conventional nitrate reagents. As a result, NO3-LDH increased dissolved oxygen (DO) from 1.05 to 3.39 mg/L, enhanced TC removal from 64.5% to 89.8% within 15 d, and reduced the combined abundance of tetracycline resistance genes (tetA, tetQ, and tetS) by 53.0%. Mechanistically, DO enrichment increased •OH generation 1.94-fold and upregulated cytochrome P450-related genes, supporting coupled enhancement of abiotic oxidation and oxygen-dependent microbial transformation. The improved oxidative microenvironment also favored the enrichment of aerobic aromatic-degrading taxa, further promoting TC attenuation. Although overall antibiotic resistance genes (ARGs) levels declined, fluoroquinolone- and macrolide-associated ARGs exhibited a transient early increase, likely triggered by an abrupt redox perturbation upon oxygen recovery that imposed oxidative stress on anaerobic microorganisms, intensified ATP-demanding stress responses, and increased membrane permeability. As interfacial redox conditions stabilized and TC concentrations decreased, these stress responses subsided and ARGs abundances declined at later stages. Overall, restoring interfacial DO strengthens oxygen-driven natural antibiotic degradation and inhibits the long-term accumulation of ARGs, providing a mechanistically grounded strategy for in situ remediation of antibiotic-contaminated sediments.}, }
@article {pmid41887505, year = {2026}, author = {Wang, Q and Zhang, J and Xia, Y and Zha, M and Li, J and Jambal, T and Dorjgotov, D and Tseveen, S and Chen, Y}, title = {Traditional fermented goat milk products in Mongolia: Analysis from the perspective of metagenomics to metabolomics.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27796}, pmid = {41887505}, issn = {1525-3198}, abstract = {Mongolia is known for its rich dairy traditions, with goat milk representing a distinctive and valuable dairy resource. Fermentation improves the quality and nutritional value of goat milk, which is closely associated with microbial activity. As traditional Mongolian fermented dairy products primarily depend on natural fermentation, investigating the microbial and metabolic changes during this process is essential for understanding product quality. In this observational study, raw goat milk (RGM) and fermented goat milk (FGM) samples were collected from Mongolia, and a total of 102 microbial species were identified using shotgun metagenomic sequencing. The RGM contained a higher proportion of viruses and nonlactic acid bacteria (non-LAB), including Macrococcus caseolyticus. Following fermentation, the microbial community composition shifted, becoming dominated by LAB species such as Lactobacillus helveticus and Lactobacillus delbrueckii, with beneficial microorganisms attaining predominant abundance. A total of 22 differential metabolites were identified between RGM and FGM. Approximately half of these metabolites were related to AA metabolism, while the remainder were involved in energy metabolism, antioxidant processes, and lipid metabolism. Spearman correlation analysis suggested that LAB, primarily Lactobacillus species, were positively associated with the abundance of metabolites such as organic acids and AA in the fermented products. In contrast, the presence of pathogenic microorganisms such as viruses showed a negative correlation with fermentation efficiency markers. It was hypothesized as a potential factor affecting product quality, possibly through disrupting host microbial metabolism. Overall, this observational study identifies understanding of the factors governing FGM quality and provides a scientific foundation for improving the goat milk industry and harnessing microbial resources in traditional fermented dairy products.}, }
@article {pmid41887507, year = {2026}, author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM}, title = {Microbiota Changes in Rumen and Milk Corresponding to Dietary Protein Intake in Transition Dairy Cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27576}, pmid = {41887507}, issn = {1525-3198}, abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively impacted milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in metabolizable protein (MP) supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (80MP) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (100MP) for an additional 14 d. Control cows (n = 6) were fed 100MP for the entire experiment. Samples of rumen content and milk were taken in the immediate Postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental Recovery phase (RP) on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated to effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the 100MP compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.}, }
@article {pmid41887601, year = {2026}, author = {Wei, Y and Liu, Q and Gong, Z and Han, GZ}, title = {Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.03.009}, pmid = {41887601}, issn = {1995-820X}, abstract = {Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that "virophage" is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7,041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7,041, 1.38%) and global environments (2,450/12,053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.}, }
@article {pmid41887858, year = {2026}, author = {Zheng, D and Li, D and Wang, J}, title = {Beyond ammonia-oxidizing bacteria-centric paradigms: Geobacter-assisted anodic anaerobic ammonia oxidation.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {399-408}, doi = {10.1016/j.jes.2025.07.035}, pmid = {41887858}, issn = {1001-0742}, mesh = {*Geobacter/metabolism/physiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Electrodes ; Anaerobiosis ; Biofilms ; Bacteria/metabolism ; *Anaerobic Ammonia Oxidation ; }, abstract = {Anodic anaerobic ammonium oxidation (anodic anammox) presents a sustainable approach for nitrogen removal, yet its bioelectrochemical mechanisms remain unclear due to biofilm complexity and undefined roles of electroactive microorganisms (EAMs). This study reveals that nitrite (NO2[-]) is the direct product of ammonia-oxidizing bacteria (AOB)-driven anodic anammox, with extracellular electron transfer (EET) mediated by indirect mechanisms via redox shuttles. Metagenomic analysis identified two ammonia oxidation pathways: (1) a novel short-range nitrification pathway (NH4[+] → NO2[-]) governed by ncd2 genes, and (2) a traditional ammonia oxidation pathway (NH4[+] → NH2OH) facilitated by amoABC. Intriguingly, Geobacter exhibited potential NH2OH oxidation capability, bridging AOB activity and electrode respiration. Functional inhibition experiments demonstrated that EAMs-derived electron shuttles and reactive oxygen species (ROS) are critical for enhancing EET efficiency, with ROS serving as a key electron acceptor for AOB under anaerobic conditions. Spatial and metabolic synergy between EAMs and AOB-via substrate cross-feeding, cofactor provision, and electron transfer-was essential for maintaining biofilm stability. These findings challenge the conventional view of AOB-driven anodic anaerobic anammox mechanisms and provide new insights into sustainable nitrogen removal in engineered bioelectrochemical systems.}, }
@article {pmid41887859, year = {2026}, author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z}, title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {409-419}, doi = {10.1016/j.jes.2025.05.033}, pmid = {41887859}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; }, abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.}, }
@article {pmid41887904, year = {2026}, author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P}, title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {867-879}, doi = {10.1016/j.jes.2025.10.021}, pmid = {41887904}, issn = {1001-0742}, mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; }, abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.}, }
@article {pmid41888119, year = {2026}, author = {Rodríguez-Varela, R and Pochon, Z and Mas-Sandoval, A and Yaka, R and Fortes-Lima, CA and García Rubio, A and Márquez-Grant, N and Marí, J and Graziani, G and Ferrer Abárzuza, A and Vicente, M and Lorca-Francisco, L and Linderholm, A and Lagerholm, VK and Arauna, LR and Pérez-Ramallo, P and Krzewińska, M and Schlebusch, CM and Götherström, A}, title = {Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41888119}, issn = {2041-1723}, support = {2019-00849_VR//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {Humans ; History, Medieval ; *Islam/history ; Spain ; *Burial/history ; *Genetic Variation ; Metagenomics ; Gene Flow ; *Leprosy/microbiology/history/genetics ; DNA, Ancient/analysis ; Male ; Cemeteries ; }, abstract = {Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of Córdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.}, }
@article {pmid41888125, year = {2026}, author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C}, title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00970-4}, pmid = {41888125}, issn = {2055-5008}, support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; }, abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.}, }
@article {pmid41888178, year = {2026}, author = {Ariaeenejad, S and Abedanzadeh, S}, title = {Enhanced stability and reusability of metagenomic laccase via immobilization on functionalized mesoporous silica for antibiotic contaminant removal.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41888178}, issn = {2045-2322}, mesh = {*Laccase/chemistry/metabolism/genetics ; *Silicon Dioxide/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Anti-Bacterial Agents/chemistry/isolation & purification/metabolism ; Enzyme Stability ; Porosity ; *Metagenome ; Water Pollutants, Chemical/chemistry ; Biodegradation, Environmental ; Metagenomics ; Doxycycline/chemistry ; Imidazoles/chemistry ; }, abstract = {The extensive application of tetracycline antibiotics in agriculture and medicine has led to persistent contamination of aquatic and terrestrial ecosystems, disrupting microbial communities and contributing to the spread of antibiotic resistance. Conventional treatment methods often suffer from poor efficiency, limited stability, and high environmental costs, underscoring the need for robust and sustainable alternatives. Here, we present a biocatalytic platform in which a metagenome-derived laccase (PersiLac1) is covalently immobilized onto imidazole-functionalized SBA-15 mesoporous silica to overcome the limitations of free laccase, including low stability and high leaching. Immobilization markedly enhanced thermal stability, reusability, and catalytic efficiency toward the degradation of doxycycline (DC) and tetracycline (TC). The optimized system exhibited minimal enzyme leaching (9.6% at 25 °C; 22.0% at 80 °C) and achieved removal efficiencies of 76.7 ± 2.8% for DC and 53.7 ± 2.1% for TC within 24 h. High removal performance was maintained even at elevated antibiotic concentrations (200 mg L[-1]), with 43.9% and 42.8% removal for DC and TC, respectively. The immobilized laccase retained over 83% (DC) and 73% (TC) of its initial activity after 10 consecutive reuse cycles. To the best of our knowledge, this is the first report of integrating a metagenomic laccase with an imidazole-functionalized SBA-15 support for antibiotic degradation, offering a unique combination of enhanced stability, high reusability, and environmentally relevant performance. These findings highlight the potential of this immobilization strategy as a sustainable and high-performance solution for the remediation of antibiotic contaminants in water systems.}, }
@article {pmid41888223, year = {2026}, author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K}, title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44250-9}, pmid = {41888223}, issn = {2045-2322}, support = {4020052//Center for International Scientific Studies & Collaborations (CISSC)/ ; }, abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.}, }
@article {pmid41888360, year = {2026}, author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ}, title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41888360}, issn = {1573-0972}, abstract = {Biological treatment of cyanide-contaminated wastewater is mediated by microbial consortia in which different organisms perform distinct, functionally specialized roles. This study investigated microbial communities involved in gold mine wastewater treatment with integrated aerobic-anoxic reactors seeded with consortia from an alkaline soda lake, Lake Chitu. Whole-genome sequencing of isolates (WGS) and metagenomic sequencing of the bioreactor were performed to characterize the consortia, resulting in the identification of 23 non-redundant genomes, comprising 14 whole-genome sequencing isolates and 19 metagenome-assembled genomes (MAGs). Most isolated genomes were similar to the recovered metagenomes of MAGs. Except for Alkalibacterium, all isolates possessed one or more genes potentially involved in cyanide or cyanate transformation, along with at least one type of terminal oxygenase; however, the gene encoding cynD, which is required for the direct hydrolysis of free cyanide (CN[-]), was not detected. Three representative Halomonas isolates harboured the nitrate reductase narGHI, nitrite reductase nirS, nitric oxide reductase norB/norC, and nitrous-oxide reductase nosZ genes for full denitrification. All of the isolates possessed several gene clusters associated with different heavy metal resistances. This study suggests that the microbial inoculum sourced from Lake Chitu harbors diverse microorganisms possessing genes potentially involved in cyanide-related metabolic pathways. The findings of this study add to our understanding of the alkaliphilic microbial population that degrades cyanide and cyanide intermediates and provide insight into how these organisms break down cyanide and resist cyanide and heavy metal inhibitory effects.}, }
@article {pmid41888867, year = {2026}, author = {Tao, M and Fan, Y and Qian, L and Liu, H and Ming, Y and Yu, X and Wu, K and Niu, M and Yan, Q and Huang, X and He, Z}, title = {Microbially driven methane and sulfur cycling processes and coupling mechanisms in mangrove sediments.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00877-9}, pmid = {41888867}, issn = {2524-6372}, support = {2021M703751//China Postdoctoral Science Foundation/ ; SML2023SP205, SML2024SP002, SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42430707, 52070196, 32370113 and 92251306//National Natural Science Foundation of China/ ; 2024A1515010931//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {BACKGROUND: Methane (CH4) as a powerful greenhouse gas is the second largest contributor to global climate warming. Mangrove sediments are an important natural source of biogenic CH4 with rich organic carbon (C) and diverse sulfur (S) compounds, ideally for studying CH4 and S cycling processes and coupling mechanisms. Here we sampled mangrove sediment cores and analyzed their key microbial groups, key environmental factors and possible coupling mechanisms for CH4 and S cycling by metagenome sequencing approaches.
RESULTS: Our results showed that Methanomicrobiales and Methanophagales were predominant methanogens, Methanospirareceae was a representative of anaerobic methanotrophic archaea (ANME), and Desulfobacteraceae and Desulfobulbaceae were abundant sulfate-reducing bacteria (SRB), while Ectothiorhodospiraceae, Chromatiaceae and Comamonadaceae were dominant S-oxidizers. Correlation network analysis revealed positive interactions among methanogens, ANME and SRB. Also, metagenome-assembled genome (MAG) analysis indicated interspecies hydrogen transfer and extracellular electron exchange via conductive pili, flagella, and cytochromes were potential coupling mechanisms between methanogens and SRB. ANME could form consortia with SRB by intermediate metabolites (e.g., acetate) and/or direct interspecies electron transfer (e.g., flagella, pili, cytochromes). Furthermore, methanogen MAGs encoded thiosulfate oxidation and partial sulfate reduction pathways, while the ANME MAGs possessed potentials for S disproportionation and incomplete sulfate reduction. Additionally, SO4[2-], total sulfur, moisture content and salinity were important environmental factors affecting the microbial community structure and gene families involved in CH4 and S cycling.
CONCLUSION: This study provides novel insights into coupling mechanisms of CH4 and S cycling processes in mangrove sediments, having important implications for mitigating global warming.}, }
@article {pmid41888912, year = {2026}, author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH}, title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02379-9}, pmid = {41888912}, issn = {2049-2618}, support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; }, abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.
RESULTS: We discovered that diatoms exude a C6-sulfated α-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.
CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome.}, }
@article {pmid41889037, year = {2026}, author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS}, title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109518}, doi = {10.1016/j.identj.2026.109518}, pmid = {41889037}, issn = {1875-595X}, abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.
METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.
RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.
CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.}, }
@article {pmid41889316, year = {2026}, author = {Niyazi, HA and Niyazi, HA and AbdulMajed, H and Juma, N and Helmi, N and Alqarni, M and Saleh, BH and Zubair, M and Alfadil, A and Alhazmi, W and Alharbi, OS and Halabi, WS and Altalhi, R and Moglad, E and Alharbi, MT and Gazzaz, M and Alharthi, TM and Altayb, HN and Ibrahem, K}, title = {Pan-genome analysis and phylogenetic characterization of Klebsiella pneumoniae from global isolates.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/17460913.2026.2617118}, pmid = {41889316}, issn = {1746-0921}, abstract = {AIMS: This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of Klebsiella pneumoniae by performing a comprehensive pan-genome and phylogenetic analysis across worldwide isolates.
MATERIALS AND METHODS: A total of 72,057 K. pneumoniae genomes were retrieved from the NCBI database, from which 91 high-quality representative genomes each from a unique country were selected based on completeness, metadata availability, and sequence quality. Genomic assemblies were assessed using QUAST, annotated with PROKKA, and analyzed for pan-genomic composition and phylogenetic relatedness using standard bioinformatics pipelines.
RESULTS: The pan-genome revealed a large accessory component, reflecting extensive genomic plasticity and adaptability. QUAST analysis indicated significant variability in genome size and contig number, while PROKKA annotation identified diverse coding sequences, tRNA, rRNA, and AMR genes. Phylogenetic clustering demonstrated both geographically localized and globally disseminated lineages, suggesting regional adaptation and intercontinental transmission.
CONCLUSIONS: This study provides a global perspective on the genomic diversity and evolutionary patterns of K. pneumoniae. The widespread presence of AMR determinants underscores the urgent need for continuous genomic surveillance and integration of metagenomic approaches to improve monitoring, infection control, and therapeutic strategies against multidrug-resistant strains.}, }
@article {pmid41889516, year = {2026}, author = {Mao, J and Jin, Q and Ye, D and Yang, Y}, title = {Case Report: A rare presentation of pulmonary tuberculosis with extensive ground-glass opacities in an immunocompetent patient: lessons from metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1696371}, pmid = {41889516}, issn = {2296-858X}, abstract = {Pulmonary tuberculosis (PTB) is typically diagnosed through sputum smear microscopy and culture. However, diagnosis is challenging in patients with atypical radiological features and negative conventional tests. Ground-glass opacities (GGOs) are common but non-specific computed tomography (CT) findings and are rarely observed in immunocompetent PTB patients. We report the first case of an immunocompetent 53-year-old female presenting with extensive bilateral GGOs without classic clinical symptoms. Conventional microbiological cultures, acid-fast staining, and serological assays were all negative. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Mycobacterium tuberculosis, further supported by a positive T-spot TB assay. Standard anti-tuberculosis therapy led to complete resolution of GGOs over nine months, confirmed by follow-up CT imaging. This case underscores the diagnostic challenge of atypical PTB presenting with non-classical CT manifestations in an immunocompetent host. It highlights the decisive role of mNGS as a complementary tool in cases where conventional methods fail, enabling timely diagnosis, precise treatment, and improved patient outcomes.}, }
@article {pmid41889550, year = {2026}, author = {Xiu, Q and He, H and Liu, Z and Ou, X and Meng, Y and Zhao, K and Yang, Q and Zhang, X and Hou, Y and Yao, S and Gao, P and Xia, W}, title = {Biosurfactant-driven desorption and remediation of heavy oil contaminated soils underpinned by molecular simulations and microbial dynamics.}, journal = {RSC advances}, volume = {16}, number = {18}, pages = {16316-16328}, pmid = {41889550}, issn = {2046-2069}, abstract = {This study integrates molecular dynamics simulations and bench-scale experiments to investigate the adsorption and desorption behaviors of heavy oil on five mineral substrates: SiO2, kaolinite, muscovite, and Ca[2+]-/Na[+]-montmorillonite. Adsorption followed Langmuir isotherms, with montmorillonite exhibiting the highest capacities (0.061-0.062 molecules per Å[2] for aromatics in simulations; 0.086-0.091 g g[-1] in bench-scale tests) and SiO2 the lowest (0.027 pcs per Å[2]; 0.013 g g[-1]). Among four biosurfactants evaluated-rhamnolipid, sophorolipid, trehalose lipid, and mannosylerythritol lipid-sophorolipid consistently achieved the greatest desorption efficiency, removing up to 99.63% of adsorbed oil from Na[+]-montmorillonite and 96.04% from field-contaminated soil. 16S rRNA and metagenomic sequencing revealed an increased abundance of hydrocarbon-degrading bacteria within the soil microbial community, highlighting a synergistic effect between biosurfactant-induced desorption and biodegradation. These findings underscore the critical roles of mineralogical properties, oil fraction characteristics, and biosurfactant selection in soil washing treatment. This work presents a viable and eco-friendly strategy for remediating crude oil-contaminated soils, with important implications for optimizing large-scale environmental restoration efforts.}, }
@article {pmid41889698, year = {2026}, author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG}, title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1733638}, pmid = {41889698}, issn = {2673-6217}, abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.
METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69 years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.
RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29 years, n = 33; 22.7%), G2 (30-39 years, n = 30; 20.7%), G3 (40-49 years, n = 27; 18.6%), G4 (50-59 years, n = 31; 21.4%), and G5 (60-69 years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.
CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.}, }
@article {pmid41889866, year = {2026}, author = {Van Camp, AG and Park, J and Ozcelik, E and Eskiocak, O and Ozler, KA and Papciak, K and Subhash, S and Alwaseem, H and Ergin, I and Chung, C and Shah, V and Yueh, B and Fein, MR and Durmaz, C and Mozsary, C and Kilic, E and Garipcan, A and Damle, N and Najjar, D and Nelson, TM and Ryon, KA and Butler, DJ and Patel, CJ and Thaiss, CA and Birsoy, K and Mason, CE and Meydan, C and Tierney, BT and Beyaz, S}, title = {Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.17.708620}, pmid = {41889866}, issn = {2692-8205}, abstract = {Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii , consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.}, }
@article {pmid41890171, year = {2026}, author = {Zhao, S and Sai, Y and Jia, M and Qiao, Y and Guo, W and Ding, W and Shao, X and Zheng, Y}, title = {Comprehensive insights into the mechanism of flavor formation in Cheonggukjang: Integration of metagenomics, volatomics, and metabolomics.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103756}, pmid = {41890171}, issn = {2590-1575}, abstract = {Microbial metabolism shapes the unique flavor profile of Cheonggukjang; however, the formation pathways of characteristic flavor compounds mediated by microbiota remain unclear, hindering precise quality control. To fill this gap, this study innovatively integrated metagenoics, volatilomics, and metabolomics to systematically decode the flavor formation mechanism during Cheonggukjang fermentation. Volatile compound analysis defined three fermentation stages for Cheonggukjang (0-18, 18-60, and 60-72 h), identifying the 60-72 h period as the most critical for flavor formation. A total of 15 key flavor compounds were identified, with 10 designated stage-specific flavor markers. LefSe analysis revealed that Bacillus subtilis, Bacillus velezensis, Caldibacillus thermoamylovorans, and Bacillus licheniformis were the key biomarkers across different fermentation stages, while redundancy analysis (RDA) indicated that total sugar as the key driver of microbial succession. Additionally, this study reconstructed the metabolic network responsible for characteristic flavor formation and identified C. thermoamylovorans, B. licheniformis, B. velezensis, B. subtilis, Bacillus paralicheniformis, and Caldibacillus hisashii as core functional microbiota modulating amino acid metabolic to drive flavor development. This study lays a theoretical framework for standardizing Cheonggukjang production and targeted regulating its flavor quality.}, }
@article {pmid41890980, year = {2026}, author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W}, title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101384}, pmid = {41890980}, issn = {2352-7714}, abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.}, }
@article {pmid41891006, year = {2026}, author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D}, title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.11.26348025}, pmid = {41891006}, abstract = {UNLABELLED: Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity, and can miss transmission involving low-abundance and co-colonizing strains. Here we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures collected between 2020 and 2025 at a single hospital. GI populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters, including six clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.
IMPACT STATEMENT: VREfm bloodstream infection is often seeded from bacteria colonizing the gut. The genetic diversity within gut and blood VREfm populations, and the role of this diversity in bacterial transmission, has been difficult to resolve as genomic surveillance typically relies on sequencing a clonal clinical isolate from each patient. Using culture-enriched metagenomic sequencing of matched GI tract and bloodstream VREfm populations from 35 patients at a single hospital, we found that the GI tract reservoir contained VREfm populations with greater strain and variant diversity than populations collected from the bloodstream. By integrating population sequencing with a large collection of VREfm clinical isolate genomes, we further demonstrate that different strains co-colonizing the GI tract of the same patient can reside in multiple putative transmission clusters, revealing potential transmission links that clone-based approaches are likely to miss. These findings demonstrate the potential utility of culture-enriched metagenomic sequencing for higher-resolution hospital surveillance of bacterial transmission. Applying this approach to other bacterial pathogens could improve our ability to detect and interpret transmission involving heterogeneous microbial populations that colonize and infect hospitalized patients.
DATA SUMMARY: Patient demographic data and clinical characteristics can be found in Table S1 (online Supplementary Material). All sequencing data generated in this study has been deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969, with sample accession numbers listed in Table S2 . Sequences used to construct the local reference strain database are available at NCBI BioProject PRJNA475751, with accession numbers listed in Table S3 . Variants identified in single-strain blood and GI populations are listed in Table S4 . Accession numbers for clinical isolate genomes included in transmission analyses are listed in Table S5 .
REPOSITORIES: Sequencing data generated in this study is deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969.}, }
@article {pmid41891018, year = {2026}, author = {Basso, M and Hildebrand, F and Winder, C and Baker, DJ and Manders, R and Barberis, M and Gibbons, SM and Cohen Kadosh, K}, title = {Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.18.26348688}, pmid = {41891018}, abstract = {Background Emerging evidence highlights the gut-brain axis as a key pathway linking diet and anxiety, yet the key determinants remain unclear. Most studies have focused on single components of diet and rarely integrate long- and short-term intake. Furthermore, prior gut-brain work has focused on microbiome composition, while functional features remain underexplored. In this study, we investigated associations between long- and short-term dietary intake, gut microbiome composition and functions, and anxiety in a subclinical cohort of 46 females (18-24 years) from the United Kingdom. Results Long-term diet quality was assessed using the Healthy Eating Index (HEI-2020) derived from a food frequency questionnaire, stratifying participants into lower and higher diet quality clusters. Short-term dietary intake was assessed via 24-hour recalls. Shotgun metagenomics of stool samples was used to assess differences in alpha and beta diversity indices, species abundances, and bacterial pathways putatively metabolizing gut-brain-axis-relevant molecules. Anxiety was measured using the State-Trait Anxiety Inventory (state subscale STAI-s). Regression models identified diet quality (HEI cluster) as the primary dietary feature of anxiety variation. The presence of Ruminococcus gnavus and Flavonifractor plautii and the abundances of Bilophila wadsworthia and Bacteroides thetaiotaomicron were positively associated with anxiety. The presence of Feacalibacterium prausnitzii and greater abundances of butyrate, propionate, and GABA synthesis pathways were inversely associated with anxiety. Non-linear models revealed a U-shaped relationship between inositol synthesis and STAI-s. Finally, we found that habitual diet quality may modulate anxiety-related responses to short-term dietary variation. Conclusions These findings reveal widespread links between long-term diet quality, microbiota composition and function, and anxiety symptoms. These results point towards several promising targets for prebiotic, probiotic, postbiotic, and dietary interventions aimed at reducing anxiety.}, }
@article {pmid41891399, year = {2026}, author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK}, title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71738}, doi = {10.1002/cam4.71738}, pmid = {41891399}, issn = {2045-7634}, support = {R21CA293626/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Liver Neoplasms/drug therapy/immunology/microbiology/complications ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; Dysbiosis/microbiology ; Drug Resistance, Neoplasm ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; }, abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.}, }
@article {pmid41891696, year = {2026}, author = {Toth, CRA and Molenda, O and Nesbø, CL and Luo, F and Devine, CE and Chen, X and Wu, K and Xiao, JZ and Puri, R and Guo, S and Bawa, N and Wang, P-H and Wei, Y and Flick, R and Edwards, EA}, title = {Identification of a highly expressed gene cluster likely coding for benzene activation enzymes in a methanogenic enrichment culture.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0208325}, doi = {10.1128/aem.02083-25}, pmid = {41891696}, issn = {1098-5336}, abstract = {UNLABELLED: The oil refinery (OR) consortium is a model methanogenic enrichment culture used to study anaerobic benzene degradation. Over half of the culture's bacterial community consists of two closely related Desulfobacterota strains, designated ORM2a and ORM2b, whose mechanisms of benzene activation are unknown. Three proteomics data sets were integrated and analyzed using high-quality OR metagenomes and metagenome-assembled genomes (MAGs), including a complete circularized ORM2a MAG, to identify active metabolic pathways and proteins expressed during methanogenic benzene degradation. Among the proteins identified were Bam-like subunits of an ATP-independent benzoyl-CoA degradation pathway, as well as downstream β-oxidation proteins yielding acetate. The most abundant proteins identified mapped to two ORM2a gene clusters of unknown function. Homologous and syntenic gene clusters were identified in the MAGs of ORM2b and a sulfate-reducing Pelotomaculum that also degrades benzene, as well as in nine contigs assembled from hydrothermal vent metagenomes. Extensive homology and structural predictions suggest that the first cluster-termed the "Magic" gene cluster-encodes for enzymes catalyzing the chemically challenging activation of benzene and subsequent transformation steps yielding benzoyl-CoA. The second ("Nanopod") gene cluster encodes a transmembrane complex that may facilitate benzene transport across the cell membrane. Phylogenomic analyses place ORM2a and ORM2b within a novel genus of strict anaerobes specialized for benzene degradation, which we propose naming "Candidatus Anaerobenzenivorax."
IMPORTANCE: Benzene is a widespread, persistent, and toxic pollutant that can accumulate in anoxic environments such as groundwater and sediments. Benzene can be metabolized in the absence of oxygen; however, despite decades of research, the biochemical mechanisms for benzene activation under anaerobic conditions remain unproven. This study provides strong genetic and proteomic evidence for a new suite of enzymes that initiate anaerobic benzene activation. These findings lay a foundation for future biochemical studies and expand our understanding of how microbes carry out difficult chemical reactions in the absence of oxygen.}, }
@article {pmid41891698, year = {2026}, author = {Li, Y and Ji, M and Tu, Q}, title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0143425}, doi = {10.1128/msystems.01434-25}, pmid = {41891698}, issn = {2379-5077}, abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.}, }
@article {pmid41892210, year = {2026}, author = {Liang, X and Li, X and Mi, N and Wu, Y and Wu, J and Chen, H and Liu, D}, title = {Early-Life Diarrhea Disrupts Antioxidant-Immune Homeostasis and Gut Microbiota in Suckling Calves.}, journal = {Biology}, volume = {15}, number = {6}, pages = {}, pmid = {41892210}, issn = {2079-7737}, support = {YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Au-tonomous Region/ ; 2024LHMS03054//nner Mongolia Natural Science Foundation Project/ ; }, abstract = {Calf diarrhea is a common early-life disorder that adversely affects growth, oxidative balance, immune function, and intestinal microbiota, thereby compromising health and production performance. This study systematically investigates the effects of naturally occurring diarrhea in 7-day-old suckling calves on oxidative stress, immune responses, intestinal barrier integrity, and gut microbiota structure and function. Fecal scores, serum antioxidant and immune indices, and intestinal permeability markers were measured, and fecal samples were subjected to metagenomic sequencing. Diarrhea-affected calves exhibited higher fecal scores, increased oxidative stress indicated by reduced total antioxidant capacity, elevated lipid peroxidation, and altered antioxidant enzyme activities. Humoral immunity was impaired, inflammatory responses were dysregulated, and intestinal barrier function was disrupted. Gut microbial diversity declined, showing a depletion in health-associated taxa and the enrichment of opportunistic pathogens. Correlation analyses revealed that pathogenic bacteria abundance positively associated with diarrhea severity, oxidative stress, inflammation, and barrier disruption, while beneficial genera correlated with antioxidant and immune function. Functional profiling indicated a microbial shift from amino acid metabolism and antioxidant homeostasis toward carbohydrate and energy metabolism under diarrheic conditions. These findings highlight the pivotal role of gut microbiota dysbiosis in diarrhea pathogenesis and provide a foundation for developing microbiome-targeted interventions to improve calf health.}, }
@article {pmid41892424, year = {2026}, author = {Gomes, E and Mesquita, TG and Serra, P and Araújo, D and Almeida, C and Machado, A and Oliveira, R and Castro, J}, title = {Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892424}, issn = {2079-6382}, support = {https://doi.org/10.54499/2024.13640.PEX//Fundação para a Ciência e Tecnologia/ ; https://doi.org/10.54499/2022.07654.PTDC//Fundação para a Ciência e Tecnologia/ ; APTA4shiga (number 14840)//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system.}, }
@article {pmid41892439, year = {2026}, author = {Gomes-Gonçalves, S and Bento, JT and Moreira, G and Mourão, J and Cruz, R and Esteves, F and Baptista, AL and Pereira, MA and Caseiro, P and Carreira, P and Figueira, L and Mesquita, JR}, title = {Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892439}, issn = {2079-6382}, support = {PRR-C05-i03-I-000190//RumiRes project-"Vigilância epidemiológica de resistências antimicrobianas e resíduos medicamentosos em Pequenos ruminantes da Região Centro"/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored.
METHODS: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal.
RESULTS: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin.
CONCLUSIONS: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.}, }
@article {pmid41892455, year = {2026}, author = {Dashti, AA and Vali, L and Walsh, F}, title = {Metagenomic Profiling of Soil Microbiomes and Resistomes in Arid Ecosystems of Kuwait.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892455}, issn = {2079-6382}, support = {(RN01/15))//Kuwait University/ ; (code EASREF).//University of Gloucestershire/ ; }, abstract = {Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics.}, }
@article {pmid41892478, year = {2026}, author = {Scarlata, GGM and Belančić, A and Štimac, D and Fajkić, A and Meštrović, T and Abenavoli, L}, title = {Bacteriophage Therapy Against Shigella spp.: A Precision Antimicrobial Strategy.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892478}, issn = {2079-6382}, abstract = {Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment.}, }
@article {pmid41892488, year = {2026}, author = {Mise, K and Wasai-Hara, S and Itoh, H}, title = {Global terrestrial distribution of N2O-reducing Acidobacteriota members.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag073}, pmid = {41892488}, issn = {1751-7370}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and soil is its largest terrestrial source. Microbial N2O reductase (NosZ) is the only known enzyme capable of reducing N2O to N2, making nosZ-harboring prokaryotes important sinks in terrestrial ecosystems. Despite being among the most abundant and ubiquitous bacterial phyla in soil, the potential role of Acidobacteriota in N2O reduction remains largely unexplored. In this study, we addressed this gap using genomic, metagenomic, and physiological analyses. We first analyzed 199,602 prokaryotic genomes, including genomes from both isolated strains and metagenome-assembled genomes. We found that 491 Acidobacteriota genomes harbored nosZ, predominantly the Sec-dependent NosZ gene (nosZII). Global metagenomic analysis of 321 soil samples revealed that Acidobacteriota nosZII is one of the most abundant groups of nosZ and distributed across different continents. Among Acidobacteriota, nosZII from the class Vicinamibacteria was the most prevalent in the soils. Finally, we provide the physiological evidence of N2O-reducing activity in Acidobacteriota by demonstrating that the Vicinamibacteria type strain, Luteitalea pratensis KCTC52215T, can reduce N2O. Taken together, these findings highlight the previously overlooked potential role of Acidobacteriota as a global N2O sink and underscore the need to include them in future studies on soil N2O dynamics.}, }
@article {pmid41892593, year = {2026}, author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A}, title = {Sulfoquinovose degradation by cow rumen microbiota.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag069}, pmid = {41892593}, issn = {1751-7370}, abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.}, }
@article {pmid41892682, year = {2026}, author = {Murgina, O and Stafeeva, K and Karaulova, S and Vostrikova, A and Kononova, S and Chursina, D and Pozdeeva, S and Makogonova, A and Burakova, I and Pogorelova, S and Morozova, P and Smirnova, Y and Syromyatnikov, M and Shutikov, V and Mikhailov, E and Gureev, A}, title = {Probiotic Bacillus subtilis, but Not a Lactobacillus spp., Ameliorates Cognitive Impairment in a Mouse Model of LPS and Zidovudine-Induced Neuroinflammation.}, journal = {Brain sciences}, volume = {16}, number = {3}, pages = {}, pmid = {41892682}, issn = {2076-3425}, support = {FZGW-2024-0003//Mikhail Syromyatnikov/ ; }, abstract = {Background/Objectives: The gut-brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut-brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut-brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions.}, }
@article {pmid41893096, year = {2026}, author = {Fan, J and Liu, S and Zhang, H and Jin, C and Wu, N}, title = {Dysbiosis of the Gut-Lung Axis and Its Immune Correlates During Pulmonary Cryptococcus neoformans Infection.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {41893096}, issn = {2309-608X}, support = {Grant No. 2023YFC2506004//National Key Research and Development Program of China/ ; }, abstract = {Cryptococcus neoformans is a major fungal pathogen responsible for life-threatening meningitis, especially in immunocompromised individuals. Although the gut-lung axis is known to regulate immune responses in respiratory infections, its role in cryptococcosis remains unclear. This study aimed to define the dynamic changes in the gut and lung microbiota and their relationship with host immunity during C. neoformans infection. Using a mouse model, we found that pulmonary infection induced significant dysbiosis in both the lung and gut microbiota, marked by decreased beneficial commensals and increased opportunistic pathogens. Integrated analysis showed these microbial shifts were closely associated with distinct immune responses: lung dysbiosis correlated with a strong IL-17-mediated pulmonary inflammatory response, while gut dysbiosis was linked to systemic immune activation in the spleen. Functional metagenomic prediction further revealed widespread disruption in microbial metabolic pathways, including energy metabolism and biosynthesis, in both sites. Importantly, a positive correlation was observed between lung and gut dysbiosis, indicating an interconnected gut-lung axis during cryptococcosis. These findings demonstrate that C. neoformans infection causes coordinated disruptions in microbiota and immunity across the gut-lung axis, underscoring the microbiome as a critical modulator of host response and suggesting potential avenues for microbiome-targeted therapies.}, }
@article {pmid41893137, year = {2026}, author = {Francis, DV and Kishorkumar, M and Ahmed, ZFR and Neumann, EG and Kurup, SS}, title = {Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {41893137}, issn = {2309-608X}, support = {21R097//ARIFSID/ ; }, abstract = {Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges.}, }
@article {pmid41893308, year = {2026}, author = {Yeerjiang, B and Manaer, T and Liu, X and Bieerdimulati, R and Nabi, X}, title = {Mechanistic Insights into Lactobacillus harbinensis and Other Probiotics Regulating Lipid Metabolism in T2DM Mice via the PPARγ-LXRα-NPC1L1 Signaling Pathway Based on Multi-Omics Analysis.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, pmid = {41893308}, issn = {2218-1989}, support = {No. 82260640//National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: Intestinal dysbiosis is a pivotal trigger of type 2 diabetes mellitus (T2DM). Our previous studies confirmed that composite probiotics derived from fermented camel milk (CPCM), containing Lactobacillus harbinensis and 13 other strains, can ameliorate glucose and lipid metabolism in T2DM mice by reshaping bile acid profiles, and its effect may be associated with the PPARγ-LXRα-NPC1L1 signaling pathway. Methods: Metagenomic analysis characterized alterations in intestinal microbiota structure and functional genes post-CPCM intervention, proteomic analysis detected changes in protein expression profiles related to glucose and lipid metabolism in mice, and Caco-2 cells were used for in vitro validation to clarify the regulatory effect of exopolysaccharides (EPS) (the active component of CPCM) on the PPARγ-LXRα-NPC1L1 signaling pathway. Results: The results showed that CPCM significantly improved glucose and lipid metabolism and remodeled the intestinal flora structure in mice, markedly enriching beneficial bacteria such as Lactobacillus and Akkermansia and enhancing the expression of functional genes related to the peroxisome proliferator-activated receptor (PPAR) signaling pathway and short-chain fatty acid synthesis in the microbiota. Proteomic analysis revealed that CPCM reversed the expression of key proteins involved in fatty acid oxidation and transport, thereby restoring the function of the PPAR signaling pathway. In vitro experiments validated that extracellular polysaccharides, the active component of CPCM, significantly upregulated the expression of PPARγ and liver X receptor α (LXRα) and inhibited the expression of Niemann-Pick C1-Like 1 (NPC1L1), a cholesterol absorption transporter, in Caco-2 cells. Conclusions: In conclusion, CPCM ameliorates glucose and lipid metabolic disorders in T2DM through multiple mechanisms: reshaping the intestinal probiotic community, enhancing its beneficial metabolic functions, restoring the activity of the PPARγ-LXRα signaling pathway, and subsequently downregulating NPC1L1.}, }
@article {pmid41893658, year = {2026}, author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Lampreht Tratar, U and Suchodolski, JS and Tozon, N}, title = {Assessment of Fecal Microbiota in Healthy Dogs and Dogs with Cutaneous Mast Cell Tumors Treated with Electrochemotherapy Combined with Gene Electrotransfer of IL-12.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893658}, issn = {2306-7381}, support = {P3-0428, P4-0053, P3-0003, and J4-2546//The Slovenian Research and Innovation Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&M University is in part funded through Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; }, abstract = {Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota.}, }
@article {pmid41893667, year = {2026}, author = {Karakaya, E and Satıcıoğlu, İB and Yarım, D and Güran, Ö and Güran, C and Alpman, U and Atalan, G and Abay, S and Aydın, F}, title = {Culture and Metagenomic Insights into the Ear Microbiota in Dogs with Healthy Ears and Otitis Externa.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893667}, issn = {2306-7381}, support = {TSA-2022-12342 and THD-2024-13751//Erciyes University/ ; }, abstract = {The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.}, }
@article {pmid41893692, year = {2026}, author = {Shehla, S and Obaid, MK and Niaz, S and Khan, MA and Ahmad, AA and Abdel-Maksoud, MA and Alamri, A and Alrokayan, S and Shoaib, M and Shams, S and Ren, Q}, title = {Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893692}, issn = {2306-7381}, support = {ORF-RC-2026-2600//King Saud University/ ; }, abstract = {Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host-microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40-49 genes), including critical genes, such as tet(X), blaOXA-427, and plasmidomes (16-22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance.}, }
@article {pmid41893724, year = {2026}, author = {Qiu, Q and Gong, T and Du, L and Li, W and Hu, Y and Li, D and Zhou, C and Liu, W}, title = {Comparative Analysis of Microbial Community Structure and Function in the Gut of South China Tigers Under Different Dietary Treatments.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893724}, issn = {2306-7381}, support = {2110499//Diagnosis and Treatment of Genetic Diseases and Training for Stereotypic Behaviors in South China Tigers at Changsha Ecological Zoo/ ; 2110499//Artificial breeding of Reeves's pheasant (Syrmaticus reevesii) at Changsha Ecological Zoo/ ; }, abstract = {The gut microbiota is a crucial component of a tiger's health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles.}, }
@article {pmid41893914, year = {2026}, author = {Pistone, D and Bevivino, G and Dipaola, MG and Bandi, C and Lombardo, F}, title = {Current and emerging molecular diagnostic approaches in the detection of human parasites.}, journal = {Parasitology research}, volume = {125}, number = {1}, pages = {}, pmid = {41893914}, issn = {1432-1955}, abstract = {Microscopy and morphological identification remain the gold standard for diagnosing most parasitic infections, yet their limited sensitivity in asymptomatic or low-burden cases, along with technical constraints, has accelerated the adoption of molecular diagnostics. Over the past three decades, advances in nucleic acid amplification and sequencing technologies have transformed parasite detection by improving sensitivity, specificity, and reproducibility, enabling earlier intervention and stronger surveillance. PCR remains the foundation of molecular diagnostics, with real-time PCR and digital PCR improving analytical performance and quantification. Multiplex qPCR supports simultaneous detection of multiple pathogens, while dPCR enables absolute quantification and rare variant detection, although broader implementation is limited by instrument cost. Isothermal amplification methods such as tHDA, NASBA, LAMP, and RPA offer rapid, low-cost amplification at constant temperature and are well suited for field diagnostics in resource-limited settings. Next-Generation Sequencing has advanced genotyping and epidemiological surveillance by resolving cryptic species, resistance mutations, and mixed infections through targeted panels, whole-genome sequencing, and metagenomics. CRISPR/Cas-based assays provide rapid and sensitive nucleic acid detection with strong potential for point-of-care deployment due to their simplicity and adaptability. Emerging biomarkers, including circulating cell-free DNA, non-coding RNAs, and microRNAs in extracellular vesicles, offer promising non-invasive diagnostic strategies, though further validation is required. This review offers a concise overview of these molecular approaches, emphasizing recent innovations such as dPCR, NGS, CRISPR/Cas systems, and biomarker-based detection. For each method, core technical principles, representative applications, and comparative strengths and limitations are presented to illustrate their diagnostic potential.}, }
@article {pmid41894043, year = {2026}, author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J}, title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41894043}, issn = {1573-7446}, support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; }, }
@article {pmid41894133, year = {2026}, author = {Zhang, X and Chen, L and Wang, F and Xu, X and Wu, Y and Xu, J and Xu, Y and He, X}, title = {Torque teno virus in the lower respiratory tract: association with immunosuppression but not mortality in severe pneumonia-a multicenter retrospective cohort study.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41894133}, issn = {1435-4373}, support = {2024C3186//Key Research and Development Program of Zhejiang Province/ ; GZY-ZJ-KJ-24030//Major Project of National-Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; }, }
@article {pmid41894264, year = {2026}, author = {Yu, Y and Hong, S and Wang, Z and Li, S and Zhang, S}, title = {Leptospirosis-induced diffuse alveolar hemorrhage: A rare case report from a non-epidemic area and literature review.}, journal = {Medicine}, volume = {105}, number = {13}, pages = {e48131}, doi = {10.1097/MD.0000000000048131}, pmid = {41894264}, issn = {1536-5964}, support = {No. LY21H100002//Zhejiang Natural Science Foundation Project/ ; No.2024C31025//Science and Technology Plan Project of zhoushan/ ; }, mesh = {Humans ; Female ; *Leptospirosis/complications/diagnosis/drug therapy ; Aged ; *Hemorrhage/etiology/diagnosis/microbiology ; *Pulmonary Alveoli/pathology ; *Lung Diseases/etiology/diagnosis/microbiology ; Shock, Septic/etiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {RATIONALE: Leptospirosis is an uncommon cause of severe pneumonia and diffuse alveolar hemorrhage (DAH), particularly in non-endemic areas, posing a significant diagnostic challenge. This case highlights the critical role of advanced molecular diagnostics in identifying this rare and life-threatening presentation.
PATIENT CONCERNS: A 65-year-old woman presented with an acute onset of high fever, chest tightness, and rapidly progressive shortness of breath.
DIAGNOSES: The patient was initially misdiagnosed with severe community-acquired pneumonia. She subsequently developed septic shock and multiple organ dysfunction syndrome. A definitive diagnosis of leptospirosis-induced DAH was confirmed through metagenomic next-generation sequencing, reverse transcription quantitative PCR, and subsequent seroconversion shown by immunoglobulin M enzyme-linked immunosorbent assay.
INTERVENTIONS: Upon diagnosis, targeted antimicrobial therapy with intravenous penicillin was initiated. Supportive care included management of septic shock and lung-protective ventilation for concomitant acute respiratory distress syndrome.
OUTCOMES: Following the confirmation of leptospirosis and initiation of targeted treatment, the patient's condition gradually stabilized. After a course of intensive care, she made a full recovery and was successfully discharged.
LESSONS: This case underscores that leptospirosis can present as fulminant DAH even in non-endemic regions. A high index of suspicion, aided by epidemiological clues and the rapid application of metagenomic next-generation sequencing/reverse transcription quantitative PCR, is crucial for timely diagnosis. Prompt targeted antimicrobial therapy combined with intensive organ support is essential for a favorable outcome in severe cases.}, }
@article {pmid41894564, year = {2026}, author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S}, title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70130}, pmid = {41894564}, issn = {1755-0998}, support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; Puerto Rico ; *Anthozoa/genetics/classification ; *Genetic Variation ; *Metagenomics/methods ; RNA, Ribosomal, 28S/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.}, }
@article {pmid41894872, year = {2026}, author = {Chen, H and Chai, Z and Chen, J and Song, C and Zheng, M}, title = {Anthraquinone-2-sulfonate enhances endogenous denitrification and phosphorus removal: Electron shuttle-mediated syntrophic partnerships.}, journal = {Water research}, volume = {298}, number = {}, pages = {125783}, doi = {10.1016/j.watres.2026.125783}, pmid = {41894872}, issn = {1879-2448}, abstract = {Endogenous denitrification (EnD) and denitrifying phosphorus removal (DPR) offer distinct advantages for low-carbon wastewater treatment, yet the nutrient removal performance is often constrained by inefficient electron transfer and nitrite/free nitrous acid (FNA) inhibition. Here, we demonstrate that anthraquinone-2-sulfonate (AQS) acts as an effective redox mediator to overcome these bottlenecks. With nitrate (NO3[-]-N) as the electron acceptor, the addition of 0.05 mmol/L AQS significantly amplified the electron transfer system activity (ETSA) by 3.66-fold. Consequently, this enhancement promoted the NO3[-]-N removal rate to 25.90 mg/(g VSS·h) (12.65-fold increase) and increased the phosphorus uptake rate to 3.69 mg/(g VSS·h) (1.95-fold improvement), achieving removal efficiencies of 96.22±1.00 % and 96.03±2.98 % for phosphorus and nitrogen, respectively. Moreover, when nitrite (NO2[-]-N) served as the electron acceptor, AQS enhanced the phosphorus uptake rate and nitrogen removal rate by 1.69-fold and 1.54-fold, respectively. Microbial analysis revealed a robust syntrophic partnership wherein Thauera, Candidatus Competibacter and Defluviicoccus (functioning as denitrifying glycogen-accumulating organisms) efficiently reduced NO3[-]-N to NO2[-]-N, which was subsequently scavenged by Dechloromonas and Candidatus Accumulibacter clade Ⅱ (functioning as denitrifying polyphosphate-accumulating organisms) for coupled phosphorus uptake. Metagenomic analysis further indicated that AQS facilitated electron transfer from Complexes I/Ⅱ to nitrate reductase and Complex Ⅲ, accelerating NO2[-]-N generation while alleviating FNA toxicity via coupled electron transfer from Cyt c to nitrite reductase. Crucially, this accelerated electron flux potentially intensified the proton motive force, suggesting an enhanced capacity for ATP generation to fuel the upregulation of phosphate transport (pit/pst) and polyphosphate synthesis (ppk) genes. These findings highlight AQS as a promising strategy to regulate electron transfer kinetics and metabolic coupling for advanced nutrient removal.}, }
@article {pmid41894881, year = {2026}, author = {Zhao, Y and Li, Y and Zheng, Y and Yan, P and Lai, Y and Wang, X and Zhuang, LL and Zhang, J}, title = {Enhanced co-removal of nutrients and glyphosate from rural sewage in siphon-driven constructed wetlands: Optimization and mechanisms.}, journal = {Water research}, volume = {298}, number = {}, pages = {125812}, doi = {10.1016/j.watres.2026.125812}, pmid = {41894881}, issn = {1879-2448}, abstract = {Constructed wetlands (CWs) often suffer from limited carbon/oxygen availability and poorly controlled redox conditions, constraining pollutant removal from rural sewage. Hence, siphon-driven CWs (S-CWs) were optimized for the co-removal of the typical rural pollutant glyphosate (N-(phosphonomethyl)glycine, PMG) and typical wastewater pollutants (carbon (C), nitrogen (N), phosphorus (P)). S-CWs exhibited strong PMG resilience, tolerating up to 8 mg/L, and achieved 50.91-92.14%, 50.93-56.82% and 96.19-97.18% for PMG, N and P removal, respectively. These results indicated superior performance compared with unaerated and aerated CWs. Mechanistic analysis showed that PMG removal was dominated by biodegradation in the aerobic, carbon-enriched inlet area of S-CWs. This process was driven by genera such as Alcaligenes and Geobacillus, and enzymes like PhnI, PhnJ via aminomethylphosphonic acid (AMPA) and C-P lyase pathways, as confirmed by metagenomics and AlphaFold 3 predictions. PMG transiently inhibited N removal by suppressing denitrification but not nitrification. However, microbial adaptation over 135 days restored N removal along the first 50% pathway, even under high PMG stress (10 mg/L). In contrast, P removal was more persistently inhibited throughout the system, as the additional PMG-derived P increased total P load and accelerated substrate adsorption saturation. Long-term operation confirmed the robustness of S-CWs, including reduced effluent toxicity, healthier plant growth, lower oxidative stress, and minimal clogging (only 1.40-13.53% porosity decline). These observations highlight the hydraulic stability and long-term suitability of S-CWs for treating PMG-laden rural wastewater.}, }
@article {pmid41895431, year = {2026}, author = {Ceruti, A and Bisia, M and Balatsos, G and Kobialka, RM and Zamil, MF and Hasan, A and Truyen, U and Lucati, F and Sanpera-Calbet, I and Palmer, JRB and Alam, MS and Michaelakis, A and Wahed, AAE}, title = {MosquitoID: Rapid metagenomic sequencing for offline mosquito surveillance.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {108071}, doi = {10.1016/j.actatropica.2026.108071}, pmid = {41895431}, issn = {1873-6254}, abstract = {Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning systems. In this study, a portable metagenomic sequencing approach using Oxford Nanopore Technologies (ONT) for field-based mosquito analysis (MosquitoID protocol) was developed, enabling species and host feeding patterns identification, and pathogen detection all coming from a single amplification-free workflow. DNA was extracted from 62 mosquito samples (Aedes albopictus, Aedes cretinus, Culex pipiens, Culiseta longiareolata) from Greece and Spain, either single-species pools (1-19 specimens),mixed-species pools, wirth reverse purification method or archived samples. Additionally, 30 pooled Aedes aegypti samples from Bangladesh underwent cDNA reverse purification. All samples were sequenced using ONT rapid barcoding kits. Offline bioinformatics analysis via Geneious screened custom BLAST databases for species, host, and virus identification. MosquitoID accurately identified mosquito species in 89% of samples overall, with main discrepancies in Aedes cretinus. Virus screening detected Phasi Charoen-like virus in cDNA samples. Host DNA sequences identified multiple species including horses, cattle, and ducks. This study demonstrates metagenomic ONT sequencing's effectiveness for rapid host, species, and virus identification. After further benchmarking, the approach shows potential for real-time disease monitoring and enhanced surveillance systems. Integrating portable next-generation sequencing with offline bioinformatics tools could significantly strengthen mosquito-borne disease prevention strategies, particularly for non-bioinformaticians and in resource-limited settings.}, }
@article {pmid41895455, year = {2026}, author = {Yin, W and Li, Y and Pan, A and Wu, J and Su, X and Xiao, X and Dong, F and Xu, L and Chen, C and Fu, H and Sun, F}, title = {Synergistic inhibition and microbial adaptation in anammox systems under long-term salinity and fulvic acid stress.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134498}, doi = {10.1016/j.biortech.2026.134498}, pmid = {41895455}, issn = {1873-2976}, abstract = {Salinity and fulvic acid frequently coexist in high-strength wastewater, yet their combined effects on anaerobic ammonium oxidation (anammox) remain unclear. This study evaluated their impacts on reactor performance, microbial community structure, and functional genes. Moderate salinity (5-10 g L[-1] NaCl) slightly enhanced anammox activity, whereas higher salinity (15 g L[-1]) and fulvic acid (> 60 mg L[-1]) significantly inhibited nitrogen removal. Under such combined stress, specific anammox activity decreased by about 40%, indicating a synergistic inhibition. Extracellular polymeric substances increased by 198%, suggesting a microbial stress-response strategy. Microbial community analysis showed a decline in Planctomycetes by 11%, and enrichment of Proteobacteria by 7% and Chloroflexi by 4%. Metagenomic results revealed suppression of key anammox genes and enrichment of denitrification genes, with quorum sensing and polysaccharide biosynthesis genes increased, suggesting EPS-mediated adaptation under combined stress. These findings provide insights for improving anammox stability in saline and humic-rich wastewater treatment systems.}, }
@article {pmid41895928, year = {2026}, author = {Movsesijan, T and Alcañiz, AJ and Roch, FF and Chaughtai, MS and Dzieciol, M and Stessl, B and Thalguter, S and Strachan, CR and Raindl, M and Wagner, M and Selberherr, E and Quijada, NM}, title = {Biofilm capacity of the psychrophilic bacteria triggers their persistence in the equipment and their spread to beef products throughout processing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118808}, doi = {10.1016/j.foodres.2026.118808}, pmid = {41895928}, issn = {1873-7145}, mesh = {*Biofilms/growth & development ; Animals ; Cattle ; *Red Meat/microbiology ; *Food Handling/instrumentation ; *Food Microbiology ; *Psychrobacter/genetics/isolation & purification/physiology ; *Equipment Contamination ; Pseudomonas/genetics/isolation & purification/physiology ; Abattoirs ; *Food Contamination/analysis ; *Meat Products/microbiology ; }, abstract = {Microbial contamination in food processing remains a persistent and complex challenge. Understanding the sources, contributing factors, and control measures is essential for effective mitigation. In this study we employed a combination of metagenomic sequencing, targeted culturomics, and whole-genome sequencing of key isolates to gain a comprehensive view of bacterial dynamics and functional capabilities throughout a working shift in a beef slaughter and cutting facility. This allowed us to identify which bacteria are i) most prevalent in the clean facility before the start of the work, ii) able to establish themselves over time, and iii) detectable in the final product. We further generated a functional profile of the microbial community within the facility, with a particular focus on antimicrobial resistance and biofilm formation genes, and the presence of specific pathogens and spoilage organisms. Both culture-based and sequencing data showed that Psychrobacter and Pseudomonas strains present in the final product were also detected on the membrane skinner, a machine used to remove all the excess tissues from meat, and in the drains even after cleaning. We found a high number of genes involved in biofilm formation in Psychrobacter immobilis, a characteristic that may explain their biofilm capacity and the survival of this species during the cleaning process and persistence throughout the facility. Taken together, our findings suggest potential sources of contamination and highlight the advantages of integrating culture-dependent methods with high-throughput sequencing technologies to enhance microbial monitoring and control strategies in food production environments.}, }
@article {pmid41895935, year = {2026}, author = {Li, H and Hu, H and Lu, W and Liu, J and Peng, Q and Wang, S and Dan, T}, title = {Metagenomic analysis of lactic acid bacteria communities in inner Mongolian fermented dairy products: influence of milk source and geography.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118849}, doi = {10.1016/j.foodres.2026.118849}, pmid = {41895935}, issn = {1873-7145}, mesh = {Animals ; *Cultured Milk Products/microbiology ; China ; *Metagenomics/methods ; *Lactobacillales/genetics/classification/isolation & purification ; Cattle ; *Milk/microbiology ; *Food Microbiology ; Fermentation ; Geography ; Horses ; }, abstract = {Inner Mongolia, a key grassland region in China, has a long-standing tradition of fermented dairy products. This study aimed to elucidate the influence of milk source and geographical origin on the community structure and functional characteristics of lactic acid bacteria (LAB) in fermented milk. Twenty-four fermented milk samples from four regions were subjected to metagenomic sequencing analysis including α/β-diversity assessment, taxonomic classification, and functional annotation. The milk source and geographical region jointly shaped the diversity of LAB. The LAB community structure in fermented mare milk displayed more pronounced geographical differentiation than that in fermented cow milk. The core dominant LAB species included Lactobacillus kefiranofaciens, Lactobacillus helveticus, and Lactococcus lactis, with L. helveticus being more abundant in fermented mare milk. The functional profiles of LAB varied depending on the milk source used. The data indicated that milk source was a primary factor associated with the core LAB composition, while geographical origin was associated with the modulation of community diversity and functional attributes. These findings provide region-specific insights into the microbial ecology of traditional Inner Mongolian fermented dairy products.}, }
@article {pmid41895941, year = {2026}, author = {Zhang, J and Li, Y and Zhao, X and Wang, Q and Li, J and Xia, Y and Jambal, T and Dorjgotov, D and Zha, M and Chen, Y}, title = {The cheese of Xilingol: A comparative study on microbial diversity and metabolic profiles across typical and meadow steppes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118860}, doi = {10.1016/j.foodres.2026.118860}, pmid = {41895941}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Milk/microbiology ; *Food Microbiology ; Animals ; Moraxella/isolation & purification/metabolism ; Lactococcus lactis/isolation & purification/metabolism ; *Microbiota ; *Metabolome ; Amino Acids/analysis ; China ; }, abstract = {Xilingol cheese (hurood), a traditional product of Inner Mongolia, acquires its superior flavor and quality from region-specific microbial communities. Understanding the microorganisms and metabolites of hurood across different grassland ecosystems is crucial. This study collected milk and hurood samples from typical and meadow steppes. A total of 179 species were identified, with Moraxella osloensis being more abundant in milk and Lactococcus lactis dominant in hurood. Additionally, 26 differential metabolites were screened from different grasslands, with 19 metabolites found in higher concentrations in hurood, such as N-lactoyl-phenylalanine and N-Acetyl-L-Histidine. These differential metabolites are mainly involved in lipid, carbohydrate, amino acid, and energy metabolism. Spearman correlation analysis revealed that L. lactis was significantly and positively correlated with differential metabolites such as O-phospho-l-serine and gluconic acid, which may affect hurood quality through carbohydrate and protein metabolism, especially amino acid metabolism. M. osloensis was positively correlated with metabolites such as 2-Methylhippuric acid and γ-Glu-Cys. Samples from typical steppe showed a richer microbial diversity, while samples from meadow steppe exhibited a higher enrichment of beneficial microorganisms and metabolites. Superior milk quality and the environmental conditions for lactic acid bacteria colonization may both promote the formation of superior flavor characteristics and functional components. This observational study offers valuable insights into the microbial and metabolic characteristics of hurood, thereby supporting efforts to improve hurood quality.}, }
@article {pmid41895971, year = {2026}, author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M}, title = {Microbiota of foods: a comprehensive review of diversity and potential implications.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118899}, doi = {10.1016/j.foodres.2026.118899}, pmid = {41895971}, issn = {1873-7145}, mesh = {*Food Microbiology ; *Fermented Foods/microbiology ; *Microbiota ; Fermentation ; Metagenomics ; Humans ; Metabolomics ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.}, }
@article {pmid41896456, year = {2026}, author = {Habot-Wilner, Z and Ostrovsky, M and Zur, D and Schwartz, S and Hagin, D and Gadoth, A and Ben-Ami, R and Paran, Y and Goldshmidt, H and Slutzkin, M and Adler, A and Levytskyi, K}, title = {Response to: 'Comment on 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections''.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {41896456}, issn = {1476-5454}, }
@article {pmid41896477, year = {2026}, author = {Shaw, J and Marin, MG and Li, H}, title = {High-resolution metagenome assembly for modern long reads with myloasm.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41896477}, issn = {1546-1696}, support = {R01HG010040//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; PDF-587396//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; }, abstract = {Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. Here we present myloasm, a metagenome assembler for modern long reads such as PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi assemblies comparable. For example, on a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm also recovers previously inaccessible within-species diversity. Here, we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with >93% similarity from an oral metagenome. Overall, we show that myloasm outperforms existing long-read metagenome assemblers across a range of environments and modern sequencing technologies.}, }
@article {pmid41896490, year = {2026}, author = {Zheng, M and Yang, X and Tian, R and Xia, X and Xu, Q and Hui, Y and Chen, S and Liu, Y and Wang, A}, title = {A Segatella Copri-centered Gut Microbiota-mediated Metabolic Dysregulation Associated with Transition from Asymptomatic to Symptomatic Intracranial Atherosclerosis.}, journal = {Translational stroke research}, volume = {17}, number = {2}, pages = {}, pmid = {41896490}, issn = {1868-601X}, support = {82504498//National Natural Science Foundation of China/ ; 82473699//National Natural Science Foundation of China/ ; 2022YFC3600600//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Intracranial Arteriosclerosis/metabolism/microbiology ; Case-Control Studies ; Aged ; Biomarkers/blood ; Metabolomics ; *Ischemic Stroke/metabolism/microbiology ; }, abstract = {The mechanisms underlying the continuum from asymptomatic intracranial atherosclerotic stenosis (aICAS) to symptomatic intracranial large-artery atherosclerotic ischemic stroke (iLAA-IS) remain unclear. We investigated the gut microbiota-metabolite axis in this transition to identify predictive biomarkers and clarify key functional pathways. In a case-control study (63 iLAA-IS cases; 56 aICAS controls), fecal shotgun metagenomics and untargeted plasma metabolomics were profiled. Using machine learning with 10-fold nested cross-validation, we identified five robust biomarkers associated with the transition: Alistipes putredinis (risk-associated) and four protective features (Segatella copri, Gln-Gly, Methionine Sulfoxide, and N6-Acetyl-L-Lysine). Integrated models incorporating these markers significantly improved predictive performance relative to conventional risk factors (e.g., mean AUC of Gln-Gly: 0.9104 vs. 0.7188). Mechanistic analyses revealed a Segatella copri-centered metabolic dysregulation: its depletion coincided with a broad loss of anabolic pathways (BCAA biosynthesis, folate-SAM-methionine metabolism, and tRNA charging), which were positively linked to amino acid-related metabolites. In contrast, the pathways of Alistipes putredinis showed no such coupling. These findings suggest that the aICAS-to-iLAA-IS transition is characterized by chronic metabolic dysregulation, involving a Segatella copri-centered microbiota-metabolite axis. This multi-omic signature offers novel insights into stroke pathogenesis and potential targets for prevention.}, }
@article {pmid41896556, year = {2026}, author = {Walsh, LH and Soni, V and Ancla, J and Somerville, V and Segata, N and Joyce, S and Sinderen, DV and Mahony, J and Shkoporov, AN and Kenny, JG and Cotter, PD and O'Sullivan, O}, title = {Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00941-9}, pmid = {41896556}, issn = {2055-5008}, support = {DOMINO-101060218//European Union's Horizon Europe programme/ ; }, abstract = {Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.}, }
@article {pmid41896639, year = {2026}, author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP}, title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41896639}, issn = {2399-3642}, support = {NIH R35 GM144276//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Behavior, Animal ; *Foxes/microbiology/physiology ; Phenotype ; Domestication ; Male ; }, abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.}, }
@article {pmid41896653, year = {2026}, author = {Zhao, Z and Yang, Y and Zhang, L and He, X and Ding, K and Chen, Y and Huo, Y and Li, P and Li, R and Ali, T and Zhao, D and Choe, H and Ma, J and Shang, D and Zhang, L}, title = {Multi-omics and network pharmacology reveal the mechanisms of Scutellaria barbata D.Don and Scleromitrion diffusum (Willd.) R.J.Wang against pancreatic cancer.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45676-x}, pmid = {41896653}, issn = {2045-2322}, support = {2022-BS-244//Liaoning Provincial Doctoral Research Startup Fund Project/ ; XLYC1907113//Liaoning Revitalization Talents Program/ ; 2022RJ19//Distinguished Young Scholars in Dalian/ ; }, abstract = {Pancreatic cancer (PC) is a common gastrointestinal malignancy whose initiation and progression may be closely linked to the gut microbiota. Previous research indicates that Scutellaria barbata D. Don and Scleromitrion diffusum (Willd.) R.J. Wang (SB-SD) exhibit diverse biological activities, such as anti-inflammatory, antioxidant, and antitumor effects, though their precise regulatory mechanisms are not fully elucidated. Here, we treated PC cells with SB-SD to assess its impact on cell viability, apoptosis, migration, and cell cycle progression, while Western blotting analyzed the expression of HSP90AA1, MAPK3, p53, CDK1, and p21. We also established a pancreatic cancer xenograft model in nude mice to evaluate the in vivo inhibitory effect of SB-SD on tumor growth. Furthermore, we employed metagenomic sequencing, untargeted metabolomics, and quantitative proteomics to comprehensively profile changes in the gut microbiota, serum metabolites, and differentially expressed proteins, with Western blotting subsequently validating BCKDK, GATM and p53 expression. The results show that SB-SD significantly inhibited PC cell proliferation, promoted apoptosis, and induced S/G2 phase cell cycle arrest, potentially via modulation of the HSP90AA1/MAPK3 signaling pathway. Measurements of tumor volume and weight, complemented by histopathological analysis, confirmed that SB-SD effectively suppressed the growth of PANC-1 xenograft tumors. Integrated multi-omics analyses suggest that the antitumor effects of SB-SD may involve the modulation of key gut microbes like Bacteroides caccae and Lactobacillus, the promotion of choline metabolism, and the regulation of BCKDK and GATM. Together, these findings not only corroborate the direct antitumor activity of SB-SD against pancreatic cancer but also offer novel mechanistic insights by constructing a microbiota-metabolite-protein interaction network.}, }
@article {pmid41896698, year = {2026}, author = {Jung, S and Militsi, E and Huck, O}, title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70215}, pmid = {41896698}, issn = {1601-0825}, abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.
METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).
RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sjögren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct β-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.
CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.}, }
@article {pmid41897379, year = {2026}, author = {Zhang, Y and Zhao, B and Li, J and Yuan, T and Liu, Y and Sun, Z}, title = {Effects and Adaptive Responses of Sulfate-Reducing Biochemical System to Acid Stress.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, pmid = {41897379}, issn = {2218-273X}, support = {41772266//State Key Laboratory of Nuclear Resources and Environment, the National Natural Science Foundation of China/ ; }, mesh = {*Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Desulfovibrio/metabolism/genetics ; Oxidation-Reduction ; *Adaptation, Physiological ; *Stress, Physiological ; Acids ; }, abstract = {A decrease in pH can affect the biochemical properties of a sulfate reduction system, but the stress responses to such pH fluctuations and acid-adaptive mechanisms of the microorganisms remain incompletely understood. Here, we compared the sulfate (SO4[2-]) reduction performance of a sulfate-reducing consortium (SRB system) and a pure Desulfovibrio sp. system (Des. system, control) under pH 7.0, 5.5, and 5.0 via batch experiments. A key novelty is the integration of microbial physiology and metagenomics to reveal adaptive mechanisms: the Des. system showed significant inhibition of growth and sulfate reduction with decreasing pH, while the SRB system maintained superior SO4[2-] removal efficiency through three synergistic adjustments: (1) physiological regulation (enhanced H[+]-ATPase activity, stress protein production, and cell membrane cyclopropane fatty acid content); (2) microbial community restructuring (enrichment of acid-resistant Bacillus and Clostridium); and (3) functional gene upregulation (sulfate import, dissimilar sulfate reduction, sulfide oxidation, and SOx system-related genes, p < 0.05). This study links physiological responses to metagenomic functional shifts under acid stress, providing critical theoretical support for applying sulfate-reducing consortia in acidic sulfate-containing wastewater remediation.}, }
@article {pmid41897502, year = {2026}, author = {Khan, A and Xiong, Z and Khan, IA and Cheng, X and Luo, Q and Jia, L and Liu, W and Huang, C and Chen, Z}, title = {Dimercaprol Reprograms Intestinal Redox Homeostasis and Organelle Crosstalk to Combat Iron-Induced Gut Dysbiosis Through NRF2/HO-1 Signaling.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41897502}, issn = {2076-3921}, support = {2024YFHZ0325//Zhengli Chen/ ; 32071161//Chao Huang/ ; 2023NSFC1929//Chao Huang/ ; }, abstract = {Gut disorders are largely caused by iron-induced microbial dysbiosis. Excess iron disrupts barrier integrity by inducing oxidative stress, leading to impaired cellular processes. The determination of therapeutic compounds that can reduce iron-induced damage and maintain gut cellular integrity is still a top objective. Dimercaprol (DP) represents a novel iron-chelating strategy for the treatment of iron-induced gut disorders. A chronic iron-overload model was established in mice via intragastric gavage of ferric citrate (FC) (286 mg/kg BW) for 16 weeks. Similarly, IPEC-J2 cells were exposed to FC (50 µmol/L) for 24 h. DP was used as a mechanistic probe to elucidate the pathways involved in iron-induced toxicity. Cells were transfected with or without NRF2 siRNA and exposed to DP post-FC. Colonic contents were assessed via metagenomics and metabolomics. Both in vivo and in vitro experiments were analyzed through a multifaceted analysis, Western blot, RT-qPCR, ELISA, transmission electron microscopy and immunofluorescence assays. Thiols in DP protect gut cells from damage by boosting their natural antioxidant defenses via the NRF2/HO-1 pathway. The DP mechanism of action is multifaceted, including enhancement of barrier integrity, protecting mitochondrial structure and function, suppression of inflammation and endoplasmic reticulum (ER) stress and restoration of gut microbial and metabolic homeostasis. These protective effects are mainly caused by the activation of the NRF2/HO-1 pathway, which makes DP a potential therapeutic agent for disorders caused by chronic gut injury induced by FC. DP provides strong protection against iron-induced gut damage by restoring organelle crosstalk, redox homeostasis and microbial-metabolic balance through NRF2/HO-1 signaling.}, }
@article {pmid41897791, year = {2026}, author = {Xie, M and Xue, F and Sun, M and Zhuang, Q and Tang, S and Huang, Y and Zhang, Y and Hu, J and Zhou, Y}, title = {Determination of the Modulatory Effects of Selenium-Enriched Egg Powder on the Physiological Immune Response and Cecal Microbiota of Kunming Mice.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, pmid = {41897791}, issn = {2304-8158}, support = {20252BAC240155//Natural Science Foundation Project of Jiangxi Province/ ; JX-202401//the Open research projects of key laboratories of the Jiangxi Province "Mechanism Research of the Regulation on Immune System by Selenium-enriched Eggs"/ ; }, abstract = {Se-enriched functional eggs are prevalent nowadays, which may help improve body health and anti-oxidant capacities. However, the modulatory effects on cecal microbiota are still limited. This study aims to investigate the underlying mechanism of Se-enriched egg powder in modulating the cecal microbiota of Kunming mice. A total of 72 mice were randomly assigned to a control treatment (CON), a conventional egg powder treatment (EP), and four gradient Se-enriched egg powder treatments (EPS1-EPS4, with the Se content ranging from 0.01 to 0.04% of total dietary content) for a 35-day feeding procedure. Parameters included growth performance, tissue Se content distribution, serum anti-oxidant capacities (GSH-Px, SOD, MDA), and immune cytokines (IgG, TNF-α), and cecal microbiota composition was further measured. Results showed dietary 0.02% (EPS2) significantly improved growth performance, physiological anti-oxidant defenses, and cytokine TNF-α (p < 0.05), while significantly reducing feed conversion ratio and malondialdehyde (MDA) compared with CON (p < 0.05). Metagenomic results revealed that Se-enriched egg powder significantly increased bacterial α-diversity and the abundance of Akkermansia, Bacteroides, and Bifidobacterium (p < 0.05), while significantly decreasing Desulfovibrio and Escherichia-Shigella (p < 0.05). In conclusion, dietary supplementation with Se-enriched egg powder effectively enhances growth performance, anti-oxidant capacity, and immunity, mainly through the promotion of beneficial bacteria diversity and suppression of pathogens.}, }
@article {pmid41897857, year = {2026}, author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L}, title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, pmid = {41897857}, issn = {2076-2615}, support = {42367014//The National Natural Science Foundation of China/ ; }, abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.}, }
@article {pmid41897913, year = {2026}, author = {An, Q and Chen, S and Ma, S and Bai, R and Lu, Z and Liu, Y and Wang, F and Wang, Q and Song, Y and Zhang, G and Lyu, Y and Wang, L and Wang, Y and Xia, Z}, title = {Shotgun Metagenomics Reveals Gut Microbiome Remodeling with Altered Taxonomic Composition and Functional Potential in Diabetic Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, pmid = {41897913}, issn = {2076-2615}, support = {1051-2225006//General Program of the 2025 Talent Fund, Veterinary Teaching Hospital, China Agricultural University/ ; }, abstract = {Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management.}, }
@article {pmid41897927, year = {2026}, author = {Fukuda, EP and Lu, Y and Fowler, E and Jessup, RW and Drewery, ML}, title = {Metagenomic Insights into the Effects of Dietary Thymol on the Structure and Function of the Rumen Microbial Community in Beef Steers Consuming Forage.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, pmid = {41897927}, issn = {2076-2615}, support = {2021-77040-34881//National Institute of Food and Agriculture/ ; 2020-38422-32250//National Institute of Food and Agriculture/ ; N/a//Translational Health Research Center/ ; }, abstract = {While essential oils are gaining momentum as a strategy to modulate rumen function and potentially reduce enteric methane in cattle, little is known about how their bioactive components, terpenes, affect rumen microbes. Our objective was to evaluate how in vivo doses of thymol affect the structure and function of the rumen microbial community via whole genome shotgun sequencing (WGS). Four beef steers were used in a 4 × 4 Latin square with four 28 d periods. Steers consumed ad libitum forage and received one of four thymol doses (0 [CON], 120 [120-T], 240 [240-T], and 480 [480-T] mg/kg forage intake). Rumen contents were separated into liquid and solid fractions, DNA was extracted, analyzed via WGS, and assessed with orthogonal contrasts. After FDR correction, no taxa were affected by thymol; however, raw p-values demonstrated responses to thymol supplementation for solid-associated uncultured Lachnospiraceae bacterium (p = 0.04), uncultured Methanobrevibacter (p = 0.05), and uncultured Coriobacteriaceae bacterium (p = 0.02). Liquid-associated uncultured Prevotellaceae bacterium (p = 0.03), Prevotella sp. (p = 0.04), and Bacteroides sp. (p = 0.02) also responded to thymol, with the highest abundances observed at various thymol doses. Genes involved in energy production and amino acid metabolism transport were observed at the highest abundances at 240-T, while genes associated with cell cycle control, cell division, and chromosome partitioning were present in the highest abundances at 120-T. The findings suggest that thymol exerts dose-dependent effects on rumen microbial abundances and functional pathways, with 240 mg/kg forage intake appearing to be the most effective dose to downregulate methanogenic enzymes while also enhancing the enzymes associated with metabolism without negatively impacting microbial diversity.}, }
@article {pmid41898277, year = {2026}, author = {Qiu, D and Suo, L and Wei, T and Lu, Z and Weng, Q and Xiao, J and Wang, X and Xu, Q and Wu, J}, title = {Mediation Role of Gut Microbiota in the Causal Relationship Between m6A Regulatory Genes and Metabolic Dysfunction-Associated Steatotic Liver Disease: A Mendelian Randomization Study.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, pmid = {41898277}, issn = {2227-9059}, support = {3502Z20227102//Qinyu Xu/ ; }, abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a globally prevalent condition with a complex pathogenesis. While both m6A RNA methylation regulators and gut microbiota have been independently implicated in MASLD, their potential causal interplay remains unexplored. This study aimed to investigate the causal relationships among m6A regulatory genes, gut microbiota, and MASLD, and to assess the mediating role of gut microbiota. Methods: We performed a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data. Genetic instruments for m6A regulators were derived from blood expression quantitative trait loci (eQTL) data. Gut microbiota and MASLD data were obtained from large-scale metagenomic and disease GWAS, respectively. The inverse-variance weighted method was the primary analysis, supplemented by sensitivity and mediation analyses to evaluate potential mediating pathways. Results: Genetically predicted levels of four m6A regulators showed significant causal associations with MASLD risk: ALKBH3 increased risk (OR = 1.17), whereas ALKBH5 (OR = 0.89), CBLL1 (OR = 0.76), and RBM15B (OR = 0.83) were protective. Nineteen gut microbial taxa were causally linked to MASLD. Among these, seven taxa were influenced by the four identified m6A genes. Although no mediation effects reached strict statistical significance, the pathway from ALKBH5 to MASLD via Parabacteroides abundance showed a suggestive indirect effect accounting for 21.9% of the total effect (p = 0.068). Given the limited statistical power of mediation analyses in MR settings, this observation should be interpreted with caution and requires validation in larger, well-powered studies. Conclusions: This MR study provides genetic evidence supporting causal roles of specific m6A regulators in MASLD and suggests that gut microbiota may partially mediate these relationships. The findings highlight a potential "m6A-gut microbiota-liver" axis in MASLD pathogenesis.}, }
@article {pmid41898335, year = {2026}, author = {Schultheiss, HP and Escher, F and Aleshcheva, G and Wiegleb, G and Baumeier, C}, title = {Diagnostic and Therapeutic Options in Myocarditis and Inflammatory Cardiomyopathy.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, pmid = {41898335}, issn = {2227-9059}, support = {KK5175802AP2, KK5463501AP2, KK5463901AP2//Federal Ministry of Economic Affairs, Germany/ ; 10169096, 10169098, 10169028//ProFIT grant of the Investitionsbank Berlin/co-funded by EFRE/ ; }, abstract = {Myocarditis and inflammatory cardiomyopathy are inflammatory diseases of the heart muscle that can have both infectious and non-infectious causes. They can be caused by an unresolved viral infection or other infection, or they can be autoimmune, toxic, or allergic in nature. The specific identification of the pathogen and/or confirmation of inflammation can only be achieved through direct tissue analysis using endomyocardial biopsy (EMB), as neither detection of the virus nor assessment of the quality and intensity of the inflammation is possible using non-invasive methods. Accordingly, the removal and analysis of an EMB is considered the diagnostic gold standard in international guidelines and statements. The sudden onset of atypical angina pectoris and initially exertion-dependent dyspnea, as well as arrhythmias, pericardial effusion, and progressive symptoms of heart failure, indicate an acute inflammatory process of the myocardium. In addition, nonspecific symptoms such as fatigue and reduced physical performance may also occur. Diagnostic evaluation includes an electrocardiogram (ECG), cardiac imaging, and laboratory tests. The analysis of the EMB is crucial for a definitive diagnosis and thus for the initiation of an etiology-based, specific and personalized therapy. This includes histological and immunohistochemical inflammation diagnostics as well as molecular virological diagnostics. These enable both the detection of viruses and the assessment of transcriptional virus activity. New analyses using metagenomic next generation sequencing (NGS) techniques provide insights of enormous diagnostic and therapeutic relevance. This applies both to the spectrum of detectable pathogens and to the possibility of confirming transcriptional viral activity. In addition, gene expression profiling enables the differentiation of specific forms of myocardial inflammation (e.g., giant cell myocarditis, cardiac sarcoidosis, and eosinophilic myocarditis) and reduces the influence of "sampling errors" in focal inflammatory processes. The treatment of heart failure or ventricular arrhythmias is always symptomatic according to general evidence-based guidelines. In severe cases, mechanical circulatory support or even a heart transplant may be necessary. Patients with histologically confirmed myocardial inflammation or intramyocardial viral infection can be offered specific, causal, and personalized therapy. These patients can be successfully treated with immunosuppressive or antiviral therapy, which significantly improves the prognosis of the disease.}, }
@article {pmid41898386, year = {2026}, author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y}, title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898386}, issn = {1422-0067}, mesh = {Humans ; Female ; *Microbiota ; *Women's Health ; *Precision Medicine ; Probiotics ; Pregnancy ; Vagina/microbiology ; Gastrointestinal Microbiome ; }, abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.}, }
@article {pmid41898595, year = {2026}, author = {Makiel, K}, title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898595}, issn = {1422-0067}, support = {//University of Physical Education, 31-571 Cracow, Poland/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolic Syndrome/diet therapy/metabolism/genetics/microbiology ; *Obesity/diet therapy/metabolism/genetics/microbiology ; *Adipokines/metabolism/genetics ; *DNA Methylation ; *Diet ; Animals ; Inflammation ; Nutrigenomics ; Multiomics ; }, abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.}, }
@article {pmid41898625, year = {2026}, author = {Chaplin, AV and Podoprigora, IV and Shcherbakova, VA and Zakharzhevskaya, NB and Evseev, PV and Vasilyeva, AA and Koshkin, FA and Kardonsky, DA and Vorobyeva, EA and Kashatnikova, DA and Kazakova, VD and Efimov, BA}, title = {Parabacteroides vesiculifaciens sp. nov., a Novel Immunomodulatory, Vesicle-Producing Gut Commensal Isolated from the Human Gut.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898625}, issn = {1422-0067}, support = {24-75-10100//Russian Science Foundation/ ; }, mesh = {Humans ; Phylogeny ; *Gastrointestinal Microbiome ; *Bacteroidetes/genetics/classification/isolation & purification ; Feces/microbiology ; Genome, Bacterial ; Animals ; HT29 Cells ; Extracellular Vesicles/metabolism ; Mice ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025[T], isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025[T] within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, "P. massiliensis", P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5-89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C15:0, iso-C17:0 3-OH, and C15:0. Conditioned medium from ASD2025[T] antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025[T] (=VKM B-3926[T] = JCM 37967[T]) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed.}, }
@article {pmid41898646, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Jimenez, M and Koralnik, IJ}, title = {Predictive Utility of ViroFind Detection of Blood and CSF Virome for Viral Presence in Human Brain Tissue.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898646}, issn = {1422-0067}, support = {DA048493/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Brain/virology ; *Virome ; HIV Infections/virology/blood/cerebrospinal fluid ; Male ; Female ; Herpesvirus 4, Human/isolation & purification/genetics ; Adult ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Torque teno virus/genetics/isolation & purification ; Viral Load ; Viruses/genetics/isolation & purification ; }, abstract = {Viral presence in the brain may contribute to chronic neurologic diseases. However, investigating these associations is limited by the difficulty of directly sampling brain tissue in living individuals. Here, we evaluated whether peripheral viral detection using unbiased target-enrichment next-generation sequencing could inform viral presence in the brain across a diverse set of viral taxa. We applied ViroFind to matched brain, blood (peripheral blood mononuclear cells, spleen, and/or lymph node), and cerebrospinal fluid (CSF) to assess the predictive utility of viral detection in blood and CSF for identifying viral presence in brain samples obtained from the National NeuroAIDS Tissue Consortium, including both HIV-infected (HIV[+]) and HIV-uninfected (HIV[-]) individuals without known active viral infection of the brain. Blood negativity was generally more informative for predicting the absence of viruses in the brain than blood positivity for predicting viral presence. CSF viral detection demonstrated limited predictive utility for brain presence across most viral taxa examined. Among blood[+] individuals, viral burden differed significantly between brain[+] and brain[-] cases for Epstein-Barr virus (EBV), parvovirus, and torque teno virus (TTV). Blood viral burden showed moderate ability to distinguish brain[+] from brain[-] cases for EBV and parvovirus, and strong discriminatory ability for TTV, with similar decision thresholds across HIV[+] and HIV[-] individuals.}, }
@article {pmid41898837, year = {2026}, author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P}, title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, pmid = {41898837}, issn = {2073-4425}, mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; }, abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.}, }
@article {pmid41898993, year = {2026}, author = {Tanachaiwiwat, P and Sanscrainte, ND and Okech, BA and Estep, AS}, title = {Insecticide Resistance Mutations, Enzymatic Activity, and Pathogen Infection in Culex quinquefasciatus from Haiti.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898993}, issn = {2075-4450}, support = {P0138_22_HS//Armed Forces Health Surveillance Directorate, Global Emerging Infection Surveillance Program/ ; 6036-10400-002-000-D//United States Department of Agriculture/ ; }, abstract = {Haiti is a Caribbean country of about 11 million people with a high burden of mosquito-transmitted disease and limited vector control, thereby making effective operational mosquito control of high importance. Previous studies have examined vector-borne disease burden and insecticide resistance markers in Haitian Aedes and Anopheles mosquitoes, but not Culex species. In this study, we examined collections of Culex quinquefasciatus from 12 locations in northern and southern Haiti for the presence of markers of insecticide resistance (using a variety of target-site mutations and biochemical assays) and pathogens (using a deep-sequencing microbiome workflow). The metagenomic analysis identified Wolbachia, Rhabdoviridae, and Plasmodium infections in all sample pools at relatively high levels, along with less frequent detections of other potential pathogens. Insecticide resistance marker examination identified variable frequencies of knockdown resistance and acetylcholinesterase resistance mutations, as well as variation in resistance-associated enzymatic activities in these populations. These findings indicate that insecticide resistance to pyrethroid and organophosphate insecticides is likely. Although there was variation among Culex mosquito populations and no clear activity pattern, enzymatic activity was significantly higher at the southern sites than at the northern sites. Similar findings in Cx. quinquefasciatus populations in other locations in the Americas strongly suggest that vector control with pyrethroid and organophosphate adulticides may be of limited efficacy.}, }
@article {pmid41900279, year = {2026}, author = {De Luca, L and Menna, F and Lupo, S and Vingolo, EM and Carlà, MM and Mancini, M and Oliverio, GW and Minutoli, L and Baldascino, A and Mazzotta, C and Aragona, P and Meduri, A}, title = {The Ocular Surface Bacterial Microbiome and the Impact of Contact Lens Use: A Literature Review.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900279}, issn = {2076-2607}, abstract = {The ocular surface microbiome plays a critical role in maintaining ocular health, preventing infections, and regulating immune responses. Contact lens (CL) wear has been linked to alterations in microbial composition, potentially leading to dysbiosis and increased susceptibility to ocular infections. This review aims to summarize current evidence on the effects of CL use on the ocular microbiome and to discuss strategies to preserve microbial homeostasis. A literature search was conducted in PubMed, Scopus, Web of Science, and Google Scholar for English-language human studies published between January 2005 and January 2025. We included original studies and systematic reviews evaluating the ocular surface bacterial community in contact lens (CL) wearers using either sequencing-based approaches (microbiome; e.g., 16S rRNA gene sequencing/metagenomics) or culture-based methods (microbiota). Two authors screened titles/abstracts and full texts. Overall, 12 studies met the inclusion criteria and were qualitatively synthesized. Across included studies, CL wear was associated with reproducible changes in the ocular surface bacterial community, most commonly a shift toward a skin-like profile and increased detection/relative abundance of opportunistic taxa (e.g., Pseudomonas, Acinetobacter, and Staphylococcus aureus) together with reduced representation of typical ocular commensals in several sequencing-based datasets. Culture-based studies reported increased recovery of opportunistic bacteria from lenses and storage cases, supporting contamination/biofilm-related mechanisms. Lens care solutions and preservatives were reported to modulate bacterial profiles and may contribute to dysbiosis, although evidence remains heterogeneous across study designs and analytic pipelines. CL use is associated with significant alterations in the ocular microbiome, increasing the risk of microbial keratitis and corneal inflammatory events. Strategies to maintain microbial balance, including careful selection of lens care products and development of antimicrobial lenses, may improve ocular surface health in CL wearers. Future longitudinal studies with standardized sampling and analytic workflows are needed to clarify causal links between CL-associated microbial changes and clinical outcomes.}, }
@article {pmid41900284, year = {2026}, author = {Kwon, H and Seo, JW and Jeong, M and Kim, Y and Chang, CL and Kim, JH and Choi, GE}, title = {Dietary Administration of a Soybean Fermented Preparation Reshapes Gut Microbial Community Structure and Colonic Mucosal Features in BALB/c Mice.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900284}, issn = {2076-2607}, support = {NRF-2022R1F1A1074419//National Research Foundation of Korea/ ; NRF-2022S1A5C2A04093562//National Research Foundation of Korea/ ; //Busan Metropolitan City and Busan Techno Park/ ; //RESEARCH FUND offered from Catholic University of Pusan in 2024./ ; }, abstract = {BACKGROUND/AIM: Fermented soybean-based products are known to influence gut microbial composition; however, the long-term effects of multicomponent soybean fermented preparations on gut microbiota and colonic mucosal features remain insufficiently characterized. This study examined the effects of a commercially available soybean fermented preparation (SFP), containing additional fermented plant and marine derived components, on gut microbial community structure and colonic histological features in BALB/c mice.
METHODS: BALB/c mice received oral SFP (1000 mg/kg) for 30 and 60 days. Gut microbial communities were analyzed using full-length rRNA operon sequencing. Colonic mucosal architecture and goblet cell density were evaluated via histological analysis (H&E).
RESULTS: SFP supplementation induced significant β-diversity separation at both 30 and 60 days (p < 0.05), indicating consistent restructuring of the gut microbial community. While alpha diversity (Observed OTUs) remained stable at 30 days, Shannon and Simpson indices were significantly reduced at 60 days (p = 0.001), indicating reduced community evenness driven by increased dominance of specific taxa, including Duncaniella. At the genus level, SFP administration was associated with increased relative abundances of Akkermansia, Lactobacillus, and Duncaniella, accompanied by reductions in several genera previously linked to dysbiosis. Histological analysis demonstrated a significant increase in goblet cell density (p < 0.01) in SFP-treated mice.
CONCLUSIONS: Long-term SFP supplementation was associated with sustained alterations in gut microbial composition and measurable histological changes in the colonic mucosa. While these findings indicate that SFP intake influences microbial structure and goblet cell abundance, further studies are required to determine the functional and physiological implications of these changes, particularly in relation to epithelial barrier function and host health.}, }
@article {pmid41900290, year = {2026}, author = {Singh, K and Mitra, S}, title = {Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900290}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) represents a critical global health challenge, with low- and middle-income countries (LMICs) disproportionately affected due to limited surveillance capacity. Advances in microbial genomics offer powerful tools for AMR detection and monitoring; however, translating these technologies into sustainable, policy-relevant surveillance systems in resource-constrained settings remains challenging. This review synthesises current approaches to genomic surveillance of AMR in LMICs and presents Bangladesh as a case study to illustrate how genomic, environmental, and clinical data can be integrated within a One Health framework. We examine key barriers to implementation, including laboratory infrastructure, bioinformatics capacity, data governance, and cross-sector coordination, alongside emerging opportunities for capacity building and regional collaboration. Using Bangladesh as a case study, we highlight practical pathways for embedding genomic surveillance into national AMR strategies, integrating human, animal, and environmental reservoirs of antibiotic resistance. We argue that genomic surveillance can move beyond data generation to inform infection prevention, antibiotic stewardship, and public health decision making when supported by context-appropriate infrastructure and interdisciplinary engagement. By focusing on operational and translational considerations rather than technology alone, this review provides actionable insights for microbiologists, public health practitioners, and policymakers seeking to strengthen AMR surveillance systems in LMICs through a One Health approach.}, }
@article {pmid41900318, year = {2026}, author = {Liu, X and Xiao, N and Yu, J and Geng, X and Zhang, M and Zhang, Y and Xu, H and Nie, C and Wang, M and Li, L}, title = {Divergent Microbial Community and Pathogenicity at a University-Urban Interface: A Comparative Analysis.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900318}, issn = {2076-2607}, support = {grant number 2022YFE0199800//National Key Research and Development Program of China/ ; grant number 24-1-8-smjk-13-nsh//Qingdao Science and Technology Wellness Promotion Demonstration Program/ ; grant number 82271658//the National Natural Science Foundation of China/ ; grant number SKLMTFCP-2023-01//SKLMT Frontiers and Challenges Project/ ; grant numbers ZR2024QD228 and ZR2024QC311//Shandong Provincial Natural Science Foundation/ ; grant number 24-4-4-zrjj-40-jch//Qingdao Natural Science Foundation/ ; grant number FDLAP24008//Opening Project of Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP)/ ; }, abstract = {Environmental metagenomics and microbial taxonomy provide essential frameworks to evaluate how population structures shape the evolution of antimicrobial resistance and microbial community dynamics within densely populated environments. To evaluate microbial community composition and pathogenic potential, high-touch surfaces at high-traffic sites on and off campus were analyzed using metagenomics and characterization of 188 bacterial isolates, including antibiotic susceptibility testing, hemolytic assays, and whole-genome sequencing. Off-campus sites showed significantly higher bacterial richness and more complex communities enriched with diverse potential pathogens. Notably, high-risk carbapenemase genes were predominantly identified in these off-campus urban environments. In contrast, on-campus environments harbored less diverse communities dominated by opportunistic, antibiotic-resistant Staphylococcus species, with metagenomic analysis confirming a concentrated enrichment of β-lactam resistance determinants associated with methicillin-resistant staphylococci. Phenotypic profiling revealed extensive antimicrobial resistance, with 84.7% of isolates exhibiting resistance to at least one antibiotic and 35.1% of Staphylococcus showing hemolytic activity. Whole-genome sequencing further revealed that these resistance and pathogenic traits are predominantly localized on mobile plasmids, highlighting a high potential for horizontal gene transfer. These findings indicate that population activities shape distinct microbial communities in closely adjacent environments and highlight the importance of monitoring high-risk resistance determinants in densely populated university settings.}, }
@article {pmid41900320, year = {2026}, author = {Cheng, H and Han, J and Liu, K and Wang, L and Meng, Q and Liu, C and Liu, X and Wang, M and Yang, F and Li, X}, title = {Integrated Metagenomic and Metabolomic Profiling of Boar Semen During Ambient-Temperature Storage.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900320}, issn = {2076-2607}, support = {2022020101//Agricultural Breeds Research Project of Henan Province/ ; HAAS2023RCQD01//the Key Technology Research and Development Program for Precision and Efficient Breeding of Local Pigs in Hainan Province/ ; }, abstract = {The reproductive efficiency of breeding boars substantially influences swine industry productivity. Sperm viability during ambient-temperature storage is critically affected by environmental factors, including microbial activity. This study aimed to elucidate the dynamics and interactions between the seminal microbiome and metabolome during boar semen storage at 17 °C. Using integrated 16S rRNA sequencing and untargeted metabolomics, we analyzed semen samples from six healthy boars (31-33 months old) collected at day 0 (control), 2, 4, and 6 of storage. Our results demonstrate that storage leads to a marked decline in microbial diversity, progressive enrichment of the opportunistic genus Proteus, depletion of key antioxidant and cofactor metabolites such as vitamin B6, and extensive metabolic reprogramming-including alterations in short-chain fatty acid, purine, and lipid oxidation pathways. Multi-omics correlation analysis further revealed strong associations between microbial succession and metabolic shifts, highlighting their combined role in driving sperm functional decline. These findings provide a mechanistic basis for improving semen preservation strategies through microbiome and metabolite-targeted interventions.}, }
@article {pmid41900339, year = {2026}, author = {Malik, PK and Mohapatra, A and Trivedi, S and Kolte, AP and Sahoo, A and Bhatta, R}, title = {In Vitro Degradation of Chlorpyrifos by the Ruminal Microbes: Insights from the Rumen Metagenome.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900339}, issn = {2076-2607}, abstract = {In vitro studies were conducted in a series to investigate if the ruminal microbes are capable of degrading chlorpyrifos. This in vitro study presents the results from three experiments: Exp. I was conducted without feed, while Exp II and III were conducted with feed, either with or without methanol for dissolving chlorpyrifos, respectively. A basal diet comprising finger millet straw and concentrate was prepared. Incubation medium with feed but without chlorpyrifos served as the control. A total of six replicates each of control and chlorpyrifos spiked were used for the incubation. The pesticide concentration in the incubation medium before and after 24 h of incubation was analyzed using GC-MS/MS. The genomic DNA was isolated from the incubation fluid of the individual samples, and the shotgun metagenomic sequencing was performed. The clean reads were taxonomically classified using the Kraken2 database, and microbial classification at different taxonomic ranks was separated using Pavian v1.0. The microbial genes in the metagenome data were predicted and assigned functional roles using the MetaErg v1.2.3 pipeline. The assigned KEGG Orthology (KO), EC numbers (Enzyme Commission number), Gene Ontology (GO), and corresponding NCBI taxonomy information relevant to chlorpyrifos metabolism/degradation were retrieved. Results from the study revealed that the chlorpyrifos concentration was decreased from 5.78 to 1.64 ppm over 24 h of in vitro incubation with feed. Similar alpha and beta diversity indices between control and chlorpyrifos treatments revealed that the richness and the evenness of the microbial population were not affected by the presence of chlorpyrifos in the rumen fluid. There was no difference in the microbiota affiliated to the major phyla such as Bacteroidota, Fibrobacterota, Bacillota, and Pseudomonadota. The EC 3.1.8.1, EC 3.1.3.1, EC 1.14.13.-, and EC 1.1.1.- reported for chlorpyrifos degradation were not detected in the metagenome, and only EC 3.1.1.1 was identified, which demonstrated that degradation of chlorpyrifos was carried out by the affiliated enzyme carboxylesterase. The presence of GO:0004035, GO:0004364, GO:0019637, GO:0016791, and GO:0042178 in the metagenome strengthens that the chlorpyrifos degradation in the present study was primarily assigned to the rumen microbiota. This in vitro study provided insights into the rumen microbiota involved in the chlorpyrifos degradation and the initial clue that the rumen microbes are capable of degrading chlorpyrifos. Further, the animal studies in different species with the variable levels of chlorpyrifos are also warranted to confirm the efficacy of rumen microbes in mixed syntrophy and determine the threshold capabilities of the ruminal microbes.}, }
@article {pmid41900342, year = {2026}, author = {Ntzouvaras, A and Koletti, A and Zografaki, ME and Marka, S and Skliros, D and Vasilakis, G and Karavidas, I and Koukouvinis, AK and Efrose, RC and Kalloniati, C and Tzovenis, I and Flemetakis, E}, title = {Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900342}, issn = {2076-2607}, support = {PRIMA2019-04//European Union research and innovation Horizon 2020/ ; }, abstract = {Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1-PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework.}, }
@article {pmid41900399, year = {2026}, author = {Yi, X and Lin, Y and Peng, Y and Liu, Y and Ning, C and Lei, J and Wang, L and Chen, C and Wu, L and Liao, J}, title = {Urbanization-Induced Shifts in Microbial Functional Genes of Wetland Nitrogen Cycling Promote Nitrous Oxide (N2O) Emissions.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900399}, issn = {2076-2607}, support = {32401392//National Natural Science Foundation of China/ ; OT-S-KTA4//Hunan Forest Quality Improvement and Efficiency Enhancement Demonstration Project Funded by the European Investment Bank Loan/ ; XLKY202216//Forestry Science and Technology Innovation Project of Hunan Province/ ; XLKY202319//Forestry Science and Technology Innovation Project of Hunan Province/ ; 2024JJ5235//Hunan Provincial Natural Science Foundation of China/ ; }, abstract = {Urban wetlands are assumed to contribute to nitrous oxide (N2O) emissions; however, the microbial mechanisms underlying enhanced N2O fluxes in urban wetlands and differences in microbial responses between aquatic and soil compartments have not been clearly identified. Here, we characterized the nitrogen (N) cycling microbial communities and their functional metabolic pathways in urban and rural wetlands using metagenomics and N2O flux measurements. Results showed that urbanization drove a 6~8-fold increase in N2O fluxes from urban wetlands compared to rural wetlands. Structural equation modeling (SEM) confirmed that urbanization intensity was a primary driver (standardized coefficients: 0.72 for soil and 0.92 for water). In wetland water, N2O emissions were negatively correlated with inorganic nutrient concentrations (coefficient = -0.62). Aquatic microbial communities exhibited substantial taxonomic shifts but preserved network connectivity, indicating adaptive strategies for surviving urban perturbations at the cost of reduced functional redundancy. In wetland soil, microbial communities maintained stability under urbanization, which was attributed to environmental buffering from heterogeneous microenvironments. Soil N2O emissions were positively linked to microbial alpha diversity (coefficient = 0.79). Furthermore, urban wetlands enriched genes mediating nitrification and denitrification while depleting genes associated with N fixation and organic N metabolism. This functional shift reflects microbial specialization in processing elevated reactive N (Nr) inputs from urban sources, trapping urban wetlands in an "N loss loop" that reinforces high N2O fluxes. This study elucidates the microbial mechanisms governing wetland N2O emissions under urbanization, thereby enhancing understanding of microbially mediated N cycling in the urban wetland ecosystem.}, }
@article {pmid41900403, year = {2026}, author = {Zhang, W and Fan, C and Yang, L and Sun, Y and Tang, L}, title = {Integrated Metagenomic and Metabolomic Analyses Reveal Rhizosphere Soil Microecological Changes in Thlaspi arvense L. Lines with Different Alkaloid Contents.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900403}, issn = {2076-2607}, support = {CARS-16-S3//The China Agriculture Research System of MOF and MARA/ ; }, abstract = {Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence both the crop's growth and the subsequent crops in rotation. However, systematic investigations comparing the rhizosphere microbiomes and metabolomes among different pennycress lines remain limited. This study employed metagenomic and metabolomic approaches to examine the dynamic changes in the rhizosphere microbial community and metabolite profiles of three pennycress lines with significantly different total alkaloid contents. The goal was to elucidate the interactions between microbes and metabolites. Results indicated significant differences in microbial community structure across the cultivars. JiL67 maintained stable community diversity, while LiN54 (with the lowest alkaloid content) showed reduced diversity. HeL43 (with the highest alkaloid content) exhibited increased diversity but also potential community homogenization, accompanied by the significant enrichment of microbial taxa capable of alkaloid tolerance. Metabolomic analysis identified metabolites such as Portulacaxanthin II, Oleanolic acid, and Soraphen A as significantly enriched in the rhizosphere soil of pennycress. This study reveals the shifts in rhizosphere microbial communities and metabolites linked to different pennycress lines and uncovers their interactive mechanisms, providing a scientific foundation for developing more economically efficient pennycress cultivation strategies.}, }
@article {pmid41900432, year = {2026}, author = {Guerrero-Torres, LE and García-Galindo, JJ and Gómez-Galindo, MF and Delgado, DIR and Retolaza Carlos, CE and Suárez-Rico, DO and Beltrán-Ramírez, A and Balleza Alejandri, LR}, title = {The Gut Microbiota in Parkinson's Disease: Mechanistic Insights into Microbial-Host Interactions.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900432}, issn = {2076-2607}, abstract = {Parkinson's disease (PD) is a multifactorial neurodegenerative disorder characterized by progressive motor and non-motor manifestations, including early gastrointestinal dysfunction. Growing evidence implicates the gut microbiota as an active modulator of host immune tone and neurodegenerative vulnerability, extending beyond descriptive taxonomic associations toward functional and metabolic mechanisms. PD-associated dysbiosis is consistently characterized by altered microbial functional capacity, including reduced short-chain fatty acid (SCFA) production, enrichment of pro-inflammatory metabolic traits, and sustained immune stimulation at the intestinal interface. These shifts promote chronic low-grade inflammation and intestinal barrier perturbations, creating conditions that may facilitate abnormal α-synuclein aggregation within the enteric nervous system. Current management predominantly relies on dopaminergic replacement and related symptomatic strategies, such as levodopa combinations, dopamine agonists, monoamine oxidase-B and catechol-O-methyltransferase (COMT) inhibitors, and device-aided therapies, which alleviate symptoms but do not halt underlying neurodegeneration or modify long-term disease course. These therapeutic limitations have intensified interest in upstream mechanisms that might be amenable to disease-modifying interventions, particularly those arising at the level of the gut microbiota and gut-immune-brain axis. This narrative review integrates clinical, metagenomic, metabolomic, and mechanistic evidence to propose a unified model in which microbiota-driven immune and metabolic perturbations may act as upstream drivers converging on α-synuclein pathology, neuroinflammation, and neurovascular dysfunction.}, }
@article {pmid41900479, year = {2026}, author = {Park, H and Kim, JS and Kim, DJ and Suk, KT}, title = {Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900479}, issn = {2076-2607}, support = {NRF-2020R1I1A3073530//National Research Foundation of Korea/ ; NRF-2020R1A6A1A03043026//National Research Foundation of Korea/ ; }, abstract = {Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field.}, }
@article {pmid41901034, year = {2026}, author = {Lee, YK and Kim, HY and Shim, D}, title = {A Triple-Hit Multi-Omics Framework for Psoriasis: Microbial Metabolic Remodeling and Immune Cell Methylome Signature Associated with an AMP-Dominant Lesional Program.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {3}, pages = {}, pmid = {41901034}, issn = {2075-1729}, support = {RS-2023-00263429//Ministry of Science and ICT (MSIT), South Korea/ ; }, abstract = {The gut-skin axis is increasingly implicated in psoriasis pathogenesis, yet the cross-compartment convergence of molecular programs remains incompletely defined. We constructed a conceptual "Triple-Hit" multi-omics framework by integrating five independent public datasets spanning gut microbial functional remodeling (shotgun metagenomics), systemic immune cell methylomes (PBMC and CD8+ T-cell EPIC 850K), and lesional skin regulatory layers (miRNA and bulk RNA-seq). In the gut compartment, functional profiles exhibited a selective reduction in microbial lipid catabolic potential, including decreased fatty acid degradation and a lowered composite lipid degradation score, alongside heterogeneous shifts across SCFA-associated metabolic pathways. Systemically, PBMC methylomes revealed widespread regional remodeling (45,396 DMRs) enriched for membrane-proximal signaling and cytoskeletal programs, while CD8+ T cells showed specific epigenetic alterations in lipid- and glycosphingolipid-associated loci, suggesting a systemic metabolic-epigenetic alignment. In the skin, we identified a compact miRNA signature (168 DE-miRNAs) and a mechanistically interpretable, directionality-constrained miRNA-mRNA bridge that aligns with an AMP-dominant inflammatory transcriptome, consistent with reduced post-transcriptional restraint. Collectively, these findings support a convergent multi-omics framework linking putative microbial metabolic remodeling, systemic immune priming, and cutaneous effector programs. This study provides a systems-level perspective on psoriasis pathogenesis, highlighting the metabolic-epigenetic-transcriptional convergence as a potential avenue for therapeutic intervention.}, }
@article {pmid41901100, year = {2026}, author = {Kim, HJ and Park, J and Oh, S and Kim, D and Kim, HJ and Jo, C and Kim, EB and Jang, A}, title = {Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901100}, issn = {2072-6643}, support = {2022R1A2C1005235//National Research Foundation of Korea/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Carnitine/pharmacology/administration & dosage ; *Obesity/microbiology/metabolism ; *Betaine/pharmacology/administration & dosage ; Male ; *Thioctic Acid/pharmacology/administration & dosage ; Mice, Inbred C57BL ; *Dietary Supplements ; Diet, High-Fat/adverse effects ; Biomarkers/blood ; Mice ; Disease Models, Animal ; Leptin/blood ; }, abstract = {Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation.}, }
@article {pmid41901112, year = {2026}, author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF}, title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901112}, issn = {2072-6643}, support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; }, mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention & control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; }, abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.}, }
@article {pmid41901564, year = {2026}, author = {Gonzalez, A and Argotsinger, J and Oram, RJ and Miller, JL}, title = {Impact of Metagenomic Next-Generation Sequencing on Antibiotic Management in Pediatric Patients.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {3}, pages = {}, pmid = {41901564}, issn = {1648-9144}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Child ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Infant ; *Anti-Bacterial Agents/therapeutic use ; Adolescent ; Pediatrics/methods ; }, abstract = {Background and Objectives: Metagenomic next-generation sequencing (mNGS) is an emerging diagnostic tool used to guide the management of infectious diseases. However, clinical criteria in which there is a clear benefit have not been identified, and more real-world clinical experience is needed to identify patient populations in which mNGS testing may have the most benefit. The aim of this article is to evaluate the utilization of mNGS to determine the impact on clinical practice for pediatric patients. Materials and Methods: This retrospective analysis included pediatric patients that had a mNGS test performed between January 2020 and September 2024. The primary outcome was the clinical impact of the mNGS test on patient management defined as either a positive impact or no impact. Secondary outcomes included test turnaround time, agreement or discordance between conventional testing and mNGS, and hospital length of stay. Results: Forty-six mNGS tests in 42 patients were evaluated. Of 60 organisms identified from the 46 tests, 27 organisms (45%) were considered clinically significant. mNGS had a positive clinical impact in 18 (39.1%) patients, primarily due to antimicrobial modifications (16, 34.8%) and new diagnoses (6, 13.0%). The majority of patients with a positive clinical impact were immunosuppressed (15/18, 83.3%). Conclusions: mNGS demonstrated utility in a subset of pediatric patients, particularly those considered immunosuppressed. Its ability to confirm or exclude infections, particularly fungal infections in this patient population, contributed to its impact. However, its limited benefit in immunocompetent patients underscores the importance of careful patient selection to optimize diagnostic and antimicrobial stewardship.}, }
@article {pmid41901695, year = {2026}, author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P}, title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901695}, issn = {2076-0817}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Aged ; Hospitalization ; Adult ; India ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.}, }
@article {pmid41901767, year = {2026}, author = {He, P and Wang, H and Li, P and Yan, Y and Gao, L and Chen, L}, title = {Pyogenic Spondylitis with Epidural Abscess Caused by Streptococcus suis Serotype 2 ST7: Tissue mNGS Confirmation and Whole-Genome Characterization of a Human Isolate.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901767}, issn = {2076-0817}, support = {2026JKP-07//Disease Prevention and Control Innovation Team of Zhejiang Province/ ; }, mesh = {Humans ; *Spondylitis/microbiology/diagnosis ; *Streptococcus suis/genetics/isolation & purification/classification/drug effects ; Aged ; *Epidural Abscess/microbiology/diagnosis ; *Streptococcal Infections/microbiology/diagnosis/drug therapy ; Male ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Serogroup ; Whole Genome Sequencing ; Animals ; Swine ; Magnetic Resonance Imaging ; Phylogeny ; }, abstract = {Streptococcus suis is an emerging zoonotic pathogen that typically causes bacteremia or meningitis in humans, whereas vertebral osteomyelitis with epidural abscess is exceedingly rare and may be missed. We describe a 65-year-old farmer with fever and severe low back pain after long-term bare-handed handling of raw pig lungs. Pre-treatment blood cultures yielded S. suis identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After transient improvement on empirical therapy, fever recurred with worsening lumbar pain. Contrast-enhanced magnetic resonance imaging (MRI) demonstrated multilevel thoracolumbar pyogenic spondylitis with an epidural abscess and a sub-ligamentous abscess beneath the posterior longitudinal ligament (PLL) extending from L2 to L5. Computed tomography-guided lumbar biopsy followed by tissue metagenomic next-generation sequencing (mNGS) detected S. suis, providing concordant evidence supporting pathogen involvement at the vertebral focus. The bloodstream isolate (SS-JX2025-01) was serotype 2, sequence type 7 (ST7). It remained susceptible to β-lactams and glycopeptides but was resistant to macrolide-lincosamide and tetracycline classes, consistent with erm(B), tet(O), tet(40), and ant(6)-Ia detected by whole-genome sequencing (WGS). Virulence profiling revealed an epf[+]/sly[+]/mrp[-] pattern with multiple adhesins and immune-evasion factors, whereas canonical 89K pathogenicity island markers were absent. Core-genome phylogeny placed SS-JX2025-01 within the Chinese ST7 lineage associated with previous outbreaks. This biopsy-supported case expands the clinical spectrum of invasive S. suis infection, highlights the value of tissue mNGS as an adjunct for supporting deep-seated foci in zoonotic infections, and underscores the importance of occupational prevention in small-scale farming households.}, }
@article {pmid41901791, year = {2026}, author = {Alessandri, G and Beligni, G and Gori Savellini, G and Mistral De Pascali, A and Gobbo, F and Montarsi, F and Mileto, D and Rizzo, L and Cusi, MG}, title = {Molecular Epidemiology of Toscana Virus in Northern and Central Italy Using Metagenomic Next-Generation Sequencing.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901791}, issn = {2076-0817}, support = {PE00000007//NextGeneration EU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases INF-ACT/ ; P2022WYNAH//Ministero dell'Università e della Ricerca, Progetti di Rilevante Interesse Nazionale PRIN2022 PNRR/ ; }, mesh = {Italy/epidemiology ; *Sandfly fever Naples virus/genetics/classification/isolation & purification ; Humans ; Phylogeny ; Molecular Epidemiology ; Animals ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Genome, Viral ; Genotype ; Phylogeography ; Psychodidae/virology ; }, abstract = {Toscana virus (TOSV) is an arthropod-borne virus, transmitted by sandflies, which represents a major cause of aseptic meningitis in Mediterranean countries during summer months. Despite its epidemiological importance, recent genomic data on circulating Italian strains remain limited. We performed comprehensive phylogenetic and genotypic characterization of 34 TOSV isolates (32 obtained from human biological samples and 2 from sandfly homogenates) collected between 2022 and 2025 from Northern/Central Italy. All the sequenced isolates clustered within Lineage A, with strains circulating in Tuscany showing significantly lower intra group genetic divergence (p < 0.05), indicative of compartmentalized local circulation. Both S and M segments exhibited negative selection and identified non-synonymous mutations deserving functional investigation. This study documents stable Lineage A predominance across Italian regions, with Tuscany showing distinct phylogeographic structuring. mNGS proves effective for TOSV genomic surveillance, supporting refined public health strategies, including targeted sandfly control in endemic foci.}, }
@article {pmid41902210, year = {2026}, author = {Zhang, Y and Ding, X and Tao, X and Tuohuti, N and Wang, X and Maimaiti, A and Su, Z and Ma, X}, title = {Viral Metagenomic Analysis Reveals High Prevalence of Dromedary Camel Bocavirus and Porcine Astrovirus in Bactrian Camel Intestinal Tissue.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902210}, issn = {1999-4915}, support = {2022KY025//Autonomous Region Science and Technology Commissioner Project of Xinjiang Uygur Autonomous Region, China/ ; }, mesh = {Animals ; *Camelus/virology ; *Bocavirus/genetics/isolation & purification/classification ; Phylogeny ; Metagenomics ; *Parvoviridae Infections/veterinary/epidemiology/virology ; *Astroviridae Infections/veterinary/epidemiology/virology ; *Intestines/virology ; China/epidemiology ; Prevalence ; *Mamastrovirus/genetics/isolation & purification/classification ; Swine ; Virome ; }, abstract = {Bactrian camels (Camelus bactrianus) are economically vital livestock in arid regions; however, their intestinal virome is poorly understood. We employed viral metagenomics to analyze intestinal tissue samples from deceased camels at a breeding facility in Urumqi, Xinjiang, China, and uncovered a diverse viral population dominated by dromedary camel bocavirus (DBoV1) and porcine astrovirus (PoAstV5). A molecular epidemiological survey of 261 anal swab samples collected across Xinjiang revealed prevalence rates of 36.40% (95/261) for DBoV1 and 26.44% (69/261) for PoAstV5, indicating their widespread circulation. Phylogenetic analyses of the DBoV1 NS1 and PoAstV5 ORF1a genes showed close relationships with known strains, with no evidence of recombination. This study expands the known viral spectrum of Bactrian camels, marking the first report of PoAstV5 in this species, a finding suggestive of cross-species transmission. These results enhance our understanding of camel viral diversity and provide critical data for managing enteric diseases in camel populations, with potential implications for livestock health and surveillance of zoonotic risks.}, }
@article {pmid41902228, year = {2026}, author = {Shankar, A and Zheng, H and Cowan, D and Jia, H and Osis, G and Burgin, A and Sheth, M and Hoff, NA and Halbrook, M and Rimoin, AW and Goldberg, TL and Chapman, CA and Ting, N and Switzer, WM}, title = {Molecular Characterization of Complete Simian Foamy Virus Genomes from Three Colobine Monkeys Reveals Highly Divergent Evolutionary Trajectories and Identifies Transmission to Humans.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902228}, issn = {1999-4915}, support = {TW009237//Canada Research Chairs Program ; NIH/ ; R01 AI084787/GF/NIH HHS/United States ; R01 AI077376-04A1/GF/NIH HHS/United States ; }, mesh = {Animals ; *Simian foamy virus/genetics/classification/isolation & purification ; *Genome, Viral ; Phylogeny ; *Retroviridae Infections/transmission/virology/veterinary ; Humans ; *Evolution, Molecular ; *Monkey Diseases/virology/transmission ; Colobus/virology ; *Colobinae/virology ; }, abstract = {Simian foamy viruses (SFVs) are ancient retroviruses that co-evolve with nonhuman primates (NHPs), although genomic data from Asian and African monkeys are limited. We report the characterization of three new SFV colobine genomes from two Asian species (Trachypithecus francoisi (Tfr) and Pygathrix nemaeus (Pne)) and one African monkey (Colobus guereza, Cgu), obtained via metagenomics analysis of peripheral blood leukocyte tissue culture isolates. Genomic analyses found conserved structural, enzymatic, and auxiliary genes flanked by long terminal repeats, with all major transcriptional and structural motifs highly preserved. An in-frame Δtas mutation in tissue culture and ex vivo specimens was identified in the SFVpne genome, which may promote viral latency. Phylogenetic analyses revealed that these colobine SFVs have distinct evolutionary trajectories without clustering together, contradicting a strict virus-host co-evolution. We developed a new generic SFV PCR assay using these genomes with increased detection sensitivity for Colobinae SFVs and identified four new human infections with Cgu-derived SFV in the Democratic Republic of Congo. Our findings indicate that SFV evolution in colobine monkeys is shaped by host switching, cross-species transmission, and high viral diversity. Our study underscores the importance of broadening SFV genomic sampling to better understand viral evolution, zoonotic risk, and improved diagnostic capabilities.}, }
@article {pmid41902303, year = {2026}, author = {Munguti, FM and LaTourrette, K and Silva, G and Maina, S and Kilalo, DC and Macharia, I and Mwango'mbe, AW and Nyaboga, EN and Garcia-Ruiz, H}, title = {Metagenomics Analysis of Viruses Associated with Cassava Brown Streak Disease in Kenya.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902303}, issn = {1999-4915}, support = {Grant ID: RU/2018/CARP+/04//MasterCard Foundation/ ; }, mesh = {Kenya ; *Plant Diseases/virology ; *Manihot/virology ; *Potyviridae/genetics/classification/isolation & purification ; Phylogeny ; Genome, Viral ; *Metagenomics ; Polymorphism, Single Nucleotide ; }, abstract = {Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of Africa, especially in Eastern, Central and Southern Africa. In Kenya, the disease continues to wreak havoc on cassava production leading to a significant reduction in crop yields and economic losses of up to USD 1 billion. Variation in virus populations make the control of CBSD challenging as virus genomic variation can affect the accuracy of diagnostic tests, lead to resistance breaking isolates and jeopardize strategies of breeding for resistance. CBSV and UCBSV populations obtained from cassava fields in Kenya were characterized. In total, 44 new complete sequences of CBSV and UCBSV were assembled and 40 sequences successfully submitted to GenBank. Single Nucleotide Polymorphism (SNP) analysis revealed that the cylindrical inclusion protein (CI) is the most stable region across the genome of CBSV and UCBSV. In contrast, protein 1 (PI) and the coat protein (CP) were the most hypervariable regions. Phylogenetic analysis showed three major geographical groupings for both UCBSV and CBSV isolates, suggesting a continued spread of the viruses through human-mediated movement of infected planting materials. The data obtained in this study can support the development of disease management strategies through improved molecular diagnostic tests and targets for breeding for resistance against CBSD.}, }
@article {pmid41903008, year = {2026}, author = {Heyse, J and Props, R and Defoirdt, T and Boon, N}, title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903008}, issn = {1573-0972}, support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; }, }
@article {pmid41903026, year = {2026}, author = {Wolthuis, JC and Schultheiss, JPD and Magnúsdóttir, S and Stigter, E and Tang, YF and Jans, J and Oldenburg, B and de Ridder, J and van Mil, S}, title = {Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {2}, pages = {}, pmid = {41903026}, issn = {1573-3890}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diagnosis/blood/metabolism/microbiology ; *Cholangitis, Sclerosing/diagnosis/blood/metabolism ; *Metabolomics/methods ; Male ; Female ; Biomarkers/blood ; Adult ; Middle Aged ; Crohn Disease/diagnosis/blood ; Colitis, Ulcerative/diagnosis/blood/metabolism ; Metabolome ; Mass Spectrometry ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract comprising two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC). Up to 8% of patients with IBD also develop primary sclerosing cholangitis (PSC), characterised by cholestasis and progressive destruction of the biliary tree, resulting in cirrhosis, end-stage liver disease and cholangiocarcinoma. Clinical outcome can currently not be improved through medication, denoting the importance of diagnosis prior to irreversible damage, which requires biomarkers of (early) disease.
OBJECTIVES: We employed direct infusion mass spectrometry (DI-MS)-based metabolomics on plasma to build predictive, potentially diagnostic models for PSC-IBC and other phenotypes including IBD subtype, stricture and fistula presence and more. We used this dataset to simultaneously investigate aetiology of these phenotypes.
METHODS: Samples of 348 IBD patients were included for analysis. The data was analysed using our previously reported tool, MetaboShiny. We built predictive models using Random Forest (RF), and subsequently combined with univariate statistics to rank m/z features connected to PSC-IBD. This ranking was used to perform mummichog enrichment analysis connected to metabolic and metagenomic changes.
RESULTS: The highest performing predictive model differentiated PSC-IBD from PSC. The metabolic signature was enriched in changes to amino acid and vitamin metabolism, alongside changes to the metagenome suggesting decreases in anti-inflammatory microbial species and increases in pro-inflammatory species.
CONCLUSION: These results demonstrate the potential of DI-MS-based metabolomics with machine learning to create diagnostic models and generate hypotheses on the metabolomic-metagenomic level. Sharing our dataset of patients will enrich future human IBD metabolomics research possibilities.}, }
@article {pmid41903099, year = {2026}, author = {Sumona, AA and Hossen, MB and Hadi, SB and Haque, MA and Haider, MN and Hossain, MT and Alam, MS}, title = {Host-derived Probiotics Enhance Immune Response and Gut Microbiome in the Freshwater Prawn Macrobrachium rosenbergii.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41903099}, issn = {1867-1314}, }
@article {pmid41903138, year = {2026}, author = {Zheng, W and Wu, C and Wang, Y and Yan, X and Han, W and Liu, X and He, C and Chen, X and Zhou, X and Zhang, L and Liu, C and Xu, J and Wang, J and Yuan, X and Song, W and Wang, X and Liang, S and Huang, J and Zhang, Y and Yang, R and Zhang, L and Qin, N and Ma, X and Xu, Q and Li, G}, title = {Mutation elevation and functional alterations in Escherichia coli are pertinent to the onset of gestational diabetes mellitus.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117143}, doi = {10.1016/j.celrep.2026.117143}, pmid = {41903138}, issn = {2211-1247}, abstract = {In the gut microbiome, purifying selection clears deleterious mutations. However, it is unknown whether this selection pressure is modifiable or what its health implications are. Here, we studied metagenomic and metabolic changes linked to gestational diabetes mellitus (GDM), and observed an increase in Escherichia coli (E. coli) mutations during host pregnancy, linking these genetic changes to host physiology. Severe depletion of bacterial genes before GDM onset was mostly traced to E. coli despite its stable abundance-indicating that functional genetic signals outweigh taxonomic shifts. E. coli and related microbes displayed pregnancy-linked single nucleotide polymorphism elevation, enriched at GDM onset in loci encoding membrane and biofilm components. These pangenomic alterations correlated with handicapped intermicrobial interactions of E. coli and with host serum metabolic abnormalities. We propose that pregnancy relaxes purifying selection, permitting mutation elevation in certain gut bacteria. Resulting functional deficits, potentially through altered ecology and metabolism, may subsequently impact host glucose regulation.}, }
@article {pmid41903180, year = {2026}, author = {Xu, Y and Akinbi, H and Shen, Z and Zhu, J and Shi, L and Du, L and Haslam, DB}, title = {Clinical Care Practices Shape Microbiome-Associated Bloodstream Infection Risk in Geographically Distinct NICUs.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag213}, pmid = {41903180}, issn = {1537-6591}, abstract = {BACKGROUND: Bloodstream infections (BSI) remain a major cause of morbidity and mortality in preterm infants. Although BSI pathogens vary geographically, the role of local microbial colonization patterns and clinical practices in driving these differences is not well understood.
METHODS: We conducted a prospective cohort study on 127 preterm infants from two geographically distinct NICUs: University of Cincinnati Medical Center (UCMC, USA) and Children's Hospital, Zhejiang University School of Medicine (ZCH, China). Six hundred and sixty-nine longitudinal stool and skin samples collected during the first three weeks of life underwent metagenomic sequencing. Associations between microbiome composition, clinical factors, and BSI epidemiology were evaluated using Generalized Linear Mixed Models and Random Forest.
RESULTS: Distinct gut and skin microbiome profiles were observed between NICUs and corresponded closely with local BSI patterns. Staphylococcus aureus predominated at UCMC, while Klebsiella pneumoniae and Enterococcus species were more common at ZCH. Skin microbiota showed strong association with BSI isolates, implicating the skin as an underrecognized potential reservoir for pathogen translocation. Linear mixed models and Random Forest machine learning approaches revealed that clinical practices, including intravenous catheter placement and antibiotic exposure had greater influence on microbiome composition than geographic location alone.
CONCLUSIONS: Our findings demonstrate that modifiable clinical care practices shape the developing microbiome of preterm infants and contribute to geographic differences in BSI epidemiology. The skin microbiome represents a potentially significant risk factor for invasive infection. Further work to clarify how specific clinical practices influence pathogen colonization may inform strategies to reduce BSI incidence in preterm infants.}, }
@article {pmid41903463, year = {2026}, author = {Rathnayake, M and Shaik, NA and Palkumbura, A and Ranaraja, A and Basnayake, Y and Basyouni, R and Taylor, A and Ambrose, N and Popowich, S and Ayalew, LE and Tikoo, S and Gomis, S}, title = {Effects of conventional and raised without antibiotic feeding systems and exposure to infectious bursal disease virus on microbial diversity of the jejunal microbiota in broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106823}, doi = {10.1016/j.psj.2026.106823}, pmid = {41903463}, issn = {1525-3171}, abstract = {Preventative use of antimicrobials in the feed in broiler chicken production is decreasing due to consumer demand. Hence broiler chickens raised without antibiotics (RWA) receive increased attention. The objective of this study was to compare jejunal microbiota in RWA and conventional feeding systems in commercial broiler chickens. A total of 6 broiler chicken farms were selected for this study, in each farm raising both conventional and RWA chicken flocks. Jejunal contents were collected from Ross 308 (n=8/flock) at 25 d of age for metagenomics analysis for 16SrRNA amplicon sequencing. Serum samples from each flock were tested for infectious bursal disease virus (IBDV) and chicken anemia virus (CAV). The 16SrRNA microbial analysis revealed that there was no substantial impact of feeding systems on the diversity of the microbial community between RWA and conventional feeding systems. The condemnation rate was significantly higher in RWA flocks compared to conventional flocks (p = 0.037). Significantly high antibody titer against IBDV was detected in 9 (75%) of 12 flocks. The microbiota significantly differed in flocks exposed to IBDV compared to flocks not exposed to IBDV irrespective of the feeding system. Alpha diversity indices revealed that richness (p = 0.025), Chao1 (p = 0.031), and Shannon index (p = 0.04) were significantly lower in flocks exposed to IBDV indicating reduced species diversity. Flocks exposed to IBDV had increased Escherichia, Anaerotignum, Clostridium, Weissella andLiquorilactobacillus genera while Furfurilactobacillus, Helicobacter, Campylobacter, Fructilactobacillus and Terrisporobacter were decreased compared to flocks not exposed to IBDV. These results suggest that broiler chickens exposed to IBDV infection irrespective of the feeding system lead reduction in microbial diversity. This study highlights the importance of control strategies of IBDV in broiler flocks since IBDV infection not only causes immunosuppression but also affects intestinal microbiota.}, }
@article {pmid41903724, year = {2026}, author = {Ouyang, E and Liu, J and Zhou, Z and Yang, H and Wang, W and Qian, K and Zhu, M and Wei, Z and Sun, X and Chen, Z}, title = {Metagenomic Surveillance of Temperature-Drived Bacterial Threats to Drinking Water Safety.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124364}, doi = {10.1016/j.envres.2026.124364}, pmid = {41903724}, issn = {1096-0953}, abstract = {Climate warming may exacerbate the risk of pathogenic bacteria and antibiotic resistance genes (ARGs) in aquatic environments. However, research on the impact of climate warming on bacterial pathogenic risks and virulence factors (VFs) communities in drinking water sources remains scarce. This study combined field multi-season monitoring with controlled laboratory temperature simulation experiments. Using 16S rRNA and metagenomic sequencing, we investigated the effects of gradually increasing temperature on pathogenic bacteria and VF community in the Gan River source area. A significant positive correlation with temperature was observed in the seasonal shifts of Legionella, Mycobacterium, and Pseudomonas during field multi-season monitoring. Our laboratory temperature simulation experiments further illustrated the differential modulation of temperature on opportunistic pathogens and their VFs. The abundance of 9 specific VFs was significantly associated with temperature. Within the high-temperature range (35-40 °C), Legionella showed a synergistic increase in both its population and the abundance of its VF (Hsp60); Mycobacterium's VF (NuoG) abundance increased significantly with increasing temperature, while the population size remained stable. Furthermore, 3 key bacterial infectious disease pathways- Bacterial invasion of epithelial cells, Staphylococcus aureus infection, and Vibrio cholerae infection were significantly enriched with elevated temperature. Furthermore, high temperatures may also weaken the microbial inactivation efficiency of the conventional chlorine disinfection process, thereby posing a potential threat to drinking water safety. This study elucidates how elevated temperature is linked to the enhanced pathogenic potential of opportunistic pathogens, mediated through the differential regulation of VFs. This provides a scientific basis for assessing aquatic microbial risks under climate warming.}, }
@article {pmid41903868, year = {2026}, author = {Manfredonia, I and Chioso, L and Mateescu, I and Konu, M and Brons, JK and Deelman-Driessen, C and Viljakainen, L and Wertheim, B and Lequime, S}, title = {Prevalence and distribution of two polycipiviruses in wild black garden ants (Lasius niger L.) in the Netherlands.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108611}, doi = {10.1016/j.jip.2026.108611}, pmid = {41903868}, issn = {1096-0805}, abstract = {Metagenomic studies have revealed diverse viruses in insects. Yet, our understanding of the ecology of insect viruses, especially in ants, remains limited, despite the insects' ecological importance. Viruses of the family Polycipiviridae are increasingly recognized as widespread yet poorly characterized components of ant viromes. In this study, we investigated the prevalence and genetic diversity of Lasius niger virus 1 (LniV-1) and Myrmica scabrinodis virus 1 (MsaV-1) in wild colonies of the black garden ant (Lasius niger L.) across the Netherlands. We surveyed 40 wild L. niger colonies, sampled at geographically distinct locations, using RT-PCR to assess viral prevalence and genetic diversity. Viral prevalence was estimated at both colony and individual levels. Amplicons were sequenced to explore potential correlations between geographic distribution and genetic diversity for both viruses. In addition, complete or almost complete viral genome sequences were obtained and assembled for one MsaV-1 genome from Groningen, The Netherlands, and one MsaV-1 and one LniV-1 from Vienna, Austria. In the Netherlands, LniV-1 was detected in 17.5% of colonies, whereas MsaV-1 was detected in 27.5%, including evidence of co-infection at the colony level. Neither the geographical distribution of infected colonies nor the inferred phylogenies for both viruses showed strong geographic structuring. The prevalence in workers within colonies was variable, ranging from 10 to 60%. These findings suggest that polycipiviruses are common in natural L. niger populations and may transmit via both horizontal and vertical routes. This study provides baseline data on ant-virus interactions in natural environments, advancing understanding of viral ecology in social insects and informing future research on virus transmission dynamics in natural ecosystems.}, }
@article {pmid41904207, year = {2026}, author = {Yan, Y and Zhen, W and Hongxia, S and Zhenhong, S and Xianghui, M and Na, W and Li, S and Defeng, W}, title = {Impact of Lactobacillus johnsonii on glycemic control and lipid metabolism in type 2 diabetes with circadian disruption.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-94359-6}, pmid = {41904207}, issn = {2045-2322}, support = {(BJK2024152)//Funded by Science and Technology Project of Hebei Education Department/ ; (20241988)//Hebei Province Medical Science Research Project Plan for 2024/ ; (No. [2020] No.23).//Project Fund of Clinical Medicine Excellent Talents funded by Hebei Provincial Department of Finance/ ; }, }
@article {pmid41904356, year = {2026}, author = {Vojtkuf, I and Čačković, A and Soares, AR and Probst, AJ and Orlić, S}, title = {Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02743-0}, pmid = {41904356}, issn = {1432-184X}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, }
@article {pmid41904418, year = {2026}, author = {Kousar, R and Latif, S and Zahoor, M and Tabassum, S}, title = {A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01413-x}, pmid = {41904418}, issn = {2730-6844}, }
@article {pmid41904571, year = {2026}, author = {Kolenda, R and Hassan, MM and Arrieta-Gisasola, A and Kamara, A and Ansorge, R and Sidorczuk, K and Acton, L and Thilliez, G and Baker, DJ and Burdukiewicz, M and Stares, MD and Browne, HP and Le Gall, G and Torres, RC and Chavez-Arroyo, A and Garrett, J and Stevens, MP and Lawley, TD and Bäumler, AJ and La Ragione, R and Hildebrand, F and Kingsley, RA}, title = {Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02322-4}, pmid = {41904571}, issn = {2049-2618}, support = {BB/W003155/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimurium ST34 clone acquired a genomic island (SGI-4) conferring high copper resistance, an adaptation relevant in the context of the widespread use of copper sulphate at therapeutic levels in pig farming. We investigated how high dietary copper influences the piglet gut microbiota and Salmonella-microbiota interactions that may explain the global spread of S. Typhimurium ST34.
RESULTS: An on-farm study combined with faecal shotgun metagenomics revealed that several potential Salmonella competitor species, including Bifidobacterium, Escherichia, and Lactobacillus, were less abundant in piglets on high-copper diets. Anaerobic and aerobic culturing alongside whole genome sequencing of 131 species and copper sulphate susceptibility testing identified copper resistance gene acquisition in selected microbes, particularly within Escherichia. Niche competition assays demonstrated that copper resistance is critical for inter-species competition under high-copper conditions, with Salmonella's Type VI Secretion System providing a distinct advantage over Escherichia in the copper-modified niche.
CONCLUSIONS: Our findings suggest that copper supplementation alters the piglet gut environment, impacting competitive dynamics between pathogenic and commensal bacteria, likely to influence the zoonotic transmission of pathogens. Video Abstract.}, }
@article {pmid41904606, year = {2026}, author = {Birkeland, S and Rohde Mæhlum, I and Senneset, M and Wik Taxerås, I and Snipen, L and Markov Arnesen, H and Boysen, P and Carlsen, H}, title = {A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649435}, doi = {10.1080/19490976.2026.2649435}, pmid = {41904606}, issn = {1949-0984}, mesh = {Animals ; *Dietary Fiber/metabolism/administration & dosage ; *Gastrointestinal Microbiome ; Mice ; *Colitis/prevention & control/microbiology/chemically induced ; Feces/microbiology ; Dextran Sulfate ; Colon/microbiology/pathology ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation & purification/metabolism ; Male ; Disease Models, Animal ; Intestinal Mucosa/metabolism/microbiology ; }, abstract = {"Feralized" mice, housed in farmyard-type environments, show a matured immunophenotype, altered intestinal barrier, and a shifted gut microbiome compared to conventionally housed laboratory mice. Since dietary fibers support gut health in part by microbial fermentation into immunomodulatory short-chain fatty acids, we hypothesized that feralization influences the intestinal barrier by enhancing the fiber-degrading properties of the microbiome. We explored whether susceptibility to low-grade dextran sulfate sodium-induced colitis differed between feralized and clean laboratory mice fed diets high or low in fermentable fibers. Feralized mice were protected against colitis, displaying low disease scores and biomarkers of inflammation in feces, plasma, and liver; and altered colonic mucosal gene expression, compared to clean mice. This protection was strongest with a fiber-rich diet, which, in contrast, worsened colitis in clean mice. Transfer of fecal microbiota from feralized mice to clean recipients conferred colitis protection. Fecal metagenome-assembled genomes revealed that the fiber-rich diet enriched the microbiome with predicted genes encoding fiber-degrading enzymes, while the low-fiber diet promoted mucin-degrading enzyme genes. However, the dominant microbial species contributing to these functions differed between feralized and laboratory mice. Differential abundance of bacterial taxa in feralized and laboratory mice further identified potential microbial modulators of colitis that merit targeted investigation in future studies. Overall, these findings suggest that fibers affect intestinal inflammation in a microbiota-dependent manner, underscoring the complex interplay between diet and microbiota in disease development.}, }
@article {pmid41904875, year = {2026}, author = {Mu, H and Hu, Y and Zhang, S and Zhang, X and Wei, Q}, title = {Anaerobic digestion model reconstruction of red mud-Pretreated food waste based on the Metagenomics: Improvement of the high-solid ADM1 incorporating SAO and DIET metabolic pathways.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129357}, doi = {10.1016/j.jenvman.2026.129357}, pmid = {41904875}, issn = {1095-8630}, abstract = {Anaerobic Digestion Model No. 1 (ADM1) can accurately describe the biochemical processes in anaerobic digestion (AD) of wastewater, but it fails in the simulation of organic waste's AD due to the different biochemical reaction pathways. To address this limitation, this study proposed an ADM1 improved method based on metagenomics information. For the red mud pretreated food waste anaerobic digestion system, an anaerobic digestion model (RF-ADM1) was developed, focusing on integrating two functional pathways: syntrophic acetate oxidation (SAO) and direct interspecies electron transfer (DIET). Feature kinetic parameters for DIET (Y_pro_ac and Y_bu_ac) were extracted to enhance the model's ability to characterize metabolic processes within this system. The coefficient of determination (R[2]) of the batch experiment reaches 0.996, while Theil's inequality coefficient (TIC) of continuous testing reaches 0.05.}, }
@article {pmid41904906, year = {2026}, author = {Zheng, Y and Wu, Q and Xia, Y and Deng, H and Zhao, Y and Luo, J and Feng, D and Ge, C}, title = {Dark side of biodegradable microplastics in mangrove ecosystem: Plastisphere as an overlooked hotspot of sulfate-reducing metabolism.}, journal = {Water research}, volume = {298}, number = {}, pages = {125802}, doi = {10.1016/j.watres.2026.125802}, pmid = {41904906}, issn = {1879-2448}, abstract = {Microplastics (MPs) have increasingly accumulated in the sulfate-rich and anoxic mangrove sediment. However, it remains unclear whether MPs serve as hotspots for sulfate-reducing microbes (SRM) and what potential risks this activity poses to this ecosystem. To address this issue, polyethylene MPs (PE-MPs) and polylactic acid MPs (PLA-MPs) were in-situ exposed to bare mudflat, invasive S. apetala and native B. gymnorhiza sediment, respectively. After 150 days of exposure, microbially-driven sulfur metabolism patterns on plastisphere in three distinct habitats were compared using metagenomic sequencing. Results showed that PLA-MPs enriched more SRM than PE-MPs and non-MPs particles. Dissimilatory sulfate reduction was one of the most abundant sulfur-metabolic pathways on plastisphere, and the abundance of genes driving this process on MPs followed an order of mudflat (9.37 % ± 0.72 %) < S. apetala (22.31 % ± 5.29 %) < B. gymnorhiza (28.69 % ± 1.10 %), indicating that MPs in B. gymnorhiza sediment fostered more active sulfate reduction, primarily driven by sat/met3, apr and dsr gene clusters. Furthermore, CO2 release from plastisphere was greater on PLA-MPs than on PE-MPs in sediments. Given the tight coupling between sulfate reduction and organic carbon degradation, these findings highlighted the potential of biodegradable MPs to affect carbon-sulfur biogeochemical processes in mangrove ecosystems.}, }
@article {pmid41905022, year = {2026}, author = {Benschop, KSM and Zwagemaker, F and Andersson-Li, L and Andrés, C and Antón, A and Berengua, C and Berginc, N and Bessaud, M and Bisseux, M and Bujaki, E and Canning, B and Christiansen, CB and Couderé, K and Broberg, EK and Cassidy, H and Castilletti, C and Celma, C and Cinek, O and Deézsi-Magyar, N and Eis-Hübinger, AM and Flipse, J and Jiřincová, H and Gatej, R and Georgieva, I and Giardina, F and González-Sánchez, A and Hack, B and Helfferich, J and Hutchings, S and Hietanen, E and Hönemann, M and Virant, MJ and Kalogera, E and Johannesen, CK and Kenicer, J and Kleines, M and Lagarejos, E and Landaas, ET and Kandulu, CC and Xavier López Labrador, F and Lunar, MM and Maier, M and Majumdar, M and Martin, J and McClure, CP and Muñoz-Almagro, C and Ošep, A and Øverbø, J and Palminha, P and Papa, A and Pariani, E and Pellegrinelli, L and Pietsch, C and Piralla, A and Poljak, M and Pomari, E and Prats-Méndez, I and Rector, A and Reuter, G and Riess, M and Ruta, S and Schibler, M and Nilsen, HS and Simmonds, P and Sourvinos, G and Szomor, K and Susi, P and Tabain, I and Vallely, P and von Eije, KJ and Weil, M and Wieczorek, M and Wollants, E and Wolthers, KC and Zuckerman, NS and Fischer, TK and Harvala, H}, title = {Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings: Expert view of the European non-polio enterovirus network (ENPEN).}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {184}, number = {}, pages = {105940}, doi = {10.1016/j.jcv.2026.105940}, pmid = {41905022}, issn = {1873-5967}, abstract = {Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (partial) VP1 gene sequencing for typing, are widely utilized. However, Next-Generation Sequencing (NGS), and bioinformatics offer a comprehensive alternative, enabling full-genome analyses for improved virus characterization, genomic epidemiological surveillance, and outbreak investigation. Despite its advantages, implementation of NGS poses challenges, particularly in standardizing and optimizing laboratory workflows (wet-lab) and bioinformatics analyses (dry-lab), methods that are not often readily accessible in many laboratories. Here, we discuss the potential of NGS as a tool for EV detection/characterization in clinical virology, public health, and research settings. We provide practical options for actions for implementing NGS to advance the understanding and management of enterovirus infections. These recommendations are based on expert discussions during the recent European non-polio enterovirus network (ENPEN) workshop held in Corfu, Greece, on 23-24 May 2024, aiming to guide harmonization of NGS practices across clinical, public health, and research settings.}, }
@article {pmid41905052, year = {2026}, author = {Liu, Z and Zhao, C and Chen, N and Zhu, K and Chen, Y and Feng, C}, title = {Synergistic and competitive interactions between solid carbon sources and current-driven sulfate reduction in a single-chamber microbial electrolysis cell.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141881}, doi = {10.1016/j.jhazmat.2026.141881}, pmid = {41905052}, issn = {1873-3336}, abstract = {Conventional microbial sulfate reduction technologies for sulfate pollution control often suffer from low efficiency, insufficient sulfur immobilization, and poor stability under extreme carbon-to-sulfur (C/S) ratios, leading to secondary pollution. To overcome these limitations, this study combined electrical stimulation with a solid-phase carbon source (wheat straw) to construct a single-chamber microbial electrolysis cell for long-term operation. Under optimal conditions (hydraulic retention time = 2.0 d, C/S = 1.5, current density = 100 mA/m[2]), the sulfate removal efficiency and the accumulation rate of dissolved sulfide reached 92.45% and 26.30%, respectively. The system maintained stable performance over 293 days and during five shock events, demonstrating a pronounced synergistic effect between electrical input and the carbon source. The iron anode facilitated the directional conversion of sulfide into FeS and S[0], enabling efficient sulfur immobilization and significantly suppressing secondary pollution. During operation, microbial activity was sustained at a high level (electron transport system activity = 0.357 μL O2·g[-1]·min[-1], ATP = 0.024 μmol). Metagenomic analysis revealed that electrical stimulation markedly enhanced the abundance of sulfur metabolism-related genes and promoted direct extracellular electron transfer process, whereas the wheat straw facilitated mediated extracellular electron transfer through the slow release of exogenous electron shuttles. The synergistic interaction between these processes optimized the electron transfer network within the system. This study elucidates the mechanisms underlying directional sulfur transformation and electron transfer during long-term operation, providing critical insights for optimizing microbial ecosystems involved in sulfate reduction and supporting the practical application of this technology in water in situ remediation.}, }
@article {pmid41905084, year = {2026}, author = {Xiang, H and Deng, Y and Xu, Y and Zhang, X and Zhang, C and Guo, B and Xu, Z and Wang, Y}, title = {Fe-S interactions and geological background shape phosphorus bioavailability in mangrove sediments.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119655}, doi = {10.1016/j.marpolbul.2026.119655}, pmid = {41905084}, issn = {1879-3363}, abstract = {Mangrove sediments act as critical phosphorus (P) sinks and potential sources in coastal ecosystems, with P release risk dominated by bioavailable phosphorus (BAP), including exchangeable P, iron-bound P (Fe-P), and organic P (OP). While Fe-S cycles tightly regulate P speciation, how the geological background mediates Fe-S-P coupling across heterogeneous mangroves remains unclear. We integrated Fe-S-P fractionation, water-soluble organic matter (WSOM) fluorescence spectroscopy, and metagenomics to compare volcanic weathering (V) and Quaternary coastal (Q) sediments in Dongzhai Harbor. Key findings are as follows: Total P in shallow V sediments (8.89-30.90 μmol/g) is higher than in Q (6.95-17.09 μmol/g). OP dominates V's BAP (48.87%) linked to OP mineralization genes (e.g., appA), whereas Fe-P dominates Q's BAP (57.31%) and is stabilized by amorphous Fe oxides. In deep V sediments, Fe-P is positively correlated with acid-volatile sulfide (AVS; R[2] = 0.57) and Fe/S reduction genes (fsr, omcF), indicating Fe-S-coupled P mobilization and release. In deep Q sediments, Fe-P remains stabilized by Feox1, and P mobilization is driven by microbial iron reduction, with iron-reduction genes (e.g., mtrA) being significantly enriched. Two distinct P release pathways are identified: in volcanic weathering zone sediments, P release shifts from OP dominance to Fe-S-coupled regulation, while in Quaternary coastal zone sediments, Fe-P mobilization relies on microbial iron reduction. These findings clarify the geological controls on Fe-S-P interactions in mangrove sediments, providing a scientific basis for site-specific P risk assessment and the formulation of targeted strategies for mangrove ecosystem restoration and coastal eutrophication control.}, }
@article {pmid41905194, year = {2026}, author = {Li, J and Silvester, R and Williams, RC and Chan-Herur, V and Goldman, M and Fidler, D and Jones, DL}, title = {Metagenomics-based source attribution of antimicrobial resistance in wastewater for improved epidemiological risk assessment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125810}, doi = {10.1016/j.watres.2026.125810}, pmid = {41905194}, issn = {1879-2448}, abstract = {Wastewater-based epidemiology (WBE) offers a powerful approach for monitoring antimicrobial resistance (AMR) at the population level. However, distinguishing between human gut-derived and sewer-derived AMR-carrying organisms remains a key challenge for accurate surveillance and risk assessment. In this study, we used genome-resolved metagenomics to distinguish human gut-derived organisms, and their associated antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and virulence-associated determinants (VFs), from taxa endemic to the sewer network. We applied this approach to wastewater samples collected from three hospital outflows (near-source healthcare sites), as well as from untreated influent and final treated effluent at the corresponding municipal wastewater treatment plants serving the surrounding communities. Along the wastewater pathway, microbial communities progressively shifted from human gut-associated to sewer adapted taxa; consequently, the final treated effluent was dominated by sewer-adapted taxa. Human gut-derived taxa were further examined in detail: 84% carried ARGs and VFs, predominantly within Bacillota and Bacteroidota; all gut-associated Pseudomonadota also harboured multiple ARGs, VFs and MGEs. Opportunistic-pathogen taxa of gut origin (Escherichia coli, Klebsiella spp., E. faecium) accounted for a substantial fraction of ARGs in hospital wastewater. Combined sewer overflow (CSO) events may allow these carriers to bypass wastewater treatment and reach receiving waters, posing public health risks. This genome-resolved framework strengthens WBE by resolving human-derived contributions for surveillance and risk assessment.}, }
@article {pmid41905375, year = {2026}, author = {Wrønding, T and Vomstein, K and Lundgaard, AT and DeLong, K and Mollerup, S and Mortensen, B and Bosma, EF and Hellerung, AM and Engel, EV and Wiil, KD and Heintz, JE and Halkjær, SI and Hugerth, LW and Hartwig, TS and Petersen, AM and Thomsen, AB and Westergaard, D and la Cour Freiesleben, N and Westh, H and van Hylckama Vlieg, JET and Ensign, LM and Nielsen, HS}, title = {Vaginal microbiota transplantation for treatment of vaginal dysbiosis without the use of antibiotics: a double-blind, randomised controlled trial in women with vaginal dysbiosis.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101294}, doi = {10.1016/j.lanmic.2025.101294}, pmid = {41905375}, issn = {2666-5247}, abstract = {BACKGROUND: A vaginal microbiota dominated by Lactobacillus species is associated with reduced risk of infection and adverse reproductive outcomes. Effective interventions to restore healthy microbiota remain scarce. In this study, we aimed to assess the efficacy of vaginal microbiota transplants (VMTs) without antibiotic pretreatment in achieving conversion to a Lactobacillus-dominated vaginal microbiome.
METHODS: This single-centre, double-blind, randomised controlled trial was done at Copenhagen University Hospital (Hvidovre, Denmark) between June 1, 2021, and March 1, 2023. We enrolled women aged 18-40 years with asymptomatic or symptomatic molecular vaginal dysbiosis (<10% total relative abundance of Lactobacillus spp and >20% relative abundance of Gardnerella spp, Fannyhessea vaginae, and Prevotella spp) who were otherwise healthy premenopausal women and not pregnant as recipients; donors were healthy women aged 18-40 years with a Lactobacillus-dominated vaginal microbiota (>80%) and a low (<5%) abundance of Gardnerella spp, F vaginae, and Prevotella spp, and negative screening for sexually transmitted infections. Participants were randomly assigned (3:1) to the intervention or placebo through a computer-generated schedule with block randomisation and stratification by hormonal contraception. Participants and investigators were masked to the group. Up to three administrations of VMT or placebo were given across three menstrual cycles, with follow-up for six cycles. The primary endpoint was resolution of dysbiosis at any timepoint during follow-up, defined as at least 70% relative abundance of Lactobacillus spp and less than 10% combined abundance of Gardnerella spp, F vaginae, and Prevotella spp, as assessed by shotgun metagenomic sequencing of vaginal samples. This analysis was done in the intention-to-treat population, excluding any participants who withdrew consent. An extension study assessed the effect of antiseptic pretreatment before additional VMT in refractory participants. This study was registered with ClinicalTrials.gov (NCT04855006) and is completed.
FINDINGS: A total of 302 women were screened, of whom 49 were enrolled. 37 women were randomly assigned to the VMT group (mean age 26·1 years [SD 3·8]) and 12 to the placebo group (27·3 years [4·8]). The primary outcome showed no significant difference in dysbiosis resolution between active and placebo groups (HR 0·65; 95% CI 0·20-2·16, p=0·49). In an extension study of refractory participants, five (50%) of the ten women who received antiseptic pretreatment followed by VMT had a microbiome conversion. Adverse events occurred in 15 (42%) VMT participants and five (42%) placebo participants; none were serious or led to withdrawal. A single pregnancy and one new human papillomavirus infection occurred, both unrelated to treatment.
INTERPRETATION: VMT without antibiotics did not significantly improve microbiome conversion in this trial. However, findings from the extension study suggest that antiseptic pretreatment might enhance efficacy. Future trials should explore optimised dosing and use donor engraftment as a primary outcome.
FUNDING: Freya Biosciences.}, }
@article {pmid41905742, year = {2026}, author = {Wu, Z and Duan, A and Liu, Y and Chen, R and Md Din, MF and Sanjaya, EH and Ali, EAE and Saad, A and Liu, Z and Chen, H}, title = {Mechanistic insights into sulfate-driven performance adaptation and membrane fouling in a UASB-SBR-AXMBR system: metabolic network reconstruction and microbial community succession.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124374}, doi = {10.1016/j.envres.2026.124374}, pmid = {41905742}, issn = {1096-0953}, abstract = {Sulfate-rich wastewater poses considerable challenges to the operational stability of biological treatment systems. This study investigated the long-term (294 days) response of a combined UASB-SBR-AXMBR process to stepwise increases in sulfate concentration from 100 to 2000 mg/L. The system maintained stable carbon and nitrogen removal performance under sulfate stress, with COD removal exceeding 90.3% and total nitrogen removal stabilizing at 85.5% via a partial nitritation-anammox (PN/A) pathway. However, high sulfate loading significantly intensified membrane fouling, with the primary driving factor likely being the co-deposition of elemental sulfur (S[0]) and soluble extracellular polymeric substances (S-EPS). Microbial analysis revealed persistent enrichment of Bacteroidota and Proteobacteria in the SBR, alongside a marked increase in Anammoxoglobus (from 17.1% to 51.2%) in the Anaerobic Ammonia Oxidation Membrane Bioreactor (AXMBR), underpinning system resilience. Metagenomic profiling further indicated adaptive shifts in key nitrogen-cycling genes (hao, amoA) and sulfur metabolism pathways. Notably, sulfate-reducing bacteria (SRB) outcompeted methanogens, redirecting carbon flow from methanogenesis to sulfur reduction, while niche diversification in the AXMBR expanded nitrogen removal pathways. These findings provide new mechanistic insights into the adaptive responses of integrated bioprocesses under sulfate stress and provide practical guidance for the treatment of high-sulfate industrial wastewaters such as monosodium glutamate effluent.}, }
@article {pmid41905975, year = {2026}, author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC}, title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45955-7}, pmid = {41905975}, issn = {2045-2322}, }
@article {pmid41906088, year = {2026}, author = {Bai, D and Wang, Z}, title = {Neurosyphilis with simultaneous brain and spinal cord involvement mimicking intracranial tumors: a case report.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04836-2}, pmid = {41906088}, issn = {1471-2377}, }
@article {pmid41906342, year = {2026}, author = {Wu, J and Tian, J and Zhang, X and Kong, Z}, title = {Metagenomic Analysis of Soybean Rhizosphere Microbiome in Black Soil: Community Composition and Functional Insights.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70505}, pmid = {41906342}, issn = {1365-3040}, support = {XDA28030201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32241045//National Natural Science Foundation of China/ ; }, }
@article {pmid41492297, year = {2025}, author = {Cordeiro, NF and Coppola, N and Ferreira, F and Vignoli, R and Bado, I}, title = {What are we eating?. Detection of antibiotic resistance mechanisms in frozen chicken nuggets imported from Brazil.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101171}, pmid = {41492297}, issn = {2352-7714}, abstract = {The rise of antibiotic resistance is a growing challenge, affecting humans, the environment, and animals. Under the One Health framework, this study investigated resistance mechanisms to critically important antibiotics in frozen chicken nuggets imported from Brazil. Eighty nugget samples were cultured on selective media containing ceftriaxone, ciprofloxacin, or colistin. Isolates were identified using MALDI-TOF, and antibiotic susceptibility was assessed by disk diffusion. Eight samples were also analyzed using shotgun metagenomic sequencing processed through the SqueezeMeta pipeline. Nineteen Enterobacterales resistant mainly to β-lactams and to a lesser extent, to quinolones and aminoglycosides, were identified. Eight Pseudomonas spp. were recovered, including one P. fulva resistant to colistin. Metagenomics revealed predominant Firmicutes, (Bacillaceae, Lactobacillaceae, and Paenibacillaceae) with low γ-Proteobacteria levels. Additionally, we detected resistance genes against several antibiotics. This study highlights the role of imported food in spreading AMR and the value of combining metagenomics with conventional microbiology to strengthen One Health surveillance.}, }
@article {pmid41492358, year = {2026}, author = {Pan, D and Jiang, M and Wang, Y and He, J and Tang, J and Liu, S and Li, M and Jiang, X and Xu, Q}, title = {Multi-omics reveals associations between the microbiota-gut-brain axis and antidepressant effects of vagus nerve stimulation.}, journal = {Neurobiology of stress}, volume = {40}, number = {}, pages = {100777}, pmid = {41492358}, issn = {2352-2895}, abstract = {BACKGROUND: Major depressive disorder is a severe mental health condition characterized by persistent depressed mood and loss of interest. Current first-line pharmacotherapies often exhibit limited therapeutic performance and adverse side effects. Transcutaneous auricular vagus nerve stimulation (taVNS) is a promising, safe, and noninvasive alternative intervention with demonstrated neuromodulatory efficacy. Nevertheless, its mechanisms remain unclear. This study investigated whether the antidepressant properties of taVNS are associated with the microbiota-gut-brain axis, focusing on the potential crosstalk between differentially expressed hippocampal proteins and the gut microbiota.
METHODS: A chronic unpredictable mild stress (CUMS) rat model of depression was established, and taVNS was administered for 14 days. Hippocampal proteomic profiling was performed using data-independent acquisition. Fecal metagenomic sequencing was conducted to characterize alterations in gut microbial communities. Key signaling pathways were validated using Western blot, qRT-PCR, HE staining, and transmission electron microscopy, all of which were employed to systematically assess behavioral, proteomic, microbial, and molecular changes.
RESULTS: Proteomics and molecular analyses revealed that taVNS upregulated hippocampal expression of glutamate ionotropic receptor N-methyl-D-aspartate type subunit 1 (GluN1) and brain-derived neurotrophic factor (BDNF), while simultaneously restoring mitogen-activated protein kinase (MAPK) signaling activity. Metagenomic profiling demonstrated that taVNS increased the abundance of Akkermansia muciniphila and reduced Ligilactobacillus reuteri. Ligilactobacillus levels were positively correlated with synaptogyrin-1 (Syngr1), indicating their potential association in enhancing the antidepressant effects mediated by the GluN1/MAPK/BDNF signaling cascade.
CONCLUSION: TaVNS significantly alleviated depression-like behaviors in CUMS-exposed rats. The underlying mechanism may involve the restoration of synaptic function of glutamatergic neurons by regulating the GluN1/MAPK/BDNF signaling pathway. In addition, taVNS reshaped the gut microbiota, markedly increasing the abundance of Akkermansia muciniphila and Ligilactobacillus murinus while reducing Limosilactobacillus reuteri and Lactobacillus johnsonii. The positive correlation between Syngr1 protein level and Ligilactobacillus abundance in the hippocampus suggests that the microbiota-gut-brain axis may play a key role in the antidepressant effects of taVNS.}, }
@article {pmid41492364, year = {2025}, author = {Solly, EF and Jaeger, ACH and Barthel, M and Six, J and Mueller, RC and Hartmann, M}, title = {Soil water limitation intensity alters nitrogen cycling at the plant-soil interface in Scots pine mesocosms.}, journal = {Plant and soil}, volume = {516}, number = {1}, pages = {705-723}, pmid = {41492364}, issn = {0032-079X}, abstract = {BACKGROUND AND AIM: More intense episodes of drought are expected to affect terrestrial nitrogen (N) cycling by altering N transformation rates, the functioning of soil microorganisms, and plant N uptake. However, there is limited empirical evidence of how progressive water loss affects N cycling at the plant-soil interface.
METHODS: We adopted [15]N tracing techniques and metagenomic analyzes of microbial genes involved in N cycling to assess how different levels of soil water availability influenced the fate of N derived from decomposing litter in mesocosms with Scots pine saplings.
RESULTS: With increasing water limitation, the release of N from decomposing litter into the soil declined rapidly. However, moderate levels of water limitation barely affected the microbial metagenome associated with N cycling and the uptake of N by the saplings. Comparatively, severe levels of water limitation impaired plant N uptake, and increased the prevalence of microbial N-cycling genes potentially involved in mechanisms that protect against water stress. Genes associated with the uptake and release of N during mineralization and nitrification declined under low soil water contents.
CONCLUSIONS: When soil water becomes largely unavailable, the cycling of N at the plant-soil interface is slowed down, and microbial and plant tolerance mechanisms may prevail over N uptake and microbial decomposition.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07758-z.}, }
@article {pmid41492410, year = {2025}, author = {Wallau, GDL and Barbier, E and Machado, LC and da Silva, AF and Dias, YJM and Dezordi, FZ and Tomazatos, A and Horváth, B and Lins, RD and Bernard, E and Cadar, D}, title = {Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats, sheds new light on bat-borne coronaviruses evolution.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf094}, pmid = {41492410}, issn = {2057-1577}, abstract = {Understanding the viral diversity harboured by wildlife is essential for effective mapping and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several high-impact zoonotic viral pathogens, including coronaviruses responsible for Severe Acute Respiratory Syndrome (SARS), the rabies virus, diverse paramyxoviruses, Marburg, Ebola, Nipah, and Hendra viruses. However, a large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazilian ecosystems. We used a meta-transcriptomic approach to characterize new virus genomes found in blood, oral, and anal samples collected from cave- and noncave bats from Northeast Brazil, Caatinga, and Atlantic Forest biomes. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nobecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain from the C-terminal domai (CTD) region could not be identified due to high dissimilarity relative to known congeners. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests potential interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown, not just in Brazil but likely in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.}, }
@article {pmid41492995, year = {2026}, author = {Sathaye, SB and Sharma, N and Bhaumik, J and Sahoo, D and Rai, AK and Singh, SP}, title = {Novel Glutamate Decarboxylase from Ethnic Food Metagenome: A Potential Biocatalyst to Produce a Nonproteinaceous Amino Acid, γ-Aminobutyric Acid.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {1}, pages = {1175-1186}, doi = {10.1021/acs.jafc.5c11421}, pmid = {41492995}, issn = {1520-5118}, mesh = {*Glutamate Decarboxylase/genetics/chemistry/metabolism ; *gamma-Aminobutyric Acid/biosynthesis/chemistry ; Metagenome ; Kinetics ; Enzyme Stability ; *Bacterial Proteins/genetics/chemistry/metabolism ; Biocatalysis ; Molecular Docking Simulation ; Hydrogen-Ion Concentration ; Molecular Dynamics Simulation ; }, abstract = {This study reports the biochemical characterization of a novel variant of glutamate decarboxylase (mtGAD), identified from an ethnic food, Kinema. The mtgad gene was cloned from the Kinema metagenome and expressed in a heterologous host, Escherichia coli. The enzyme mtGAD was extracted and purified for biochemical characterization. The enzyme showed optimal activity for γ-aminobutyric acid (GABA) synthesis at 50 °C and pH 4.5. The kinetic parameters of mtGAD were computed to be 29.2 mM Km, 561.8 s[-1] kcat, and 23.2 mM[-1] s[-1] kcat/Km. The in silico protein structure analysis, followed by molecular docking and molecular dynamics simulation, revealed that the binding with pyridoxal-5'-phosphate (PLP; a cofactor for mtGAD) reduces the fluctuations in the structure at high temperatures, contributing to the thermal stability of mtGAD. Furthermore, the conversion of about 60% monosodium glutamate (MSG) into GABA was achieved in approximately 3 h of catalytic reaction with 200 mM MSG, treated with 6.67 U mtGAD. A high turnover number with moderate thermal and pH stability makes mtGAD a potential biocatalyst for GABA production.}, }
@article {pmid41493186, year = {2026}, author = {Queiroz, VF and Jivaji, AM and Aylward, FO}, title = {Tiny giants in a big ocean.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0299225}, pmid = {41493186}, issn = {2165-0497}, mesh = {*Seawater/virology ; Phylogeny ; Pacific Ocean ; Genome, Viral ; Oceans and Seas ; Metagenomics ; }, abstract = {Prasinoviruses infect some of the most abundant photosynthetic eukaryotes in the ocean, shaping microbial dynamics and playing a major role in nutrient cycling. Despite their ecological significance, they have only been explored in a few marine systems. In a recent study, A. B. de Silva, S. W. Polson, C. R. Schvarcz, G. F. Steward, and K. F. Edwards (Microbiol Spectr 13:e02583-24, 2025, https://doi.org/10.1128/spectrum.02583-24) describe four new prasinoviruses isolated from the tropical North Pacific. The comparative analyses highlighted the placement of these viruses within known prasinovirus lineages while also revealing novel genetic features. To assess their ecological reach, the authors mapped metagenomic reads from global data sets, demonstrating that these viruses are not confined to the Pacific but are globally distributed. These findings expand our understanding of prasinovirus diversity and evolution and highlight their widespread occurrence across oceanic regions.}, }
@article {pmid41493376, year = {2026}, author = {Shklyar, AA and Mesentsev, YS and Smirnov, AV and Nassonova, ES}, title = {Nucleophaga amutiana, sp. nov.-a novel intranuclear parasite of amoebae from the Far East of Russia expands the diversity and biogeography of microsporidia-like organisms.}, journal = {Mycologia}, volume = {118}, number = {2}, pages = {330-344}, doi = {10.1080/00275514.2025.2586430}, pmid = {41493376}, issn = {1557-2536}, mesh = {Phylogeny ; Russia ; RNA, Ribosomal, 18S/genetics ; *Amoeba/microbiology ; DNA, Ribosomal/genetics/chemistry ; Sequence Analysis, DNA ; Molecular Sequence Data ; Phylogeography ; }, abstract = {The genus Nucleophaga comprises poorly studied intranuclear parasites that infect amoebae. Currently classified within the phylum Rozellomycota, this genus belongs among numerous lineages with unresolved taxonomic positions, primarily identified through metagenomic studies. Three species of Nucleophaga were described at the morphological and molecular levels-N. amoebae, N. terricolae, and N. striatae, all isolated in Europe. Here, we report the discovery of a fourth species of the genus, isolated from the Far East of Russia, infecting nuclei of Thecamoeba sp. A detailed light microscopic study revealed several remarkable morphological features of this organism. For the first time, the division of Nucleophaga plasmodium was illustrated. Experimental infections demonstrated that Thecamoeba quadrilineata and T. foliovenanda can support the development of the parasite, whereas Nucleophaga showed abnormal development in T. onigiri and was unable to survive in T. vumurta. Phylogenetic analysis, based on the nuc 18S rRNA gene sequences, placed the new isolate as a distinct lineage within the genus Nucleophaga. Based on its molecular characteristics, the studied isolate was described as a new species, Nucleophaga amutiana.}, }
@article {pmid41493379, year = {2026}, author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA}, title = {A mathematical framework to correct for compositionality in microbiome data sets.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {1}, pages = {e0112625}, pmid = {41493379}, issn = {1098-5336}, mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.}, }
@article {pmid41493389, year = {2026}, author = {Buchheister, S and Bolsega, S and Rösel-Birk, S and Smoczek, A and Scheele, T and Bleich, A and Basic, M}, title = {To stain or not to stain: unraveling potential bacterial contamination in germ-free husbandry using bacterial viability staining.}, journal = {Journal of applied microbiology}, volume = {137}, number = {1}, pages = {}, doi = {10.1093/jambio/lxag001}, pmid = {41493389}, issn = {1365-2672}, support = {395357507//German Research Foundation/ ; 01EA1906F//Federal Ministry of Education and Research/ ; }, mesh = {Animals ; Mice ; Germ-Free Life ; *Bacteria/isolation & purification/genetics ; *Microbial Viability ; *Staining and Labeling/methods ; RNA, Ribosomal, 16S/genetics ; *Animal Husbandry/methods ; Intestines/microbiology ; Microscopy, Phase-Contrast ; Microscopy, Fluorescence ; }, abstract = {AIMS: Hygienic monitoring (HM) of germ-free (GF) mouse colonies is exceptionally challenging. The test accuracy of the applied diagnostic methodology has to be outstanding to provide proof of absence of all living microorganisms confirming the GF status. In this context, microscopy of native intestinal content serves as a highly sensitive diagnostic tool for the detection of bacterial contaminants. However, with this method residual microorganisms may be detected. To overcome this risk of false-positive results, we complemented our analyses with a bacterial viability staining of the intestinal content of GF mice.
METHODS AND RESULTS: Intestinal contents of GF mice (n = 13) from five isolators were analyzed by bacterial culture and phase-contrast microscopy. Additionally, 16S rRNA gene PCR analysis and metagenomic sequencing were performed. To distinguish between live and dead bacteria, intestinal content was stained by a Bacterial Viability Kit and analyzed by fluorescence microscopy. While culture medium proved sterility of the sample material, increased amounts of scattered bacterial structures were detected during microscopic analysis, indicating potential contamination. Molecular techniques pointed to a presence of environmental bacteria. However, viability staining revealed the presence of only dead (double-stained) bacteria in all samples. Likewise, non-viable bacteria have been identified in samples obtained from irradiated feed, probably being the source of bacterial structures found in GF mice.
CONCLUSIONS: Altogether, detected bacterial structures were proven to be non-viable and therefore should not be interpreted as isolator contaminants. Thus, in our hands, with the herein described report of suspected contamination, we prove that bacterial viability staining served as a highly valuable screening tool, enhancing diagnostic quality of the HM of GF colonies.}, }
@article {pmid41493405, year = {2025}, author = {Seidel, F and Nygren, TM and Opgen-Rhein, B and Hecht, T and Boehne, M and Weickmann, J and Anderheiden, F and Reineker, K and Böcker, D and Rentzsch, A and Wiegand, G and Fischer, M and Kiski, D and Frede, W and Ruf, B and Tarusinov, G and Papakostas, K and Logeswaran, T and Schiebel, A and Voges, I and Kaestner, M and Kramp, J and Kerst, G and Khedim, M and Gatzweiler, E and Wannenmacher, B and Knirsch, W and Meyer-Dobkowitz, L and Donner, B and Klingner, J and Rau, C and Haller, S and Brinkmann, A and Nitsche, A and Noldt, M and Schmoock, G and Herzmann, C and Degenhardt, U and Bühler, S and Enders, M and Hermes, J and Rolfs, N and Manuylova, T and Schwarzkopf, E and Beudt, J and Siffczyk, C and Schubert, S and Sandfort, M and Klingel, K}, title = {Severe Myocarditis Increase in Children Associated With Parvovirus B19 Infection: MYKKE Registry and German Surveillance Data.}, journal = {JACC. Heart failure}, volume = {}, number = {}, pages = {102854}, doi = {10.1016/j.jchf.2025.102854}, pmid = {41493405}, issn = {2213-1787}, abstract = {BACKGROUND: Following a surge in myocarditis in Germany since August 2023, many with parvovirus B19 (B19V) detection, concerns arose about causes and countermeasures.
OBJECTIVES: The authors aimed to verify the association among B19V, myocarditis increase, and severity.
METHODS: Data from the pediatric multicenter registry (MYKKE) from 27 centers were analyzed. B19V myocarditis cases were defined by polymerase chain reaction (PCR) positivity in blood or myocardium with clinical or histopathologic myocarditis evidence. Comprehensive clinical, histopathologic, and epidemiologic analyses were conducted. Past patients were hospitalized from 2013 to July 2023, current from August 2023 to November 2024. Registry data were compared with surveillance and consultant laboratory data. Specimens of current cases underwent metagenomic analysis and B19V sequencing.
RESULTS: Since 2013, 922 myocarditis patients including 126 (13.6%) with B19V myocarditis were enrolled. With 57 of 126 (45.2%) current cases, B19V myocarditis increased, compared with other myocarditis causes. Most current cases were patients who were <2 years of age (64.9%), 56.1% were female. The ratio of B19V myocarditis to incidence did not increase compared with the earlier period. Current cases presented with more reduced ejection fraction (29.0% vs 34.5%; P = 0.007), linked to severe cardiac T-cell infiltration and high numbers of B19V copies. Increased severity was associated with younger age. Phylogenetic analysis identified B19V genotype 1A, without sequence variants indicating increased virulence.
CONCLUSIONS: The increase in pediatric myocarditis since August 2023 was associated with B19V, more likely explained by disproportionately young current cases and young children's vulnerability than a virulent strain. Raising clinicians' awareness and proactive, interdisciplinary approaches are essential for improving prevention of B19V infection, management of myocarditis, and treatment strategies in this vulnerable cohort. (Myocarditis Registry for Children and Adolescents [MYKKE]; NCT02590341).}, }
@article {pmid41494246, year = {2026}, author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F}, title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.}, journal = {Waste management (New York, N.Y.)}, volume = {212}, number = {}, pages = {115332}, doi = {10.1016/j.wasman.2026.115332}, pmid = {41494246}, issn = {1879-2456}, mesh = {*Oligochaeta/physiology ; *Quorum Sensing ; Animals ; *Composting/methods ; *Sewage/microbiology ; Biodegradation, Environmental ; Humic Substances ; Microbiota ; Bacteria/metabolism ; Acyl-Butyrolactones/metabolism ; }, abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.}, }
@article {pmid41494287, year = {2026}, author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y}, title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.}, journal = {Redox biology}, volume = {89}, number = {}, pages = {104005}, pmid = {41494287}, issn = {2213-2317}, mesh = {Animals ; *Citrobacter rodentium/drug effects/pathogenicity ; Oxidation-Reduction/drug effects ; Rats ; *Antioxidants/pharmacology/administration & dosage/chemistry ; *Colon/microbiology/drug effects/metabolism ; Delayed-Action Preparations/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy/metabolism ; Male ; Coumaric Acids/pharmacology/administration & dosage ; }, abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.}, }
@article {pmid41494342, year = {2026}, author = {Hu, P and Chen, S and Qian, Y and Hong, Y and Lin, JG and He, B and Gu, JD}, title = {Efficient nitrogen removal by coupling with methane metabolism in three landfill leachate wastewater treatment systems.}, journal = {Journal of hazardous materials}, volume = {502}, number = {}, pages = {141035}, doi = {10.1016/j.jhazmat.2026.141035}, pmid = {41494342}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/metabolism ; *Nitrogen/metabolism/isolation & purification ; *Methane/metabolism ; *Wastewater/microbiology/chemistry ; Denitrification ; Bacteria/metabolism/genetics ; Nitrification ; *Waste Disposal, Fluid/methods ; Ammonia/metabolism ; }, abstract = {High concentration of ammonium-nitrogen (NH4[+]-N) is a widley known characteristic of landfill leachate, and therefore, a thorough understanding of the active nitrogen-related microorganisms is essential for designing an efficient landfill leachate treatment system. Here, we analyze the microbial nitrogen cycling and metabolic interactions at three full-scale landfill leachate treatment plants. Specifically, using metagenomics and metatranscriptomics techniques, we elucidate the mechanisms underlying high NH4[+]-N removal rates achieved through distinct N removal strategies (nitrification-denitrification system at Jilong (JL), denitrification-ammonia oxidation-partial nitrification system at Xinfeng (XF), and simultaneous nitrification-denitrification-ammonia oxidation system at Wenshan (WS)), all three plants achieved efficient NH4[+]-N removal of 96 %, 97.96 % and 97.33 % for JL, XF, and WS, respectively. Highly active methane (CH4)-associated microorganisms, particularly CH4-catabolizing bacteria, exhibited strong interactions with denitrifying bacteria in all three treatment plants, promoting effective nitrogen removal in the landfill treatment systems. In addition, enhanced anammox activity in WS treatment plant in 2023 and 2015 was compared using nitrogen-15 isotope labeling and in situ transcriptome analysis. By comparing microbial metabolic activity, strong interactions were observed between anammox bacteria and other nitrogen-transforming microbes. Meanwhile, detailed physicochemical parameter analysis revealed that optimal Fe[3] [+] concentrations significantly promote the enrichment and enhanced activity of anammox bacteria. Collectively, this study highlights strategies for microbial-mediated high-efficiency ammonia nitrogen removal in full-scale landfill leachate and explains the underlying mechanisms that may lead to increased abundance and activity of anammox bacteria.}, }
@article {pmid41494802, year = {2026}, author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C}, title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337480}, pmid = {41494802}, issn = {1468-3288}, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.
OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.
DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, Índice de Alimentación Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6 months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.
RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.
CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.}, }
@article {pmid41495312, year = {2026}, author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA}, title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {40}, pmid = {41495312}, issn = {1432-184X}, mesh = {*Carbon Dioxide/metabolism ; *Geologic Sediments/microbiology ; *Carbon Cycle ; *Hydrogen/metabolism ; Formates/metabolism ; Autotrophic Processes ; Seawater/microbiology ; Acetic Acid/metabolism ; Lakes/microbiology ; Biodiversity ; Phylogeny ; *Bacteria, Anaerobic/metabolism/genetics/classification/isolation & purification ; *Bacteria/metabolism/classification/genetics ; Metagenome ; Metagenomics ; }, abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.}, }
@article {pmid41495321, year = {2026}, author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K}, title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4066}, pmid = {41495321}, issn = {2045-2322}, support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Poecilia/genetics/physiology ; Male ; *Predatory Behavior ; Rivers ; *DNA, Environmental/analysis/genetics ; *Introduced Species ; Japan ; *Pigmentation ; Ecosystem ; DNA Barcoding, Taxonomic ; Color ; }, abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.}, }
@article {pmid41495863, year = {2026}, author = {Ali, H and Rafiq, M and Manzoor, M and Gillani, SW and Degen, A and Iqbal, A and Wang, W and Rafiq, MK and Shang, Z}, title = {Seasonal shifts in vegetation, soil properties, and microbial communities in Western Himalayan forests.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {22}, pmid = {41495863}, issn = {2524-6372}, support = {31961143012//Natural Science Foundation of China/ ; ANSO-SBA-2023-02//Science-based Advisory Program of The Alliance of National and International Science Organizations for the Belt and Road Regions/ ; }, abstract = {BACKGROUND: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.
RESULTS: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p < 0.001) in summer than in winter while the community maturity index was higher (p < 0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p < 0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p < 0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p < 0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R = 0.222, p = 0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R[2]=0.64-0.72 for key paths) than in winter (R[2]=0.52-0.63).
CONCLUSIONS: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.}, }
@article {pmid41495893, year = {2026}, author = {Bouras, G and Grigson, SR and Mirdita, M and Heinzinger, M and Papudeshi, B and Mallawaarachchi, V and Green, R and Kim, RS and Mihalia, V and Psaltis, AJ and Wormald, PJ and Vreugde, S and Steinegger, M and Edwards, RA}, title = {Protein structure-informed bacteriophage genome annotation with Phold.}, journal = {Nucleic acids research}, volume = {54}, number = {1}, pages = {}, pmid = {41495893}, issn = {1362-4962}, mesh = {*Genome, Viral ; *Molecular Sequence Annotation/methods ; *Bacteriophages/genetics ; *Viral Proteins/chemistry/genetics ; *Software ; Protein Conformation ; }, abstract = {Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here, we introduce Phold, an annotation framework utilizing protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high-quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency, and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveal that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold.}, }
@article {pmid41496069, year = {2026}, author = {Zhao, Y and Wang, H and Lu, Y and Lou, D}, title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.}, journal = {Medicine}, volume = {105}, number = {1}, pages = {e46594}, pmid = {41496069}, issn = {1536-5964}, support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTDã€"2025〕046//The Program for High level Innovative Talents in the Guizhou Province/ ; }, mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; }, abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.
METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.
RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.
CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.}, }
@article {pmid41496236, year = {2026}, author = {Huang, C and Huang, P and Zhang, Y and Bartlam, M and Wang, Y}, title = {Ecological filtering enhanced by smaller PBS biodegradable microplastics constrains ARG dynamics in the soil plastisphere.}, journal = {Environment international}, volume = {207}, number = {}, pages = {110030}, doi = {10.1016/j.envint.2025.110030}, pmid = {41496236}, issn = {1873-6750}, mesh = {*Microplastics ; *Soil Microbiology ; Soil/chemistry ; *Soil Pollutants/analysis ; *Drug Resistance, Microbial/genetics ; Biodegradable Plastics ; Particle Size ; }, abstract = {Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.}, }
@article {pmid41496335, year = {2026}, author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K}, title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {194}, number = {}, pages = {118923}, doi = {10.1016/j.biopha.2025.118923}, pmid = {41496335}, issn = {1950-6007}, mesh = {Animals ; *Deoxyadenosines/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Cellular Senescence/drug effects ; Mice ; Rats ; *Hypertension, Pulmonary/drug therapy/microbiology/pathology/metabolism ; Male ; Humans ; Mice, Inbred C57BL ; Myocytes, Smooth Muscle/drug effects/metabolism/pathology ; Pulmonary Artery/drug effects/pathology/metabolism ; Rats, Sprague-Dawley ; Macrophages/drug effects/metabolism ; Disease Models, Animal ; Vascular Remodeling/drug effects ; }, abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.
OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.
METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).
RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.
CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.}, }
@article {pmid41496502, year = {2026}, author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO}, title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611543}, pmid = {41496502}, issn = {1949-0984}, mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Eubacteriales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; }, abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.}, }
@article {pmid41496862, year = {2025}, author = {Rojas-Vargas, J and Samperio-Ramos, G and Camacho-Ibar, VF and Pajares, S}, title = {Taxonomic and functional stability of sedimentary microbial communities in a pristine upwelling-influenced coastal lagoon.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf241}, pmid = {41496862}, issn = {2730-6151}, abstract = {Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.}, }
@article {pmid41496864, year = {2025}, author = {Shi, H and Zhang, X and Liu, L and Thompson, F and Li, X and Sun, H and Mi, H and Zhang, XH and Zhang, Y}, title = {Vertically stratified carbon fixation and coupling processes in deep-sea sediment.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf242}, pmid = {41496864}, issn = {2730-6151}, abstract = {Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH4[+]) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.}, }
@article {pmid41496931, year = {2026}, author = {Mehmood, MS and Danaf, N}, title = {Helicobacter pylori persists in pancreatic ductal adenocarcinoma despite eradication therapy.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {1}, pages = {955-956}, pmid = {41496931}, issn = {2049-0801}, abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with global 5-year survival below 12%. Recent molecular analyses have revealed that Helicobacter pylori may persist within the pancreatic ductal microenvironment despite successful gastric eradication. In a 2024 multicenter study, H. pylori DNA was detected in 41.6% of PDAC tissues, including patients with documented eradication. Metagenomic sequencing identified H. pylori 16S rRNA reads comprising up to 2.5% of total microbial DNA, supporting selective intrapancreatic survival. Mechanistically, CagA/VacA-mediated STAT3 and NF-κB activation drives cytokine release, oxidative stress, and mismatch repair suppression, enhancing oncogenic inflammation and genomic instability. Chronic colonization increased pancreatic intraepithelial neoplasia by more than 60% in murine models, underscoring its pathogenic potential. These findings suggest that H. pylori persistence represents a novel microbial co-factor in PDAC, warranting further exploration as a diagnostic biomarker and therapeutic target.}, }
@article {pmid41497123, year = {2026}, author = {Mehmood, MS and Hajj, F}, title = {Noninvasive early detection of colorectal cancer through gut microbiome-derived biomarkers.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {1}, pages = {997-998}, pmid = {41497123}, issn = {2049-0801}, abstract = {Colorectal cancer (CRC) remains a major global burden, with 1.9 million new cases and 935000 deaths reported in 2024. Despite available screening tools, nearly 45% of cases are still diagnosed at advanced stages, where the 5-year survival rate falls below 14%, compared to >90% in early detection. The limitations of colonoscopy its invasiveness, cost, and poor compliance (<40% globally) demand innovative, noninvasive diagnostic solutions. Gut microbiome profiling has recently emerged as a transformative approach, with specific bacterial signatures such as Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius showing AUC values between 0.85 and 0.93 for early CRC identification. Integrating metagenomic and metabolomic data enhances diagnostic accuracy to 89% sensitivity and 91% specificity. Moreover, altered microbial metabolites including decreased short-chain fatty acids and elevated secondary bile acids correlate with a 2.3- to 3.1-fold higher risk of carcinogenesis. Novel CRISPR-Cas13a-based assays further allow sub-attomolar detection of microbial RNA transcripts, underscoring a new frontier in microbiome-driven cancer diagnostics. Collectively, gut microbiome-derived biomarkers represent a noninvasive, mechanistically grounded, and highly sensitive platform for early CRC detection with significant translational potential.}, }
@article {pmid41497396, year = {2025}, author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T}, title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.}, journal = {iScience}, volume = {28}, number = {12}, pages = {114029}, pmid = {41497396}, issn = {2589-0042}, support = {R01 HG011392/HG/NHGRI NIH HHS/United States ; }, abstract = {Metagenomic read classification is a fundamental task in computational biology but remains challenging due to the scale and diversity of sequencing data. We present a run-length compressed BWT-based index using the move structure for efficient multi-class classification. Our method finds all super-maximal exact matches (SMEMs) of length ≥ L between a read and a reference and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs and their class identifiers into a single classification. We are the first to perform run-length compressed read classification using full rather than semi-SMEMs. We evaluated on long and short reads across two datasets: a large bacterial pan-genome with few classes and a smaller 16S rRNA gene database spanning thousands of genera. Our method outperforms SPUMONI 2 in accuracy and runtime while maintaining run-length compressed memory complexity and surpasses Cliffy in memory efficiency with comparable accuracy.}, }
@article {pmid41498484, year = {2026}, author = {Huang, T and Ge, H and Wu, Z and Zhang, Y and Wang, L and Dang, C and Fu, J}, title = {Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.}, journal = {Biotechnology and bioengineering}, volume = {123}, number = {4}, pages = {995-1010}, doi = {10.1002/bit.70155}, pmid = {41498484}, issn = {1097-0290}, support = {22306068//National Natural Science Foundation of China/ ; 42476142//National Natural Science Foundation of China/ ; //2022 HUST-UTS Key Partnership Research Seed Funding/ ; 2024AFD091//Hubei Provincial Natural Science Foundation of China/ ; }, mesh = {*Quorum Sensing/drug effects ; *Sewage/microbiology ; *Acyl-Butyrolactones/metabolism ; *Silver/toxicity ; Bioreactors/microbiology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics/metabolism ; }, abstract = {Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 [+]-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.}, }
@article {pmid41498995, year = {2026}, author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A}, title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {1}, pages = {32}, pmid = {41498995}, issn = {1573-0972}, support = {42430404//National Natural Science Foundation of China/ ; }, }
@article {pmid41499358, year = {2026}, author = {Cao, A and Lin, Y and Guan, S and Chen, Y and Zhai, W and Zhou, Y and Feng, S and Guan, Y and Zhang, Y and Huang, M and Wang, X and Long, H}, title = {Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.}, journal = {Clinical and translational medicine}, volume = {16}, number = {1}, pages = {e70579}, pmid = {41499358}, issn = {2001-1326}, support = {82474002//National Natural Science Foundation of China/ ; 82020108031//National Natural Science Foundation of China/ ; 82404752//National Natural Science Foundation of China/ ; 81973398//National Natural Science Foundation of China/ ; WKZX2023CX020006//Development Center for Medical Science & Technology National Health Commission of the People's Republic of China/ ; 2025A1515012521//Natural Science Foundation of Guangdong Province/ ; 2020B1212060034//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017B030314030//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017YFC0909300//National Key Research and Development Program/ ; B16047//The 111 project/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy ; Female ; Male ; *Neoadjuvant Therapy/methods ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy ; Gastrointestinal Microbiome/drug effects ; Metabolomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Neoadjuvant anti-programmed cell death 1 (PD-1) immunochemotherapy has shown promising efficiency in the treatment of early-stage non-small-cell lung cancer (NSCLC), but it has not consistently yielded durable responses. Biomarkers for the prediction of efficacy are warranted.
METHODS: We performed shotgun metagenomic and plasma/faecal metabolomic studies in 44 NSCLC patients who underwent neoadjuvant tislelizumab plus platinum-based doublet chemotherapy. Samples were collected at baseline and before surgical resection, and the major pathologic response (MPR) was evaluated.
RESULTS: MPR patients showed a significantly higher gut-microbial alpha diversity, an enrichment of Ruminococcaceae, Lachnospiraceae and Clostridiales species, and an increased plasma level of tryptophan metabolites at baseline. On the contrary, non-MPR patients were characterized by enrichment of Prevotella species in faecal samples and higher plasma levels of linoleic acid metabolites. A high predictive accuracy was achieved using a small panel of differential microbial (Clostridium sp. M62/1 and Eisenbergiella tayi) or metabolomic features (linoleic acid, oxindole-3-acetic acid and quinolinic acid) with AUCs > .85.
CONCLUSIONS: The baseline characteristics of the gut microbiota and plasma metabolites could provide early predictions of the response to neoadjuvant anti-PD-1 immunochemotherapy.
TRIAL REGISTRATION: NCT05244837.
KEY POINTS: Baseline metagenomic and metabolomic signatures were significantly associated with the major pathologic response of neoadjuvant anti-PD-1 immunochemotherapy. Integrated microbial model (consists of Clostridium sp. M62/1 and Eisenbergiella tayi) and metabolomic model (consists of linoleic acid, oxindole-3-acetic acid and quinolinic acid) could provide early predictions of the response.}, }
@article {pmid41499369, year = {2026}, author = {Chen, K and Luo, S and Jiang, C and Gu, S and Yang, F and Liu, X and Wang, S and Qu, X and Zhang, Q and Zhang, P and Gong, Y and Zeng, H and Qiu, D and Miao, W and Xiong, J}, title = {HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70092}, pmid = {41499369}, issn = {1755-0998}, support = {2023S016//Ningbo Public Welfare Science and the Technology Program Project/ ; 2022xjkk0204//Third Xinjiang Scientific Expedition Program/ ; SNJNP2022008//Background Resources Survey in Shennongjia National Park/ ; 2019 QZKK0304//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; SNJGKL2022008//Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; 32122015//National Natural Science Foundation of China/ ; 32300355//National Natural Science Foundation of China/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Ecosystem ; *Metagenomics/methods ; *Aquatic Organisms/classification/genetics ; Fungi/genetics/classification ; Computational Biology/methods ; Bacteria/classification/genetics ; }, abstract = {Aquatic ecosystems host diverse organisms across all six life kingdoms, yet their complex interactions remain poorly understood, primarily due to limitations in transkingdom species detection methods. To address this limitation, we developed HiMBar (https://github.com/Xchenkai2019/HIFI_barcoding), a high-fidelity (HiFi) metagenomic barcoding approach that utilises long, highly accurate reads to extract multiple full-length marker genes (such as rRNA genes, COI, rbcL) directly from environmental DNA sequencing reads. These genes are subsequently clustered into operational taxonomic units (OTUs) for species identification, eliminating the need for PCR amplification or sequence assembly. HiMBar outperforms existing DNA-based methods in accuracy, recall and consistency. Applying HiMBar, we identified a stable interaction network among Cyanobacteria, Planctomycetota, Verrucomicrobiota and Fungi. Further analysis revealed that glucose metabolism plays a key role in maintaining these interactions. Our study offers a powerful tool for transkingdom species monitoring and provides a case study for exploring transkingdom interactions and their molecular mechanisms.}, }
@article {pmid41499519, year = {2026}, author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E}, title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0323038}, pmid = {41499519}, issn = {1932-6203}, mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation & purification ; Food Microbiology ; }, abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.}, }
@article {pmid41499533, year = {2026}, author = {Liu, T and Song, Z and Zhang, L and Liu, F and Sun, L}, title = {Clinicopathological Features of Orf Virus Infection in the Human: A Rare Case Report of Extensive Skin Infections and Meta-Analysis.}, journal = {Journal of medical virology}, volume = {98}, number = {1}, pages = {e70794}, doi = {10.1002/jmv.70794}, pmid = {41499533}, issn = {1096-9071}, support = {//Beijing Ditan Hospital, Xuzhou Hospital, Capital Medical University, Special Program for Clinical Research and Scientific Innovation Transformation (KCZL202510)./ ; //Training Program for High-level Public Health Technical Talents Construction Project (academic backbone-03-21)/ ; }, mesh = {Humans ; *Orf virus/isolation & purification/genetics ; *Ecthyma, Contagious/pathology/virology/diagnosis ; Male ; Adult ; Animals ; Female ; Sheep ; Middle Aged ; Skin/pathology/virology ; Young Adult ; }, abstract = {The Orf virus is responsible for causing contagious ecthyma in sheep and goats. Humans are primarily infected with Orf virus result in zoonotic skin diseases. We reported a rare case of orf virus infection affecting the face and thoracodorsal regions and performed pathological examination and metagenomic pathogen detection technology(MethPath[TM]) test on the patient. A meta-analysis of the reported cases was also presented. All cases of human infection with orf virus were searched in PubMed and web of science databases. The pathology revealed eosinophilic inclusion bodies visible in the epidermal cells, and the demonstrated orf virus infection by MetaPath™. We identified 99 articles reporting 159 cases of human orf virus infection. The average (±SD) age of all patients was 34.96 ± 16.82 years. Male gender was predominant; hand infections were the most frequent. 81.3% of the patients were infected by contact with sheep. The observed recovery time averaged 42.7 days, with a median of 40 days. The most typical histopathological finding is characterized by the presence of eosinophilic inclusions within vacuolated epidermal cells. When facial nodular lesions are present, obtaining a detailed medical history is essential to aid in considering orf virus infection in the differential diagnosis.}, }
@article {pmid41499817, year = {2026}, author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z}, title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119669}, doi = {10.1016/j.ecoenv.2025.119669}, pmid = {41499817}, issn = {1090-2414}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Phthalic Acids/toxicity ; Mice, Inbred C57BL ; Mice ; Male ; *Plasticizers/toxicity ; Dysbiosis/chemically induced ; *Intestines/drug effects ; Cytokines/metabolism ; }, abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.
METHODS: C57BL/6 mice (n = 10 per group) were orally gavaged with DnPP (1-100 mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).
RESULTS: DnPP exposure induced dose-dependent villus degeneration (100 mg/kg/d, P < 0.05) and colon shortening (P < 0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-α) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P < 0.001) and elevated antibiotic resistance genes (CARD, P < 0.05).
CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.}, }
@article {pmid41499829, year = {2026}, author = {Huang, Z and Liu, H and Wang, C and Wang, J and Tian, C and Feng, J and Shen, J and Wang, X}, title = {Regulation of carbon cycling in plateau lakes by trophic states and seasonal variations: A focus on dissolved organic matter and microbial interactions.}, journal = {Water research}, volume = {292}, number = {}, pages = {125312}, doi = {10.1016/j.watres.2025.125312}, pmid = {41499829}, issn = {1879-2448}, mesh = {*Lakes/chemistry/microbiology ; Seasons ; *Carbon Cycle ; Eutrophication ; Carbon ; Microbial Interactions ; Microbiota ; }, abstract = {Plateau lakes are highly sensitive to climate change and anthropogenic disturbances. The intensification of seasonal variations caused by global warming has complicated the biogeochemical interactions between dissolved organic matter (DOM) and microbial communities. However, how DOM's chemical composition regulates microbial community dynamics and carbon cycling under varying trophic states and seasonal conditions remains unclear. Here, we employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing to investigate the seasonal and trophic controls on DOM composition, microbial communities, and carbon cycling in plateau lakes. The results showed that in the dry season, DOM in the eutrophic lake exhibited pronounced aromaticity, with carboxyl-rich alicyclic molecules (CRAMs) constituting 42.80 % of the molecular pool. Conversely, during the wet season, sulfur- and nitrogen-containing compounds like CHOS and CHONS significantly increased, particularly in the eutrophic lake. The oligotrophic lake displayed the highest molecular lability, characterized by hydrogen-to-carbon (H/C) ratios of 1.24 and molecular lability indices (MLB%) of 34.76 %. Eutrophication altered microbial interaction networks, enhancing interspecies interactions and metabolic specialization. This metabolic shift drove preferential utilization of labile sugars in dry seasons and facilitated the degradation of recalcitrant carbon substrates in wet seasons, thereby optimizing carbon source partitioning. Notably, mesotrophic and oligotrophic lakes fostered resource cooperation by reducing network modularity and shaping carbon cycling through the coordinated action of multiple microbial groups. This study elucidates that carbon cycling in plateau lakes is governed by synergistic effects of trophic states and seasonal dynamics, with DOM serving as a critical mediator in microbial-driven carbon cycling dynamics.}, }
@article {pmid41499832, year = {2026}, author = {Wang, Y and Yao, C and Zhou, J and Liu, B and Qi, L and Wang, B and Ma, C and Hou, L and Liu, M and Zheng, Y}, title = {Co-occurring aquatic acidification and hypoxia promote methane emissions from estuarine ecosystems.}, journal = {Water research}, volume = {292}, number = {}, pages = {125307}, doi = {10.1016/j.watres.2025.125307}, pmid = {41499832}, issn = {1879-2448}, mesh = {*Methane ; *Estuaries ; *Ecosystem ; Geologic Sediments/chemistry ; Climate Change ; Hydrogen-Ion Concentration ; }, abstract = {Estuaries worldwide are experiencing intensifying acidification and hypoxia, driven synergistically by anthropogenic activities and global climate change. Nevertheless, their combined impact on the emissions of the potent greenhouse gas methane (CH4) and its underlying regulatory mechanisms remains poorly understood, undermining our ability to project climate feedbacks. Here, we integrated [13]C stable isotope tracing, DNA/mRNA-based qPCR, and amplicon/metagenomic sequencing to unravel how acidification-hypoxia interactions regulate the complex balance between CH4 production and consumption in estuarine sediments. Results showed that aquatic acidification and hypoxia combined to significantly increase CH4 emissions from estuarine sediments (P < 0.05), in a non-additive (antagonistic) manner where oxygen availability was the dominant factor governing this response. Notably, acidification increased CH4 emissions by suppressing methanotrophy more strongly than methanogenesis, whereas hypoxia preferentially stimulated methanogenic activity over CH4 oxidation. These response patterns were further demonstrated by metagenomic sequencing and mRNA-based quantitative PCR analyses, which revealed coordinated shifts in both the relative abundance and transcriptional activity of key functional genes. These findings uncover a previously overlooked mechanism whereby the worldwide co-occurrence of acidification and hypoxia in estuarine ecosystems jointly promote CH4 emissions, providing a scientific basis for improving predictive models of the global CH4 cycle and its climate feedbacks under combined anthropogenic and climatic stressors.}, }
@article {pmid41499920, year = {2026}, author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S}, title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {57}, number = {}, pages = {106558}, doi = {10.1016/j.clnu.2025.106558}, pmid = {41499920}, issn = {1532-1983}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Child ; Child, Preschool ; Female ; Male ; *Pediatric Obesity/microbiology ; Longitudinal Studies ; Cross-Sectional Studies ; Feces/microbiology ; Body Mass Index ; Risk Assessment ; *Thinness/microbiology ; Overweight/microbiology ; Cohort Studies ; Bacteria/classification ; }, abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.
METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.
RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.
CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.
CLINICALTRIALS: gov ID NCT06317883.}, }
@article {pmid41499937, year = {2026}, author = {Wu, X and Zhang, T and Feng, J and Park, S}, title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {150}, number = {}, pages = {157758}, doi = {10.1016/j.phymed.2025.157758}, pmid = {41499937}, issn = {1618-095X}, mesh = {Humans ; *Parkinson Disease/drug therapy/microbiology/metabolism ; Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; Caco-2 Cells ; Animals ; *Methylamines/metabolism ; Rats ; *5-Hydroxytryptophan/metabolism ; PC12 Cells ; Male ; *Plant Extracts/pharmacology ; Female ; Faecalibacterium prausnitzii ; Aged ; }, abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.
PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.
METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPKα signaling pathways.
RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPKα signaling.
CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPKα signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.}, }
@article {pmid41500047, year = {2026}, author = {Gutfreund, MC and Callado, GY and Pardo, I and Hsieh, MK and Celeghini, PD and Lopes, GOV and Marra, PS and Cheng, YR and Kobayashi, T and Pinho, JRR and Generoso, JR and Bulgarelli, L and Mendonça, EA and Deliberato, RO and Amgarten, DE and Malta, FM and Edmond, MB and Marra, AR}, title = {Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic literature review and meta-analysis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {4}, pages = {117248}, doi = {10.1016/j.diagmicrobio.2025.117248}, pmid = {41500047}, issn = {1879-0070}, mesh = {Humans ; *Communicable Diseases/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Child ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; Child, Preschool ; Infant ; }, abstract = {BACKGROUND: Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.
METHODS: This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (≤21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.
RESULTS: Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82-0.86) and 0.71 (95% CI: 0.66-0.75), respectively, compared with 0.40 (95% CI: 0.37-0.43) and 0.82 (95% CI: 0.78-0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.
CONCLUSIONS: mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.}, }
@article {pmid41500138, year = {2026}, author = {Bellekom, B and Troman, C and Fitz, S and Akello, JO and Grassly, NC and Shaw, AG}, title = {Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater.}, journal = {The Science of the total environment}, volume = {1013}, number = {}, pages = {181333}, doi = {10.1016/j.scitotenv.2025.181333}, pmid = {41500138}, issn = {1879-1026}, mesh = {*Wastewater/virology ; *SARS-CoV-2/isolation & purification/genetics ; *Metagenomics/methods ; *Environmental Monitoring/methods ; }, abstract = {Timely and accurate pathogen detection is critical for the successful implementation of wastewater surveillance and has broad implications for public health. A wide range of surveillance tools are currently available, offering both quantitative and qualitative insights into the wastewater virome. Careful consideration of molecular methodology is required to successfully implement an effective wastewater surveillance scheme. Using SARS-CoV-2 as a model organism, we compared detection success across multiple approaches, including targeted (RT-PCR, qPCR, random priming RT-PCR) and target-agnostic (Rapid SMART-9N metagenomics) methods. We also estimated the copy number required for reliable detection, examined how the ratio of target to off-target genomes in wastewater affects detection and genome coverage using metagenomics, and assessed the efficacy of hybrid capture enrichment of target genomes in improving metagenomic detection. Our results show significant differences between methods, targeted RT-PCR and qPCR were more likely (68 % and 65 % respectively) to detect SARS-CoV-2 than target agnostic approaches. The inclusion of carrier RNA during extraction significantly increased the likelihood of target detection. Our target-agnostic metagenomic approach was consistently unable to detect our target, and, even in the presence of high concentrations that are atypical for wastewater, detection was limited. Target enrichment increased SARS-CoV-2 detection and maximum coverage by metagenomics (SMART-9N), though was outperformed by targeted amplicon sequencing. Overall, our findings support the use of targeted approaches for the routine surveillance of viral pathogens in wastewater. Whilst metagenomics provides broad insights into the virome, enrichment strategies are essential when using it to detect specific viruses, particularly in complex wastewater matrices.}, }
@article {pmid41500299, year = {2026}, author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J}, title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.}, journal = {Environmental research}, volume = {292}, number = {}, pages = {123688}, doi = {10.1016/j.envres.2026.123688}, pmid = {41500299}, issn = {1096-0953}, mesh = {*Sulfamethoxazole/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; *Toluidines/toxicity ; *Microbiota/drug effects ; *Herbicides/toxicity ; *Soil Pollutants/toxicity ; Anti-Bacterial Agents ; Ecosystem ; Bacteria/drug effects ; }, abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.}, }
@article {pmid41501123, year = {2026}, author = {Alexandrino, DAM and Semedo, M and Cao, W and Azevedo, J and Magalhães, C and Osório, H and Jia, Z and Campos, A and Mucha, AP and Almeida, CMR and Carvalho, MF}, title = {Insights into the biodegradation of two persistent fluorinated fungicides by coupling metabolic modelling with metaproteogenomics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {2126}, pmid = {41501123}, issn = {2045-2322}, mesh = {Biodegradation, Environmental ; *Fungicides, Industrial/metabolism/chemistry ; *Triazoles/metabolism ; Proteomics/methods ; *Bacteria/metabolism/genetics ; *Pyrroles/metabolism ; Halogenation ; }, abstract = {Epoxiconazole (EPO) and fludioxonil (FLU) are fluorinated fungicides known for their extremely high environmental persistence and significant ecotoxicological impact. Given their decades-old use in the agrochemical sector, EPO and FLU became frequent pollutants of terrestrial and aquatic ecosystems. And yet, not much is known regarding how these pesticides biodegrade in the natural environment or how to develop suitable bioremediation approaches capable of tackling their inherent recalcitrance. As such, this work focused on providing new insights into the bacterial degradation of EPO and FLU, by surveying the catabolic activity of a previously obtained EPO-enriched bacterial consortium through chemical and metaproteogenomic analyses guided by different metabolic modelling tools. The bacterial consortium was capable of extensively degrading EPO and FLU in 21 days, with fungicide removals of over 90% and defluorination efficiencies of up to 80%, but none of the subproducts predicted in silico were identified for either pesticide. Despite this, the combination of metabolic modelling tools and metaproteogenomic surveys suggested that EPO and FLU were first attacked in their N-heterocyclic moieties and that the targets of defluorination were the resulting aromatic fluorinated intermediates. This catabolic cascade is consistent with the experimental data gathered in this study and with the existing literature on this topic. Also, the degrading consortium remained stable at the taxonomical and functional levels, highlighting its catabolic plasticity in biodegrading and defluorinating two chemically distinct fluorinated compounds. This work offers a conceptual framework with novel observations that can guide future efforts to further elucidate the pathways of microbial transformation of these pesticides, ultimately contributing to better environmental risk management practices for these pollutants.}, }
@article {pmid41501250, year = {2026}, author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X}, title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3801}, pmid = {41501250}, issn = {2045-2322}, support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Myositis/microbiology ; Middle Aged ; Adult ; China ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; Bacteria/genetics/classification ; Virome ; Machine Learning ; Case-Control Studies ; Metagenome ; Asian People ; Aged ; East Asian People ; }, abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.}, }
@article {pmid41501434, year = {2026}, author = {Zell, R and Groth, M and Selinka, L and Selinka, HC}, title = {A metagenomic analysis of urban river samples reveals high numbers of sequences related to mycoviruses.}, journal = {Archives of virology}, volume = {171}, number = {2}, pages = {46}, pmid = {41501434}, issn = {1432-8798}, mesh = {*Rivers/virology ; Phylogeny ; Genome, Viral ; *Metagenomics ; *Fungal Viruses/genetics/classification/isolation & purification ; Germany ; Open Reading Frames ; }, abstract = {Mycoviruses have been classified into 35 virus families so far. In addition to numerous mycoviruses with proven fungal or oomycetes hosts, many newly discovered viruses from environmental water and soil samples and various animal or plant specimens exhibit significant similarity to classified mycoviruses, thereby expanding the known sequence space of fungal and related viruses. In this study, we searched for mycoviruses in two environmental water samples that had been collected from the Teltow Canal and the Havel River in Berlin, Germany. Viral sequences with similarity to members of 16 virus families were identified. The most common viruses in our samples were botourmia-like viruses with moderate similarity to members of the genus Ourmiavirus. Notably, 58 of the ourmia-like sequences from the Teltow Canal and Havel River and 10 ourmia-like sequences from other sources exhibited a dicistronic genome layout. The second open reading frame (ORF) of these viruses encoded a putative capsid protein with an S domain that showed little similarity to the structural proteins of the classified ourmiaviruses. The second-largest virus group (59 sequences) was assigned to the order Ghabrivirales, and 13 of these sequences exhibited similarity to members of the suborder Alphatotivirineae (families Orthototiviridae, Pseudototiviridae, Botybirnaviridae, and Chrysoviridae). Thirty-three sequences clustered with members of the suborder Betatotivirineae - three of them with members of the family Artiviridae. Fifteen highly divergent toti-like sequences suggest the need to establish a new higher-order taxon within the order Ghabrivirales. Other virus sequences were assigned to the families Mitoviridae (three unuamitoviruses and 10 highly divergent mitovirus-like sequences), Narnaviridae (five "alphanarnavirus"-like sequences), Amalgaviridae (two zybavirus-like sequences), Hypoviridae (one partial RdRP sequence), and Mymonaviridae (one partial RdRP sequence), and one was not classified (Sclerophthora macrospora B-like virus). Notable results include a clade of highly divergent mitovirus-like sequences with a standard translation code, three narnavirus-like sequences with a reverse-frame ORF, and a clade of four Ghabrivirales-like replicase sequences that were found to have numerous termination codons regardless of which translation table was used.}, }
@article {pmid41501755, year = {2026}, author = {Li, JL and Hu, W and Pu, LH and Sun, J and Ortúzar, M and Lv, ZH and Yang, ZF and Zhu, D and Xie, KQ and Yang, LQ and Yin, YR}, title = {Molecular cloning and characterization of a GH10 thermophilic xylanase from hot spring and its potential application in promoting probiotic growth.}, journal = {BMC biotechnology}, volume = {26}, number = {1}, pages = {16}, pmid = {41501755}, issn = {1472-6750}, support = {202101AU070138 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; }, abstract = {BACKGROUND: Xylan is widely found in plant cell walls, and xylanase, an essential enzyme in xylan breakdown, has promising applications in energy, food, feed, and healthcare sectors.
RESULTS: This study presents the discovery of a novel GH10 family xylanase gene, termed Lc-Xyn81, isolated from the hot spring of Eryuan, Dali, Yunnan Province, employing enrichment culture and metagenomic approaches. The amino acid sequence of Lc-Xyn81 shares 72.29% identity with that of Blastocatellia bacterium. The gene was amplified via specific PCR, cloned, and heterologously expressed in Escherichia coli. The recombinant Lc-Xyn81 was purified using Ni-affinity chromatography, followed by enzymatic characterization. Lc-Xyn81 demonstrated optimal activity at 75 °C and pH 6.6. It maintained over 80% relative activity between 65 and 75 °C, and its activity increased to over 120% after incubation at 70 °C for 40–100 min with a half-life of 180 min at 70 °C. Additionally, incubation at pH 5.0–7.0 for 12 h boosted its activity to over 140%. Lc-Xyn81 was activated by divalent metal ions such as Co²⁺ (128.55%), Mn²⁺ (119.84%), and Cu²⁺ (112.27%). The enzyme exhibited activity against beechwood xylan (213.68 U/mg), corncob xylan (143.40 U/mg), and sugarcane bagasse xylan (80.39 U/mg). The primary degradation products were xylobiose and xylotetraose, which significantly promoted the growth of L. lactis. Kinetic analysis indicated that the Km value of Lc-Xyn81 for beechwood xylan is 4.62 mg/mL, and its Vmax value is 312.5 µmol/min/mg.
CONCLUSIONS: In summary, Lc-Xyn81, a thermophilic and thermostable xylanase, exhibits considerable potential for industrial applications in lignocellulose degradation and prebiotic production.
GRAPHICAL ABSTRACT: [Image: see text]
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12896-025-01096-9.}, }
@article {pmid41501865, year = {2026}, author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H}, title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {56}, pmid = {41501865}, issn = {2049-2618}, support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; }, mesh = {Animals ; *Heteroptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Predatory Behavior ; Biological Evolution ; Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Symbiosis ; Adaptation, Physiological ; Feeding Behavior ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.
RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.
CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.}, }
@article {pmid41502126, year = {2026}, author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM}, title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.}, journal = {Environmental microbiology}, volume = {28}, number = {1}, pages = {e70226}, doi = {10.1111/1462-2920.70226}, pmid = {41502126}, issn = {1462-2920}, support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; }, mesh = {*Oxygen/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Metagenomics ; Pacific Ocean ; *Microbiota/genetics ; *Metagenome ; Photosynthesis/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Chlorophyll/metabolism ; Nitrites/metabolism ; }, abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.}, }
@article {pmid41502155, year = {2026}, author = {Kim, SS and D'Agostino, E and Needham, DM}, title = {Dynamics and Eco-Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness.}, journal = {Environmental microbiology}, volume = {28}, number = {1}, pages = {e70215}, pmid = {41502155}, issn = {1462-2920}, support = {//Helmholtz Association/ ; NE 2754/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Nitrification ; *Archaea/genetics/metabolism/classification/isolation & purification ; Seasons ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Phylogeny ; Ammonia/metabolism ; Genomics ; Nitrogen/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Nitrates/metabolism ; }, abstract = {Nitrification is widespread across marine systems, yet the ecological and evolutionary drivers shaping nitrifier populations remain largely unknown. The Baltic Sea, a brackish basin with pronounced gradients in salinity, oxygen, nutrients and strong seasonality, is a valuable model environment to investigate these questions. Here, we combined metagenomics and rRNA gene sequencing to characterise the spatiotemporal dynamics and genomic diversity of nitrifiers, alongside physicochemical measurements. Nitrifiers were persistently abundant throughout aphotic waters, with vertical niche partitioning and seasonal peaks in surface waters from late fall to early spring. The seasonal peaks were positively correlated with nitrite, nitrate and diverse other prokaryotes, and negatively correlated with solar radiation and chlorophyll. To probe the genomic basis of these ecological patterns of the numerically dominant nitrifier, we recovered five novel genomes of ammonia-oxidising archaea through metagenomics of bulk samples and selective enrichments, including the dominant taxon from aphotic depths. Comparative genomics showed high gene conservation, with variation largely in genes linked to interactions with the external environment and nitrogen and phosphorus metabolism between central surface and deep types. Together, our study provides insights into niches of Baltic Sea nitrifiers and begins the process of understanding the mechanisms and functional implications of these patterns.}, }
@article {pmid41502165, year = {2026}, author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES}, title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.}, journal = {Environmental microbiology}, volume = {28}, number = {1}, pages = {e70225}, pmid = {41502165}, issn = {1462-2920}, support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; }, mesh = {*Hot Springs/microbiology ; *Thermus/metabolism/growth & development/genetics ; *Nitrogen/metabolism ; *Carbon/metabolism ; Iceland ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; Metagenomics ; }, abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.}, }
@article {pmid41502197, year = {2025}, author = {Hasan, I}, title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.}, journal = {Acta medica Indonesiana}, volume = {57}, number = {4}, pages = {433-435}, pmid = {41502197}, issn = {2338-2732}, mesh = {Humans ; *Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; *Liver Cirrhosis/complications ; Indonesia/epidemiology ; *Liver/metabolism ; *Brain/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; }, abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.}, }
@article {pmid41502282, year = {2025}, author = {Sheng, YP and Kong, LJ and Chu, PP and Xia, YL and Shen, CT and Sun, JF}, title = {[Clinical Analysis of Torque Teno Virus Infection after Hematopoietic Stem Cell Transplantation in Children].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {33}, number = {6}, pages = {1784-1789}, doi = {10.19746/j.cnki.issn.1009-2137.2025.06.036}, pmid = {41502282}, issn = {1009-2137}, mesh = {Humans ; *Torque teno virus ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *DNA Virus Infections ; Child ; Male ; Female ; Incidence ; Child, Preschool ; Adolescent ; }, abstract = {OBJECTIVE: To investigate the incidence, clinical characteristics, and complications of Torque teno virus (TTV) in children after hematopoietic stem cell transplantation (HSCT).
METHODS: A total of 40 children with hematological diseases who underwent HSCT were selected, and metagenomic next-generation sequencing (mNGS) technology was used to detect the gene sequences of pathogenic microorganisms in the blood. Combined with clinical data, the characteristics of TTV infection were analyzed.
RESULTS: Among the 40 pediatric patients post-HSCT, the TTV positive rate was 42.5% (17/40). There were no statistically significant differences between the TTV-positive group and the TTV-negative group in sex, age, white blood cell count(WBC), red blood cell count(RBC), hemoglobin, platelet count, neutrophil count, lymphocyte count, and high-sensitivity C-reactive protein (all P >0.05). The incidence of TTV infection was significantly higher in children who underwent haploidentical HSCT and in those with bone marrow stem cells (BMSC) as the transplant source (P <0.05). However, there were no significant differences in the TTV infection rate among patients with different disease types, different HLA matching statuses, or different engraftment times of neutrophils and platelets (all P >0.05). Among 17 children infected with TTV, 13(76.5%) had co-infections with other viruses, mainly including cytomegalovirus (58.8%, 10/17), human polyomavirus (41.2%, 7/17), and Epstein-Barr virus (17.6%, 3/17). In children with TTV infection, the most common complications were sepsis (82.4%), graft-versus-host disease (GVHD) (70.6%), pulmonary infection (41.2%), and hemorrhagic cystitis (17.6%). The incidence of GVHD in the TTV-positive group was significantly higher than that in the TTV-negative group (P <0.05).
CONCLUSION: TTV infection is common in children undergoing HSCT, and it is prone to be complicated with cytomegalovirus infection and GVHD, which has an important influence on the clinical outcomes.}, }
@article {pmid41502470, year = {2026}, author = {Shukla, A and Yadav, M and Malik, MZ and Aditya, AK and Kumar, A and Tandon, R and Shalimar, and Ray, AK}, title = {Soil influences on rural versus urban human gut microbiota and implications on cardio-metabolic health: a comparative pilot study.}, journal = {3 Biotech}, volume = {16}, number = {1}, pages = {62}, pmid = {41502470}, issn = {2190-572X}, abstract = {UNLABELLED: Humans are exposed to surrounding soil environment and this exposure has reduced with growing urbanisation. Limited evidence exists on how rural and urban soils shape human gut microbiome and related functions. Here, we performed metagenomic analysis, functional prediction, gene ontology using QIIME2, PICRUSt, and DAVID by taking human stool and soil samples (n = 20) from rural and urban settings to characterise gut microbiota and their resemblance to their respective soil microbiota and its functional implications. Our findings demonstrated that soil environment affects gut microbial diversity and abundance of its immediate human inhabitants in both groups and observed shared microbial and functional properties in rural- and urban-guts characteristic of their respective soil microbiota. In rural-group, phylum Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, class Actinobacteria were major overlapping features, while in the urban-counterpart phylum Proteobacteria, Firmicutes, class Gammaproteobacteria were observed. We also demonstrated implication of this differential composition on human health in both settings, and observed enrichment of cytokines like IL-12, IFN-ϒ, and oxidative phosphorylation pathway in rural group vital to metabolic homeostasis. While enrichment of response to toxic substances, methane metabolism, and potentially low levels of alanine in the urban counterpart, linked to impaired immune response and metabolism, suggests urban group may be prone to the cardio-metabolic disease risk. These observations were consistent with other findings emphasising rural groups have healthy sets of microbiome compared to their urban counterpart. In conclusion, our findings unveil the significance of soil microbiota in evolution and shaping of human gut microbiota, thereby potentially beneficial to human health.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04675-x.}, }
@article {pmid41502854, year = {2025}, author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX}, title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1744013}, pmid = {41502854}, issn = {2297-1769}, abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.
METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.
RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.
CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.}, }
@article {pmid41502900, year = {2025}, author = {Hou, Y and Xie, W and Duan, J and Li, X and Wu, Z}, title = {Challenge of Cupriavidus gilardii infection in an immunocompromised child: a case report.}, journal = {Translational pediatrics}, volume = {14}, number = {12}, pages = {3498-3503}, pmid = {41502900}, issn = {2224-4344}, abstract = {BACKGROUND: Cupriavidus gilardii is a multidrug-resistant (MDR) pathogen found in soil and water. Human infection is extremely rare, with only two pediatric cases reported to date, and its clinical features and the antimicrobial strategies remain unclear. The pathogen's MDR nature often poses a therapeutic challenge. This case provides valuable clinical evidence regarding the management of C. gilardii infection in immunocompromised pediatric patients.
CASE DESCRIPTION: A 4-year-old boy with acute lymphoblastic leukemia developed severe immunosuppression after reinduction cyclophosphamide, cytarabine (Ara-C), mercaptopurine (CAM) chemotherapy according to the SCCCG-ALL-2023 protocol. The patient initially presented with recurrent fever, septic shock, and progressive respiratory distress. Despite an aggressive empirical antibiotic regimen including meropenem, imipenem, piperacillin-tazobactam, linezolid, and levofloxacin, his condition continued to worsen. Blood cultures and metagenomic next-generation sequencing (mNGS) subsequently confirmed C. gilardii infection. Based on susceptibility testing, therapy was adjusted to a combination of ceftazidime-avibactam (CAZ-AVI) and tigecycline. After this adjustment, the patient showed marked clinical improvement, with decreased inflammatory indicators and nearly completed clearance of the pathogen. Unfortunately, on hospital day 26, he developed sudden massive hemoptysis due to Aspergillus pulmonary artery invasion and died despite emergency treatment.
CONCLUSIONS: This case demonstrates that CAZ-AVI may offer effective antimicrobial control for C. gilardii infection in immunocompromised pediatric patients. Although the patient succumbed to secondary fungal complications, successful microbiological control demonstrates that CAZ-AVI may serve as a potential salvage therapy for rare MDR Gram-negative bacteria and provides clinical insight into the management of uncommon pediatric infections.}, }
@article {pmid41502951, year = {2025}, author = {Oliveira, RA and McSpadden, E and Pandey, B and Lee, K and Yousef, M and Chen, RY and Triebold, C and Haro, F and Aksianiuk, V and Patel, R and Shriram, K and Ramanujam, R and Kuehn, S and Raman, AS}, title = {Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41502951}, issn = {2692-8205}, support = {R35 GM146702/GM/NIGMS NIH HHS/United States ; }, abstract = {Engineering functional microbiomes is challenging due to complex interactions between bacteria and their environments[1-6]. Using a set of 848 gut commensal strains and clearance of multi-drug resistant Klebsiella pneumoniae (Kp-MH258) as a target function, we engineered a functional 15-member synthetic microbiome-SynCom15-through a statistical approach agnostic to strain phenotype, mechanism of action, bacterial interactions, or composition of natural microbiomes. Our approach involved designing, building, and testing 96 metagenomically diverse consortia, learning a generative model using community strain presence/absence as input, and distilling model constraints through statistical inference. SynCom15 cleared Kp-MH258 across in vitro, ex vivo, and in vivo environments, matching the efficacy of a fecal microbiome transplant in a clinically relevant murine model of infection. The mechanism of suppression by SynCom15 was related to fatty acid production coupled with environmental acidification. SynCom15 also suppressed other pathogens-Clostridioides difficile, Escherichia coli, and other K. pneumoniae strains-but through different mechanisms. Sensitivity analysis revealed models trained on strain presence/absence captured the statistical structure of pathogen suppression, illustrating that community representation was key to our approach succeeding. Our framework, 'Constraint Distillation', could be a general and efficient strategy for building emergent complex systems, offering a path towards synthetic ecology more broadly.}, }
@article {pmid41503361, year = {2025}, author = {Uddin, MN and Hartog, C and Murray, E and Loveless, JB and Roberson, L and Aslan, A and Cubas, F and Rowles, LS}, title = {Advancing Circular Bioeconomy through a Systems-Level Assessment of Food Waste and Industrial Sludge Codigestion.}, journal = {ACS environmental Au}, volume = {5}, number = {5}, pages = {479-489}, pmid = {41503361}, issn = {2694-2518}, abstract = {Disposal of food waste (FW) in landfills remains an unsustainable practice for organic waste management. Simultaneously, pulp and paper mills produce significant amounts of recalcitrant organic waste that is difficult to decompose due to its high lignocellulosic content. In this study, we developed an innovative approach to improve the digestion of pulp and paper mill sludge (PPMS) by amending FW to produce a low chemical oxygen demand (COD) sludge while recovering methane in the process. This codigestion process was evaluated through lab-scale biogas production experiments coupled with a comprehensive economic and environmental sustainability assessment. Biomethane production results revealed that the FW-PPMS codigestion methane yield was 36% higher on average than the PPMS monodigestion. Additionally, metagenomic analysis revealed that microbial communities for both systems transitioned from highly heterogeneous to more adapted uniform communities after digestion. Improved microbial communities contributed to higher COD removal (92%) in the FW-PPMS system compared to monodigestion (80% removal). The sustainability analysis revealed that the codigestion of FW-PPMS had median costs of 236.64 USD·tonne[-1]·day[-1] and emissions of 228.30 kg CO2 eq·tonne[-1]·day[-1], a significant reduction compared to directly disposing the FW in landfills (median costs of 405.13 USD·tonne[-1]·day[-1] and emissions of 556.27 kg CO2 eq·tonne[-1]·day[-1]). A nationwide contextual analysis revealed that out of six regions, the US Northeast had the lowest median costs and emissions, while the Mountain Plains region had the highest, highlighting the importance of geographical and infrastructural factors in implementation. Overall, codigesting FW with PPMS is revealed to be a sustainable waste management option to decrease landfill disposal of valuable organic waste.}, }
@article {pmid41503489, year = {2026}, author = {Goddard, TR and Carlson-Jones, JA and Judith, M and Ooi, CY and Andrew, T and Warner, MS and John, W and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA}, title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41503489}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.}, }
@article {pmid41503526, year = {2026}, author = {Phillips, K and Acker, KP and Han, JY and Salvatore, CM and Permar, SR and Rolón, RM and Marino, J and Dysart, C and Berman, DM and Chiu, CY and Kidd, SE and Westblade, LF and Dubois, MM}, title = {Trichosporon inkin meningitis in a pediatric patient diagnosed via metagenomic sequencing.}, journal = {ASM case reports}, volume = {1}, number = {2}, pages = {}, pmid = {41503526}, issn = {2996-2684}, abstract = {BACKGROUND: Trichosporon has emerged as an important cause of invasive fungal infections in immunocompromised patients. There are limited data on invasive Trichosporon infections in children.
CASE SUMMARY: We report a case of culture-negative Trichosporon inkin meningitis diagnosed via metagenomic next-generation sequencing of plasma and cerebrospinal fluid in an infant with retinoblastoma. In addition, we highlight the role of β-1,3-D-glucan in the diagnosis and therapeutic monitoring of trichosporonosis, and cross-reactivity of the cryptococcal antigen lateral flow assay with T. inkin.
CONCLUSION: This diagnosis, which was challenging to make in the absence of a positive culture, highlights the utility of metagenomic sequencing methods and fungal biomarkers in identifying infectious agents and ensuring timely diagnosis and management of patients with rare fungal infections of the central nervous system.}, }
@article {pmid41503531, year = {2026}, author = {Burd, EM}, title = {Metagenomic next-generation sequencing reveals cross-reactivity of lateral flow cryptococcal antigen assay with Trichosporon inkin.}, journal = {ASM case reports}, volume = {1}, number = {2}, pages = {}, pmid = {41503531}, issn = {2996-2684}, abstract = {Metagenomic next-generation sequencing (mNGS) in plasma, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid is a relatively new technology that offers a means to potentially provide a diagnosis in cases where infection is suspected, but conventional diagnostic testing has not revealed a pathogen. There have been many publications of individual cases and overall appraisals of its utility in detecting bacteria, fungi, and DNA viruses associated with otherwise undiagnosed systemic infections. A recent article by Phillips et al. published in ASM Case Reports (2:e00053-25, 2025, https://doi.org/10.1128/asmcr.00053-25) presents a case of meningitis in an immunosuppressed child that was ultimately determined to be caused by Trichosporon inkin using mNGS. Elevated ß-1,3-D-glucan (BDG) levels in CSF and serum projected a diagnosis of fungal meningitis. Bacterial, fungal, and mycobacterial cultures were negative. Positive lateral flow cryptococcal antigen titers in serum and CSF complicated the anticipated diagnosis since Cryptococcus spp. are thought to not have sufficient cell wall BDG to produce positive test results. Given the ultimate diagnosis of T. inkin meningitis and the known cross-reactivity with Trichosporon asahii per package insert, the unexpected cryptococcal antigen results raised the possibility of additional cross-reactivity. The authors uncovered this possibility by testing three known clinical isolates of T. inkin which generated positive results. This case adds to the growing literature that highlights the utility of mNGS in providing a diagnosis in otherwise unresolved cases and shows that mNGS can be further instructive in elucidating limitations in commonly used diagnostic tests.}, }
@article {pmid41503571, year = {2026}, author = {Bajaj, JS and Fagan, A and Sterling, RK and Sikaroodi, M and Gallagher, ML and Lee, H and Matherly, SC and Bartels, A and Mousel, T and Davis, BC and Puri, P and Fuchs, M and Thacker, LR and McGinley, JP and Khoruts, A and Gillevet, PM}, title = {The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.}, journal = {JHEP reports : innovation in hepatology}, volume = {8}, number = {1}, pages = {101634}, pmid = {41503571}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of HE recurrence among THEMATIC trial participants.
METHODS: The THEMATIC trial enrolled patients with cirrhosis and HE who received oral or enema FMT vs. placebo (1-3 administrations) and were followed for 6 months. Outcomes included safety and HE recurrence. Serum, urine, and stool samples were collected at baseline and post-FMT for all participants. Stool metagenomics, serum and urine metabolomics, inflammatory cytokines, and clinical data were analyzed. Differences between patients with and without HE recurrence were assessed using pathway, random forest, and latent factor analyses.
RESULTS: HE recurred in 10 of 60 patients (17%), with significantly higher recurrence in the placebo vs. the FMT groups (40% vs. 8%; p = 0.005). Due to the low recurrence rate in the FMT arms, all patients with recurrence were combined and compared with those without recurrence. Stool metagenomics showed that the abundance of short-chain fatty acid (SCFA) producers (Faecalibacterium, Eubacterium, Bacteroides, Blautia spp.) was lower, while that of GABA-producing taxa (Lactobacillus, Bifidobacterium spp.) was higher, in patients with recurrence. Urine and serum metabolomes separated HE recurrence groups on PLS-DA, with serum butyrate and isobutyrate being most significantly associated (p = 0.008). Pathway analyses revealed upregulation of GABA and neurotransmitter pathways in patients with HE recurrence. Random forest and latent factor analysis indicated that SCFA producers and secondary bile acids were protective, whereas IL-6, GABA producers, nicotine metabolites, and primary bile acids were associated with HE recurrence.
CONCLUSIONS: Secondary analysis of the THEMATIC randomized controlled trial indicates that HE recurrence in patients on lactulose and rifaximin is associated with distinct microbiome and metabolomic profiles, particularly involving SCFAs, GABA metabolism, bile acids, and IL-6.
IMPACT AND IMPLICATIONS: Fecal microbiota transplantation (FMT) reduced hepatic encephalopathy (HE) recurrence in patients receiving lactulose and rifaximin in the THEMATIC trial, but the multi-omic mechanisms underlying this effect were unclear. In this secondary analysis, we found that HE recurrence - regardless of FMT or placebo assignment - was associated with distinct multi-omic signatures, including reduced short-chain fatty acid-producing and increased pathobiont taxa, lower urinary and serum short-chain fatty acids, secondary bile acids, and acetaminophen derivatives, and higher GABA-related and nicotine metabolites, along with elevated IL-6 levels. Notably, patients with greater donor microbiota engraftment had lower rates of HE recurrence. These findings suggest that HE recurrence after FMT reflects a multifactorial process involving alterations in gut metagenomics, systemic metabolomics, inflammation, and donor engraftment.
TRIAL REGISTRATION: www.clinicaltrials.gov: NCT03796598.}, }
@article {pmid41503705, year = {2026}, author = {Liu, W and Du, Y and Ning, J and Zheng, S and Qiu, W and Wang, Y}, title = {Geogenic Ammonium Enrichment in Alluvial-Lacustrine Aquifer Systems: Coupled Controls of Microbial Pathways and Organic Matter Composition.}, journal = {Environmental science & technology}, volume = {60}, number = {2}, pages = {2088-2100}, doi = {10.1021/acs.est.5c11156}, pmid = {41503705}, issn = {1520-5851}, mesh = {*Groundwater/chemistry ; *Ammonium Compounds ; Nitrogen ; Nitrates ; }, abstract = {Elevated geogenic ammonium (NH4[+]) reported globally in alluvial-lacustrine aquifer systems is generally attributed to the mineralization of natural organic matter (OM). However, the contribution of microbial nitrogen (N) metabolism remains unclear. This study integrated hydrogeochemical profiling, metagenomic sequencing, and molecular-level OM characterization to elucidate how microbial nitrogen transformation and organic N mineralization could drive geogenic NH4[+] accumulation in groundwater. A distinct shift in microbial N metabolism pathways was identified along the NH4[+] enrichment gradient. Under N-limited and strongly reducing conditions, N fixation and dissimilatory reduction of nitrate to ammonium provided additional NH4[+] sources, whereas nitrification served as the primary sink by oxidizing NH4[+] to nitrate. At low NH4[+] levels, NH4[+] was mainly produced via deamination of simple mono-N compounds (CHO+1N) found in highly unsaturated low-oxygen (O) compounds and low-O polyphenols. In contrast, at high NH4[+] levels, urease-mediated hydrolysis of multi-N compounds (CHO+nN) in highly unsaturated high-O compounds became dominant. Co-occurrence network analysis revealed tight, pathway-specific linkages between functional genes and NH4[+]-associated OM compounds, highlighting the substrate-dependent nature of geogenic NH4[+] production. These findings could advance our understanding of microbially mediated NH4[+] enrichment mechanisms and offer implications for the management of NH4[+] and other geogenic contaminants in organic-rich aquifers.}, }
@article {pmid41503787, year = {2026}, author = {Wang, Y and Yu, Y and Xu, N and Zhang, Z and Chen, B and Song, M and Zhang, Q and Wang, T and Ma, Y and Lu, T and Sun, L and Qian, H}, title = {Genes for Vitamin B Synthesis and Their Distribution in Microbial Producers.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {2}, pages = {2069-2078}, doi = {10.1021/acs.jafc.5c11883}, pmid = {41503787}, issn = {1520-5118}, mesh = {Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Vitamin B Complex/biosynthesis ; *Bacterial Proteins/genetics/metabolism ; Soil/chemistry ; Metagenome ; Phylogeny ; }, abstract = {B vitamins (VBs) are essential micronutrients, yet their microbial production across natural habitats remains poorly understood. We analyzed 126,931 metagenome-assembled genomes to map the distribution of VB producers and constructed a database of 87 VB synthesis genes, identifying VB-independent producers and their environmental drivers. Soil and freshwater habitats harbored the greatest diversity of VB1, VB2, VB7, VB9, and VB12 producers, whereas marine systems contained fewer. Biosynthetic capacity was rare for VB5 and was limited for VB3 and VB6. Gammaproteobacteria are prolific producers, synthesizing up to eight VB types. Soil sulfur content and conductivity significantly enhanced VB production potential, linking beneficial microbes to improved soil health. We further validated VB3 and VB7 synthesis in Acinetobacter kookii, supporting our predictive framework. Because the identified producers include both beneficial and pathogenic taxa, careful evaluation is required. This work provides a robust gene database and a foundation for optimizing microbial VB production in agriculture and biotechnology.}, }
@article {pmid41503791, year = {2026}, author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q}, title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611645}, pmid = {41503791}, issn = {1949-0984}, mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation & purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.
RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.
CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.}, }
@article {pmid41503923, year = {2026}, author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H}, title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70231}, pmid = {41503923}, issn = {1744-7917}, support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; }, abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.}, }
@article {pmid41504158, year = {2025}, author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F}, title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {6}, pages = {42590}, doi = {10.31083/IJVNR42590}, pmid = {41504158}, issn = {0300-9831}, support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; }, abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).
METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.
RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.
CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.}, }
@article {pmid41504449, year = {2026}, author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H}, title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0305125}, pmid = {41504449}, issn = {2165-0497}, support = {32460813//National Natural Science Foundation of China/ ; 2022MS03074, 2025MS03005, 2023YFDZ0079, 2023YFDZ0068, 2025YFDZ0123//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; NJYT22054//Education Department of Inner Mongolia Autonomous Region/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle/microbiology ; *Animal Feed/analysis ; *Poaceae/metabolism ; Fermentation ; Metagenomics ; *Dietary Fiber/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome ; Female ; Metabolomics ; Mongolia ; Digestion ; Fungi/classification/genetics/metabolism/isolation & purification ; Metagenome ; }, abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.}, }
@article {pmid41504847, year = {2026}, author = {Wang, W and Li, Y and Sun, J and Jiang, C and Hao, J}, title = {Semi-Rational Design of a Deep-Sea Metagenomic Sucrose Phosphorylase for Enhanced α-Arbutin Biosynthesis.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {3}, pages = {1923-1938}, pmid = {41504847}, issn = {1559-0291}, support = {2022YFC2805101//National Key Research and Development Program of China/ ; 2022QNLM030003-2//Qingdao Marine Science and Technology Center/ ; 2023TD71//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, }
@article {pmid41505541, year = {2026}, author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C}, title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6781}, pages = {eadu2182}, doi = {10.1126/science.adu2182}, pmid = {41505541}, issn = {1095-9203}, mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; }, abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.}, }
@article {pmid41505640, year = {2026}, author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G}, title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {2}, pages = {2438-2451}, pmid = {41505640}, issn = {1520-5118}, mesh = {*Silage/analysis/microbiology ; Fermentation ; Animals ; Rumen/metabolism/microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Lactiplantibacillus plantarum/metabolism ; Animal Feed/analysis ; Digestion ; Gastrointestinal Microbiome ; }, abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.}, }
@article {pmid41505815, year = {2026}, author = {Liu, F and Sun, S and Zhang, Y and Wang, F and Yang, X and Zhang, B and Fan, S and Jia, H}, title = {Possible tuberculous meningitis presenting with predominant voiding dysfunction in an elderly patient: A case report.}, journal = {Journal of infection and public health}, volume = {19}, number = {3}, pages = {103128}, doi = {10.1016/j.jiph.2025.103128}, pmid = {41505815}, issn = {1876-035X}, mesh = {Humans ; Male ; Aged ; *Tuberculosis, Meningeal/diagnosis/drug therapy/complications ; Antitubercular Agents/therapeutic use ; *Urination Disorders/etiology ; Mycobacterium tuberculosis/isolation & purification ; }, abstract = {Tuberculous meningitis (TBM) typically presents with neurological symptoms. Voiding dysfunction in TBM is usually attributed to spinal cord involvement. We report a rare case of possible TBM co-existing with possible prostatic tuberculosis, presenting primarily with urinary symptoms in the absence of spinal pathology. A 69-year-old male presented with a two-year history of progressive urinary retention, urgency, and frequency. Initial management for benign prostatic hyperplasia was ineffective. He subsequently developed fever, headache, and dizziness. Cerebrospinal fluid (CSF) analysis revealed lymphocytic pleocytosis and elevated protein. Despite extensive testing, including CSF culture, Xpert MTB/RIF, and metagenomic next-generation sequencing (mNGS), no pathogen was identified. However, a history of untreated testicular tuberculosis, pulmonary nodules on CT, and a prostatic nodule on MRI raised suspicion of disseminated tuberculosis. A clinical diagnosis of possible TBM was made based on a Marais score of 11. An intensive anti-tuberculosis regimen including moxifloxacin and linezolid led to complete resolution of neurological and urinary symptoms. This case suggests that voiding dysfunction in TBM patients may stem from concurrent genitourinary tuberculosis rather than spinal cord involvement. It highlights the importance of considering hematogenous dissemination from latent genitourinary foci in elderly patients and the utility of the Marais criteria for the diagnosis of TBM when microbiological evidence is elusive.}, }
@article {pmid41506424, year = {2026}, author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z}, title = {Response of sediment microbial community composition and function to mangrove restoration from an aquaculture pond in Southern China.}, journal = {Environmental research}, volume = {292}, number = {}, pages = {123718}, doi = {10.1016/j.envres.2026.123718}, pmid = {41506424}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; China ; Aquaculture ; *Wetlands ; *Microbiota ; Ponds/microbiology ; Bacteria/classification ; *Environmental Restoration and Remediation ; }, abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.}, }
@article {pmid41506449, year = {2026}, author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M}, title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.013}, pmid = {41506449}, issn = {2090-1224}, abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.
OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.
METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).
RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2] = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.
CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.}, }
@article {pmid41506454, year = {2026}, author = {Shi, T and Chen, H and Xu, S and Lin, Y and Zheng, X and Ruan, H and Shi, W and Zhang, R and Chen, H and Chen, T and Wang, H}, title = {The clinical application of metagenomic next-generation sequencing in pathogen identification of postoperative spinal implant infection.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.spinee.2026.01.004}, pmid = {41506454}, issn = {1878-1632}, abstract = {BACKGROUND CONTEXT: Postoperative spinal implant infection (PSII) poses significant diagnostic challenges and can lead to serious clinical outcomes. Traditional microbial culture methods are limited by prolonged turnaround times and low sensitivity, which have long hindered a comprehensive understanding of the pathogen spectrum in PSII. Metagenomic next-generation sequencing (mNGS) offers rapid, broad-spectrum, and highly sensitive pathogen detection, providing a promising solution to the diagnostic difficulties associated with PSII.
PURPOSE: This study aimed to evaluate the clinical utility of mNGS for the pathogenic diagnosis of PSII.
STUDY DESIGN/SETTING: Retrospective cohort study.
PATIENT SAMPLE: A retrospective analysis was conducted on clinical data from 122 patients with suspected surgical site infection following spinal implant-related surgery between January 2020 and July 2025.
OUTCOME MEASURES: Identification of pathogenic bacteria in patients.
METHODS: According to the National Healthcare Safety Network (NHSN) criteria, patients were classified into the PSII group (n=89) and the non-PSII group (n=33). Pathogen spectrum characteristics of PSII detected by mNGS were analyzed, and the diagnostic performance of mNGS was compared with that of traditional microbial culture, laboratory tests, and imaging studies.
RESULTS: The pathogen detection rate of mNGS was significantly higher than that of traditional culture (79.78% vs. 38.20%, p <.001). mNGS successfully detected pathogens in 42.70% (38/89) of culture-negative PSII cases. The main pathogens identified by mNGS included Staphylococcus aureus and coagulase-negative staphylococci (20.00% each, 15/75), Mycobacterium tuberculosis (18.67%, 14/75), and anaerobic bacteria (14.67%, 11/75). Among the 33 patients positive by both mNGS and culture, species-level concordance was 69.70%. No significant difference in the distribution of major pathogens was observed between early-onset (≤3 months) and late-onset (>3 months) infection groups. Antibiotic appropriateness evaluation revealed that only 32.58% (29/89) of patients had initial antibiotic regimens that provided complete coverage against the detected pathogens. The overall diagnostic performance of mNGS for PSII was superior to that of culture, with significantly higher sensitivity (79.78% vs. 38.20%), specificity (100.00% vs. 93.94%), positive predictive value (100.00% vs. 94.44%), negative predictive value (64.71% vs. 36.05%), accuracy (85.25% vs. 53.28%), and AUC (0.8989 vs. 0.6607).
CONCLUSION: mNGS significantly improves the detection of difficult-to-culture pathogens such as M. tuberculosis and anaerobic bacteria in PSII. It is recommended to combine mNGS with conventional methods, thereby improving diagnostic accuracy, guiding rational antibiotic use, and enhancing treatment outcomes.}, }
@article {pmid41506577, year = {2026}, author = {Sagar, K and Priti, K and Chandra, H}, title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.}, journal = {Journal of microbiological methods}, volume = {241}, number = {}, pages = {107390}, doi = {10.1016/j.mimet.2026.107390}, pmid = {41506577}, issn = {1872-8359}, mesh = {*Artificial Intelligence ; *Metagenome/genetics ; *Metagenomics/methods ; Microbiota/genetics ; Computational Biology/methods ; Machine Learning ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.}, }
@article {pmid41506580, year = {2026}, author = {Nichols, S and Estandía, A and Young, CM and Knowles, LS and Palinauskas, V and Okamura, B and Clegg, SM}, title = {Host whole genome sequence data represent an untapped resource for characterising affiliated parasite diversity.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {104768}, doi = {10.1016/j.ijpara.2025.104768}, pmid = {41506580}, issn = {1879-0135}, abstract = {Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.}, }
@article {pmid41507173, year = {2026}, author = {Han, Y and Liao, J and Li, C and Xing, F and Peng, J and Liu, X and Xie, W and Wu, F and Jian, H and Cheng, R and Dong, X}, title = {Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1427}, pmid = {41507173}, issn = {2041-1723}, mesh = {*Archaea/genetics/virology ; *Seawater/microbiology/virology ; *Bacteria/genetics/virology/classification ; Genome, Viral/genetics ; *Viruses/genetics ; Metagenome ; Phylogeny ; Geologic Sediments/microbiology/virology ; Ecosystem ; Cold Temperature ; }, abstract = {Cold seeps host diverse microbes and viruses with numerous unexplored defense and anti-defense systems. Analysis of 3813 microbial and 13,336 viral genomes from 191 metagenomes across 17 cold seep sites reveals extensive microbial defense repertoires, with over 60% representing candidate systems. Experimental validation confirms that several candidates protect against viral infection. These defense systems frequently co-occur, suggesting potential synergistic interactions, and are broadly distributed across sediments. In response, viruses have evolved diverse anti-defense genes, and the concurrent presence of multiple viral and microbial systems highlights intricate coevolution. Functionally critical lineages, such as anaerobic methanotrophic archaea, sulfate-reducing bacteria, and diazotrophs, appear to modify their defensive strategies under ecological and environmental pressures; for example, sulfate-reducing bacteria harbor multiple Gabija systems while corresponding viruses carry anti-Gabija genes, illustrating specific coevolutionary adaptations. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in deep-sea ecosystems.}, }
@article {pmid41507585, year = {2026}, author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B}, title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {415-428}, pmid = {41507585}, issn = {2058-5276}, support = {R21 AA030654/AA/NIAAA NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Feces/microbiology/chemistry ; *Ethanol/metabolism ; Male ; Female ; Middle Aged ; Adult ; Cohort Studies ; Metagenomics ; Fecal Microbiota Transplantation ; Escherichia coli/metabolism/genetics ; Fermentation ; Bacteria/metabolism/genetics/classification/isolation & purification ; Proteobacteria/metabolism/genetics/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; *Alcoholic Intoxication/microbiology ; Klebsiella pneumoniae/metabolism/genetics ; Metabolomics ; Metabolic Networks and Pathways/genetics ; }, abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.}, }
@article {pmid41507619, year = {2026}, author = {Mohamad, M and Sergaki, C and Patel, VC}, title = {Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {3}, pmid = {41507619}, issn = {2731-8745}, abstract = {Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.}, }
@article {pmid41507780, year = {2026}, author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L}, title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {126}, pmid = {41507780}, issn = {1471-2180}, support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Microbiota/drug effects/genetics ; *Bacteria/drug effects/genetics/classification/isolation & purification ; Animal Husbandry/methods ; *Anti-Bacterial Agents/pharmacology ; Farms ; *Drug Resistance, Bacterial ; Soil Microbiology ; Poultry Diseases/microbiology ; *Anti-Infective Agents/pharmacology ; }, abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.
STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.
RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.
CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.}, }
@article {pmid41507798, year = {2026}, author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J}, title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {130}, pmid = {41507798}, issn = {1471-2180}, support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Lung/microbiology ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Nontuberculous Mycobacteria/genetics/isolation & purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Adult ; }, abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.
OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.
METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.
RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.
CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.}, }
@article {pmid41508107, year = {2026}, author = {Bay, P and Cappy, P and Rodriguez, C and Mongardon, N and Petit, M and Voiriot, G and Sonneville, R and Pineton de Chambrun, M and Urbina, T and Pham, T and Decavèle, M and Benghanem, S and Contou, D and Lepeule, R and Melica, G and de Prost, N and Angebault, C and Mekontso Dessap, A and Woerther, PL and Razazi, K}, title = {Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.}, journal = {Critical care (London, England)}, volume = {30}, number = {1}, pages = {18}, pmid = {41508107}, issn = {1466-609X}, abstract = {BACKGROUND: Infection are the leading cause of intensive care unit (ICU) admission, yet conventional microbiological methods frequently fail to identify the causative pathogen. Metagenomic next-generation sequencing (mNGS) is an emerging, unbiased, pan-pathogen diagnostic tool. However, its real-world microbiological and clinical impact in the ICU remains poorly characterized. This study aimed to assess the microbiological yield and clinical impact of mNGS when implemented in routine ICU practice.
METHODS: This retrospective multicenter study was conducted across ten tertiary-care ICUs in the Greater Paris area between January 2018 and April 2024. All patients for whom an mNGS analysis was requested by clinicians from a microbiological sample were included. Any additional pathogens identified by mNGS were independently classified as causative, possibly causative, or non-causative by two reviewers. The independent reviewers also categorised therapeutic changes attributable to mNGS as escalation, de-escalation, discontinuation, or other decision support. Discrepancies were adjudicated by a third reviewer.
RESULTS: A total of 144 mNGS analyses were performed in 132 critically ill patients (median age 55 years), 31% of whom were immunocompromised. The number of mNGS analyses requested increased each year. The most common sample types were cerebrospinal fluid (CSF) (n = 60/144, 41.7%) and pleural fluid (n = 21/144, 14.6%). Pathogens were identified by mNGS in 58 samples (40.3%), with a higher yield in pleural fluid (n = 11/21, 52.4%) than in CSF (n = 16/60, 26.6%). Of the 107 pathogens identified, 43 (40.2%) were detected exclusively by mNGS, notably anaerobic bacteria in pleural fluid and abscess samples. mNGS identified an additional pathogen in 34 cases (25.8%) of the 132 patients included, which was deemed causative in 18 cases (13.6%). mNGS findings influenced therapeutic management in seven patients (5.3%) including five cases of antibiotic de-escalation, one appropriate antibiotic escalation, and one case of clinical decision support.
CONCLUSION: In this real-life ICU cohort, mNGS identified additional pathogens in 25.8% of patients, deemed causative in 18 cases (13.6%), and a direct therapeutic impact was observed in 5.3% of cases. However, the median turnaround time of 14 days likely limited its clinical impact. Further studies are needed to better define the role of mNGS in the diagnostic management of critically ill patients.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13054-025-05764-2.}, }
@article {pmid41508143, year = {2026}, author = {Gong, Y and Shen, S and Cao, Z and Zou, X and Zhou, S and Jiang, R and Kang, X and Liu, S and Tian, Y}, title = {Prophylactic impact of cecal fermentation broth against gut microbiota dysbiosis of broiler chickens challenged with Escherichia coli.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {11}, pmid = {41508143}, issn = {2524-4671}, support = {2024CXZX009//The Science and Technology Innovation Fund of Henan Agricultural University/ ; 30601985//The Scientific Studio of Zhongyuan Scholars/ ; }, abstract = {BACKGROUND: The intestinal microorganisms make an important contribution to the development of the host immune system and resistance to pathogen infections, especially early in life. Our previous study found that early inoculation with cecal fermentation broth could change the colonization patterns of intestinal microorganisms and enhance the immune performance in broilers. However, it remains unknown whether cecal fermentation broth inoculation can be used as a novel form of treatment against pathogenic infections.
RESULTS: In this study, a pathological model of avian pathogenic Escherichia coli (E. coli) was established to investigate the mechanism of cecal fermentation broth against pathogen infection in broilers. A total of 180 newly hatched broilers were randomly divided into three groups: (1) negative control (Con) group, inoculated with sterile normal saline from 1 to 4 days of age; (2) positive control (NS + E.coli) group, inoculated with sterile normal saline from 1 to 3 days of age, infected with E.coli at 4 days of age; (3) fermentation broth prevention (FerB + E.coli) group, inoculated with fermentation broth from 1 to 3 days of age, infected with E.coli at 4 days of age. Subsequently, 8 individuals were randomly selected from each group for weighing followed by slaughter to determine relevant indicators at 7, 10, 14 and 21 days of age. The results showed that early inoculation with fermentation broth significantly alleviates the negative effects on growth performance and intestinal permeability caused by E. coli infection. Furthermore, enhanced small intestinal health was observed, as indicated by the increase in villus height and the ratio of villus height to crypt depth (V/C). The relative abundance of Bacteroidetes was higher in the prevention group, and the number of functional genes detected was significantly greater. Additionally, the concentration of propionic acid was substantially elevated in the prevention group, while butyric acid concentrations were significantly reduced in the challenge group.
CONCLUSION: This study demonstrates that early intervention with cecal fermentation broth improves intestinal barrier function and immune performance in broilers by increasing the relative abundance of intestinal Bacteroides and promoting propionic acid synthesis. These findings provide a novel strategy for preventing intestinal inflammatory disorders in broilers, such as avian colibacillosis.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00514-9.}, }
@article {pmid41508161, year = {2026}, author = {Villafuerte, AB and Comeau, AM and Soria, R and Ortega, R and Wright, RJ and Miralles, I}, title = {Linking microbial taxonomy and function in N and P metabolism: a study of organic amendments in semiarid restored soils.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {23}, pmid = {41508161}, issn = {2524-6372}, support = {FIRESOIL CNS2023-14150//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; BIOQUALIRES-PID2021-1275910B-100//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; P_FORT_GRUPOS_2023/69//Research Plan of the University of Almeria/ ; TECHBIOSOL-PID2024-156189OB- I00//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {BACKGROUND: Arid and semi-arid regions cover approximately 41% of Earth's surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments are widely used to restore degraded soils because they improve physical, chemical, and biological properties. However, little is known about how these amendments alter microbial communities and the relationship between microbial taxonomy and function, particularly in nitrogen and phosphorus cycling. To address this knowledge gap, the effects of different organic amendments (gardening compost, greenhouse horticultural compost, sewage sludge and two blends of the above) on soil properties, microbial communities and their contributions to nitrogen metabolism and phosphorus turnover in degraded soils from a limestone quarry in the Gádor Range (Almería, SE-Spain) six months after their application were investigated.
RESULTS: Organic amendments increased nutrient content (total organic carbon, total nitrogen and available phosphorus), microbiological activity, and bacterial biomass compared to unamended soils, with the largest increases in sewage-sludge-treated soils. Shotgun metagenomic assays revealed that organic amendments modified bacterial community composition and differentially influenced potential function pathways, contributing more strongly to nitrogen metabolism than phosphorus turnover, particularly within the phosphonate pathway. Across soils, Pseudomonadota and Actinomycetota were the dominant phyla. Sludge-amended soil showed higher relative abundance of Pseudomonas, associated with denitrification processes (nirK, nosZ, norB) and phosphonate degradation via C-P lyase (phnJ). Genera such as Streptomyces were linked to ammonium assimilation (glnAd, gltBD) and phosphonate synthesis (pmmS), and were more abundant in soil with vegetable-compost and unamended soils. Both nitrogen and phosphorus metabolisms exhibited phylogenetically unrestricted functional patterns, indicating high functional redundancy at phylum and genus levels.
CONCLUSIONS: This research establishes key relationships between taxonomy and function in restored soils and demonstrates how organic amendments rephase microbial communities and their potential roles in nutrient cycling. Although dominant taxa and functions were identified, many microorganisms involved in nitrogen and phosphorus turnover remain insufficiently characterized. Further research across restoration contexts is needed to compare nutrient-cycling responses and to deepen understanding of taxonomy-function linkages in soils amended with organic residues.}, }
@article {pmid41508436, year = {2026}, author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L}, title = {Corrigendum to "Aldehyde metabolism in Maotai-flavor baijiu: insights from integrated metagenomic and metaproteomic analyses" [Food Res. Int. 221(Part 3) (2025) 117518].}, journal = {Food research international (Ottawa, Ont.)}, volume = {225}, number = {}, pages = {117954}, doi = {10.1016/j.foodres.2025.117954}, pmid = {41508436}, issn = {1873-7145}, }
@article {pmid41508467, year = {2026}, author = {Chang, H and Zhang, Q and Soro, PL and Zhang, W and Ma, L and Feng, Z and Gu, C}, title = {Integrative metagenomic, metabolomic, and transcriptomic analyses unravel flavor development driven by a defined starter cocktail in cocoa fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {225}, number = {}, pages = {118042}, doi = {10.1016/j.foodres.2025.118042}, pmid = {41508467}, issn = {1873-7145}, mesh = {*Fermentation ; *Cacao/microbiology/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Saccharomyces cerevisiae/metabolism/genetics ; Gene Expression Profiling ; Odorants/analysis ; Transcriptome ; Food Microbiology ; Hanseniaspora/metabolism ; Gas Chromatography-Mass Spectrometry ; }, abstract = {This study investigated the impact of a defined starter cocktail (Hanseniaspora uvarum XY23.1, Saccharomyces cerevisiae XY23.2, Lactiplantibacillus plantarum XY23.1, and Gluconobacter oxydans XY23.2) on Trinitario cocoa fermentation in Hainan, China. A multi-omic approach integrating shotgun metagenomics, metabolomics (LC-MS and GC-MS), and transcriptomics was employed to comprehensively assess microbial succession, metabolite dynamics, and functional gene expression. Starter inoculation accelerated cocoa fermentation and stabilized microbial succession, and the four introduced strains remained dominance during the process. Metabolomic analysis revealed that the inoculated group had a remarkable increase in the content of the aromatic volatiles phenylethyl alcohol, 3-methylbutyl acetate, and delta-decalactone, which contributes to fruity and floral aroma characteristics. Shotgun metagenomics revealed enrichment of genes involved in carbohydrate utilization, amino acid catabolism, and acetate ester biosynthesis. Transcriptomics also indicated that S. cerevisiae upregulated Ehrlich pathway and glyoxylate cycle under co-culture conditions, demonstrating its central role in aroma formation and redox balance, while H. uvarum upregulated sugar transporters and stress-response genes, demonstrating a putative regulatory role in nutrient competition and interspecies interaction. Overall, our findings elucidate that defined starter cultures can shape cocoa fermentation toward improved consistency and aroma outcomes, providing a foundation for designing function-driven microbial consortia for controlled fermentation applications.}, }
@article {pmid41508656, year = {2026}, author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL}, title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.}, journal = {Cancer research communications}, volume = {6}, number = {1}, pages = {70-76}, pmid = {41508656}, issn = {2767-9764}, support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; }, mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Prospective Studies ; Male ; Female ; *Specimen Handling/methods ; Middle Aged ; Australia ; Aged ; Occult Blood ; Adult ; *Neoplasms/microbiology ; Surveys and Questionnaires ; Metagenomics/methods ; }, abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.
SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.}, }
@article {pmid41508741, year = {2026}, author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P}, title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.}, journal = {Environmental microbiology reports}, volume = {18}, number = {1}, pages = {e70262}, pmid = {41508741}, issn = {1758-2229}, support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Lakes/virology ; *DNA Viruses/genetics/classification/isolation & purification ; *Geologic Sediments/virology ; Tibet ; Metagenomics ; Phylogeny ; *Biodiversity ; Metagenome ; }, abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.}, }
@article {pmid41509203, year = {2025}, author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G}, title = {Quantum implementation of multi-pattern string matching for k-mer detection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41509203}, issn = {2692-8205}, support = {R35 GM155468/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.
METHOD: We implement two quantum algorithms for DNA multi pattern string matching for k-mer detection based on Grover's amplitude amplification with quantum random access memory (QRAM). The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O(√S) query complexity for S text positions but requiring O(m·L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O(√S · √m) in total.
RESULTS: We present two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.
CONCLUSIONS: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.}, }
@article {pmid41509497, year = {2025}, author = {Shen, Z and Eckert, J and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA}, title = {Skin microbiome composition and function in the development of atopic diseases during infancy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41509497}, issn = {2692-8205}, support = {R00 AR084058/AR/NIAMS NIH HHS/United States ; UM1 AI109565/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome.
OBJECTIVE: To determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.
METHODS: We analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status.
RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae. At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae. Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.
CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.}, }
@article {pmid41509546, year = {2026}, author = {Steriade, C}, title = {The Gut Feeling Behind Autoimmune Encephalitis.}, journal = {Epilepsy currents}, volume = {}, number = {}, pages = {15357597251412104}, pmid = {41509546}, issn = {1535-7597}, abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.
METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.
RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.
SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.}, }
@article {pmid41510275, year = {2025}, author = {De Vlaminck, I and Mzava, O and Djomnang, LA and Cheng, A and Gomez-Escobar, L and Lenz, J and Belcher, E and Schenck, E}, title = {Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41510275}, issn = {2693-5015}, support = {K23 HL151876/HL/NHLBI NIH HHS/United States ; DP2 AI138242/AI/NIAID NIH HHS/United States ; R21 AI133331/AI/NIAID NIH HHS/United States ; R21 AI124237/AI/NIAID NIH HHS/United States ; R01 AI146165/AI/NIAID NIH HHS/United States ; }, abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated response to infection. Early identification of pathogens and accurate assessment of organ injury are critical for improving outcomes, but current methods are often inadequate, especially after initiation of antibiotic treatment. Metagenomic sequencing of cell-free DNA (cfDNA) offers a promising alternative, enabling simultaneous pathogen detection and tissue-of-origin profiling. Contamination, however, can limit its accuracy in low-biomass samples. Here, we apply the Sample-Intrinsic Microbial DNA Found by Tagging and Sequencing (SIFT-seq) assay, which reduces contamination and allows detection of pathogens and organ injury simultaneously. We analyzed 142 plasma specimens: 105 from sepsis patients, 103 collected after initiation of antibiotic treatment, 24 from non-sepsis ICU controls, and 13 from healthy controls. SIFT-seq identified sepsis-causing pathogens in good agreement with pre-antibiotic blood cultures, revealed elevated immune activity and organ injury in sepsis patients, and, when combined with the SOFA score in a multivariate model, improved diagnostic performance (AUC = 0.874). These findings highlight the potential of integrated cfDNA profiling to enhance sepsis diagnosis.}, }
@article {pmid41510411, year = {2025}, author = {Zhao, J and Wang, Y and Zhang, H and Feng, J}, title = {A Case of Severe Fever With Thrombocytopenia Syndrome Co-infected With Pseudomonas aeruginosa and Aspergillus fumigatus.}, journal = {Cureus}, volume = {17}, number = {12}, pages = {e98752}, pmid = {41510411}, issn = {2168-8184}, abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne infectious disease with a high mortality rate. Co-infections with SFTS virus (SFTSV) and other pathogens can exacerbate the condition, leading to rapidly progressive multiple organ failure. We reported a case of SFTS complicated by Pseudomonas aeruginosa and Aspergillus fumigatus. Despite active symptomatic supportive treatment (including anti-virus, anti-infection, anti-antifungal treatment, liver protection, and other advanced life supports), the patient's condition deteriorated rapidly, leading to multiple organ failure. The patient was discharged home and died on the same day. The next day, her blood test results reported that SFTSV, Pseudomonas aeruginosa and Aspergillus fumigatus were detected through metagenomic next-generation sequencing (mNGS). It suggests that early pathogen screening and targeted anti-infective treatment are crucial for improving the prognosis.}, }
@article {pmid41510448, year = {2025}, author = {Tohya, M and Murase, K and Minagawa, M and Saiura, A and Nakagawa, I and Kirikae, T and Watanabe, S}, title = {Single-Cell Sequencing of a Bile Sample From an Acute Cholecystitis Patient.}, journal = {Cureus}, volume = {17}, number = {12}, pages = {e98748}, pmid = {41510448}, issn = {2168-8184}, abstract = {Single-cell sequencing is a novel approach to genome sequencing of clinical samples. However, there are only few studies using single-cell sequencing of genomes for bacterial infections. A 71-year-old woman presented to the emergency department with epigastric pain, 38.5°C fever, and a history of hypertension and hyperuricemia. From blood test results, acute cholecystitis was suspected. The surgery went well and bilirubin calcium stones were found in the gallbladder. Single-cell sequencing was used to investigate a bile sample from a patient with acute cholecystitis. The sample, cultured on a MacConkey agar plate, produced four colonies, all identified as Escherichia coli by bacteriological and biochemical properties. Whole genome sequences of the four strains were determined using the single-cell amplified genome (SAG) sequencing technique. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all four were 99.98-100% and 100%, respectively, indicating that they were the same bacterial species. Compared with type strains, these four strains were closest to Shigella sonnei (ANI 98.65-98.66%; dDDH 88.5%) than E. coli (ANI 96.79-96.80%; dDDH 74.2%), despite lacking stx1, stx2 and ipaH, which Shigella species harbor. 16S metagenome analysis identified E. coli as the predominant bacterial genome in the sample, comprising 93.15%. SAG raw data had a relatively high level of quality, with 98.4-98.7% of the read numbers used after quality trimming. However, the genome sequencing coverage was only 9.45-42.88% when compared to a complete genome of an isolate with a mapping quality set above 99%, resulting in gaps compared to conventional whole genome sequence data of these isolates. The procedures of the SAG sequencing technique should be revised to improve the sequencing coverage and reduce gaps in the sequence data. Nonetheless, single-cell genome sequencing can provide novel information for bacterial infections.}, }
@article {pmid41510663, year = {2026}, author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y}, title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {2}, pages = {1998-2011}, doi = {10.1021/acs.jafc.5c09250}, pmid = {41510663}, issn = {1520-5118}, mesh = {*Citrus/metabolism/microbiology/growth & development/physiology/genetics ; *Plant Roots/metabolism/microbiology/physiology/growth & development ; Microbiota/drug effects ; *Iron/metabolism/analysis ; Rhizosphere ; Bacteria/genetics/isolation & purification/classification/metabolism ; *Azetidinecarboxylic Acid/analogs & derivatives/metabolism/pharmacology ; Soil Microbiology ; *Proline/analogs & derivatives/metabolism/pharmacology ; Fertilizers/analysis ; }, abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.}, }
@article {pmid41511078, year = {2026}, author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P}, title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41511078}, issn = {2057-5858}, support = {INV-044643/GATES/Gates Foundation/United States ; }, mesh = {*Feces/microbiology/virology ; Animals ; *Marsupialia/microbiology/virology/classification ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Viruses/genetics/classification ; }, abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.}, }
@article {pmid41511092, year = {2026}, author = {Jabir, T and Venkatachalam, S and Surya Prakash, L}, title = {Metagenome-assembled genomes of bacterial communities in the eastern Southwest Indian Ridge, Indian Ocean.}, journal = {Microbiology resource announcements}, volume = {15}, number = {2}, pages = {e0087025}, pmid = {41511092}, issn = {2576-098X}, support = {MoES/EFC/28/2018-II//Ministry of Earth Sciences/ ; }, abstract = {This paper presents high-quality metagenome-assembled genomes (MAGs) recovered from hydrothermal plume at the 67.67°E vent field along the eastern Southwest Indian Ridge. A total of 24 high-quality MAGs were obtained having 21 different genera. These MAGs, associated with chemosynthetic pathways including methane, metal, and sulfur metabolism, offer crucial insights into microbial transformation in deep-sea hydrothermal vents.}, }
@article {pmid41511111, year = {2026}, author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M}, title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0140525}, pmid = {41511111}, issn = {2379-5077}, support = {82571963//National Natural Science Foundation of China/ ; 2025A1515012162, 2024A1515010590//Natural Science Foundation of Guangdong Province/ ; JCYJ20250604145739052 and JCYJ20240813144117023//Shenzhen Science and Technology Program/ ; Y2024001//Resear Initaion Fund of Longgang District Maternity & Child Healthcare Hospital of Shenzhen City/ ; Postdoctoral fellow stationed in Shenzhen second batch in 2022//Shenzhen Municipal Human Resources and Social Security Bureau/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/metabolism/etiology/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; *Machine Learning ; Female ; Infant, Newborn ; *Jaundice, Neonatal/complications/metabolism ; *Metabolome ; Feces/microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Infant ; Child, Preschool ; }, abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.
IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.}, }
@article {pmid41512665, year = {2026}, author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY}, title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106384}, pmid = {41512665}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Poultry Diseases/microbiology/prevention & control ; Cecum/microbiology ; *Salmonella Infections, Animal/microbiology/prevention & control ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology/administration & dosage ; Random Allocation ; Anti-Bacterial Agents/pharmacology ; Amoxicillin/pharmacology ; *Bacillaceae/physiology ; *Lactobacillaceae/physiology ; }, abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.}, }
@article {pmid41512717, year = {2026}, author = {Li, L and Shang, G and Guo, Y and Zhang, J and Qi, Y and Wang, H and Flores, M and Belloch, C and Liu, Y and Jing, W and Li, X and Woldemariam, KY}, title = {Unlocking the genomic landscape of Staphylococcus equorum and understanding the functional role and technological application in dry-cured fermented meat products: A review.}, journal = {International journal of food microbiology}, volume = {449}, number = {}, pages = {111618}, doi = {10.1016/j.ijfoodmicro.2025.111618}, pmid = {41512717}, issn = {1879-3460}, mesh = {*Meat Products/microbiology/analysis ; *Staphylococcus/genetics/metabolism ; Fermentation ; Food Microbiology ; Fermented Foods/microbiology ; Genome, Bacterial ; Animals ; }, abstract = {In Dry-cured fermented meat products, the role of Staphylococcus equorum has been given less attention. S. equorum enhances the flavour, colour, texture, and nutritional quality, and produces antimicrobial compounds that inhibit pathogens in dry-cured fermented meat products. This review aims to provide a comprehensive evaluation of S. equorum as a potential starter culture in dry-cured fermented meat products, examines the main genomic and metabolic characteristics, and highlights the regulatory mechanisms. S. equorum is a gram-positive, catalase-positive coccus with high salt tolerance and optimal growth at 4-10 °C and pH 5-5.6. Modern PCR-based sequencing and metagenomics allow accurate identification of S. equorum using the major genes, including superoxide dismutase (sodA) and recombinase A (recA). Identification of this species has been made from different dry-cured fermented meat products, including Spanish dry-cured ham and "Chorizo" sausages from Spain, artisanal "Soppressata" fermented sausage from Italy. The functional role of S. equorum in protein and lipid hydrolysis contributes to key flavour and aroma compounds. Moreover, it has potential in the prevention of secondary lipid oxidation (superoxide dismutase (SOD)), contributes to nitrate reductase activity (NOS pathway), and biosynthesis of antibacterial peptide (micrococcin P1), which improves the quality and safety of dry-cured fermented meat products. Keeping this into account, the studies conducted on the S. equorum application as a starter culture in dry-cured fermented meat products are in their early stages and require further investigation and analysis.}, }
@article {pmid41512751, year = {2026}, author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R}, title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {140812}, doi = {10.1016/j.jhazmat.2025.140812}, pmid = {41512751}, issn = {1873-3336}, mesh = {*Biofilms ; *Ecosystem ; Gene Transfer, Horizontal ; *Ships ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Water Microbiology ; }, abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.}, }
@article {pmid41512763, year = {2026}, author = {Liu, X and Li, J and Ma, C}, title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141076}, doi = {10.1016/j.jhazmat.2026.141076}, pmid = {41512763}, issn = {1873-3336}, mesh = {Animals ; *Aflatoxin B1/toxicity ; Bees/drug effects/microbiology/genetics ; Metagenomics ; Transcriptome/drug effects ; Gene Expression Profiling ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.}, }
@article {pmid41512899, year = {2026}, author = {Chu, VT and Spottiswoode, N and Ward, R and Yokoe, DS and Ramirez-Avila, L and Phelps, MS and Glascock, A and Crawford, ED and Kamm, J and Hao, S and Li, L and Dynerman, D and Waltari, E and Nafees, S and Kalantar, KL and Caldera, S and Madera, S and Guerrero, ES and Ivashin, D and Serpa, PH and Love, C and Mwakibete, LL and Doernberg, SB and Kistler, A and Alvino, R and Engel, J and Chiu, CY and Pak, C and Cunningham, G and Reyes, H and Buie, B and Messacar, K and Leroue, M and Prince, BC and Detweiler, AM and Stanley, K and Caughell, C and McNeil, N and Neff, N and Nichols, A and Miller, S and DeRisi, JL and Tato, CM and Langelier, CR}, title = {Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.}, journal = {The Lancet. Microbe}, volume = {7}, number = {2}, pages = {101277}, doi = {10.1016/j.lanmic.2025.101277}, pmid = {41512899}, issn = {2666-5247}, mesh = {Humans ; *Cross Infection/prevention & control/epidemiology/microbiology ; *Academic Medical Centers ; *Infection Control/methods ; *Genomics/methods ; Disease Outbreaks/prevention & control ; Whole Genome Sequencing ; High-Throughput Nucleotide Sequencing ; San Francisco/epidemiology ; }, abstract = {Advances in genomic technologies have revolutionised practices for hospital infection prevention and control programmes. In this Personal View, we describe a genomic epidemiology service called the Rapid Response (RR) programme at University of California, San Francisco, a large academic medical centre. In collaboration with the hospital infection-prevention team, the RR programme uses whole-genome sequencing and metagenomic next-generation sequencing for outbreak investigations, special interest analyses of emerging pathogens, and surveillance of high-priority microbes. Over 7 years (2017-24), the RR programme conducted a diversity of outbreak investigations and other analyses; most investigations ruled out transmission, and the rapid turnaround of genomic results averted further resource-intensive work. Longitudinal surveillance enabled early detection of changing incidence trends and guided timely infection-prevention responses. Our experiences with the RR programme build upon growing evidence that genomic epidemiology programmes enhance hospital infection prevention and control, augment priority pathogen surveillance, and improve patient safety.}, }
@article {pmid41513032, year = {2026}, author = {Liu, S and Liu, Z and Xia, X}, title = {Primary cutaneous blastomycosis in a Chinese-Canadian girl following an insect bite.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108374}, doi = {10.1016/j.ijid.2026.108374}, pmid = {41513032}, issn = {1878-3511}, mesh = {Humans ; Female ; *Blastomycosis/diagnosis/drug therapy/microbiology ; *Blastomyces/isolation & purification/genetics ; Antifungal Agents/therapeutic use ; *Insect Bites and Stings/complications/microbiology ; China ; Canada ; Itraconazole/therapeutic use ; Animals ; High-Throughput Nucleotide Sequencing ; East Asian People ; }, abstract = {BACKGROUND: Blastomycosis is a disease caused by the dimorphic fungus Blastomyces species. This infection occurs most frequently among individuals residing in the midwestern, southeastern, and south-central United States, as well as in Canadian provinces bordering the Great Lakes and the St. Lawrence Seaway. Sporadic cases have been reported in China, the diagnosis of imported cases remains a significant challenge.
CASE PRESENTATION: We report a diagnostically challenging case of primary cutaneous blastomycosis in a Chinese-Canadian girl, presenting as two nodules of different sizes on her left lower leg and left arm. The patient was initially diagnosed with insect bite dermatitis in Canada, which showed poor response to treatment. Direct microscopic examination revealed large spherical yeast cells, some with broad-based budding, initially interpreted as protothecosis or coccidioidomycosis. However, metagenomic next-generation sequencing (mNGS) indicated Blastomyces dermatitidis, which was subsequently confirmed by fungal culture and ITS sequencing. The patient was prescribed oral itraconazole at 50 mg/day and has since returned to Canada to continue treatment.
CONCLUSIONS: For diagnosing infections caused by highly pathogenic pathogens such as imported blastomycosis, the combination of metagenomic next-generation sequencing (mNGS) and direct microscopic examination represents a valuable diagnostic approach.}, }
@article {pmid41513932, year = {2026}, author = {Ruiz-Ruiz, S and Piquer-Esteban, S and Pérez-Rocher, B and Pérez-Brocal, V and Arnau, V and Artacho, A and Diaz, W and Jiménez-Hernández, N and Pons, J and Castro, JA and Moya, A}, title = {Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4921}, pmid = {41513932}, issn = {2045-2322}, support = {grant number CD15/00067//the Carlos III Health Institute (ISCIII)/ ; project number PMPTA23/00001//the Carlos III Health Institute (ISCIII)/ ; grant Conselleria d´Educació, Cultura, Universitats i Ocupació, cofinançat per la Unió Europea FSE+ 2021-2027, ACIF/2021/341//ACIF fellowship from the Generalitat Valenciana/ ; grant number FPU20/05756//Spanish Ministry of Universities, Vocational Training ans Sports/ ; project number PID2019-105969GB-I00 funding by MICIU/AEI/10.13039/501100011033//the Spanish Ministry of Science and Innovation and Universities/ ; project number SAF2015-65878-R funding by MICIU/AEI/10.13039/501100011033/ and by FEDER Una manera de hacer Europa//the Ministry of Science, Innovation and Universities/ ; project number CIPROM/2021/042//Conselleria d´Educació, Cultura, Universitats i Ocupació/ ; }, abstract = {UNLABELLED: While a proportion of the microbiota plays a beneficial role, there is no conclusive evidence that the entire microbiome is mutualistic. Here, we have studied the intestinal microbiota of three healthy age groups from the Valencian Region (Spain). We have periodically obtained stool samples to determine the 16S rRNA gene amplicons, metagenomes, and metatranscriptomes, and we have observed that the microbiota’s stability differs with age, being less stable in infants. Regarding analyses of the conserved microbiota across the three age groups throughout the study period, shared genera account for about 60%. In addition, we identified a core of microbial taxa present in all individuals, which could represent mutualistic symbionts. Finally, in a previous study, we detected that tryptophan and indole production by intestinal bacteria decreases substantially with host age. Metagenomics and metatranscriptomics analyses show that tryptophanase mRNA synthesis in the genus Akkermansia is approximately 10 times lower in adults and the elderly than in children, consistent with this enzyme’s low levels or absence in these groups. Consequently, this supports the hypothesis that an uncoupling might occur between some microbiota taxa and the human host at older ages.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-35033-3.}, }
@article {pmid41514032, year = {2026}, author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S}, title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {39}, pmid = {41514032}, issn = {1432-184X}, support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; }, mesh = {*Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Salt-Tolerant Plants/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Metagenome ; }, abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.}, }
@article {pmid41514203, year = {2026}, author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S}, title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41514203}, issn = {1471-2180}, mesh = {Animals ; Cattle/microbiology/growth & development ; *Gastrointestinal Microbiome ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation & purification ; Male ; RNA, Ribosomal, 16S/genetics ; *Diet/veterinary ; Fermentation ; Metagenomics ; DNA, Bacterial/genetics ; }, abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.}, }
@article {pmid41514270, year = {2026}, author = {González-Rovira, M and Sainz-Bueno, JA and García-Díaz, L and Martínez-Pancorbo, C and Sánchez, J and Gutiérrez, G and Magoutas, K and Mesías-Pérez, A and Mellado, E and Payne, M and Sousa, C and Moreno, ML}, title = {Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {273}, pmid = {41514270}, issn = {1479-5876}, support = {PID2024-157768OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; SUBN/2019/005//Federación de Asociaciones de Celíacos de España (FACE)/ ; US-15332/I+D+I//FEDER ANDALUCIA/ ; }, abstract = {BACKGROUND: The evidence of a low-biomass microbial community in the amniotic fluid (AF) is challenging the traditional concept of a sterile womb. To clarify microbial presence and host responses, a comprehensive, multi-methodological approach is required.
METHODS: We designed an optimized culturing strategy that maximized microorganism recovery by implementing differential centrifugation and concentration of AF samples, followed by plating onto four distinct selective media types and incubation under both stringent aerobic (up to two weeks) and prolonged anaerobic (up to four weeks) conditions, including an initial pre-enrichment step in Brain Heart Infusion (BHI) broth for low-abundance organisms. These results were combined with PacBio 16S rRNA gene sequencing, Illumina shotgun metagenomics, and antimicrobial peptides (AMP) detection. Using this approach, we characterized microbial presence in 154 AF samples across gestational stages. Data normality was assessed with the Shapiro-Wilk test, guiding the selection of both parametric and non-parametric tests, and a p-value of < 0.05 was considered statistically significant.
RESULTS: We detected culturable microorganisms in 33.1% of samples, with a higher proportion in elective caesarean Sect. (55.0%) compared to amniocentesis (29.5%), suggesting increased microbial load toward term. We applied stringent contamination controls, and repeatedly recovered viable microorganisms Bacillus, Cutibacterium, Micrococcus, and Staphylococcus, with Cutibacterium acnes and Staphylococcus epidermidis common. Both sequencing methods revealed a low-biomass, low-diversity microbial community with high inter-individual variability. Notably, striking microbial discordance in diamniotic twin pregnancies, challenged intrauterine homogeneity. Higher Human Beta Defensin (HBD) -1 levels correlated with absence of culturable bacteria or microbial DNA, while levels of HBD-1, HBD-3, and LL-37 were reduced in Staphylococcus-positive samples, suggesting a dynamic interplay between specific bacteria and host defences.
CONCLUSIONS: Our findings indicate that viable bacteria and/or DNA can transiently access the prenatal environment microbial balance. We propose a novel perspective of a potential regulatory axis between microorganisms and AMP.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07601-0.}, }
@article {pmid41514433, year = {2026}, author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y}, title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {60}, pmid = {41514433}, issn = {2049-2618}, support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Gastrointestinal Microbiome ; Female ; Milk/chemistry/metabolism ; *Rectum/microbiology ; Metagenomics ; Lactation ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; Dairying ; Longevity ; }, abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.
RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.
CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.}, }
@article {pmid41514445, year = {2026}, author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C}, title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {61}, pmid = {41514445}, issn = {2049-2618}, support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; Female ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Stress, Physiological ; Milk/metabolism ; Oxidative Stress ; Metabolomics ; Archaea/classification/genetics/isolation & purification ; Methane/metabolism ; }, abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.
RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.
CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.}, }
@article {pmid41514452, year = {2026}, author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K}, title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {24}, pmid = {41514452}, issn = {2049-2618}, support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium für Forschung, Technologie & Raumfahrt/ ; }, mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics/classification/isolation & purification ; Metagenomics/methods ; *Eukaryota/genetics/classification ; Metagenome ; Genetic Variation ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.
RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.
CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.}, }
@article {pmid41514654, year = {2025}, author = {Liu, KYP and Huang, A and Pepin, C and Shen, Y and Tsang, P and Poh, CF}, title = {Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.}, journal = {Cancers}, volume = {18}, number = {1}, pages = {}, pmid = {41514654}, issn = {2072-6694}, abstract = {The oral microbiome has become an emerging focus of oral cancer research, with growing evidence linking microbial communities to disease development, progression, and prognosis. However, there is limited consensus on optimal sampling strategies, storage methods, and analytical approaches. This narrative review critically evaluates current strategies for sampling, preservation, DNA extraction, sequencing, and data analysis in oral microbiome research related to oral cancer. We compared commonly used sampling methods, including saliva, oral rinse, swab, brush, and tissue biopsy, and reviewed preservation conditions, extraction kits, sequencing platforms, and analytical pipelines reported in recent oral microbiome studies. Sampling approaches affect microbial yield and site specificity. Saliva and oral rinse samples are convenient and noninvasive but may dilute lesion-specific microbial signals, whereas lesion-directed swabbing or brushing yields greater microbial biomass and biological relevance. Preservation media and storage temperature significantly influence microbial stability, and DNA extraction methods vary in their ability to remove host DNA. Although 16S rRNA gene sequencing remains the most common approach, shotgun metagenomics offers higher resolution and function insights but is still limited by clinical applicability. Differences in data pre- and post-processing models and normalization strategies further contribute to inconsistent microbial profiles. Given that oral mucosal sites differ markedly in structure and microenvironment, careful consideration is required to ensure that collected samples accurately represent the biological question being addressed. Methodological consistency across all workflow stages-from collection to analysis-is essential to generate reproducible, high-quality data and to enable reliable translation of oral microbiome research into clinical applications for cancer detection and risk assessment. Together, these insights provide a framework to guide future study design and support the development of clinically applicable microbiome-based biomarkers.}, }
@article {pmid41514742, year = {2025}, author = {Song, Y and Hu, Z and Yang, X and An, Y and Lu, Y}, title = {Duckweed as a Sustainable Aquafeed: Effects on Growth, Muscle Composition, Antioxidant and Immune Markers in Grass Carp.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {1}, pages = {}, pmid = {41514742}, issn = {2076-2615}, support = {2020B1111530002//Guangdong Foundation for Program of Science and Technology Research/ ; }, abstract = {Duckweed (Spirodela polyrhiza), a fast-growing aquatic plant rich in protein and bioactive compounds, offers a sustainable alternative to conventional aquafeed protein sources. This study evaluated the effects of incorporating 25-75% duckweed meal into a commercial feed on grass carp (Ctenopharyngodon idella) over a 6-week trial. Fish meal, wheat starch, and vegetable oil was added in amounts to obtain isonitrogenous and isoenergetic diets. Additionally, another grass carps were used for extended feeding until they reached approximately 1000 g, using the feed with the optimal duckweed inclusion rate (25%). Fish fed a diet consisting of 75% commercial feed and 25% duckweed meal (F75D25) exhibited significantly higher weight gain. Muscle analysis revealed increased protein content (up 15%, p < 0.05) and improved amino acid and fatty acid profiles. Liver, muscle, and blood assays showed elevated antioxidant enzyme activities (SOD up 20%, LYS up 18%; p < 0.05) and immune markers (CRP, GOT; p < 0.05), indicating enhanced health status. Transcriptomic and metagenomic analyses confirmed the upregulation of immune-related genes (e.g., SOD1, IL-6; fold change > 2, p < 0.01) and beneficial shifts in gut microbiota (e.g., increased Firmicutes). These findings highlight duckweed's potential as a nutrient-rich, health-promoting ingredient for sustainable aquaculture diets.}, }
@article {pmid41514837, year = {2026}, author = {Li, L and Zhang, H and Zhan, L and Guan, W and Hu, J and Wei, Z and Wu, W and Wu, Y and Xing, Q and Wu, J and Li, Z and Liu, Q and Chen, J and Yuan, A and Guo, D and Ouyang, K and Yang, J and Hu, W and Zhao, X}, title = {Synergistic Regulation of Bile Acid-Driven Nitrogen Metabolism by Swollenin in Ruminants: A Microbiota-Targeted Strategy to Improve Nitrogen Use Efficiency.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {1}, pages = {}, pmid = {41514837}, issn = {2076-2615}, support = {32160804//National Natural Science Foundation of China/ ; 32202762//National Natural Science Foundation of China/ ; 32360855//National Natural Science Foundation of China/ ; 32460886//National Natural Science Foundation of China/ ; 20224BAB215037//Jiangxi Provincial Natural Science Foundation/ ; 20252BAC240611//Jiangxi Provincial Natural Science Foundation/ ; 20224ACB205007//Jiangxi Provincial Natural Science Foundation/ ; 20232BBF60009//Key Project Under the Key R&D Program of Jiangxi Provincial Department of Science and Technology/ ; }, abstract = {The annual nitrogen loss from the livestock production sector poses a significant threat to the global natural environment. Therefore, it is urgent to focus on improving the nutrient utilization efficiency of ruminants and promoting the sustainable development of livestock production. Twelve 60-day-old Ganxi goats with similar body weights were selected and randomly assigned to two dietary treatment groups. The control group was fed only a basal diet, while the treatment group was supplemented with 32 mg/d of Swollenin. The experiment lasted for 30 days. At the end of the experimental period, the goats were euthanized, and their intestinal contents were collected, rapidly frozen, and stored at -80 °C for subsequent metagenomic and metabolomic analyses. In the Swollenin group, we observed changes in gut microbiota structure and significantly enhanced feed conversion efficiency compared to the control group. Notably, genera such as Bacteroides, Ruminococcus, and Bifidobacterium exhibited significantly higher abundance. Following Swollenin supplementation, the gene abundance associated with the secondary bile acid biosynthesis pathway in the intestinal tract of young goats was significantly higher. The levels of primary bile acids (BAs), including taurocholic acid, glycocholic acid, taurochenodeoxycholic acid, and glycochenodeoxycholic acid, were significantly lower, while the concentrations of secondary BAs such as ursodeoxycholic acid and deoxycholic acid were significantly higher. The abundance of nitrogen-fixing and nitrogen-assimilating genes in the gut of young goats in the Swollenin group was significantly higher. Furthermore, co-occurrence network analysis revealed a strong correlation between bile acid metabolism and nitrogen metabolism pathways. These results suggest that nutritional regulation may serve as a preventive strategy to optimize the symbiotic development of animals and their gut microbiota, ultimately improving nitrogen utilization.}, }
@article {pmid41515159, year = {2025}, author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR}, title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.}, journal = {Nutrients}, volume = {18}, number = {1}, pages = {}, pmid = {41515159}, issn = {2072-6643}, support = {na/MRA/Melanoma Research Alliance/United States ; na//Andrew Sabin Family Fellowship/ ; na//MD Anderson Melanoma Moon Shot/ ; 1P30CA016672/NH/NIH HHS/United States ; 1R01CA291965/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; }, mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Patient Reported Outcome Measures ; *Cancer Survivors/psychology ; *Diet ; Aged ; Adult ; *Immunotherapy/adverse effects ; Quality of Life ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Depression ; Anxiety ; Prospective Studies ; Exercise ; }, abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.}, }
@article {pmid41515236, year = {2025}, author = {Zhang, Z and Wang, S and Sun, G and Pan, D}, title = {Intermittent Fasting and Probiotics for Gut Microbiota Modulation in Type 2 Diabetes Mellitus: A Narrative Review.}, journal = {Nutrients}, volume = {18}, number = {1}, pages = {}, pmid = {41515236}, issn = {2072-6643}, support = {82204030//National Natural Science Foundation of China/ ; 2025M770748//China Postdoctoral Science Foundation/ ; 2024T170134//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Humans ; Blood Glucose/metabolism ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Dysbiosis ; *Fasting ; *Gastrointestinal Microbiome/physiology ; Intermittent Fasting ; *Probiotics/therapeutic use/administration & dosage ; }, abstract = {Background: Type 2 diabetes mellitus (T2DM) is a global epidemic in which gut microbiota dysbiosis contributes to impaired glucose homeostasis and chronic inflammation. Intermittent fasting (IF) and probiotic supplementation have independently demonstrated glycemic benefits in T2DM, largely through microbiota remodeling. This narrative review synthesizes evidence up to October 2025 to clarify the microbiota-dependent mechanisms of IF and probiotics, and to evaluate the biological plausibility and preliminary clinical data for their combined application in T2DM management. Methods: We conducted a comprehensive literature review of preclinical and clinical studies (PubMed, Embase, Web of Science, and Cochrane Library) examining IF regimens (primarily time-restricted feeding and 5:2 protocols) and multi-strain probiotics containing Lactobacillus and Bifidobacterium species in T2DM or relevant models. Mechanistic pathways, microbial compositional shifts, and metabolic outcomes were qualitatively synthesized, with emphasis on overlapping signaling (short-chain fatty acids, bile acids, GLP-1, and barrier function). Results: IF consistently increases Akkermansia muciniphila and, variably, Faecalibacterium prausnitzii abundance, restores microbial circadian rhythmicity, and enhances SCFA and secondary bile acid production. Multi-strain probiotics modestly reduce HbA1c (-0.3% to -0.6%) and fasting glucose, outperforming single-strain preparations. Both interventions converge on reduced endotoxaemia and improved intestinal integrity. Preclinical models indicate potential synergy, whereas the only direct human trial to date showed neutral results. Conclusions: IF and probiotics engage overlapping microbiota-mediated pathways, supporting their combined use as an adjunctive strategy in T2DM. Adequately powered randomized trials incorporating deep metagenomics, metabolomics, and hard clinical endpoints are now required to confirm additive or synergistic efficacy.}, }
@article {pmid41516078, year = {2025}, author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD}, title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.}, journal = {International journal of molecular sciences}, volume = {27}, number = {1}, pages = {}, pmid = {41516078}, issn = {1422-0067}, support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/therapy ; Middle Aged ; Biomarkers/blood ; *Artificial Intelligence ; Feces/microbiology ; Inflammation/microbiology ; Metagenomics/methods ; Treatment Outcome ; Young Adult ; Multiomics ; }, abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.}, }
@article {pmid41516169, year = {2025}, author = {Uvarova, YE and Khlebodarova, TM and Vasilieva, AR and Shipova, AA and Babenko, VN and Zadorozhny, AV and Slynko, NM and Bogacheva, NV and Bukatich, EY and Shlyakhtun, VN and Korzhuk, AV and Pavlova, EY and Chesnokov, DO and Peltek, SE}, title = {Genetic Characterisation of Closely Related Lactococcus lactis Strains Used in Dairy Starter Cultures.}, journal = {International journal of molecular sciences}, volume = {27}, number = {1}, pages = {}, pmid = {41516169}, issn = {1422-0067}, support = {075-15-2025-516//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical program for genetic technologies development for 2019-2030)/ ; FWNR- 2022-0022//Ministry of Science and Higher Education project "Study of metabolic control networks in living systems under environmental interaction, including in genetically modified organisms."/ ; }, mesh = {*Lactococcus lactis/genetics/classification/isolation & purification/metabolism ; *Cheese/microbiology ; Food Microbiology ; Phylogeny ; Genome, Bacterial ; Fermentation ; Microbiota/genetics ; }, abstract = {The complex microbiota of cheese starters plays a key role in determining the structure and flavour of the final product, primarily through their acid-forming capacity, protease activity, and exopolysaccharide synthesis. However, the specific microbial communities underlying the unique qualities of artisanal cheeses remain poorly understood. This study presents the microbiological and molecular genetic characterisation of the microbiome isolated from an artisanal cheese starter in Kosh-Agach, Altai, Russia. Metagenomic analysis of this starter revealed the presence of three bacterial genomes corresponding to those of Lactococcus lactis. Pure cultures from this starter were obtained by sequential subculture, and seventeen colonies displaying distinct characteristics on differential media were selected. Genome sequencing was performed for each colony. Bioinformatic analysis based on the rpoB gene grouped the isolates into three clusters, each corresponding to a distinct strain of Lactococcus lactis subsp. diacetilactis. This classification was further confirmed by microbiological and microscopic analyses. A notable finding was that none of the strains produced the characteristic aroma compounds of L. l. subsp. diacetilactis, namely, diacetyl and CO2. The functional properties and metabolic characteristics of this starter consortium are discussed.}, }
@article {pmid41517247, year = {2026}, author = {Shah, SMH and Volpe, S and Colonna, F and Valentino, V and De Filippis, F and Torrieri, E and Cavella, S}, title = {Combined Effect of Plasma-Activated Water, Edible Coating, and Active Packaging on Cherry Tomato Shelf-Life: Kinetics and Microbiome Approach.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41517247}, issn = {2304-8158}, support = {817936//European Commission/ ; }, abstract = {Cherry tomatoes are highly appreciated for their nutritional value but remain highly perishable due to rapid respiration and senescence. This study evaluated a multi-hurdle strategy combining plasma-activated water (PAW), sodium caseinate-based edible coating, and antioxidant active packaging to preserve minimally processed (MP) cherry tomatoes stored at 1 °C, 4 °C, and 8 °C for 15 days. Quality evolution was monitored through physical, chemical, nutritional, and microbiological parameters and described using pseudo-zero- and first-order kinetic models, with temperature dependence expressed by the Arrhenius equation. The combined treatment (prototype) slowed the degradation rates of pH, titratable acidity, total polyphenols, and antioxidant capacity, as reflected by consistently lower kinetic rate constants across all temperatures. Prototype samples showed better retention of polyphenols and antioxidant capacity, particularly at 1 °C and 4 °C, without detrimental effects on visual appearance. Metagenomic analysis revealed that the multi-hurdle treatment reshaped the microbial community, reducing the relative abundance of potentially problematic taxa such as Acinetobacter johnsonii and limiting the occurrence of antimicrobial resistance (AMR) genes at the end of storage. This study provides the first integrated assessment of PAW, edible coating, and antioxidant active packaging as a synergistic multi-hurdle strategy, demonstrating their combined ability to extend shelf life while modulating the microbiome and resistome of minimally processed cherry tomatoes.}, }
@article {pmid41517713, year = {2026}, author = {Sun, Z and Xu, K and Huo, L and Zhang, X and Chen, B}, title = {Family psittacosis cluster diagnosed by metagenomic next-generation sequencing in Hangzhou City, Eastern China: A case series.}, journal = {Medicine}, volume = {105}, number = {2}, pages = {e47139}, pmid = {41517713}, issn = {1536-5964}, mesh = {Humans ; *Psittacosis/diagnosis/drug therapy/microbiology ; *Chlamydophila psittaci/genetics/isolation & purification ; China ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Female ; Metagenomics/methods ; Adult ; Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; Animals ; Moxifloxacin/therapeutic use ; }, abstract = {RATIONALE: Psittacosis, a human infection caused by Chlamydia psittaci (C psittaci), is often underdiagnosed due to its nonspecific presentation and the limitations of conventional diagnostic methods. This diagnostic challenge can lead to missed outbreaks and delays in appropriate treatment. This report aims to highlight the critical role of metagenomic next-generation sequencing (mNGS) in rapidly identifying C psittaci and facilitating the investigation of a family cluster, thereby providing a clearer rationale for its application in similar scenarios.
PATIENT CONCERNS: In this study, we report a family cluster of psittacosis cases. All affected individuals had a history of direct or indirect contact with backyard poultry during a visit to a rural village before symptom onset. The index case (Case 1) presented with fever and chills and was subsequently hospitalized. The 2 secondary cases (Cases 2 and 3) exhibited similar clinical manifestations and were treated at the same hospital, where doctors promptly collected specimens for testing based on their shared medical history.
DIAGNOSES: The diagnosis of C psittaci pneumonia was confirmed by mNGS analysis of bronchoalveolar lavage fluid obtained from 3 patients through bronchoscopy.
INTERVENTIONS: Combination therapy involving intravenous moxifloxacin and doxycycline was administered for the treatment of infectious pneumonia.
OUTCOMES: Following timely diagnosis and targeted antimicrobial therapy, all 3 patients attained full clinical recovery.
LESSONS: C psittaci pneumonia presents with nonspecific clinical and radiographic features that are indistinguishable from other causes of community-acquired pneumonia. mNGS markedly enhances diagnostic accuracy and shortens the time to diagnosis, proving to be an invaluable tool for early identification and management of outbreaks, particularly in patients with avian or poultry exposure.}, }
@article {pmid41517763, year = {2026}, author = {Zhu, Q and Liu, Q}, title = {Early diagnosis of Lemierre syndrome using targeted next-generation sequencing combined with metagenomics capture: A case report and literature review.}, journal = {Medicine}, volume = {105}, number = {2}, pages = {e46988}, pmid = {41517763}, issn = {1536-5964}, support = {2022KC22269//Project of Xuzhou Key Research and Development Program/ ; }, mesh = {Humans ; Female ; *Lemierre Syndrome/diagnosis/microbiology/therapy ; Adolescent ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Fusobacterium necrophorum/isolation & purification/genetics ; Early Diagnosis ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {RATIONALE: Lemierre syndrome (LS) is a rare but life-threatening complication of acute oropharyngeal infections. It is characterized by septic thrombophlebitis of the internal jugular vein and subsequent metastatic abscess formation. The most common causative pathogen of LS is Fusobacterium necrophorum (FN). This paper presents the case of a 17-year-old female patient with LS, in whom FN was rapidly detected and LS was diagnosed using targeted next-generation sequencing (tNGS) combined with metagenomics capture (MetaCAP). This approach enabled timely detection of FN and guided appropriate treatment.
PATIENT CONCERNS: The patient, a female 17-year-old student, experienced a fever after catching a cold, with a peak temperature of 39.8 °C on May 22, 2024, accompanied by chills and shivering, sore throat, right chest pain, back pain, cough, and hemoptysis.
DIAGNOSES: The patient was initially diagnosed with non-severe community-acquired pneumonia at admission on May 26, 2024. She was finally diagnosed with LS after FN was detected using bronchoalveolar lavage fluid tNGS combined with serum MetaCAP.
INTERVENTIONS: The patient received targeted antimicrobial therapy and thorough thoracic drainage in the shortest time after being definitely diagnosed with LS using tNGS and MetaCAP technologies.
OUTCOMES: The clinical symptoms of the patient were significantly improved. A chest computed tomography scan on July 15, 2024 indicated complete resolution of exudates and solid lesions in both lungs.
LESSONS: This case underscores the significant role of tNGS combined with MetaCAP in the early detection of FN and timely diagnosis of LS, systematically explores the epidemiology, clinical features, diagnosis and treatment of LS, thus providing a reference for clinicians to rapidly diagnose and treat LS.}, }
@article {pmid41518158, year = {2026}, author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S}, title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.}, journal = {Aging cell}, volume = {25}, number = {2}, pages = {e70365}, pmid = {41518158}, issn = {1474-9726}, support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R + D + I/ ; //ERDF/ESF/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; *Aging ; Comorbidity ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; }, abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.}, }
@article {pmid41518205, year = {2026}, author = {Ren, H and Jiao, X and Wang, R and Liu, J and Wu, D and Liu, J and Wang, M and Shangguan, W and Cao, S and Chen, P}, title = {DSN-based host DNA depletion for simultaneous detection of DNA and RNA pathogens in next-generation sequencing.}, journal = {Letters in applied microbiology}, volume = {79}, number = {1}, pages = {}, doi = {10.1093/lambio/ovaf145}, pmid = {41518205}, issn = {1472-765X}, support = {GZL202309043419000025//Shenzhen Science and Technology Program/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Bacteria/genetics/isolation & purification ; DNA, Bacterial/genetics ; *Deoxyribonucleases/metabolism ; *DNA/genetics ; }, abstract = {In recent years, nucleic acid sequencing has been increasingly used in clinical pathogen detection. Typically, 20-100 million metagenomic reads are generated per sample, but 90%-99% originate from host nucleic acids, leaving only 1-2 million for microbial identification-potentially compromising detection sensitivity. Here, we present a novel duplex-specific nuclease (DSN)-based method to reduce host nucleic acid content in next-generation sequencing. Validated using mock communities and clinical samples, it yielded a 2- to 3-fold increase in pathogen RPM (reads per million) in metagenomic NGS (mNGS) and a more pronounced 3- to 10-fold improvement in probe-based targeted NGS (tNGS). Optimal performance was achieved with: 65°C annealing temperature; 2 μg Cot-1 DNA and 50 μmol rProbe as driver DNA; and 150 mmol·L-1 tetramethylammonium chloride (TMAC)-using 25 ng input nucleic acid for library preparation. The DSN workflow adds less than 30 min to library preparation and enables rapid, low-loss microbial enrichment, enhancing pathogen detection in clinical NGS. While effective, its host depletion efficiency could be further improved by expanding driver DNA coverage to additional abundant human genomic regions, such as LINE and LTR repeats.}, }
@article {pmid41518728, year = {2026}, author = {Sun, J and Lyons, R and Weigh, KV and Lieske, S and Newsham, KK and Hopkins, DW and Dennis, PG}, title = {Putative drivers of maritime Antarctic soil resistomes in the early 21st century: A baseline for monitoring environmental change and human influence.}, journal = {The Science of the total environment}, volume = {1014}, number = {}, pages = {181361}, doi = {10.1016/j.scitotenv.2026.181361}, pmid = {41518728}, issn = {1879-1026}, mesh = {Antarctic Regions ; *Soil Microbiology ; *Environmental Monitoring/methods ; Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Humans ; }, abstract = {Antibiotic resistance genes (ARGs) are present in all ecosystems and encode the defences that microorganisms have naturally evolved to defend themselves against antimicrobial agents. The use and synthesis of antibiotics by humans, however, has led to a proliferation of ARGs, resulting in their consideration as emerging environmental pollutants, even in some of the most pristine terrestrial ecosystems on Earth. Here we used shotgun metagenomics to characterise the abundance and diversity of ARGs in 29 maritime Antarctic soils collected in the 2007-2008 austral summer that varied in edaphic conditions and levels of human visitation. In total, 1831 ARGs were identified, spanning 29 naturally occurring ARGs that confer resistance to either single or multiple drug classes, such as glycopeptide, fluoroquinolone and tetracycline. The ARG profiles were not significantly associated with predicted levels of human visitation and harboured novel and potentially ancient ARGs, suggesting that these soils were relatively pristine. Furthermore, we observed that the abundance and diversity of ARGs was strongly associated with soil pH and mean annual surface air temperature (MASAT), as well as moisture content, C:N ratio, DOC and Mg concentration, albeit to a lesser extent. Our study provides a useful baseline for future studies, greatly expands the geographical coverage of Antarctic soil resistomes, and highlights putative environmental drivers of ARGs for the early 21st century including pH and MASAT, the latter of which is predicted to rise towards the end of this century.}, }
@article {pmid41518802, year = {2026}, author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG}, title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141026}, doi = {10.1016/j.jhazmat.2026.141026}, pmid = {41518802}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Nitrosamines/metabolism ; Bacteria/metabolism/genetics ; Multiomics ; Triazines ; }, abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.}, }
@article {pmid41518812, year = {2026}, author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Yu, Z and Liu, J}, title = {Urban habitat types modulate soil contamination and bacterial functional traits through antibiotic resistance genes and metal(loid) interactions.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141092}, doi = {10.1016/j.jhazmat.2026.141092}, pmid = {41518812}, issn = {1873-3336}, mesh = {*Soil Pollutants/analysis ; *Soil Microbiology ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; *Metals/analysis ; Cities ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Urban soils are important reservoirs for contaminants, including metal(loid)s and antibiotic resistance genes (ARGs), posing threats to ecosystem function and public health. However, the variation in these contaminants across urban habitat types remains poorly understood. This study integrated shotgun metagenomics, 16S rRNA sequencing, quantitative PCR, and multivariate modeling to investigate the co-distribution of ARGs, metal(loid)s, and bacterial functional traits across six urban habitat types: afforestation areas, croplands, orchards, parks, ruderals, and semi-natural remnants. Our findings revealed habitat-specific contamination patterns, with croplands and orchards showing the highest ARG risks and strong co-selection signals mediated by mobile genetic elements (MGEs) and biocide/metal resistance genes (BMRGs). In contrast, ruderals and remnants exhibited significantly lower ARG abundances (<1.2 × 10[4] copies/g) and metal(loid) concentrations (Cd < 0.05 mg/kg and Pb < 10 mg/kg), as well as nearly 50 % fewer plasmid-associated ARGs, indicating reduced horizontal gene transfer potential. Integrative modeling identified functional genes and BMRGs as the most consistent drivers of MGE dynamics, while MGEs showed limited direct influence on ARGs, suggesting that mobility alone may not explain the spread of resistance in urban soils. Metagenomic analyses linked ARG profiles to disruptions in bacterial functions essential for nutrient cycling and ecosystem services, indicating that resistance risks in urban soils are closely tied to declines in functional capacity. A substantial overlap in ARGs between orchard soils and fruits underscored the potential for soil-to-human transmission. These results provide a cross-habitat framework that links contaminant profiles, resistance mobilization, and functional consequences in urban soils.}, }
@article {pmid41518832, year = {2026}, author = {Hellwig, P and Seick, I and Meinusch, N and Benndorf, D and Wiese, J and Reichl, U and Heyer, R}, title = {Molecular community data meets anaerobic digestion Model 1 (ADM1) - a study about the correlation between metagenome-centric metaproteomics data of a two-step full-scale anaerobic digester and its corresponding mathematical model.}, journal = {Water research}, volume = {292}, number = {}, pages = {125272}, doi = {10.1016/j.watres.2025.125272}, pmid = {41518832}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Metagenome ; *Bioreactors/microbiology ; Models, Theoretical ; Proteomics ; }, abstract = {Advanced models, such as the Anaerobic Digestion Model No 1 (ADM1), are essential for operating, planning, and optimizing renewable energy production in anaerobic digester plants (AD-P)s. In this study, the ADM1da model was employed to simulate a two-step AD-P in an industrial setting. The ADM1da model is an extended ADM1 model for mixed substrates, accounting for substrate-specific disintegration, temperature effects, biogas-related mass reduction, and mineral solids content. ADM1 models can represent the anaerobic digestion processes, although the biological assumptions are coarse and reflect the knowledge and available tools for microbial communities at the time of development. Meanwhile, metagenome-centric metaproteomics provides deeper insight into the metabolic activities of microbial communities in AD-Ps. Until now, this data has not been integrated with ADM1 models. The objective of this study is to assess the feasibility of incorporating metagenome-centric metaproteome data into the ADM1 model. In a novel approach, 49 high-quality metagenome-assembled genomes (MAGs) with associated protein abundances were systematically classified into the trophic groups defined by the ADM1 model using specifically developed grouping rules. Abundances of MAGs were more variable than the process parameter-dependent dynamics of ADM1. Depending on the grouping rules, 32%-78% of all high-quality MAGs were successfully categorized into ADM1 trophic groups. However, some MAGs, e.g., Methanotrix, were multifunctional (acetoclastic and hydrogenotrophic methanogenesis) and required assignment to multiple groups. Unfortunately, more precise grouping rules resulted in greater discrepancies between metaproteomics data and the model. Additionally, 22% of the MAGs could not be assigned. The metagenome-centric metaproteome data imply that ADM1 probably needs extension to cover the observed microbial function of syntrophic acetate oxidizers, hydrolytic bacteria, lactate- and ethanol-fermenting bacteria, and mortality by phages. It was also observed that changes in process parameters, such as those caused by seasonal feeding, led to significant changes in the protein abundance Integrating metagenome-centric metaproteomic data into ADM1 trophic groups was shown to be feasible.Some trophic groups detected in protein data but not implemented in ADM1 imply the need for data-driven model enhancement and approval. In the future, more accurate models considering molecular data could support a deeper understanding of microbial community dynamics in AD-Ps.}, }
@article {pmid41519162, year = {2026}, author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P}, title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf283}, pmid = {41519162}, issn = {1938-291X}, support = {NP104- 3020-32000-20-00D//USDA/ ; }, abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.}, }
@article {pmid41519314, year = {2026}, author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K}, title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111198}, doi = {10.1016/j.ygeno.2026.111198}, pmid = {41519314}, issn = {1089-8646}, mesh = {Animals ; *Hyperlipidemias/metabolism/genetics ; *Circadian Rhythm/genetics ; *Liver/metabolism ; Mice ; *Gastrointestinal Microbiome ; Male ; Diet, High-Fat/adverse effects ; Lipid Metabolism/genetics ; Transcriptome ; Mice, Inbred C57BL ; Multiomics ; }, abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.
RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.
DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.
CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.}, }
@article {pmid41519702, year = {2026}, author = {Zhang, Y and Tian, J and Xu, Y}, title = {Endogenous endophthalmitis secondary to neisseria meningitidis: a case report.}, journal = {BMC ophthalmology}, volume = {26}, number = {1}, pages = {16}, pmid = {41519702}, issn = {1471-2415}, support = {No.20241205//Medical Science Research Project of Hebei/ ; }, abstract = {BACKGROUND: Bacterial endogenous endophthalmitis (BEE) represents a rare but severe ophthalmological emergency which caused by hematogenous spread of bacterial infection. As its characteristics of insidious onset and rapid progression, BEE may lead to vision loss or even enucleation without immediate treatments. In recent years, with increasing numbers of immunosuppression and prevalence of resistant strains, incidence of BEE has risen, and its diagnosis and treatment face new challenges.
CASE PRESENTATION: A 15-year-old female patient was admitted to department of ophthalmology due to blurred vision and photophobia and lacrimation in the left eye for two days, and was first diagnosed as endophthalmitis and secondary glaucoma. During the diagnosis and treatment process, after smear culture of left chamber and vitreous aspirates, as well as the metagenomic next-generation sequencing (mNGS), final diagnosis of infectious endophthalmitis secondary to Neisseria meningitidis (N. meningitidis) was decided and a targeted treatment plan was developed. After intraocular injection and systemic antibiotic therapy, the patients was discharged after full control of the infection and improved endophthalmitis. Combined with literature review, this study discussed the application value of mNGS in diagnosing endogenous endophthalmitis.
CONCLUSION: mNGS shows significant value in the diagnosis of endogenous endophthalmitis in terms of improving positive rate of pathogen detection in intraocular fluid of infectious endophthalmitis and providing strong support for clinical treatments. The successful treatment of this case further confirms the promise of mNGS in ophthalmic infectious diseases. With the continuous progress of technology, mNGS is expected to be popularized and applied in more medical institutions to benefit more patients.}, }
@article {pmid41519950, year = {2026}, author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J}, title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {41519950}, issn = {1530-0447}, abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.
METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.
RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.
CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.
IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.}, }
@article {pmid41519985, year = {2026}, author = {Bodhe, I and Gokuladoss, V}, title = {Sustainable CO2 valorization for PHB production towards circular economy: metagenomic insights on enriched indigenous microbial cultures.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {1552}, pmid = {41519985}, issn = {2045-2322}, abstract = {UNLABELLED: This study developed resilient mixed microbial cultures (MMCs) from diverse indigenous sources 2 through strategic pretreatment and enrichment, robust conversion of CO2 and bicarbonate into volatile fatty acids (VFAs) and polyhydroxybutyrate (PHB) was achieved. This article establishes a sustainable biotechnological platform, transforming waste CO2 into valuable bio-products and biodegradable polymers, thereby bridging a circular bioeconomy approach. In Phase I, CO2 was converted into VFAs (2.017, 2.307, 3.243, and 3.467 g/L) by anaerobic MMC and PHB (3.2% (0.082 g/L)) by aerobic cultures, respectively.The reduction in pH was observed to 3.45 ± 0.22 due to pretreatment methods, indicated acetogenic dominance. In phase II, VFA was recirculated for PHB production (6.5 ± 0.24%) and molecular confirmation was done using FTIR and NMR.ted The anaerobic MMC achieved a CO2 reduction efficiency of 70 ± 1.78%, while aerobic cultures showed 45 ± 1.26%, contributing to the production of biodegradable PHB, thus closing loop towards circular bio-economy. This study also shows carbon balance and thermodynamic feasibility of converting CO2 into PHB via microbial fermentation, highlighting the energy requirements and process efficiency. Metagenomic analysis of microbial consortia, using 16S rRNA (V3-V4) sequencing, identified key bacteria for CO2 bioconversion. Anaerobic genera like Pseudomonas and Halomonas dominated VFA production, while aerobic bacteria such as Brevundimonas, Achromobacter were predominant in PHB synthesis. KEGG analysis predicts genetic pathways for CO2 fixation.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-26791-7.}, }
@article {pmid41521100, year = {2026}, author = {Zhu, NQ and Zhang, QB and Wang, ZX and Li, RD}, title = {Bacteroides in Bile Detected by Metagenomic Next-Generation Sequencing: Potential Novel Indicator for Early Allograft Dysfunction After Liver Transplantation.}, journal = {Transplantation proceedings}, volume = {58}, number = {1}, pages = {107-113}, doi = {10.1016/j.transproceed.2025.11.001}, pmid = {41521100}, issn = {1873-2623}, mesh = {Humans ; *Liver Transplantation/adverse effects ; Male ; *Bacteroides/isolation & purification/genetics ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Bile/microbiology ; Adult ; Risk Factors ; *Metagenomics/methods ; *Postoperative Complications/microbiology ; Retrospective Studies ; Allografts/microbiology ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) is an effective method for the detection of microorganisms. Early allograft dysfunction (EAD) is a common complication after liver transplantation. The association between early postoperative microorganisms in bile and EAD is unclear, so we evaluated the association of microorganisms and other potential risk factors with EAD.
METHODS: A total of 100 patients who underwent orthotopic liver transplantation with biliary T tube placement in Huashan Hospital Fudan University from March 2021 to July 2022 were studied. Clinical data, the occurrence of EAD, and bile microorganisms' information detected by mNGS were collected.
RESULTS: EAD occurred in 22 recipients (22%). Patients with EAD had a longer length of postoperative hospital stay. Bacteroides spp. detected by mNGS in bile was identified as an independent risk factor for EAD. Also, operation time, the MELD score of the recipient, and donor AST level were also independent risk factors for EAD.
CONCLUSION: Bacteroides spp. detected by mNGS in bile after liver transplantation was identified as an independent risk factor for EAD, which may reflect the translocation of intestinal flora into the biliary tract and may serve as a potential early warning indicator of poor quality of the donor liver. Recipients with EAD had longer LOS, which may indicate a poor short-term prognosis.}, }
@article {pmid41521588, year = {2026}, author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I}, title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70117}, doi = {10.1111/jfd.70117}, pmid = {41521588}, issn = {1365-2761}, support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; }, abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.}, }
@article {pmid41521629, year = {2026}, author = {Shelton, BR and Larrere, J and Yusta Belsham, D and Omacini, M and Argüelles-Moyao, A and Buscardo, E and Alves da Silva, DK and Zhao, X and Nakamura, N and Ángeles-Argáiz, R and Paz, C and Matías-Ferrer, N and Hart, MM}, title = {Fungal ecology in the age of 'omics.}, journal = {The New phytologist}, volume = {250}, number = {2}, pages = {822-833}, pmid = {41521629}, issn = {1469-8137}, mesh = {*Fungi/genetics/physiology ; *Ecology ; *Genomics ; *Plants/microbiology ; *Computational Biology ; }, abstract = {The advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its interactions with the macroscopic world, than ever before. However, fungal studies that use meta'omic technologies have been sparse compared with bacterial and plant-focused studies. In this review, we highlight the ways that meta'omics can help to address pressing questions in belowground plant-fungal ecology, show consistencies that are emerging - and discrepancies that still exist - among analysis pipelines, and advocate for reporting standards that will allow meta'omic research to more fully benefit fungal ecology.}, }
@article {pmid41522492, year = {2026}, author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R}, title = {Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2610588}, pmid = {41522492}, issn = {2000-2297}, abstract = {BACKGROUND: The oral cavity is a known reservoir of antibiotic resistance genes (ARGs), but little is known about their subgingival distribution across health states and regions.
OBJECTIVE: This study aimed to characterize and compare the subgingival resistome and mobile genetic elements (MGEs) in healthy subjects (HS) and periodontitis patients (PP) from Belgium, Chile, Peru and Spain.
DESIGN: Subgingival samples pooled from the deepest site of each quadrant of 40 HS and 40 PP were analyzed via shotgun metagenomic sequencing. After human DNA depletion, the microbial composition was assessed with MetaPhlAn 4.0; ARGs were identified using MEGAHIT and AMRFinderPlus; and MGEs with MGEfinder.
RESULTS: ARG richness was significantly higher in PP (mean 3.98) than in HS (2.15). PP from Peru showed more ARGs than HS from Chile and Spain. In total, 28 ARGs were found, conferring resistance to eight antibiotic classes. β-lactam, tetracycline and aminoglycoside resistance were more abundant in PP. Macrolide resistance was lower in Chilean samples than in Peruvian and Spanish ones. Additionally, 99 MGE-associated genes were detected, with 16 differing by diagnosis and 78 by country.
CONCLUSIONS: Subgingival resistome profiles vary significantly by periodontal status and geography, underscoring the influence of clinical and regional factors on antimicrobial resistance in the oral microbiome.}, }
@article {pmid41522496, year = {2026}, author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S}, title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20566}, pmid = {41522496}, issn = {2167-8359}, mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; }, abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.}, }
@article {pmid41522572, year = {2025}, author = {Pfliegler, WP and Németh, B and Bodnár, V and Pusztahelyi, T and Carbone, I and Pócsi, I}, title = {Global population genomics redefines domestication and clinical diversity in the Aspergillus flavus-oryzae complex.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e172343}, pmid = {41522572}, issn = {2210-6340}, abstract = {Aspergillus flavus is a globally important human pathogen and agricultural contaminant, while its domesticated relative A. oryzae is widely used in food fermentation and biotechnology. Despite their importance, the evolutionary relationship, population structure and domestication history of these fungi remain unresolved. Here, we present the first global population genomic analysis of 639 A. flavus and A. oryzae isolates from clinical, environmental and food-fermentation sources across multiple continents. Our analyses reveal a complex evolutionary landscape comprising well-separated clades interspersed with highly admixed mosaic groups and potential evidence for multiple independent domestication events giving rise to A. oryzae. Clinical A. flavus isolates are distributed across several clades and mosaic groups, some overlapping with fermentation strains, highlighting an apparent role of domestication and admixture in shaping pathogen diversity. These results challenge current species boundaries and provide a framework for understanding evolutionary history, taxonomy and pangenomic architecture in these fungi, with broad implications for pathogenicity, food safety, biocontrol and metagenomic surveillance.}, }
@article {pmid41523161, year = {2025}, author = {Sanchez, G and Simakov, O and Nyholm, S and Nishiguchi, M and McFall-Ngai, M and Lami, R and Heath-Heckman, E and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {351}, pmid = {41523161}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a specimen of Sepioteuthis lessoniana (bigfin reef squid; Mollusca; Cephalopoda; Myopsida; Loliginidae). The genome sequence has a total length of 5,056.23 megabases. Most of the assembly (86.4%) is scaffolded into 44 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 28,970 protein-coding genes.}, }
@article {pmid41523242, year = {2025}, author = {Qi, W and Tian, L and Li, Z and Xu, J and Wang, T}, title = {Pathogen spectrum and management strategies for opportunistic infections in lung cancer in the immunotherapy era: recent advances from fungi to mycobacteria.}, journal = {American journal of cancer research}, volume = {15}, number = {12}, pages = {5140-5167}, pmid = {41523242}, issn = {2156-6976}, abstract = {Lung cancer is one of the most common cancers and the leading cause of cancer death worldwide. Opportunistic infections (OI) are increasingly recognized in this population due to disease-related immune dysfunction and treatment-induced immunosuppression. Compared with the chemotherapy era, the use of immune checkpoint inhibitors and targeted agents has shifted the OI profile. Pneumocystis jirovecii pneumonia (PJP) and invasive pulmonary aspergillosis (IPA) are reported more often in older adults and patients with lymphopenia, while tuberculosis (TB) and nontuberculous mycobacteria (NTM) cluster in those with structural lung disease (e.g., bronchiectasis, cavities) and prolonged immunosuppression. High-risk features include absolute lymphocyte count <500/µL, corticosteroids ≥20 mg prednisone-equivalent for ≥4 weeks, airway obstruction, prior TB, chronic obstructive pulmonary disease/interstitial lung disease (ILD), and recent broad-spectrum antibiotics. Diagnosis should integrate high-resolution computed tomography (HRCT) patterns (e.g., diffuse ground-glass for PJP; nodules with halo sign for IPA), microbiology [bronchoalveolar lavage fluid (BALF) culture/microscopy, galactomannan (GM)/β-D-glucan (BDG)], and metagenomic next-generation sequencing, interpreted against host factors and treatment timeline, while carefully distinguishing immune-related pneumonitis and TKI-associated ILD. Prophylaxis with TMP-SMX is recommended for high-risk patients; voriconazole (or isavuconazole) is first-line for IPA with attention to drug-drug interactions; TB/NTM regimens require coordination with anticancer therapy, especially where rifamycins interact with TKIs. Vaccination (influenza, pneumococcus, zoster) and antimicrobial stewardship are essential. Future work should validate risk scores prospectively and clarify microbiome-immunotherapy-infection relationships.}, }
@article {pmid41523323, year = {2026}, author = {Chen, J and Wu, Y and Tang, J and Guo, J and Zhai, Y}, title = {Pertussis is identified among common respiratory diseases: A case report.}, journal = {SAGE open medical case reports}, volume = {14}, number = {}, pages = {2050313X251411124}, pmid = {41523323}, issn = {2050-313X}, abstract = {Pertussis, caused by Bordetella pertussis, is increasingly recognized in adults who often present with atypical symptoms, leading to underdiagnosis. We report a case of a 64-year-old woman with a persistent cough and sore throat initially treated as refractory community-acquired pneumonia. Despite empirical antibiotic therapy, her symptoms persisted. Conventional diagnostic tests, including sputum and bronchoalveolar lavage fluid cultures, were negative. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Bordetella pertussis with high sequence coverage (7497 reads). The patient showed no clinical improvement with azithromycin, prompting a switch to trimethoprim-sulfamethoxazole, after which she improved and was discharged to complete a 14-day course. At 1-month follow-up, she was asymptomatic with resolved radiographic findings. This case highlights that pertussis can mimic refractory pneumonia in adults without typical features such as whooping cough, and underscores the diagnostic value of metagenomic next-generation sequencing when conventional methods fail. Clinicians should consider pertussis in adults with prolonged cough unresponsive to standard community-acquired pneumonia therapy and be aware of potential macrolide resistance, which may necessitate alternative antibiotics like trimethoprim-sulfamethoxazole.}, }
@article {pmid41523444, year = {2025}, author = {Hofmann, SP and Bieri, U and von Stauffenberg, F and Schneider, S and Singer, G and Greiner, M and Hefermehl, LJ}, title = {Atypical Polypoid Bladder Lesion Mimicking Urothelial Carcinoma in a Young Male: A Case Report About a Possible Autoimmune-Triggered Granulomatous Inflammation With Secondary Colonization.}, journal = {Cureus}, volume = {17}, number = {12}, pages = {e98879}, pmid = {41523444}, issn = {2168-8184}, abstract = {Gross hematuria is a critical clinical symptom requiring thorough diagnostic evaluation, particularly due to its association with urothelial carcinoma. However, other differential diagnoses must also be considered, including renal carcinoma, infection, urolithiasis, and autoimmune disease. We report the case of a 28-year-old male presenting with gross hematuria, flank pain, and dysuria. Imaging revealed bladder wall thickening and bilateral narrowing of the renal pelvis. Cystoscopy showed a large, polypoid lesion suggestive of urothelial carcinoma. Transurethral resection (TUR-B) was performed; however, histological analysis revealed granulation tissue with inflammatory infiltrates, multinucleated giant cells, and necrosis but no evidence of malignancy. Metagenomic sequencing identified Peptoniphilus sp. SAHP1, Anaerococcus mediterraneensis, and Trichomonas vaginalis, though their pathogenic role remained uncertain. Shortly after, the patient developed systemic inflammatory symptoms, including exanthema and gingivostomatitis. Biopsy of skin lesions showed leukocytoclastic vasculitis, and serologic testing yielded borderline myeloperoxidase-specific antineutrophil cytoplasmic antibody (MPO-ANCA) positivity. Under corticosteroid therapy, all symptoms, including the bladder lesion, regressed completely. This case highlights a rare constellation of findings mimicking urothelial carcinoma, ultimately pointing to a probable autoimmune vasculitic process with possible secondary microbial colonization. It underscores the diagnostic challenges posed by atypical presentations and the need for integrative interpretation of clinical, histological, and molecular findings in complex cases.}, }
@article {pmid41524715, year = {2026}, author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S}, title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {41524715}, issn = {2050-084X}, support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; }, mesh = {*Dysbiosis/microbiology ; *Microbial Interactions ; Humans ; *Microbiota ; Metagenomics ; Models, Biological ; }, abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.}, }
@article {pmid41524778, year = {2026}, author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK}, title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {105}, pmid = {41524778}, issn = {1432-072X}, support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; }, }
@article {pmid41524860, year = {2026}, author = {Parab, C and Yadav, KD and Prajapati, V}, title = {Metagenomic Insights into Microbial Community Succession and its Functional Changes during Natural Fermentation of Food Waste.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {3}, pages = {2053-2081}, pmid = {41524860}, issn = {1559-0291}, mesh = {*Fermentation ; *Metagenomics ; *Microbiota ; *Bacteria/genetics/metabolism ; *Food ; Food Loss and Waste ; }, abstract = {Food waste is a global concern, necessitating sustainable management strategies. While fermentation offers a promising approach to valorizing food waste, studies about microbial dynamics and functionality assessment of semi-controlled naturally fermented food waste are still seldom. This study employed whole-genome metagenomic sequencing to investigate the microbial succession and functional pathways during natural fermentation of food waste over 15 days. Physicochemical analysis revealed that pH decreased from 5.20 to 4.32 on day 3 and then neutralized. Protein, lipids, and carbohydrate were in the range of 4.03-4.90%, 9.99-17.78%, and 85.44-77.84%, respectively. Taxonomic profiling revealed clear community restructuring from an initially diverse consortium dominated by Enterobacter, Klebsiella, Pseudomonas, and Acinetobacter (collectively > 45% relative abundance at day 0) to a highly specialized lactic acid bacteria (LAB) community (> 80% by day 15). Lactobacillus helveticus and Limosilactobacillus panis emerged as the late-stage co-dominant species, together accounting for 60-75% of the total reads. Functional annotation based on the PFAM, eggNOG, GO, and EC databases revealed a progressive reduction in gene family richness and metabolic breadth, with early samples being enriched in carbohydrate-active enzymes, membrane transporters, and amino acid metabolism pathways. By contrast, late-stage communities were dominated by LAB-associated fermentative functions, including lactate and acetate production, stress-response modules, and transport systems supporting acid tolerance, driven mainly by Lactobacillus, Weissella, Streptococcus, Gluconobacter, Aeromonas, Saccharomyces, Klebsiella, and Cronobacter. These findings provide insights into the microbial dynamics and functional adaptations during natural fermentation of food waste, contributing to the development of optimized waste valorization strategies.}, }
@article {pmid41524878, year = {2026}, author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M}, title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.}, journal = {Annals of surgical oncology}, volume = {33}, number = {4}, pages = {3203-3213}, pmid = {41524878}, issn = {1534-4681}, mesh = {Humans ; *Esophageal Neoplasms/therapy/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality ; Prognosis ; Survival Rate ; *Esophagectomy/mortality ; Aged ; Neoadjuvant Therapy/mortality ; Follow-Up Studies ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Bacteria/genetics/isolation & purification ; }, abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.
PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.
RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.
CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.}, }
@article {pmid41524921, year = {2026}, author = {Nayab, GE and Ur Rahman, R and Hanan, F and Khan, I and Fahim, M}, title = {Metagenomic Exploration of the Bacteriome Reveals Natural Wolbachia Infections in Yellow Fever Mosquito Aedes aegypti and Asian Tiger Mosquito Aedes albopictus.}, journal = {Current microbiology}, volume = {83}, number = {2}, pages = {133}, pmid = {41524921}, issn = {1432-0991}, mesh = {Animals ; *Aedes/microbiology/classification ; *Wolbachia/genetics/classification/isolation & purification ; Phylogeny ; Pakistan ; Metagenomics ; *Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; *Microbiota ; *Metagenome ; Electron Transport Complex IV/genetics ; DNA, Bacterial/genetics ; }, abstract = {Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present in various insect genera, including Aedes, has demonstrated promising results globally. In this study we collected Aedes species and investigated its microbiomes with a particular focus on identifying the endosymbiont Wolbachia. Mosquitoes were collected via Gravitraps in the Peshawar region of Pakhtunkhwa province in the northwest of Pakistan. The identity of the mosquitoes was initially confirmed through morphological characters followed by molecular identification using species-specific Cytochrome oxidase I (COI) primers. The DNA from female Ae. aegypti and Ae. albopictus was further subjected to 16 S rRNA sequencing. The hypervariable regions V3/V4 of 16 S rRNA were used for sequencing using the paired-end Illumina MiSeq platform. The phylogenetic analysis of the COI gene in our samples demonstrated similarity to Aedes species previously documented in Pakistan. In comparative analysis of the microbiomes, Ae. albopictus was found to harbor 921 bacterial species, while Ae. aegypti only had 239 species. The metagenomic analysis revealed single-strain Wolbachia pipientis infection in Ae. aegypti, while Ae. albopictus harbored a double-strain infection involving a supergroup A strain (referred to as Wolbachia pipientis in 16 S EzBioCloud database) and a supergroup B strain (referred to as Wolbachia bourtzisii in16S EzBioCloud database).}, }
@article {pmid41524947, year = {2026}, author = {Shafi, Z and Shahid, M and Singh, R}, title = {Food-borne bacterial pathogens: emerging approaches in detection and prevention.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {109}, pmid = {41524947}, issn = {1432-072X}, mesh = {*Food Microbiology/methods ; *Foodborne Diseases/prevention & control/microbiology/diagnosis ; *Bacteria/isolation & purification/genetics/classification/pathogenicity ; Humans ; Food Safety ; Computational Biology/methods ; }, abstract = {Food-borne bacterial pathogens remain a major public health concern, causing extensive illness and economic losses worldwide. Conventional detection methods are often slow and insufficient for identifying viable but non-culturable pathogens. Recent microbiological, biotechnological and bioinformatic advances have markedly improved food safety monitoring. Rapid molecular assays (PCR, qPCR, microarrays), next-generation sequencing, metagenomics, and emerging CRISPR-based diagnostics enable faster and more accurate pathogen detection and outbreak tracing. Bioinformatic tools-including genomic databases, phylogenetics, and machine-learning models-support predictive risk assessment and real-time surveillance. Preventive innovations such as bacteriophages, probiotics, antimicrobial peptides, nanotechnology-based interventions, and engineered microbes provide sustainable alternatives to chemical preservatives. Key challenges include variability across food matrices, biosafety considerations, and limited integration of multi-omics approaches into routine workflows. Overall, these emerging strategies offer improved precision and responsiveness for detecting and preventing food-borne bacterial pathogens.}, }
@article {pmid41525137, year = {2026}, author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW}, title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41525137}, issn = {2057-5858}, mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; Secondary Metabolism/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Genome, Bacterial ; Sequence Analysis, DNA ; }, abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.}, }
@article {pmid41525322, year = {2026}, author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI}, title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013883}, pmid = {41525322}, issn = {1553-7358}, support = {S10 OD032203/OD/NIH HHS/United States ; UH3 AG064704/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Aging/genetics/physiology ; *Longevity/genetics/physiology ; Aged ; Male ; Computational Biology ; Female ; Aged, 80 and over ; Feces/microbiology ; Metagenome/genetics ; Middle Aged ; }, abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.}, }
@article {pmid41525910, year = {2026}, author = {Fourgeaud, J and Veyrenche, N and Laloum, I and Jais, JP and Roger, C and Rabant, M and Mallet, V and Beaufrère, A and Fontaine, H and Leruez-Ville, M and Durand, F and Anglicheau, D}, title = {Occult rat hepatitis E virus infection as a cause of cirrhosis and posttransplant recurrence: insights into the role of metagenomics.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2026.01.005}, pmid = {41525910}, issn = {1600-6143}, abstract = {We report the case of a kidney-transplant recipient (2011) who developed persistent elevation of liver enzymes beginning in 2015. Extensive investigations including standard hepatitis E virus PCR failed to identify a cause. In 2019, she developed decompensated cirrhosis and underwent liver-kidney transplantation in 2021. Posttransplant, liver function tests remained abnormal. Given suspicion of an unidentified pathogen, metagenomic next-generation sequencing was performed on the graft and identified rat hepatitis E virus. Retrospective testing of native liver and serum samples confirmed infection since 2015. Ribavirin therapy resulted in normalization of liver enzymes and viral clearance.}, }
@article {pmid41525926, year = {2026}, author = {Sbampato, V and De Marco, G and Tsoupras, A and Khan, A and Beaugé, A and Dayer, R and Tabard-Fougère, A and Ceroni, D}, title = {Next-generation sequencing for diagnosing primary osteoarticular infections compared to conventional culture: A systematic review and meta-analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108380}, doi = {10.1016/j.ijid.2026.108380}, pmid = {41525926}, issn = {1878-3511}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Child ; *Arthritis, Infectious/diagnosis/microbiology ; Metagenomics/methods ; Sensitivity and Specificity ; Osteoarthritis/diagnosis/microbiology ; }, abstract = {BACKGROUND: Osteoarticular infections (OAIs) in children is a significant diagnostic challenge for healthcare professionals. Traditional culture techniques are often time-consuming and demonstrated low sensitivity. This systematic review aims to evaluate the diagnostic yield of metagenomic next-generation sequencing (mNGS) compared to standard culture for detecting pathogens in OAIs.
METHODS: A systematic review (PROSPERO CRD420251131272) of three databases (2000-2025) was performed. Study quality was assessed using the QUADAS-2 tool. A meta-analysis was performed using a random-effects model to calculate pooled positive detection rate with 95% confidence intervals (95% CI). Heterogeneity was quantified (I[2]), and sensitivity analysis with leave-one-out and subgroups were performed.
FINDINGS: From 35 included studies (>3000 patients), mNGS demonstrated a significantly higher pooled positive detection rate (81%; 95% CI: 75%-85%) than traditional culture (35%; 95% CI: 29%-41%) with high heterogeneity (>80%). mNGS performed consistently in pediatric (79%) and adult (81%) subgroups and was particularly effective for spinal infections (82%).
INTERPRETATION: The mNGS demonstrates a significantly higher diagnostic yield than standard culture for pathogen detection in OAIs. Its simplicity of execution, its fast-processing methods, and high sensitivity are promising factors that could lead to a more reliable detection of the causative microorganism responsible for an OAI.
LEVEL OF EVIDENCE: level I.}, }
@article {pmid41525981, year = {2026}, author = {Yan, Y and Gao, Y and Gao, M and Chen, J and Cui, L and Ma, Y}, title = {Decipherment of dissolved organic matter compositions on waste activated sludge under in situ multi-enzyme pretreatment: novel bioavailability-oriented evaluation framework.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133995}, doi = {10.1016/j.biortech.2026.133995}, pmid = {41525981}, issn = {1873-2976}, mesh = {*Sewage/chemistry/microbiology ; *Organic Chemicals/analysis ; Methane/biosynthesis ; Biological Availability ; Anaerobiosis ; Hydrolysis ; Biodegradation, Environmental ; *Enzymes/metabolism ; }, abstract = {This study systematically elucidated the dissolved organic matters (DOM) molecular conversion and biological response mechanisms during anaerobic digestion (AD) of waste activated sludge (WAS) under different multi-enzyme pretreatment durations. Fourier transform ion cyclotron resonance mass spectrometry analysis revealed that the biodegradable protein-like and amino sugar-like substances were converted into recalcitrant aromatic nitrogen-containing compounds via hydrolysis, condensation, and cyclization processes as extended pretreatment duration, significantly reducing DOM bioavailability. Metagenomic sequencing further indicated that the DOM deterioration inhibited the enrichment of hydrolytic and acidogenic bacteria, thereby suppressed the acetotrophic methanogenesis and methane production. Based on these insights, a novel DOM bioavailability-oriented evaluation framework was proposed for WAS pretreatment optimization, focusing on three key metrics, including the relative abundance of biodegradable substrates, key microorganisms and functions, and methanogenic pathways. Expectantly this study may provide theoretical and data support for future precise design of enzymatic pretreatment process and high-efficiency AD of WAS.}, }
@article {pmid41526357, year = {2026}, author = {Cronin, P and Siegers, JY and Heang, V and Tok, S and Sin, S and Sievers, B and Omondi, V and Nuon, S and Chhel, K and Nouhin, J and Chim, V and Seng, B and Hak, M and San, S and Tum, S and Claes, FF and Firth, C and Su, YCF and Smith, GJD and Karlsson, EA}, title = {Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1525}, pmid = {41526357}, issn = {2041-1723}, support = {75N93021C00016/AI/NIAID NIH HHS/United States ; U01 AI151378/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Metagenomics/methods ; Cambodia/epidemiology ; Ducks/virology ; *Viruses/genetics/isolation & purification/classification ; Chickens/virology ; *Environmental Monitoring/methods ; Influenza in Birds/virology ; *Poultry/virology ; *Poultry Diseases/virology ; Cloaca/virology ; Influenza A Virus, H5N1 Subtype/genetics/isolation & purification ; Humans ; }, abstract = {Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose a threat to humans. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission. Traditional sampling strategies are time-consuming, expensive and carry significant biosafety risks. Here, we assess the performance of metagenomics on environmental samples (ES) versus traditional poultry swabs for detecting viral pathogens in two Cambodian LBMs between January 2022 and April 2023. ES, including air (n = 35), cage swabs (n = 17), carcass wash water (n = 17) and drinking water (n = 9) are collected alongside oropharyngeal and cloacal swabs from chickens (n = 30) and ducks (n = 29). ES is sensitive in detecting 40 viruses from pathogen families including Orthomyxoviridae and Coronaviridae. Air samples capture the greatest diversity of poultry viruses. Viral contigs from ES show high sequence identity to poultry swab contigs when aligned to the same gene. We show ES outperforms poultry samples in detecting the highly pathogenic influenza A/H5N1, including clades 2.3.4.4b and 2.3.2.1c, which are found in the environment but are missed by poultry swabs. Our findings show metagenomics on ES replicates traditional surveillance, offering broader coverage and improved pathogen detection. This approach could be pivotal for mitigating zoonotic spillover and enhancing pandemic preparedness.}, }
@article {pmid41526362, year = {2026}, author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R}, title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {40}, pmid = {41526362}, issn = {2055-5008}, mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Virulence Factors/genetics ; *Bacteria/genetics/drug effects/classification/pathogenicity/isolation & purification ; Cohort Studies ; Metagenome ; }, abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.}, }
@article {pmid41526579, year = {2026}, author = {Fang, H and Pu, M and Jiang, A and Haiti, F and Liu, Y and Ailijiang, N and Mamat, A and Tu, X}, title = {Prevalence of antibiotic resistance gene in different wastewater treatment systems and effluent-irrigated soils through metagenomic analysis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5167}, pmid = {41526579}, issn = {2045-2322}, support = {XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; 51968067//National Natural Science Foundation of China/ ; 2024TSYCCX0014//the "Tianshan Yingcai" Cultivation Program/ ; }, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Water Purification/methods ; *Genes, Bacterial ; Agricultural Irrigation ; Seasons ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Metagenome ; }, abstract = {Wastewater treatment systems (WWTS) are considered to be the main source of antibiotic resistance genes (ARGs) spreading into the environment. In this study, samples were collected from WWTS influent, biological treatment tank effluent, and recycled water treatment plant (RTP) effluent during summer and winter, followed by metagenomic sequencing. The study investigated the differences in antibiotic resistance gene transfer between two typical wastewater treatment plants (WWTPs) processes and the impact of recycled water irrigation on ARG dissemination in soil. The WWTS (HD and MD) adopting two combined processes of "Adsorption-Biodegradation Process(AB)+ Anaerobic-Anoxic-Oxic Process(AAO)" and "AAO + Membrane Bioreactor(MBR)" as the research objects for the first time.The primary ARGs types identified were multidrug resistance, tetracycline, macrolide, and aminoglycoside resistance genes. The top three ARGs subtypes by relative abundance in the influent, biological treatment tank effluent, and total effluent were msrE, mphE, and ANT(6)-Ia, respectively. Seasonal variations did not significantly influence the distribution of ARGs in the two WWTSs. The AAO and AB processes increase the relative abundance and diversity of ARGs, while ARGs relative abundance decreases after RTP treatment but may proliferate new ARGs subtypes. Additionally, the efficiency of reducing the relative abundance of ARGs in summer is higher than that in winter. The two WWTSs were able to efficiently remove msrE and mphE. The abundance and diversity of ARGs and microorganisms were maximum in soil samples from the RTP. The microbial genera significantly related to ARGs may become its potential host, such as Rhodanobacter had significant correlations with ropB2, carA, and oleB. These results provide new insights into the control of ARGs contamination and focus on the risks associated with irrigated wastewater.}, }
@article {pmid41526915, year = {2026}, author = {Shao, D and Li, Y and Chen, S and Ma, S and Liu, Y and Huang, W and Liu, D and Lyu, Y and Xia, Z and Wang, Y}, title = {Improved RNA-based metagenomic sequencing for rapid pathogen detection in pets.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41526915}, issn = {1746-6148}, support = {2022YFD18000400//National Key Research and Development Program of China/ ; PC2023A01002//Pinduoduo-China Agricultural University Research Fund/ ; }, abstract = {UNLABELLED: In veterinary medicine, particularly in pet clinics, the accurate and rapid detection of pathogens is crucial for effective disease diagnosis and treatment. Traditional diagnostic methods are often time-consuming and fall short in identifying a broad spectrum of pathogens. The newly developed metagenomic transcriptomics next-generation sequencing (mtNGS) technology is a promising tool for the rapid detecting RNA- and DNA-based pathogens. However, its application in pet clinics has been limited due to high costs, complex operational procedures, and the absence of unified protocols. Here we established a standardized mtNGS workflow for pathogen detection tailored to various clinical sample types from pets. This workflow involves the extraction of total RNA without rRNA depletion and sequencing using Illumina platforms. It also incorporates Bowtie2 to eliminate host genome sequences and MetaPhlAn3 to identify microbial compositions. Our mtNGS technology was evaluated in 16 diverse clinical cases involving body fluids, fecal samples, nasopharyngeal swabs, and tissue samples from dogs, cats, and parrots. Notably, it detected pathogens in all cases, including an identification of Mycobacterium intracellulare in a cat, highlighting its utility in diagnosing zoonotic diseases. These results, corroborated by traditional techniques, demonstrate that the mtNGS-based diagnostic approach is particularly advantageous in cases where conventional diagnostics are insufficient or when multiple co-infections are suspected. This method exhibits potential in diagnosing complex clinical diseases that are challenging to identify using traditional techniques, thus representing a promising tool and can be widely applied in veterinary diagnostics.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-025-05174-0.}, }
@article {pmid41526953, year = {2026}, author = {Quijia-Pillajo, J and Naik, S and Chapin, LJ and Owen, JS and Jones, ML}, title = {Calcium phosphate-solubilizing bacteria promote growth and alleviate phosphorus deficiency in French marigold with minimal impact on the rhizosphere microbiome.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {24}, pmid = {41526953}, issn = {2524-6372}, support = {2021-09976//NIFA Agriculture and Food Research Initiative - Foundational Knowledge of Agricultural Production Systems/ ; }, abstract = {BACKGROUND: Plant roots are surrounded by communities of microbes that influence plant growth, development, and disease resistance. In soilless culture, microbial diversity in root-associated communities primarily originates from the substrate, irrigation water, and applied microbial inoculants. Phosphate solubilizing bacteria (PSB) capable of mobilizing phosphate from insoluble Ca3(PO4)2 were identified from a greenhouse rhizobacteria collection. Plant growth promoting efficacy was investigated at different substrate pH. The influence of the inoculum composition on plant growth responses to the bacteria was also evaluated. Finally, we analyzed the impact of PSB inoculation on microbiome composition and function.
RESULTS: From 1044 isolates in the rhizobacteria collection, 14 solubilized more than 25% of the phosphorus provided in vitro. Only eight bacterial strains resulted in growth promotion benefits in planta when inoculated as a substrate drench onto marigolds grown in a peat-based substrate (pH 7.0) and fertilized with insoluble Ca3(PO4)2. In a follow up experiment, two newly identified (Pantoea sp. C2G6 and Enterobacter soli C4A1) and three previously identified PSB (Pantoea trifolii C2B11, Pantoea formicae C8D10, and Bacillus velezensis) that have demonstrated superior phosphate-mineral solubilization were evaluated. The PSB were tested at a substrate pH of 6.0 and 6.5 using water, 1% glucose, 2% Micromate, or 0.1X Luria-Bertani (LB) broth as inoculant supplements. All five bacteria promoted growth and improved plant health at both pH levels. A greater benefit to marigold growth and health was observed in plants growing at pH 6.5. C2B11, C8D10, C2G6, and B. velezensis treatment resulted in a significant increase in shoot P content. Microbiome diversity and community structure exhibited no significant alterations in response to PSB treatment. Genes enriched in PSB treated rhizospheres were mostly related to colonization, competition, and biofertilization traits.
CONCLUSIONS: PSB isolated from the rhizosphere of floriculture crops grown in soilless substrates promoted growth and enhanced health of marigolds grown under P limitation. They also enhanced growth under optimal or slightly basic pH, but their efficacy was not improved by the inoculant supplements evaluated in this experiment. The native microbial community in peat-based soilless substrate was resilient to PSB inoculation.}, }
@article {pmid41527012, year = {2026}, author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P}, title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.}, journal = {Alzheimer's research & therapy}, volume = {18}, number = {1}, pages = {23}, pmid = {41527012}, issn = {1758-9193}, mesh = {Humans ; *Alzheimer Disease/microbiology ; Male ; Female ; Aged ; *Microbiota ; *Dysbiosis/microbiology ; *Mouth/microbiology ; Aged, 80 and over ; Middle Aged ; Saliva/microbiology ; }, abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.
METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.
RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.
CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.
TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.}, }
@article {pmid41527052, year = {2026}, author = {Zhou, L and Xu, Y and Wang, L and Li, X}, title = {Trichoderma harzianum fungemia following COVID-19-related immune dysregulation in an immunocompetent patient: a case diagnosed by mNGS.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {298}, pmid = {41527052}, issn = {1471-2334}, support = {No.2020SCZT062//Jilin Provincial Department of Finance,China/ ; }, abstract = {BACKGROUND: Trichoderma harzianum is a filamentous saprophytic fungus rarely implicated in human infections. Invasive Trichoderma infections are uncommon and are typically observed in immunocompromised hosts.
CASE PRESENTATION: We report a 68-year-old immunocompetent male farmer who developed persistent fever and dizziness after COVID-19 infection. Initial empirical antibacterial and antiviral therapy failed to relieve symptoms. Repeated blood cultures and serological fungal tests were negative, whereas metagenomic next-generation sequencing (mNGS) of whole blood identified T. harzianum sequences (794 reads), confirming fungemia. The patient experienced severe infusion reactions to amphotericin B and visual disturbances with voriconazole, but responded well to posaconazole therapy. Fever subsided within seven days, mNGS sequence reads declined markedly, and no recurrence occurred during 12 weeks of follow-up.
CONCLUSIONS: This case represents the first documented instance of T. harzianum fungemia in an immunocompetent individual following transient immune dysregulation associated with COVID-19. The report underscores the diagnostic value of mNGS in detecting rare opportunistic fungi when conventional cultures are negative and highlights posaconazole as a potential therapeutic option.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12568-4.}, }
@article {pmid41527141, year = {2026}, author = {Liu, YY and Xia, F and Yimuran, R and Nuermamaiti, A and Yang, Y and Zhou, JT}, title = {Assessing whether rectal swabs reflect appendiceal microbiota profiles in acute appendicitis: a 16S rRNA-based comparative study.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {10}, pmid = {41527141}, issn = {1757-4749}, support = {2023D01A93//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, abstract = {BACKGROUND: Acute appendicitis is associated with characteristic changes in the intestinal microbiota, but direct sampling of appendiceal contents is invasive and cannot be performed in healthy controls. We therefore evaluated whether rectal swabs could partially capture appendiceal microbiome signatures in adults with acute appendicitis.
METHODS: In a prospective cross-sectional study, we enrolled adults with acute appendicitis and healthy volunteers between October 2023 and December 2024. Four types of samples were collected: feces from healthy controls (HC), appendiceal luminal contents from patients with acute appendicitis (AC), intraoperative rectal swabs from patients with acute appendicitis (RS), and initial postoperative feces from patients with acute appendicitis (IF; first stool within 24 h after surgery). 16 S rRNA gene (V3-V4) sequencing was performed, and reads were processed with QIIME2. Alpha and beta diversity, differential taxonomic composition, and PICRUSt2-based functional predictions were compared across matrices. Genus-level and functional concordance between paired AC-RS samples was assessed.
RESULTS: After quality control, 64 AC, 34 RS, 24 IF, and 29 HC samples were included. Phylogenetic diversity (PD whole-tree) was higher in AC and RS than HC, with AC also higher than RS; IF showed lower PD than AC. Bray-Curtis principal coordinate analysis showed AC forming a distinct cluster separated from HC and RS along PC1, whereas IF overlapped with HC and RS. AC, RS, and IF were enriched for Escherichia/Shigella and Fusobacterium and depleted in butyrate-producing genera such as Faecalibacterium compared with HC. In the 21 paired AC-RS cases, genus-level relative abundances and several predicted functional pathways showed concordance, indicating that RS captured many but not all appendiceal dysbiosis features.
CONCLUSIONS: Our findings suggest that intraoperative rectal swabs may partially reflect appendiceal microbiome alterations at the genus and pathway levels and may serve as a minimally invasive adjunct for microbiome profiling in acute appendicitis. However, these associations are inferred from 16 S amplicon data in a modestly sized, antibiotic-exposed cohort and should be validated using shotgun metagenomics in larger, clinically stratified populations.}, }
@article {pmid41527156, year = {2026}, author = {Buffoni, M and Kerkvliet, JJ and Enting, H and Kers, JG and Rogers, M and Visser, JAGM and Paganelli, FL and Willems, RJL and Schürch, AC}, title = {Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {3}, pmid = {41527156}, issn = {2524-4671}, abstract = {BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR) due to their antimicrobial properties and the ability of bacteria to evolve resistance to these drugs. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons.
RESULTS: In this study, we used metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. We also explored the mobile resistome, ARGs located on mobile genetic elements (MGEs) such as plasmids, which are capable of disseminating, investigating ARGs identifying with the potential to disseminate within and beyond farm settings. Our exploratory findings in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identified 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans.
CONCLUSIONS: Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00497-7.}, }
@article {pmid41527291, year = {2026}, author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J}, title = {Alterations of the gut virome in patients with Parkinson's disease.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {81}, number = {3}, pages = {}, doi = {10.1093/gerona/glag001}, pmid = {41527291}, issn = {1758-535X}, support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; }, mesh = {Humans ; *Parkinson Disease/virology/microbiology ; *Gastrointestinal Microbiome ; *Virome ; Male ; Female ; Aged ; Case-Control Studies ; Middle Aged ; Metagenomics ; }, abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.}, }
@article {pmid41527828, year = {2026}, author = {Kaur, I and Shaw, B and Multani, A and Malhotra, S and Dong, HV and Lukose, C and Prabaker, K and Saleh, T and Sim, YB and Tymchuk, CN and Uslan, DZ and Zhou, H and Brewer, TF and Yang, S}, title = {Clinical utility of serial plasma cell-free DNA metagenomic next-generation sequencing assays.}, journal = {Infection control and hospital epidemiology}, volume = {47}, number = {3}, pages = {1-3}, pmid = {41527828}, issn = {1559-6834}, abstract = {This single center retrospective observational study of serial plasma metagenomic next-generation sequencing testing shows that >95% of serial testing was without meaningful clinical impact. Only 5/173 cases were adjudicated as having significant clinical impact.}, }
@article {pmid41528122, year = {2026}, author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW}, title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41528122}, issn = {2057-5858}, mesh = {*Intensive Care Units ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Humans ; Queensland ; *Environmental Monitoring/methods ; Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Metagenomics/methods ; Cross Infection/microbiology ; }, abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.}, }
@article {pmid41528142, year = {2026}, author = {Boey, JS and Tee, HS and Waite, DW and Handley, KM}, title = {Genetic mechanisms for estuarine carbohydrate degradation and linked transcriptional activity.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0185225}, pmid = {41528142}, issn = {1098-5336}, support = {1806//Genomics Aotearoa/ ; 2101//Genomics Aotearoa/ ; }, mesh = {*Estuaries ; *Carbohydrate Metabolism/genetics ; *Bacteria/genetics/metabolism ; Geologic Sediments/microbiology ; *Transcription, Genetic ; Polysaccharides/metabolism ; Metagenome ; }, abstract = {The current understanding of carbohydrate substrate degradation is largely derived from incubation experiments involving specific substrates. In estuaries, carbohydrates are often grouped together with other sources of carbon, for analytical purposes, and measured as total and fractional organic matter. Here, we describe putative carbohydrate degradation at the polysaccharide level by the prokaryotic community in an estuary. Samples were collected along a freshwater-to-marine salinity gradient from both the water column and underlying benthic sediments. Metagenomic and metatranscriptomic data were used to determine carbohydrate-active enzyme (CAZyme)-encoding metagenome-assembled genomes and associated transcriptional activity across the gradient. Previous work demonstrated assimilation of xylan (a component of hemicellulose) in estuaries. We show the genetic mechanisms associated with the degradation of xylan, as well as arabinogalactan (also from hemicellulose), and various other glycans were widespread among estuarine taxa and actively expressed. In addition, results show different carbohydrate degradation strategies between planktonic and benthic organisms. For example, results indicate that sediment communities harbored a greater variety and density of CAZyme-encoding genes and capacity to degrade complex plant biomass (cellulose and hemicellulose) and dedicated more gene transcription overall to CAZymes than planktonic communities. In contrast, planktonic prokaryotes tended to express a greater fraction of their CAZyme-encoding gene repertoires. The transcription of gene clusters associated with degrading beta-1,3-glucans such as laminarin was prevalent in the water column. Microbial activity to degrade alpha-glucans such as glycogen was predicted to be ubiquitous but was greatest in planktonic communities. Taken together, results highlight differences in the capacity of planktonic and benthic communities to degrade carbohydrates, which reflect differences in substrate availability and complexity.IMPORTANCEEstuaries are productive ecosystems that combine various forms of organic carbon from autochthonous (e.g., algal primary producers and mangroves) and allochthonous (e.g., terrestrial plant) sources. The degradation and recycling of this organic carbon is driven by heterotrophic bacteria that are expected to harbor diverse genetic mechanisms for carbohydrate degradation to match the diversity and complexity of organic carbon encountered in the environment. Results here illustrate the diversity of carbohydrate-active enzymes (notably glycosyl hydrolases) encoded by estuarine communities and the different substrate prioritizations of planktonic and benthic communities.}, }
@article {pmid41528333, year = {2026}, author = {Velioglu, EM and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, SS}, title = {Corrigendum: Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.}, journal = {Journal of medical microbiology}, volume = {75}, number = {1}, pages = {}, doi = {10.1099/jmm.0.002120}, pmid = {41528333}, issn = {1473-5644}, }
@article {pmid41528680, year = {2026}, author = {Wu, C and Zeng, B and Ning, Z and Wang, W and Wang, Y and Zhang, Q and Lu, D}, title = {Cloning and Characterization of a PL6 Alginate Lyase Aly94 from the Marine Bacteria.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41528680}, issn = {1559-0305}, support = {32201039//National Natural Science Foundation of China/ ; ZR2022QC247//Natural Science Foundation of Shandong Province/ ; 2023YX040//Weifang Science and Technology Development Plan Project (Medical Category)/ ; }, abstract = {Microbial alginate lyases are essential biocatalysts for analyzing alginate structure and sustainably producing bioactive alginate oligosaccharides (AOS). In this study, we characterized Aly94, a novel alginate lyase from the polysaccharide lyase family 6 (PL6) family, identified from a marine sediment metagenomic library. Biochemical analyses showed Aly94 exhibits optimal activity at 40 ℃ in 50 mM NaH2PO4-Na2HPO4 buffer (pH 7.0). Adding 20 mM NaCl significantly increases its catalytic efficiency. The enzyme exhibits a strong preference for polyguluronate (polyG) over polymannuronate (polyM), with specific activities of 4.19 U/mg (polyG), 0.25 U/mg (polyM), and 2.45 U/mg (alginate). When degrading substrates-particularly polyG-Aly94 primarily generates trisaccharides. Although Aly94 acts as an endolytic alginate lyase, it also could digest the monosaccharides from small oligosaccharide chains (∆G3, ∆G4). These catalytic properties, combined with its polyG-specific depolymerization, made Aly94 a promising candidate for biotechnological applications requiring controlled alginate saccharification and high-value AOS production.}, }
@article {pmid41529347, year = {2026}, author = {Singh, S and Bajaj, A and Manickam, N}, title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.}, journal = {The Science of the total environment}, volume = {1014}, number = {}, pages = {181331}, doi = {10.1016/j.scitotenv.2025.181331}, pmid = {41529347}, issn = {1879-1026}, mesh = {*Microbiota ; Biodegradation, Environmental ; Rivers/microbiology ; *Soil Microbiology ; Bacteria/classification ; *Plastics/metabolism ; India ; *Soil Pollutants/metabolism/analysis ; Waste Disposal Facilities ; Water Pollutants, Chemical/analysis ; Biodiversity ; }, abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).}, }
@article {pmid41529381, year = {2026}, author = {Haars, J and Cumlin, T and Ladenvall, C and Lennerstrand, J and Kaden, R}, title = {Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel.}, journal = {Virology}, volume = {616}, number = {}, pages = {110789}, doi = {10.1016/j.virol.2026.110789}, pmid = {41529381}, issn = {1096-0341}, mesh = {Humans ; *Nanopore Sequencing/methods ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Virus Diseases/virology ; *Whole Genome Sequencing/methods ; Nasopharynx/virology ; }, abstract = {The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within samples. This study presents a novel protocol called Twist-ONT, integrating Twist CVRP with Oxford Nanopore Technologies (ONT) long-read sequencing. Using clinical nasopharyngeal/throat swab and plasma samples PCR-positive for a variety of different viruses, the protocol's capability for viral species classification was demonstrated. It is also shown how high-quality whole-genome assemblies and consensus sequences can be generated from the sequencing reads of this protocol. This protocol facilitates further studies into the viromes of clinical samples and viral genomics in general using ONT sequencing.}, }
@article {pmid41529435, year = {2026}, author = {Xiao, Y and Sheng, ZM and Taubenberger, JK}, title = {Precursors to the 1918 pandemic: Finding Rickettsia felis and Mucor co-infection associated with a death in 1912.}, journal = {International journal of paleopathology}, volume = {52}, number = {}, pages = {69-75}, pmid = {41529435}, issn = {1879-9825}, support = {Z01 AI000986/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; Female ; *Coinfection/history/microbiology ; *Mucormycosis/history/complications ; History, 20th Century ; *Mucor/isolation & purification/genetics ; *Pandemics/history ; Infant ; *Pneumonia/history/microbiology ; }, abstract = {OBJECTIVE: To investigate potential molecular evidence of the presence of infuenza A in a patient who died in 1912.
MATERIALS: Two to three paraffin curls from a formalin-fixed paraffin-embedded (FFPE) lung sample from an autopsy case of a one-and-a-half-year-old girl who reportedly died of acute pneumonia at the Royal London Hospital on February 1, 1912.
METHODS: RNA was extracted from the sample. Real-time reverse transcription PCR (RT-PCR) was performed to screen for influenza A virus, followed by total RNA library preparation and high-throughput sequencing on the Illumina NextSeq platform. Bioinformatic analysis was conducted on the obtained reads, which included metagenomic classification and sequence alignment to reference genomes.
RESULTS: Real-time RT-PCR and next-generation sequencing both revealed no evidence of influenza A virus infection. However, metagenomic analysis identified a significant number of reads matching Rickettsia felis, with 233 unique reads specifically aligning to its OmpB gene, and over 4 million fungal reads classified within the Mucor genus, although the exact species could not be determined. These findings provide suggestive molecular evidence of co-infection with R. felis and a Mucor species.
CONCLUSIONS: This study demonstrates the utility of modern molecular techniques in evaluating early diagnoses. Despite records attributing the cause of death to acute pneumonia, no influenza A virus RNA was detected. The identification of R. felis and Mucor sequences suggests that this rare co-infection may have contributed to the infant's death.
SIGNIFICANCE: Retrospective diagnosis is enhanced by the use of modern molecular and bioinformatic techniques. This case study provides important paleopathological insight into the etiology of recorded "acute pneumonia", indicating the presence of pathogens other than influenza A leading up to the 1918 pandemic.
LIMITATIONS: Contamination during autopsy, tissue processing, or storage cannot be ruled out. Due to the lack of remaining material, histopathological confirmation of Mucor or Rickettsia infection was not possible.
Molecular and bioinformatic research into other cases of suspected influenza A.}, }
@article {pmid41529629, year = {2026}, author = {Chen, Z and Zhao, Y and Jin, L and Ma, R and Zhao, H and Ren, H and Huang, H}, title = {Insights into the molecular mechanism driving transformation and detoxification of erythromycin in anoxic biofilters.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141116}, doi = {10.1016/j.jhazmat.2026.141116}, pmid = {41529629}, issn = {1873-3336}, mesh = {*Erythromycin/metabolism/toxicity/chemistry ; *Water Pollutants, Chemical/metabolism/toxicity/chemistry ; Filtration ; *Anti-Bacterial Agents/metabolism/toxicity/chemistry ; Molecular Docking Simulation ; Anaerobiosis ; Water Purification/methods ; Wastewater ; }, abstract = {Erythromycin (ERY), the most prevalent macrolide antibiotic detected in aquatic environments worldwide, has attracted considerable scientific interest. This concern stems from its persistent environmental presence, largely due to the limited removal efficiency of conventional wastewater treatment processes. Anoxic biofilters were established with two nutritional modes (heterotrophic/autotrophic) and two filter media (bio-ceramic/poly-urethane particle) to reveal the migration and transformation patterns of ERY. Through non-targeted and targeted analysis, 18 transformation products (TPs) were identified, including 11 previously unreported TPs. By integrating metagenomic analysis with molecular docking, key genes, enzymes, and pathways were identified. Linking the molecular mechanism of ERY transformation with toxicity prediction can categorize the toxicity of TPs from high to low into four levels. It is worth noting that the hydrolysis, phosphorylation, and oxidation of hydroxy process is most conducive to reducing the environmental toxicity of ERY. This study elucidated the fate characteristics of ERY in anoxic biofilter at the molecular level. This work provides a theoretical basis for optimizing biofilter operation to mitigate ERY. It also offers insights for developing green, advanced wastewater treatment technologies aimed at ensuring water quality health.}, }
@article {pmid41529631, year = {2026}, author = {Wang, Y and Qian, Y and Shi, C and Bi, J and Dong, P and Zou, Y and Yang, Y and Tao, Y and Li, H}, title = {Seasonal dynamics and stability of gut antibiotic resistance genes in plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi).}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141112}, doi = {10.1016/j.jhazmat.2026.141112}, pmid = {41529631}, issn = {1873-3336}, mesh = {Seasons ; Animals ; *Lagomorpha/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Bacteria/genetics ; }, abstract = {The extreme ecosystems of the Tibetan Plateau harbor an alarming reservoir of antibiotic resistance genes (ARGs) within wildlife gut microbiomes-an emerging contaminant with significant implications for One Health. However, seasonal dynamics and pathogenic risks of these ARGs remain poorly understood. Through a 2.5-year study comparing the subterranean plateau zokor (Eospalax baileyi) and the surface-dwelling plateau pika (Ochotona curzoniae), we demonstrate how species-specific ecological strategies shape distinct ARG transmission patterns. Our results demonstrated striking eco-evolutionary trade-offs: surface pikas showed 1.3 times higher ARG diversity with strong seasonal variation, influenced by temperature-modulated bacterial community turnover and mobile genetic elements (MGEs). Conversely, subterranean zokors maintained stable, were enriched with high-risk ARGs dominated by mepA and tetO, reflecting their isolated niche. Both species consistently carried pathogenic-ARG complexes (Clostridium-bacA, Staphylococcus-Ermb) across seasons, genders, and ages, indicating established resistance reservoirs in plateau food webs. Metagenomic binning revealed co-transfer potential between ARGs and MGEs. This pioneering longitudinal study exposes a dual pattern: seasonal changes cause temporary turnover of ARGs, which harbor lower resistance risk in surface-dwelling animals, while subterranean hosts retain stable, higher-risk resistance. These findings establish critical baselines for monitoring antimicrobial resistance in vulnerable ecosystems and underscore the need for integrated One Health strategies.}, }
@article {pmid41529636, year = {2026}, author = {Díaz-Moreno, N and Lebrero, R and Cantera, S}, title = {Toluene bioconversion into ectoines by halophile mixed microbial cultures.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141045}, doi = {10.1016/j.jhazmat.2026.141045}, pmid = {41529636}, issn = {1873-3336}, mesh = {*Toluene/metabolism ; Biodegradation, Environmental ; *Amino Acids, Diamino/metabolism ; Paenibacillus/metabolism ; Rhodococcus/metabolism ; Biomass ; *Bacteria/metabolism/genetics ; }, abstract = {Toluene, which has been listed in the Pollutant Release and Transfer Register (PRTR) of many countries, is one of the most emitted pollutants to the atmosphere. This study demonstrates for the first time a new perspective in toluene treatment based on its continuous bioconversion into high-value chemicals, specifically ectoine and hydroxyectoine, which hold considerable commercial relevance in the cosmetic industry with market prices reaching 1000 € kg[-1]. Specific ectoine and hydroxyectoine contents of 27.3 mg gTSS[-1] were achieved together with toluene elimination capacities of 7.2 ± 1.9 g m[-3] h[-1] and a maximum biomass concentration of 1.8 g L[-1]. Ectoine synthesis predominated initially, later shifting toward hydroxyectoine, reaching a combined amount of 71.2 mg L[-1] (ectoine:hydroxyectoine 32:68) by the end of the assay. Metagenomic analysis revealed key pathways and taxa involved in toluene degradation and ectoine and hydroxyectoine synthesis. Members of Paenibacillus, Rhodococcus and Microbacterium were identified as possessing the enzymes required for toluene degradation via the TOL pathway, while Gordonia, the most abundant genus, was primarily associated with the degradation of intermediates such as benzoate, muconate, or oxoadipate derivatives and their bioconversion into ectoine. These findings revealed a potential metabolically diverse consortium with functional complementarities, where metabolic synergies overcome species-specific limitations and promote the elimination and subsequent valorization of toluene into high-value products fostering sustainable industrial innovation.}, }
@article {pmid41529797, year = {2026}, author = {Cao, X and Zhang, L and Tu, H and Li, T and Wang, G and Xiao, L and Zhang, Y and Liu, P and Li, Y and Li, J and Li, X and Hu, B and Zhang, S and Li, B}, title = {Membrane aerated biofilm reactor for largely enhanced nitrogen removal in low carbon/nitrogen ratio municipal wastewater: integrating nitrification, partial denitrification, and anammox.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133994}, doi = {10.1016/j.biortech.2026.133994}, pmid = {41529797}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Bioreactors/microbiology ; *Biofilms ; *Denitrification ; *Nitrification ; *Carbon/analysis ; *Wastewater/chemistry/microbiology ; *Membranes, Artificial ; *Water Purification/methods/instrumentation ; Oxidation-Reduction ; Ammonia/metabolism ; Cities ; }, abstract = {This study first established an integrated nitrification-partial denitrification-anammox (INPDA) process in a single-stage membrane aerated biofilm reactor (MABR) under low dissolved oxygen concentrations (0.12-0.27 mg/L) and low carbon/nitrogen ratios (1.0-3.0), without the need for anaerobic ammonia-oxidizing bacteria (AnAOB) inoculation. The optimal effluent total nitrogen (TN) concentration reached below 5 mg/L, achieving a 92.7% TN removal efficiency. Nitrifiers (including Ellin6067 and Nitrospira) oxidized a portion of ammonium to nitrate, which was subsequently reduced to nitrite by partial denitrifier Thauera utilizing influent organic carbon. Subsequently, AnAOB Candidatus Brocadia converted remaining ammonium and available nitrite into nitrogen. Metagenomics further confirmed a 32.96-fold increase in anammox-associated gene (hdh) abundance during INPDA establishment. Notably, this elevated hdh abundance remained stable even as carbon/nitrogen ratio increased, demonstrating process robustness. This study established a promising single-stage MABR strategy to advance mainstream anammox application.}, }
@article {pmid41530018, year = {2026}, author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW}, title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {25}, number = {2}, pages = {232-239}, doi = {10.1016/j.jcf.2025.12.011}, pmid = {41530018}, issn = {1873-5010}, mesh = {Humans ; *Cystic Fibrosis/microbiology/diagnosis ; *Bronchoalveolar Lavage/methods ; *Metagenomics/methods ; Child, Preschool ; Male ; Female ; Specimen Handling/methods ; Oropharynx/microbiology ; Microbiota ; Child ; *Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.
METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).
RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.
CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.}, }
@article {pmid41530166, year = {2026}, author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG}, title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1533}, pmid = {41530166}, issn = {2041-1723}, support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Food Chain ; *Soil Microbiology ; *Soil/chemistry ; *Bacteria/metabolism/genetics/classification ; Microbiota ; Animals ; Phylogeny ; Metagenomics ; }, abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.}, }
@article {pmid41530170, year = {2026}, author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S}, title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {29}, pmid = {41530170}, issn = {2052-4463}, support = {Laboratoire international associé program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; }, abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.}, }
@article {pmid41530663, year = {2026}, author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX}, title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {40}, pmid = {41530663}, issn = {1471-2164}, support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; }, abstract = {UNLABELLED: The gut microbiota of the Tibetan antelope (Pantholops hodgsonii) plays a vital role in host nutrition, particularly by contributing to the biosynthesis of essential micronutrients such as vitamins B and K2. In this study, we integrated existing P. hodgsonii gut metagenome-assembled genomes with healthy and Blastocystis-infected gut metagenomic samples to investigate microbial strategies for vitamins B and K2 production, as well as the potential modulation of these biosynthetic pathways in the gut of P. hodgsonii. From a total of 33,925 metagenome-assembled genomes, we identified 14,549 non-redundant genomes encoding 182 KEGG orthologs linked to vitamin biosynthesis. Among these, 2,115 high-quality genomes were predicted to synthesize at least one vitamin de novo, yet only 2.9% could produce four or more vitamins. Comparative analyses across multiple host species, including humans, chickens, cats, and mice, revealed that members of the phyla Bacillota_A and Bacteroidetes consistently serve as primary contributors to microbial vitamin biosynthesis. Blastocystis infection was associated with a significant increase in the abundance and diversity of vitamin biosynthesis genes, reflecting adaptive shifts in microbial metabolism. Detailed genomic analyses of the thiamine biosynthesis pathway highlighted the core contributions of Bacillota_A, Bacteroidota, Verrucomicrobiota, and Methanobacteriota, underscoring complex taxonomic cooperation. These results provide novel insights into the functional specialization and taxonomic composition of the P. hodgsonii gut microbiota, offering novel insights into microbial adaptation and metabolic cooperation that support host nutritional homeostasis and resilience in extreme environments.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12269-3.}, }
@article {pmid41530817, year = {2026}, author = {Li, R and Liao, X and Fu, X and Li, X and Liao, X and Cen, S and Zeng, J and Huang, L and Chi, H and Zou, Y}, title = {Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {33}, pmid = {41530817}, issn = {1749-8546}, support = {2022A1515140011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010012//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 20231800936162//Dongguan Science and Technology of Social Development Program/ ; 20221800905632//Dongguan Science and Technology of Social Development Program/ ; }, abstract = {BACKGROUND: Promoting intestinal barrier repair and epithelial regeneration is a core therapeutic objective in managing ulcerative colitis (UC). Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora, and Glycyrrhiza uralensis, is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.
PURPOSE: This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.
METHODS: Mice developed colitis after drinking water with a 3.5% (w/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.
RESULTS: High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.
CONCLUSION: HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel "microbiota-tryptophan metabolism-AhR-ISC differentiation" axis underlying HQD's therapeutic efficacy in UC.}, }
@article {pmid41530889, year = {2026}, author = {Bonacolta, AM and Keeling, PJ}, title = {Modern microbialites harbor an undescribed diversity of chromerid algae.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {25}, pmid = {41530889}, issn = {2524-6372}, support = {GBMF9201//Gordon and Betty Moore Foundation/ ; }, abstract = {BACKGROUND: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.
RESULTS: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.
CONCLUSIONS: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.}, }
@article {pmid41530917, year = {2026}, author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF}, title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611544}, pmid = {41530917}, issn = {1949-0984}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Big Data ; *Software ; Colorectal Neoplasms/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Computational Biology/methods ; Gastrointestinal Microbiome ; Reproducibility of Results ; }, abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.}, }
@article {pmid41531057, year = {2026}, author = {Fan, YT and Chang, S and Wang, ER and Zhu, YY and Wang, SJ and Yin, XY}, title = {[Distribution， Diffusion Regularity， and Influencing Factors of Antibiotic Resistance Genes in the Water Transfer Chain from Luanhe River to Tianjin Based on Metagenomics].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {47}, number = {1}, pages = {256-268}, doi = {10.13227/j.hjkx.202410104}, pmid = {41531057}, issn = {0250-3301}, mesh = {Rivers/microbiology ; China ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Water Microbiology ; Environmental Monitoring ; Water Supply ; }, abstract = {Yuqiao Reservoir is an important drinking water source for Tianjin. As the source of the "Water Diversion Project from Luanhe River to Tianjin"， there are more than one hundred types of contamination of antibiotic resistance genes （ARGs） in the Panjiakou and Daheiting Reservoirs. However， the level of ARGs in the upstream water transfer chain of Yuqiao Reservoir （Linhe River， Shahe River， and Lihe River） has not yet been studied. It is necessary to characterize the dynamic mechanism of ARGs in this basin to gain a deeper understanding of water ecosystem security. In this study， metagenomic methods were used to investigate the distribution characteristics of ARGs and mobile genetic elements （MGEs） in the surface water of the water transfer chain from Luanhe River to Tianjin during different periods， combined with the correlation mechanisms among microbial community structure and environmental factors. The results showed that the water transfer chain of the Luan River to Tianjin contained 21 types of ARGs with 1 161 subtypes. The main types of ARGs were multidrug， macrolide-lincosamide-streptogramin b （MLSB）， and tetracycline， with macB and tetA58 being the dominant ARGs. The predominant types of MGEs were integration/excision （IE） and replication/recombination/repair （RRR）. Compared to that during the flood period， there was a significant positive correlation between ARGs and MGEs during the dry period. Correlation analysis indicated that temperature， dissolved oxygen， and nitrate showed significant correlation with various ARGs （P < 0.05）. The abundance of ARGs was more easily affected by multiple environmental factors， but the composition of ARGs showed correlations only with total phosphorus and dissolved total phosphorus. Proteobacteria was the most dominant phylum， and several dominant microbial genera， such as Acidovorax and Rhodoferax， also showed significant correlation with ARGs， especially during the dry period. The co-occurrence network analysis revealed the most significant co-occurrence relationship between ARGs and MGEs， and some microbial genera related to nutrient elements and photosynthesis also showed co-occurrence relationships with major ARGs. This project aims to profoundly understand the biogeochemical cycle mechanisms of ARGs in the upstream water transfer chain of the reservoir， and it can provide a scientific basis for decision-making to control the transmission of resistance genes within the regional basin.}, }
@article {pmid41531093, year = {2026}, author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W}, title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {47}, number = {1}, pages = {650-662}, doi = {10.13227/j.hjkx.202411219}, pmid = {41531093}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Gossypium/growth & development ; Metagenomics ; Soil/chemistry ; Biodegradation, Environmental ; *Agriculture/methods ; Microbiota ; }, abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.}, }
@article {pmid41531535, year = {2025}, author = {Walia, A and Selvarajan, R and Ogola, HJO and Chauhan, R and Bala, J and Verma, SK and Kumar, R}, title = {Genome-resolved analysis of traditional fermented biofertilizers as scalable solutions for soil restoration.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1725475}, pmid = {41531535}, issn = {1664-302X}, abstract = {Soil degradation threatens global food security by eroding nutrient reserves and biological resilience. Microbial solutions that regenerate soil fertility through ecological processes offer a sustainable alternative to chemical intensification, yet lack mechanistic validation linking genomic potential to field performance. Fermented microbial consortia, naturally assembled through traditional practices worldwide, represent promising but underexplored technologies for biological soil restoration. Here, we integrate shotgun metagenomics, metagenome-assembled genome (MAG) reconstruction, and two-season field trials to evaluate Jeevamrit, a cattle-derived fermented biofertilizer widely used across South Asia, as a model system for understanding microbial-mediated soil restoration. Metagenomic profiling revealed that Jeevamrit fermentation of cattle dung and urine produces a functionally rich microbial consortium dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Thirty high-quality MAGs encoded genes for nitrogen fixation (nifHDK), phosphate solubilization (phoA, pstS), potassium transport (trkA, phoR), siderophore biosynthesis, and phytohormone production (trpA, miaB), alongside enriched CAZymes (GH13, PL1) and biosynthetic clusters (NRPS, PKS, terpenes) supporting nutrient turnover and rhizosphere signaling. Field application in severely degraded Himalayan rice soils substantially improved soil health relative to controls: soil organic carbon increased from 0.53%-0.68% to 0.76%-1.04% (up to 96% increase), microbial biomass carbon rose from ~72 mg C kg[-1] to 186-282 mg C kg[-1] (159% increase), available phosphorus increased 39.5%, and grain yield improved 74%, while pH and electrical conductivity remained stable. Principal component analysis confirmed that SOC, microbial biomass, and nutrient availability drove treatment differentiation, corroborating genomic predictions. This genome-to-field framework establishes fermented microbial consortia as multifunctional solutions that restore soil fertility through ecological intensification rather than chemical supplementation. By demonstrating that traditional farmer innovations can be genomically validated and mechanistically understood, this work provides a replicable model for scaling nature-based, low-cost soil restoration technologies to address global agricultural sustainability challenges.}, }
@article {pmid41532447, year = {2026}, author = {Ning, W and Hu, G and Yuan, D and Arick, MA and Hsu, CY and Magbanua, ZV and Pechanova, O and Peterson, DG and Dong, Y and Udall, JA and Grover, CE and Wendel, JF}, title = {Comparative Population Genomics of Relictual Caribbean Island Gossypium hirsutum.}, journal = {Molecular ecology}, volume = {35}, number = {2}, pages = {e70239}, pmid = {41532447}, issn = {1365-294X}, support = {141589//National Science Foundation Plant Genome Program/ ; 22-605//Cotton Incorporated/ ; 58-6066-0-066//USDA ARS Non-Assistance Cooperative Agreements/ ; 58-6066-0-064//USDA ARS Non-Assistance Cooperative Agreements/ ; //Iowa State University/ ; }, mesh = {*Gossypium/genetics ; *Genetics, Population ; Genetic Variation ; Phylogeny ; Gene Flow ; Genome, Plant ; Puerto Rico ; Guadeloupe ; Metagenomics ; Domestication ; Genomics ; Islands ; }, abstract = {Gossypium hirsutum is the world's most important source of cotton fibre, yet the diversity and population structure of its wild forms remain largely unexplored. The complex domestication history of G. hirsutum combined with reciprocal introgression with a second domesticated species, G. barbadense, has generated a wealth of morphological forms and feral derivatives of both species and their interspecies recombinants, which collectively are scattered across a large geographic range in arid regions of the Caribbean basin. Here we assessed genetic diversity within and among populations from two Caribbean islands, Puerto Rico (n = 43, five sites) and Guadeloupe (n = 25, one site), which contain putative wild or introgressed forms. Using whole-genome resequencing data and a phylogenomic framework derived from a broader genomic survey, we parsed individuals into feral derivatives and truly wild forms. Feral cottons display uneven levels of genetic and morphological resemblance to domesticated cottons, with diverse patterns of genetic variation and heterozygosity. These patterns are inferred to reflect a complex history of interspecific and intraspecific gene flow that is spatially highly variable in its effects. Wild cottons in both Caribbean islands appear to be relatively inbred, especially the Guadeloupe samples. Our results highlight the dynamics of population demographics in relictual wild cottons that experienced profound genetic bottlenecks associated with repeated habitat destruction superimposed on a natural ecogeographical distribution comprising widely scattered populations. These results have implications for conservation and utilisation of wild diversity in G. hirsutum.}, }
@article {pmid41532487, year = {2026}, author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK}, title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/1040841X.2026.2614431}, pmid = {41532487}, issn = {1549-7828}, abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.}, }
@article {pmid41533582, year = {2026}, author = {Ahrendt, SR and Haridas, S and Stong, S and Salamov, A and Steindorff, A and LaButti, K and Riley, R and Shabalov, I and Lukashin, I and Dusheyko, S and Schulz, F and Romero, MF and Villada, JC and Grigoriev, IV and Mondo, SJ}, title = {Comparative mitogenomics of kingdom Fungi - evolutionary insights and metagenomic applications.}, journal = {Nucleic acids research}, volume = {54}, number = {2}, pages = {}, pmid = {41533582}, issn = {1362-4962}, support = {//U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; *Metagenomics/methods ; *Fungi/genetics/classification ; Genome, Fungal ; Phylogeny ; RNA, Transfer/genetics ; Molecular Sequence Annotation ; }, abstract = {Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.}, }
@article {pmid41533915, year = {2026}, author = {Pang, J and Wei, Z and Zhang, Z and Xu, X and Peng, Y and Chen, Q and Wei, Y and Liu, J and Zhang, Y and Shi, Q and Wang, Z and Zhang, Y and Chen, K and Zhou, M and Lu, X and Liang, Q}, title = {Genomic Landscape Reveals Correlation of Endosymbiont Ralstonia With Acanthamoeba Keratitis Severity.}, journal = {Investigative ophthalmology & visual science}, volume = {67}, number = {1}, pages = {17}, pmid = {41533915}, issn = {1552-5783}, mesh = {Animals ; *Acanthamoeba Keratitis/microbiology/parasitology/diagnosis/genetics ; Mice ; *Acanthamoeba/genetics/microbiology ; *Symbiosis ; *Ralstonia/genetics/physiology ; Humans ; Whole Genome Sequencing ; Disease Models, Animal ; Female ; In Situ Hybridization, Fluorescence ; Microscopy, Electron, Transmission ; Cornea/parasitology/pathology ; Male ; Genome, Bacterial ; Severity of Illness Index ; Genomics ; }, abstract = {PURPOSE: To identify the basic genomic profile of Acanthamoeba, obtain information on Acanthamoeba endosymbionts, and analyze the correlation between these endosymbionts and the prognosis of Acanthamoeba keratitis (AK) patients.
METHODS: Whole-genome sequencing was conducted on 30 cornea-derived Acanthamoeba strains. Pan-genome analysis was performed, and endosymbionts were identified by metagenomic analysis. Gimenez staining, fluorescence in situ hybridization, and transmission electron microscopy were used to prove the existence of endosymbionts. Linear discriminant analysis effect size was used to associate endosymbiont species with AK clinical prognosis. The correlation between the endosymbiont Ralstonia and pathogenicity was experimentally validated by assessing the biological characteristics of Acanthamoeba and by performing clinical and histopathological evaluations in AK mouse models.
RESULTS: Whole genome sequencing revealed that the Acanthamoeba genome size was 37.1-105.0 Mb and GC content was 53.9%-60.5%. Pan-genomic analysis indicated an open state of the Acanthamoeba genome. Metagenomic analysis identified the presence of endosymbionts within Acanthamoeba, notably the endosymbiont Ralstonia, which was associated with poor prognosis at the genus level (P = 0.047). Acanthamoeba harboring the endosymbiont Ralstonia exhibited an increased migration area, enhanced adhesion, and had a more pronounced cytopathic effect. The size of clinical scores and corneal ulcers showed a significant increase in mouse models induced by Acanthamoeba with endosymbiont Ralstonia.
CONCLUSIONS: Whole-genome sequencing highlighted the symbiotic relationship between Acanthamoeba and associated microorganisms. The presence of the endosymbiont Ralstonia influenced the biological characteristics of Acanthamoeba and was correlated with clinical poor prognosis in AK, suggesting its potential as a target for clinical intervention.}, }
@article {pmid41534271, year = {2026}, author = {Zhou, W and Duan, C and Xue, M and Li, S and Fan, X and Wu, H}, title = {Diversity and potential environmental risks of DNA viruses on international ships' ballast water at Shanghai port, China.}, journal = {Marine pollution bulletin}, volume = {225}, number = {}, pages = {119198}, doi = {10.1016/j.marpolbul.2025.119198}, pmid = {41534271}, issn = {1879-3363}, mesh = {China ; *DNA Viruses/genetics ; *Ships ; *Water Microbiology ; *Environmental Monitoring ; Drug Resistance, Microbial/genetics ; }, abstract = {Over 10 billion tons of ballast water is transferred annually globally, transporting many microorganisms such as bacteria and viruses into new environments and harming local ecology, economy and human health. Numerous studies on bacteria in ballast water have shown its remarkable bacterial diversity and potential risks in recent years. However, the diversity of viruses present in ballast water and their potential environmental implications remain extremely limited in our understanding. In this investigation, we utilized viral metagenomic sequencing to evaluate the viral diversity and distribution in ballast water sourced from five distinct shipping routes that docked at Shanghai Port. Additionally, we compared the distribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) harbored by viruses in ballast water from different routes. The viral diversity and community composition exhibited significant differences in the ballast water samples collected along distinct shipping routes. The virus diversity index varies across different routes, and notably, for the Shannon and Pielou indices, the DJ and GG routes were significantly lower than other routes. Although Caudoviricetes was the dominant viral group, the abundances of Megaviricetes and Faserviricetes were also relatively high, albeit showing variations among different routes. 224 ARGs were identified, including 143 single resistance genes (SARGs) and 81 multiple resistance genes (MARGs), and their distribution varied across different shipping routes. Similarly, certain types of VFs also exhibit differences across various routes, including nutritional/metabolic processes, biofilm formation, and exotoxins. Moreover, the comparison of viral environmental risks showed that ballast water from routes through the Indian Ocean and the South China Sea posed a greater environmental risk. In summary, the results of our research have uncovered the virus diversity and potential risks associated with different routes. This underscores the imperative of implementing targeted management strategies for each individual route.}, }
@article {pmid41534337, year = {2026}, author = {Huang, X and Ni, Y and Ma, Z and Xie, Z and Ding, Z and Xu, H and Wei, H and Jin, Q and Zhou, R}, title = {Polymer type and aging drive the selective enrichment of antibiotic resistance genes and pathogens in microplastics biofilms.}, journal = {Water research}, volume = {292}, number = {}, pages = {125364}, doi = {10.1016/j.watres.2026.125364}, pmid = {41534337}, issn = {1879-2448}, mesh = {*Biofilms ; *Microplastics ; *Drug Resistance, Microbial/genetics ; Polymers ; Wetlands ; Polyesters ; }, abstract = {Microplastics (MPs) biofilms are critical vectors for antibiotic resistance in aquatic environments. In this study, in situ incubation coupled with metagenomic sequencing was employed to investigate microbial colonization patterns, antibiotic resistance gene (ARG) profiles, and mobile genetic element (MGE) dissemination characteristics of biofilms on MPs surfaces of different polymer types and aging states within a unique wetland ecosystem. Results demonstrated that microorganisms preferentially colonized the hydrophobic surface of conventional polypropylene (PP) over biodegradable polylactic acid (PLA). Aging treatments further enhanced MP-microbe interactions. Microbial community analysis revealed selective enrichment of microbial communities in MPs biofilms, including clinically relevant pathogens such as Acinetobacter baumannii. Notably, despite showing lower microbial colonization, PLA enriched a higher abundance of priority antibiotic-resistant pathogens and high-risk ARGs, which further amplified following environmental aging. Co-occurrence network analysis identified seven key MGEs strongly correlated with multiple ARGs and exhibited the highest abundance on PLA-derived biofilms, indicating a high potential for horizontal gene transfer mediating the propagation of antibiotic resistance. Furthermore, Enterobacteriaceae were identified as critical co-hosts of ARGs and MGEs within the plastisphere, potentially playing a central role in maintaining antibiotic resistance. Our findings highlight a significant ecological threat from biodegradable and aged MPs in amplifying antibiotic resistance.}, }
@article {pmid41534338, year = {2026}, author = {Potgieter, S and Oosthuizen-Vosloo, S and Langenfeld, K and Dowdell, KS and Vedrin, M and Lahr, R and Pinto, AJ and Raskin, L}, title = {Biofiltration, seasonality, and distribution system factors influence nitrifier communities in a full-scale chloraminated drinking water system.}, journal = {Water research}, volume = {292}, number = {}, pages = {125288}, doi = {10.1016/j.watres.2025.125288}, pmid = {41534338}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; Nitrification ; Chloramines ; Filtration ; Water Purification ; Seasons ; RNA, Ribosomal, 16S ; Bacteria ; Nitrites ; }, abstract = {Nitrification in chloraminated drinking water systems has been widely studied, although limited information is available on the role of biofiltration in shaping the nitrifier communities within drinking water distribution systems (DWDS). Additionally, the co-occurrence of comammox and canonical nitrifiers in drinking water systems remains unclear. This study investigates how biofiltration shapes nitrifier communities in a full-scale drinking water system where chloramine is a secondary disinfectant, and biofilters are backwashed with chloraminated water. Samples were collected monthly for one year from biofilter effluent, finished water, and three DWDS sites with varying water ages, water quality, and nitrite concentrations. Nitrifier abundances were quantified using droplet digital PCR, which showed contrasting temporal trends between the ammonia-oxidizing bacteria amoA gene and both nitrite-oxidizing bacteria 16S rRNA gene and comammox amoB gene abundances. Genome-resolved quantitative metagenomics revealed Nitrosomonas cluster 6a species, canonical Nitrospira species, and Nitrospira-like comammox species as the dominant nitrifiers. The same populations were detected in biofilter effluent and across DWDS sites, indicating that biofilter operation contributed to the persistence of nitrifiers in the DWDS. Further, DWDS site-specific factors, such as water age and disinfectant degradation, influenced the presence and abundance of individual nitrifier populations. These findings advance our understanding of how upstream treatment processes influence microbial community structure and nitrifier persistence in full-scale chloraminated DWDSs, and highlight the importance of considering biofilter operation, alongside disinfection practices, within integrated nitrification control strategies.}, }
@article {pmid41534355, year = {2026}, author = {He, S and Wang, Z and Zhong, Z and Shi, C and Li, D and Yin, F}, title = {Soil salinization alters biogeochemical cycles in agricultural ecosystems by reducing carbon-cycling microorganisms.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119706}, doi = {10.1016/j.ecoenv.2026.119706}, pmid = {41534355}, issn = {1090-2414}, mesh = {*Soil Microbiology ; *Salinity ; *Soil/chemistry ; *Carbon Cycle ; Ecosystem ; Agriculture ; Bacteria/genetics/metabolism ; Microbiota ; Metagenomics ; }, abstract = {Salinity stress can decline crop yield in agricultural systems. Beyond the environmental conditions that drive agricultural plant growth, the diverse roles of microbes represent a critical, often overlooked factor in shaping crop health and productivity. Salinization exerts a profound effect on soil microbial communities, with consequences for biogeochemical cycles. However, the salinity adaptation mechanisms of microorganisms participating in biogeochemical cycles remain incompletely understood, which hold considerable promise for microbial solutions in saline agriculture. In this study, metagenomics-based technology was employed to analyze agricultural soils within a region-scale irrigation area characterized by varying degrees of salinization. According to the results of generalized linear models, bell-shaped trends were observed for the diversity and abundance of biogeochemical cycling genes along the soil salinity gradient, all of which peaked at a salinity of approximately 7.5 ‰. Further comparisons indicated reduced total abundance of all biogeochemical cycling genes in high salinity soils (>7.5 ‰) compared to those in low salinity soils (<7.5 ‰). Furthermore, correlation analysis indicated the coupling of different biogeochemical cycling genes, which were observed to be possessed by similar functional microorganisms, with a predominance of Gammaproteobacteria and Alphaproteobacteria. The presence of elevated salt levels resulted in a decline in the abundance of various microorganisms that play roles in biogeochemical cycling, including members of the Alphaproteobacteria, Actinomycetia, Limnocylindira, and Gemmatimonadetes phyla. Concurrently, there was an enrichment of a limited number of salt-tolerant bacteria, predominantly classified under the Bacteroidia and Bacilli taxonomic groups. The coupling of different biogeochemical cycling genes in some metagenome-assembled genomes (MAGs) was confirmed through metagenomics binning. Three MAGs (strains of Methylophaga, Salinimicrobium, and Sediminibacterium, respectively) with diverse biogeochemical cycling functions were recognized as potential plant-growth-promoting bacteria under salinity stress. These findings contribute to the existing body of knowledge on the salinity adaptability of soil microbial communities and offer guidance for the management of saline agriculture.}, }
@article {pmid41534561, year = {2026}, author = {Chai, X and Zhang, X and Chen, D and Rong, D}, title = {Whole blood metagenomic next-generation sequencing in the diagnosis of bloodstream infection in patients with hematologic diseases.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108375}, doi = {10.1016/j.ijid.2026.108375}, pmid = {41534561}, issn = {1878-3511}, mesh = {Humans ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Aged ; *Hematologic Diseases/complications/microbiology/blood ; Adult ; Cell-Free Nucleic Acids/blood ; *Sepsis/diagnosis/microbiology/blood ; Aged, 80 and over ; *Bacteremia/diagnosis/microbiology/blood ; }, abstract = {OBJECTIVES: This study aimed to evaluate the value of cell-free DNA (cfDNA) in plasma and genomic DNA (gDNA) in nucleated cell layer of whole blood samples detected by metagenomic next-generation sequencing (mNGS) in the diagnosis of bloodstream infection in patients with hematologic diseases.
METHODS: Whole blood samples collected from hematologic patients with suspected bloodstream infections were divided into the plasma and nucleated cell layers. The DNA of plasma and nucleated cell layers was extracted for mNGS. The pathogenic results were compared between whole blood (plasma plus nucleated cell layers) and plasma layer. In addition, the factors influencing the prognosis at discharge were analyzed.
RESULTS: In total, 92 patients were included. The positive rate of mNGS in whole blood was higher than those of the single plasma layer (58.70% vs 53.26%) and the culture layer (58.70% vs 17.39%). The consistency of plasma and nucleated cell layers was 57.6%. The proportion of fungi detected in nucleated cell layer was higher than that in plasma layer (30.2% vs 17.0%). A total of 10 patients had extra pathogens detected in whole blood compared with the single plasma layer, and the positive rate of mNGS increased by 10.87%. gDNA microbe reads and non-host ratios in the extra-detection group were significantly higher than those in the non-extra-detection group. cfDNA microbe reads, non-host ratios, and microbe percentage showed no significant differences between the two groups. The maximum Sequential Organ Failure Assessment (SOFA) score and age in the death group were significantly higher, whereas cfDNA/gDNA species richness was significantly lower compared with the survival group. The maximum SOFA score and cfDNA Shannon diversity index were found as risk factors for improved prognosis. The maximum SOFA score and cfDNA concentration were combined for the diagnosis of poor prognosis at discharge, with the highest area under the curve at 0.95.
CONCLUSIONS: Simultaneous metagenomic sequencing of plasma layer and nucleated cell layer contributes to the detection of pathogens in patients with bloodstream infections. cfDNA detection has a certain significance in predicting the prognosis of patients with bloodstream infections.}, }
@article {pmid41534666, year = {2026}, author = {Chang, Y and Qiu, S and Collins, G and Hu, Y and Lee, PH and Zhan, X}, title = {Iron modulation of sulfur-mediated autotrophic denitrification: denitrification efficiency, microbial succession, and metabolic pathways.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133997}, doi = {10.1016/j.biortech.2026.133997}, pmid = {41534666}, issn = {1873-2976}, mesh = {*Denitrification/drug effects ; *Sulfur/metabolism ; *Autotrophic Processes/drug effects ; *Iron/pharmacology/metabolism ; *Metabolic Networks and Pathways/drug effects ; Nitrates/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {The application of iron sulfide-mediated autotrophic denitrification is promising for nitrate reduction in carbon-deficient wastewater and polluted groundwater. Previous studies have shown distinct functional microbial communities in different iron sulfide-mediated autotrophic denitrification systems, obscuring how iron modulates their composition and activity. In this study, iron-modulated sulfur autotrophic denitrification efficiency, microbial succession, and key pathways were investigated at different iron levels. Results showed that 1 mM Fe[2+] enhanced denitrification efficiency (91.1 %) and prevented cell encrustation. Metagenomic analysis indicated that phylum Campylobacterota (16.0 %) and genus Sulfurimonas (14.4 %) were enriched under iron-modulated conditions. Iron modulated nitrate reduction by improving the relative abundance of complete denitrification genes (napA, napB, and nosZ) and stimulating sulfur metabolism through the SOX complex pathway (soxZ and soxY). These findings reveal the role of iron in modulating sulfur-mediated autotrophic denitrification and provide new insights into the microbial mechanisms involved in iron-sulfur coupling systems.}, }
@article {pmid41534755, year = {2026}, author = {Liu, K and Peng, W and Yang, X and Zeng, Y and Liu, Y and Yu, K and Zhu, Y and Gou, H and Li, L and Zhang, C}, title = {Efficacy and multi-omics regulatory effects of Guilou Tongluo formula in patients with chronic obstructive pulmonary disease combined with pulmonary hypertension: A prospective, multicenter, randomized controlled trial.}, journal = {Journal of ethnopharmacology}, volume = {361}, number = {}, pages = {121204}, doi = {10.1016/j.jep.2026.121204}, pmid = {41534755}, issn = {1872-7573}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/drug therapy/complications/physiopathology ; Male ; *Drugs, Chinese Herbal/therapeutic use/adverse effects/pharmacology ; Female ; Middle Aged ; Aged ; *Hypertension, Pulmonary/drug therapy/physiopathology/complications ; Prospective Studies ; Treatment Outcome ; Multiomics ; }, abstract = {Pulmonary hypertension (PH) is a serious and common complication in patients with chronic obstructive pulmonary disease (COPD), and this clinical gap has been newly emphasized in the GOLD 2025 guidelines. Guilou Tongluo Formula (GLTLF) is a traditional Chinese herbal prescription widely used in clinical practice for the treatment of COPD combined with PH (COPD-PH). However, there is a lack of high-quality clinical trials to support its efficacy, and the underlying mechanisms of action remain unclear.
AIM OF THE STUDY: This study aims to evaluate the efficacy and safety of GLTLF in the treatment of COPD-PH, and to explore the potential mechanisms underlying its therapeutic effects.
MATERIALS AND METHOD: A total of 104 patients with COPD-PH were randomized to receive either conventional therapy alone (Control group) or in combination with GLTLF (GLTLF group). Clinical efficacy was assessed by changes in traditional Chinese medicine (TCM) syndrome scores, pulmonary artery systolic pressure (PASP), pulmonary function, arterial blood gases, COPD Assessment Test (CAT), modified Medical Research Council (mMRC) grade, WHO functional class (WHO-FC), 6-min walk distance (6MWD), and laboratory parameters. Potential mechanisms were explored via gut metagenomic and metabolomic analyses.
RESULTS: Clinical efficacy evaluation indicated that the TCM syndrome scores were significantly reduced in both groups post-treatment (P < 0.001). PASP, FEV1, and FEV1/FVC improved significantly in the GLTLF group (P < 0.05), and were superior to the control group post-treatment (P < 0.05). PaO2, PaCO2, BNP, and D-dimer improved after GLTLF intervention (P < 0.05). Both groups had increased 6MWD (P < 0.001), with the GLTLF group performing better (P = 0.006). CAT score, mMRC grade, and WHO-FC improved in both groups (P < 0.05), with superior outcomes in the GLTLF group (P < 0.05). Metagenomic sequencing revealed that GLTLF altered the structure and function of the gut microbiota in patients with COPD-PH. Metabolomic analysis identified a total of 87 differential metabolites following GLTLF intervention, which were significantly enriched in 18 metabolic pathways.
CONCLUSION: GLTLF can effectively treat patients with COPD-PH, enhance clinical efficacy, and modulate both metabolic status and gut microbiota composition.}, }
@article {pmid41534886, year = {2026}, author = {Idrees, S and Chen, H and Sadaf, T and Rehman, SF and Johansen, MD and Paudel, KR and Liu, G and Wang, Y and Luecken, MD and Hortle, E and Philp, AS and Budden, KF and O'Rourke, M and Kaiko, GE and Lucas, SEM and Dickinson, JL and Allen, PC and Powell, JE and Zhang, LY and Chambers, DC and Corte, T and Caramori, G and Sauler, M and Wark, PA and Gote-Schniering, J and Lehmann, M and Conlon, TM and Kapellos, TS and Yildirim, AÖ and Faner, R and Dharmage, SC and Wheelock, CE and van den Berge, M and Nawijn, MC and Polverino, F and Belz, GT and Chotirmall, SH and Segal, LN and Faiz, A and Hansbro, PM}, title = {Multi-omics to study chronic respiratory diseases and viral infections.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {35}, number = {179}, pages = {}, pmid = {41534886}, issn = {1600-0617}, mesh = {Humans ; Chronic Disease ; *Metabolomics/methods ; *Genomics/methods ; *Proteomics/methods ; *Virus Diseases/genetics/metabolism/diagnosis/virology ; Host-Pathogen Interactions ; Epigenomics ; *Respiratory Tract Infections/genetics/virology/metabolism/diagnosis ; Animals ; Metagenomics ; *Lung/metabolism/virology/physiopathology ; *Respiration Disorders/genetics/metabolism/diagnosis ; Multiomics ; }, abstract = {Despite recent advances, the underlying mechanisms of the development and progression of many chronic respiratory diseases remain to be elucidated. Factors such as heterogeneity and complexity of human diseases and difficulty interpreting large datasets hinder research into chronic respiratory diseases. Omics assesses the changes in specific biological entities, such as mRNA expression, epigenetics/epigenomics, genomics, proteomics, metagenomics and metabolomics, and provides valuable insights into the roles of these processes in chronic respiratory diseases. High-throughput omics at bulk, single-cell and spatial levels empower the exploration of disease-related changes through untargeted data-driven statistical methods. Multi-omics is the exploration and integration of multiple biological processes, which compared to a single-omics, can provide a substantially greater and more holistic overview of the pathogenic mechanisms that underpin complex diseases. Multi-omics analysis can comprehensively characterise the mechanisms that drive chronic respiratory diseases, capturing unique biological signatures and cellular interactions at different omics levels. Use of these methods has begun to identify key factors and biomarkers in chronic respiratory diseases. Here, we review current omics approaches and highlight recent advances in respiratory research achieved using multi-omics and integrative methods. Our review provides a valuable resource for researchers and clinicians in this area.}, }
@article {pmid41535070, year = {2026}, author = {Zhang, W and Liu, Y and Li, G and Xu, J and Chen, E and Schönhuth, A and Luo, X}, title = {Strain-level metagenomic profiling using pangenome graphs with PanTax.}, journal = {Genome research}, volume = {36}, number = {2}, pages = {405-420}, pmid = {41535070}, issn = {1549-5469}, mesh = {*Metagenomics/methods ; *Metagenome ; *Software ; Phylogeny ; *Genome, Bacterial ; }, abstract = {Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, most existing strain-level taxonomic classifiers rely on the sequence representation of multiple linear reference genomes, which fails to capture the sequence correlations among these genomes, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pangenome graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pangenome graphs possess the capability to depict the full range of genetic variability present across multiple evolutionarily or environmentally related genomes. PanTax provides a comprehensive solution to taxonomic classification for strain resolution, compatibility with both short and long reads, and compatibility with single or multiple species. Extensive benchmarking results demonstrate that PanTax drastically outperforms state-of-the-art approaches, primarily evidenced by its significantly higher F1 score at the strain level, while maintaining comparable or better performance in other aspects across various data sets.}, }
@article {pmid41535300, year = {2026}, author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC}, title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {36}, pmid = {41535300}, issn = {2055-5008}, support = {NCI202346//New Cornerstone Science Foundation/ ; }, mesh = {Humans ; Pilot Projects ; Male ; *Autism Spectrum Disorder/microbiology/therapy/complications ; Female ; Child ; *Synbiotics/administration & dosage ; *Anxiety/therapy/microbiology ; Gastrointestinal Microbiome ; Feces/microbiology ; Metagenomics ; Treatment Outcome ; Bacteria/classification/genetics/isolation & purification ; Metabolomics ; }, abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.}, }
@article {pmid41535304, year = {2026}, author = {Courtine, D and Lepère, C and Wawrzyniak, I and Moné, A and Billard, H and Colombet, J and Monjot, A and Cruaud, C and Da Silva, C and Aury, JM and Debroas, D and Bronner, G}, title = {A multi-Omic resource for exploring microbial eukaryotes in the meromictic freshwater Lake Pavin.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {252}, pmid = {41535304}, issn = {2052-4463}, support = {ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {*Lakes/microbiology ; *Eukaryota/genetics ; France ; *Metagenome ; Metagenomics ; Multiomics ; }, abstract = {Although recent advances in high-throughput sequencing have greatly expanded our understanding of microbial diversity and function in aquatic ecosystems, progress in studying freshwater microbial eukaryotes has been more limited, mainly due to their large genomes, immense diversity, and largely uncharacterised physiologies. In this work, we present a comprehensive multi-omic dataset, eukaryote-centred, including targeted-metagenomic (18S rDNA V4 and V9), metagenomic, metatranscriptomic and single amplified genomes (SAGs). Both the oxic and anoxic layers of Lake Pavin (France), a permanently stratified freshwater lake, were sampled at four distinct times throughout 2018, by day and night, targeting microbial eukaryotes of two size classes (0.65-10 µm and 10-50 µm). This dataset comprises 106 eukaryotic metagenome-assembled genomes (MAGs), over 9 million unigenes and 11 SAGs, encompassing several under-represented taxa in public databases (e.g. Perkinsea, Chytridiomycota, Cryptista). Altogether, this dataset represents a resource for exploring the functional diversity and spatio-temporal dynamics of microbial eukaryotes.}, }
@article {pmid41535683, year = {2026}, author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q}, title = {Identification of antimicrobial peptides from ancient gut microbiomes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1788}, pmid = {41535683}, issn = {2041-1723}, support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science & Technology)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Antimicrobial Peptides/pharmacology/isolation & purification/chemistry ; Feces/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Metagenomics/methods ; Mice ; Bacteria/drug effects ; }, abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.}, }
@article {pmid41535719, year = {2026}, author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L}, title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.}, journal = {Cell research}, volume = {36}, number = {2}, pages = {103-120}, pmid = {41535719}, issn = {1748-7838}, support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/immunology/microbiology/complications ; Risk Factors ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; }, abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.}, }
@article {pmid41535941, year = {2026}, author = {Parida, S and Nandi, D and Verma, D and Yi, M and Yende, A and Queen, J and Gabrielson, KL and Sears, CL and Sharma, D}, title = {A pro-carcinogenic oral microbe internalized by breast cancer cells promotes mammary tumorigenesis.}, journal = {Cell communication and signaling : CCS}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12964-025-02635-9}, pmid = {41535941}, issn = {1478-811X}, support = {90047965//Breast Cancer Research Foundation/ ; BC191572//Congressionally Directed Medical Research Programs/ ; }, abstract = {The intricate relationship between microbiota and breast cancer presents an additional risk factor that can have a profound impact on disease progression. Focusing on dysbiosis, our metagenomic analysis shows overabundance of an oral pathogenic microbe F. nucleatum and co-habitation of associated biofilm forming oral microbes in cancerous breast. Mammary gland colonization with F. nucleatum results in the development of metaplastic lesions accompanied with inflammation, DNA damage and hyper-proliferation in healthy mice. Exhibiting the impact of circulating F. nucleatum introduced via hematogenous route, breast tumor bearing mice show accelerated tumor growth and metastatic progression. Increased proliferation, migration, self-renewal and chemoresistance in breast cancer cells as well as non-tumorigenic breast epithelial cells bearing pathogenic BRCA1 mutation is observed upon F. nucleatum exposure which is internalized by the cells in a Gal-GalNAc dependent manner. Of interest, cells harboring BRCA1 mutations exhibit greater cell surface accumulation of Gal-GalNAc sugar residue. This work sheds light on the oncogenic impact of a pro-carcinogenic oral bacterium, F. nucleatum, on normal mammary epithelium and breast cancer, implicates the impairment of DNA damage and repair pathways as its functional mediators, and proposes the concept of increased vulnerability of BRCA1 mutant breast cancer cells owing to their preferential internalization of F. nucleatum.}, }
@article {pmid41536169, year = {2026}, author = {Abdulkareem, AA and Gul, SS and Abdulbaqi, HR and Sha, AM and Preshaw, PM}, title = {Assessing Evidence to Include Filifactor alocis as a Novel Candidate in Socransky's Complexes.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {e70018}, doi = {10.1111/omi.70018}, pmid = {41536169}, issn = {2041-1014}, abstract = {Socransky's complexes have identified a range of bacteria as key contributors to the onset and progression of periodontal disease. However, advancements in microbiological detection methods have allowed for exploration of the microbiome in periodontal health/disease in greater detail. In recent years, Filifactor alocis has emerged as a potential periodontal pathogen. Therefore, the aim of this review was to investigate whether this bacterium could be included in Socransky's model by summarizing the available evidence. A comprehensive literature search performed using PubMed, ScienceDirect, and Scopus databases was undertaken. The retrieved articles were filtered according to defined eligibility criteria, which yielded 24 studies. Data were extracted from these observational and clinical studies to synthesize findings. Findings regarding the host immune response were derived from in vitro and experimental animal models and narratively summarized. Observational studies and clinical trials showed heterogeneity and a lack of standardized outcomes. However, the general trend indicated a higher prevalence of F. alocis at diseased sites than at healthy sites. In addition, periodontal treatment was found to significantly reduce F. alocis levels and was associated with improvements in clinical periodontal parameters. Experimental models and in vitro studies showed that F. alocis exhibits a range of virulence attributes and pathogenic behavior similar to that of putative pathogenic periodontal bacteria. The evidence is not sufficient to include F. alocis as a new member of Socransky's model. However, this review suggests that this bacterium has the potential to be included in Socransky's complexes in the future after further research which would require to be highly standardized to enhance comparability and generalizability of findings.}, }
@article {pmid41536238, year = {2026}, author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C}, title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2607043}, pmid = {41536238}, issn = {1949-0984}, mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; Longitudinal Studies ; Adult ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Pregnancy in Obesity/microbiology/metabolism ; Infant ; Male ; Body Mass Index ; Mexico ; }, abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.}, }
@article {pmid41537457, year = {2026}, author = {Chari, NR and DeAngelis, KM and Aguilar, AA and Chan, ALH and Burgin, GA and Frey, SD and Taylor, BN}, title = {Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41537457}, issn = {1751-7370}, support = {DEB-1456610//Long-Term Research in Environmental Biology/ ; DEB-1832110//U.S. National Science Foundation (NSF) Long-Term Ecological Research Program/ ; }, mesh = {*Plant Roots/metabolism/microbiology ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; *Biomass ; Soil/chemistry ; Carbon/metabolism ; *Bacteria/genetics/classification ; *Plant Exudates/metabolism ; Climate Change ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; Forests ; *Microbiota ; DNA, Ribosomal/chemistry/genetics ; }, abstract = {Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.}, }
@article {pmid41537461, year = {2026}, author = {Choi, KY and Kang, S and Cook, S and Li, D and Choi, YY and Seo, EH and Han, X and Park, JE and Lee, S and Lee, S and Chung, JY and Chong, A and Choi, SM and Ha, JM and Song, MK and Lee, JS and Choo, IH and Kim, JH and Song, HC and Kim, BC and Kim, H and Farrer, LA and Gim, J and Jun, GR and Lee, KH}, title = {The Gwangju Alzheimer's & Related Dementias (GARD) cohort: Over a decade of Asia's largest longitudinal multimodal study.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {22}, number = {1}, pages = {e70981}, pmid = {41537461}, issn = {1552-5279}, support = {25-BR-03-05//the KBRI Basic Research Program through the Korea Brain Research Institute, funded by the Ministry of Science and ICT/ ; NRF-2014M3C7A1046041//the Original Technology Research Program for Brain Science of the National Research Foundation funded by the Korean government, MSIT/ ; RS-2024-00407198//Brain Pool program funded by the Ministry of Science and ICT through the National Research Foundation of Korea/ ; 2023-ER1007-01//Korea National Institute of Health research project/ ; //by the Technology Innovation Program (20022810, Development and Demonstration of a Digital System for the evaluation of geriatric Cognitive impairment) funded By the Ministry of Trade, Industry & Energy (MOTIE, Korea)/ ; RS-2024-00433283//the Technology Innovation Program funded by the Ministry of Trade, Industry & Energy, Republic of Korea/ ; HR22C141105//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; }, mesh = {Humans ; Longitudinal Studies ; Male ; *Alzheimer Disease/epidemiology/diagnostic imaging/genetics/diagnosis ; Female ; Aged ; *Cognitive Dysfunction/epidemiology/diagnostic imaging ; Disease Progression ; Republic of Korea/epidemiology ; Cohort Studies ; Middle Aged ; Biomarkers ; Magnetic Resonance Imaging ; Aged, 80 and over ; Neuroimaging ; Proteomics ; Genomics ; }, abstract = {INTRODUCTION: Alzheimer's disease (AD) is a major public health concern in Korea, with a high prevalence among older adults. A community-based longitudinal study is essential for tracking disease progression, identifying biomarkers, and developing targeted prevention and treatment strategies. The Gwangju Alzheimer's & Related Dementias (GARD) cohort was established to address these needs through a multimodal approach.
METHODS: Participants aged ≥60 years undergo comprehensive clinical evaluations, neuroimaging, and biospecimen collection for multi-omics analyses (genomics, transcriptomics, proteomics, and metagenomics) at baseline and systematic follow-up visits.
RESULTS: From over 17,000 screened individuals, 12,877 were enrolled. Baseline diagnoses include 5,123 cognitively unimpaired (CU), 3,250 mild cognitive impairment (MCI), and 2,125 AD dementia. The resource includes magnetic resonance imaging scans (n = 10,843) and extensive multi-omics data: genomic (n = 10,775), proteomic (n = 116), and microbiome (n = 595).
DISCUSSION: The integrated GARD dataset provides a powerful and scalable resource for identifying novel biomarkers, understanding disease heterogeneity, and advancing precision medicine for AD.
HIGHLIGHTS: Gwangju Alzheimer's & Related Dementias (GARD) is a large-scale, longitudinal, community-based cohort study in South Korea. The study focuses on early detection and monitoring of dementia progression. GARD includes cognitive testing, imaging, biospecimens, and multi-omics data. We aim to identify Korean-specific biomarkers predictive of cognitive decline. Supports East Asian insights and fills gaps in global Alzheimer's research.}, }
@article {pmid41537582, year = {2026}, author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D}, title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.}, journal = {mSphere}, volume = {11}, number = {2}, pages = {e0084225}, pmid = {41537582}, issn = {2379-5042}, support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Acinetobacter/genetics/classification/isolation & purification ; Soil Microbiology ; *Microbiota ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; }, abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.}, }
@article {pmid41537586, year = {2026}, author = {Belay, KH and Abdelrazek, S and Kaur, S and Mazloom, R and Bily, D and Gyatso, T and Avin, FA and Bonkowski, J and Liyanapathiranage, P and Rodriguez Salamanca, L and Heath, LS and Baysal-Gurel, F and Vinatzer, BA}, title = {Genomic insights into Ceratobasidium sp. associated with vascular streak dieback of woody ornamentals in the United States using a metagenomic sequencing approach.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0252325}, pmid = {41537586}, issn = {2165-0497}, support = {2023-67013-39920//U.S. Department of Agriculture/ ; 838//Virginia's Agricultural Council/ ; }, mesh = {*Plant Diseases/microbiology ; Phylogeny ; *Genome, Fungal ; United States ; Metagenomics/methods ; Wood/microbiology ; *Ascomycota/genetics/classification/isolation & purification ; *Basidiomycota/genetics/classification/isolation & purification ; }, abstract = {UNLABELLED: Woody ornamentals are integral to urban landscapes and play important roles in habitat restoration and ecological conservation, yet their national and international trade facilitates the spread of plant diseases with significant ecological and economic consequences. Vascular streak dieback (VSD) recently emerged on woody ornamentals in the United States and was found to be associated with the fungal pathogen Ceratobasidium sp. (Csp), but little is known about its genomic diversity and associated microbial communities. We thus applied metagenomic sequencing to 106 symptomatic samples that had tested positive for Csp and had been collected from 34 woody ornamental species in seven states. Taxonomic profiling identified Csp as the only putative pathogen of which we recovered 17 high-quality draft genomes. Phylogenomic and pangenome analyses revealed that U.S. Csp isolates form a tight genetic cluster, distinct in gene content from C. theobromae, a pathogen of cacao, avocado, and cassava in Southeast Asia. Comparative analyses highlighted gene content differences, including candidate effectors and secondary metabolite clusters, which may underlie host interactions and offer diagnostic targets. These findings provide the first genomic insights into the U.S. Csp population, suggest the recent introduction of a single genetic lineage with a broad host range, and establish a framework for improved detection, monitoring, and management of VSD in woody ornamentals.
IMPORTANCE: Identification of the pathogen that causes an emerging disease, be it of humans, animals, or plants, is a prerequisite to develop effective treatment and/or management practices and to try to control the disease outbreak to prevent further pathogen spread. Vascular streak dieback (VSD) is an emerging disease of ornamental bushes and trees in the United States. Identification of the pathogen has been hindered by the difficulty in growing the fungal pathogen found to be associated with diseased plants in pure culture. Here, we succeeded in sequencing the DNA of the likely pathogen directly from plant tissue or from the fungal mass growing out of collected plant tissue. The sequences were assembled into genomes, which allowed us to precisely identify the pathogen, compare it to related pathogens of other plants, and predict how it causes disease. These results can now be used to inform management and control of VSD.}, }
@article {pmid41537603, year = {2026}, author = {Zou, Y and Zhou, J and Zeng, Y and Chen, B and Liu, L and Xu, G}, title = {Mining and engineering of ene-reductases from marine sediment metagenome for prochiral ACE inhibitor synthesis.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0233325}, pmid = {41537603}, issn = {1098-5336}, support = {42376097//National Natural Science Foundation of China/ ; }, mesh = {*Metagenome ; *Geologic Sediments/microbiology ; *Angiotensin-Converting Enzyme Inhibitors/metabolism/chemical synthesis ; Substrate Specificity ; *Bacterial Proteins/genetics/metabolism/chemistry ; China ; Escherichia coli/genetics ; }, abstract = {The development of sustainable biocatalytic processes for pharmaceutical synthesis represents a major goal in green chemistry. Ene-reductases (ERs) are attractive biocatalysts for asymmetric hydrogenation of activated alkenes, yet their industrial application is often constrained by limited substrate scope and stability. In this study, we explored the deep-sea sediment metagenome of the South China Sea and identified 41 putative ER genes, with 22 successfully solubly expressed in Escherichia coli. Biochemical characterization revealed broad substrate specificity, achieving up to 90% conversion for diverse α,β-unsaturated compounds. Notably, three enzymes (S2gene2614772, S2gene1139, and S2gene22028) exhibited exceptional adaptability, maintaining high activity over a wide pH range (5.5-8.5) and at low temperatures (15°C). However, none of the wild-type ERs showed significant activity toward the prochiral substrate 2-oxo-4-phenyl-3-butenoic acid, a key intermediate for angiotensin-converting enzyme inhibitors (ACEIs). Through directed evolution, we obtained a mutant (S2gene22028-G102S) with 30-fold enhanced activity, reaching 90% conversion at 10 mM substrate. Scale-up synthesis (5 mmol substrate) afforded 2-oxo-4-phenylbutyric acid (OPBA) at 11 mg/mL, demonstrating industrial potential. This study highlights marine metagenomes as valuable sources of novel ERs and provides an efficient biocatalytic route to ACEI precursors.IMPORTANCEThe development of sustainable biocatalysts for pharmaceutical synthesis is a pivotal goal in green chemistry. This study leverages the untapped enzymatic diversity of the South China Sea deep-sea sediment metagenome to discover novel ene-reductases (ERs). We not only identified robust ERs with broad substrate promiscuity and exceptional adaptability to low temperature and pH fluctuations but also successfully engineered a variant to overcome the key biocatalytic challenge in the synthesis of 2-oxo-4-phenylbutyric acid (OPBA), a critical precursor to angiotensin-converting enzyme inhibitors. Our work underscores marine metagenomes as a valuable reservoir for discovering industrially relevant biocatalysts and demonstrates the power of combining metagenomic mining with protein engineering to enable greener manufacturing routes for high-value pharmaceuticals.}, }
@article {pmid41538320, year = {2026}, author = {}, title = {Correction to 'MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis'.}, journal = {Nucleic acids research}, volume = {54}, number = {2}, pages = {}, doi = {10.1093/nar/gkag015}, pmid = {41538320}, issn = {1362-4962}, }
@article {pmid41538522, year = {2026}, author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S}, title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA virome.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {120}, number = {}, pages = {e250131}, pmid = {41538522}, issn = {1678-8060}, mesh = {Animals ; *Mosquito Vectors/virology/classification ; *Arboviruses/genetics/isolation & purification ; Colombia ; *Culicidae/virology/classification ; *Virome/genetics ; *RNA, Viral/genetics ; Metagenomics ; Seasons ; Caribbean Region ; *RNA Viruses/genetics/classification ; Arbovirus Infections/transmission ; }, abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.
OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.
METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across Córdoba, Sucre, Bolívar, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50™ platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.
FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.
MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.}, }
@article {pmid41538947, year = {2026}, author = {Zhang, X and Feng, Y and Jiang, X and Sun, W and Zhang, C and Han, J and Hou, Y and You, X and Zhang, H and Wang, X and Wu, X and Wang, J}, title = {Unveiling hidden risks of chiral fungicide benzovindiflupyr: Stereoselectivity in soil antibiotic resistance gene transmission.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141088}, doi = {10.1016/j.jhazmat.2026.141088}, pmid = {41538947}, issn = {1873-3336}, mesh = {*Soil Microbiology ; Stereoisomerism ; *Fungicides, Industrial/chemistry/pharmacology/toxicity ; *Soil Pollutants/chemistry/toxicity ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal ; Soil/chemistry ; }, abstract = {Antibiotic resistance gene (ARG) dissemination is closely associated with modern agricultural practices. However, the stereoselective effects of widely applied chiral pesticides on resistance evolution remain insufficiently investigated. This study systematically explored the differential effects of benzovindiflupyr enantiomers on transmission of ARGs through long-term soil incubation experiments combined with metagenomic and in vitro studies. Results demonstrated that 1S,4R-enantiomer exhibited significantly longer half-life than 1 R,4S-enantiomer. 1 R,4S-enantiomer induced extreme enrichment of a few ARGs. 1S,4R-enantiomer persistently increased abundance of multiple ARGs. Compared with 1 R,4S-enantiomer, 1S,4R-enantiomer more consistently enhanced abundance of mobile genetic elements (MGEs) related to conjugative transfer. Moreover, 1 R,4S-enantiomer primarily enriched specific genera within Pseudomonadota. 1S,4R-enantiomer simultaneously promoted abundance of multiple genera across both Pseudomonadota and Bacteroidota, driving cross-phylum genera to correlate with shared ARGs. Genomic analysis confirmed that Pseudomonadota under 1S,4R-enantiomer treatment carried more ARGs and MGEs. In vitro transformation experiments ultimately validated that 1S,4R-enantiomer significantly enhanced transformation efficiency across multiple ARGs consistently, substantially exceeding 1 R,4S-enantiomer effects. Overall, 1S,4R-enantiomer poses more significant risks for horizontal transfer of ARGs. This study elucidates enantioselective effects of chiral pesticides on transmission of ARGs, providing a foundation for improving chiral agrochemical risk assessment.}, }
@article {pmid41539094, year = {2026}, author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z}, title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {151}, number = {}, pages = {157804}, doi = {10.1016/j.phymed.2026.157804}, pmid = {41539094}, issn = {1618-095X}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Rats, Inbred SHR ; *Drugs, Chinese Herbal/pharmacology ; Male ; Rats ; *Antihypertensive Agents/pharmacology ; *Lipid Metabolism/drug effects ; Blood Pressure/drug effects ; Dysbiosis/drug therapy ; Fecal Microbiota Transplantation ; Hypertension/drug therapy ; *Prehypertension/drug therapy ; Disease Models, Animal ; }, abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.
PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.
METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.
RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.
CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.}, }
@article {pmid41539238, year = {2026}, author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K}, title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106371}, pmid = {41539238}, issn = {1525-3171}, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Bacillus subtilis/chemistry ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Clostridium butyricum/chemistry ; Animal Feed/analysis ; Diet/veterinary ; *Metabolic Networks and Pathways/drug effects ; Thailand ; Metagenomics ; Dietary Supplements/analysis ; *Metagenome ; }, abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.}, }
@article {pmid41539415, year = {2026}, author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL}, title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111204}, doi = {10.1016/j.ygeno.2026.111204}, pmid = {41539415}, issn = {1089-8646}, mesh = {*Fruit/metabolism/microbiology ; *Fermentation ; *Vegetables/metabolism/microbiology ; *Microbiota ; *Fertilizers ; Lactuca/growth & development ; Germination ; Sugars/metabolism ; }, abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.}, }
@article {pmid41539526, year = {2026}, author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q}, title = {Microbial taxonomic and functional responses to heavy metal gradients in mining-impacted stream sediments.}, journal = {Environmental research}, volume = {293}, number = {}, pages = {123778}, doi = {10.1016/j.envres.2026.123778}, pmid = {41539526}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Metals, Heavy/analysis/toxicity ; *Mining ; Archaea/drug effects/classification ; *Water Pollutants, Chemical/analysis/toxicity ; Bacteria/drug effects/classification ; *Rivers/microbiology/chemistry ; China ; Fungi/drug effects/classification ; *Microbiota/drug effects ; Environmental Monitoring ; }, abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1 %, 12.4 %, and 12.9 % of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4 %) and Acidithiobacillus (5.0 %), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8 %) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.}, }
@article {pmid41539568, year = {2026}, author = {Farhat, I and Kaminski, H and Woerther, PL and Rodriguez, C and Pierre, C and Cheval, J and Korbi, S and Couzi, L and Merville, P and Jambon, F and Moreau, K}, title = {Spiroplasma infection complicated by macrophage activation syndrome and fulminant hepatitis in a kidney transplant recipient.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2026.01.008}, pmid = {41539568}, issn = {1600-6143}, abstract = {A 65-year-old kidney transplant recipient was admitted with isolated fever. Initial tests revealed pancytopenia and elevated C-reactive protein levels but failed to detect any pathogen. A bone marrow aspirate was performed because of signs suggestive of hemophagocytic lymphohistiocytosis, but the results were negative. The patient subsequently developed fulminant hepatitis. Liver biopsy showed severe acute cytolytic hepatitis with a neutrophil-rich infiltrate, suppurative hepatocytic necrosis, and hemophagocytosis. Etoposide, N-acetylcysteine, and piperacillin-tazobactam were initiated. However, the patient died from hemorrhagic complications of the biopsy. Posthumous shotgun metagenomics on liver samples identified Spiroplasma ixodetis.}, }
@article {pmid41539598, year = {2026}, author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H}, title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.027}, pmid = {41539598}, issn = {2090-1224}, abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.
METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.
RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).
CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.}, }
@article {pmid41539600, year = {2026}, author = {Li, W and Guo, H and Wang, Q and Peng, D and Wang, Y and Lu, Z}, title = {Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.022}, pmid = {41539600}, issn = {2090-1224}, abstract = {INTRODUCTION: Taihe Silky Fowl (TSF) has a long growth cycle and slow growth rate, how to effectively improve the growth rate of TSF has become the primary concern for breeders. Currently, extensive research has established the gut microbiota's role in modulating growth rate of commercial chicken breeds, while the specific microbial mechanisms influencing TSF growth rate remain poorly understood.
OBJECTIVES: Therefore, this study aimed to identify growth rate-associated key microbial species in TSF through multi-omics approaches, experimentally validate their growth-promoting roles via controlled interventions, and elucidate the species-metabolite-host interaction mechanisms.
METHODS: Cecal metagenome and metabolome was used to search for differential key microbiota and metabolites of TSF with different growth rate, the whole genome of key microbiota was used to identify the relationship between microbiota and metabolites, and gavage key microbiota to TSF was used to demonstrate the effectiveness of probiotics and preliminarily explore their mechanisms of action.
RESULTS: Cecal metagenome analysis demonstrated a significant enrichment of Phocaeicola vulgatus (P. vulgatus) in high-growth-rate fowls, Erysipelotrichaceae bacterium was significantly enriched in low-growth-rate fowls. The differential metabolites between the two groups were significantly enriched in tryptophan metabolism pathway. Subsequently, gene analysis revealed that P. vulgatus encoded tryptophan biosynthesis genes. In feeding experiment, oral gavage P. vulgatus improved the TSF final body weight, average growth rate and average daily gain, increased cecal P. vulgatus abundance, enriched the metabolites in tryptophan metabolism pathway both in the cecum and serum, and upregulated cecal tissue gene expression in the 'intestinal immune network for IgA production' pathway resulting in the higher secretory IgA (sIgA) concentrations in cecal tissue and luminal content than the control group.
CONCLUSION: P. vulgatus promoted the growth rate of TSF by optimizing the cecal microbiota, elevating cecal tryptophan metabolites and stimulating sIgA production via sIgA gene upregulation in cecal tissues, thereby enhancing host immune modulation. These findings elucidated the microbiota-metabolite-host axis governing TSF growth regulation, providing both mechanistic insights and practical applications for probiotic-based strategies to enhance growth performance and gut health in this valuable poultry breed.}, }
@article {pmid41539626, year = {2026}, author = {Vijande, C and Balboa, S and Lazzari, M and Lema, JM and Pabst, M}, title = {Multi-omics reveals wastewater sludge bacteria with genomic potential to degrade poly(ethylene terephthalate).}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134003}, doi = {10.1016/j.biortech.2026.134003}, pmid = {41539626}, issn = {1873-2976}, mesh = {*Polyethylene Terephthalates/metabolism ; *Sewage/microbiology ; *Wastewater/microbiology ; Biodegradation, Environmental ; *Bacteria/genetics/metabolism ; Biofilms ; *Genomics/methods ; Spectroscopy, Fourier Transform Infrared ; *Genome, Bacterial/genetics ; Metagenomics ; Multiomics ; }, abstract = {Plastic pollution is a growing concern, especially poly(ethylene terephthalate) (PET), one of the most produced plastic polymers. Although several microorganisms capable of degrading PET have been identified, little is known about those present in wastewater treatment plants (WWTPs). This study explores their ability to degrade PET and the enzymes involved. Activated sludge from two facilities-one urban WWTP and one industrial WWTP-was cultivated with PET of different crystallinities. The inoculum source primarily determined differences in microbial community composition. Metagenomics revealed more than 300 genes homologous to PET-degrading enzymes in all biofilms; however, metaproteomics confirmed expression of only a few of these enzymes in industrial WWTP-derived biofilms. This inoculum demonstrated the ability to degrade PET breakdown products within 24 h. In addition, FTIR analysis revealed initial signs of surface alteration. In conclusion, this study reveals the presence of microorganisms in industrial wastewater treatment sludge that possess the genetic potential to degrade PET.}, }
@article {pmid41539627, year = {2026}, author = {Wang, Z and Yang, Y and Qiu, B}, title = {Synergistic improvement of methane production and phosphorus recovery from anaerobic digestion of waste activated sludge by Fe2O3-assisted electroactive microorganisms.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134004}, doi = {10.1016/j.biortech.2026.134004}, pmid = {41539627}, issn = {1873-2976}, mesh = {*Methane/biosynthesis ; *Phosphorus/isolation & purification/metabolism ; *Sewage/microbiology ; Anaerobiosis ; *Ferric Compounds/pharmacology ; Electron Transport ; Bioreactors/microbiology ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {Conductive materials and electroactive microorganisms (EAM) are key factors on enhancing methane production in anaerobic digestion of waste actived sludge via the direct interspecies electron transfer (DIET). However, their combined impact on simultaneous methane production and phosphorus recovery remains unclear. The Fe2O3 and EAM were added together to synergistically improve anaerobic processes, resulting in a 1.53-fold increase in methane production and a remarkable 12.03-fold enhancement in phosphorus removal. The co-additon of Fe2O3 and EAM promoted Fe(III/II) redox cycling, increased enzyme activity, and enhanced electron transport system (ETS) functionality while enriching DIET-associated bacteria (e.g., Brooklawnia, Anaerolineae) and methanogens (Methanosarcina). Metagenomic analysis revealed the upregulated genes related to phosphorus and iron metabolism, ETS, and DIET-coupled electron bifurcation. Notably, Fe2O3 may act as an alternative to cytochromes and pili in mediating DIET in electron transfer processes.}, }
@article {pmid41539628, year = {2026}, author = {Peng, Y and Liu, H and Xing, T and Zhen, F and Wu, D and Sun, Y}, title = {Instability mechanisms of overloaded anaerobic digestion: Insights from volatile fatty acid metabolism.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134006}, doi = {10.1016/j.biortech.2026.134006}, pmid = {41539628}, issn = {1873-2976}, mesh = {*Fatty Acids, Volatile/metabolism ; Anaerobiosis ; Methane/metabolism/biosynthesis ; Bioreactors/microbiology ; }, abstract = {To clarify the mechanisms driving process instability under overload stress, a long-term semi-continuous overload instability simulation experiment was conducted. High-throughput sequencing and metagenomics were used to determine the response of the process parameters, community composition, and volatile fatty acid (VFA)-related metabolic functional genes to the organic loading rate (OLR). When the OLR increased to 12.5 kg VS/m[3]/d, the methane yield remained low at 226.40 ± 10.78 mL CH4/g VS. Further increasing the OLR to 20 kg VS/m[3]/d completely destabilized the reactor, resulting in a final methane yield as low as 0.29 mL CH4/g VS, a hydrogen partial pressure as high as 357.37 Pa, and concentrations of butyrate, propionate, and acetate of 4328.49 ± 538.18, 1036.13 ± 75.48, and 9939.67 ± 427.68 mg/L, respectively. Organic overload stress caused reactor instability mainly by blocking VFA metabolism. When the OLR was ≥ 11 kg VS/m[3]/d, the relative abundances of key genes (aceE, buk, ptb, atoD) in the butyrate and propionate metabolic pathways decreased, resulting in the accumulation of butyrate and propionate. Despite a shift in syntrophic acetate oxidation metabolism from the methyl to the carbonyl branch under overload, the latter's recovery was insufficient to compensate for the severe impairment of the methyl branch, ultimately leading to acetate accumulation. VFA accumulation caused severe inhibition of acetogens and some methanogens, while hydrolytic and acidogenic bacteria dominated the microbiome (relative abundance: 94.18 %). As a result, the microbial metabolic balance was broken. Our results provide new insights into the mechanisms driving process instability under overload stress.}, }
@article {pmid41539810, year = {2026}, author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C}, title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {226}, number = {}, pages = {118184}, doi = {10.1016/j.foodres.2025.118184}, pmid = {41539810}, issn = {1873-7145}, mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; }, abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.}, }
@article {pmid41539847, year = {2026}, author = {Kong, M and Zhou, W}, title = {Clinical characteristics and outcomes of Rickettsia japonica infection: A retrospective case series of five patients.}, journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)}, volume = {44}, number = {1}, pages = {503047}, doi = {10.1016/j.eimce.2025.503047}, pmid = {41539847}, issn = {2529-993X}, mesh = {Humans ; Retrospective Studies ; Middle Aged ; Male ; Aged ; Female ; *Rickettsia Infections/diagnosis/drug therapy/microbiology ; *Rickettsia/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; }, abstract = {OBJECTIVE: To characterize the clinical manifestations of Rickettsia japonica (R. japonica) infection and to generate evidence facilitating early diagnosis and targeted treatment.
METHODS: We retrospectively reviewed the clinical data of five patients with R. japonica infection who were treated in the Emergency Department, Xiling Campus, Yichang Central People's Hospital, between January 2023 and December 2024.
RESULTS: All patients were residents of Yichang City, Hubei Province, aged 58-70 years, and 80% (4/5) were farmers. The onset of illness occurred exclusively between May and September, and all patients reported a definite history of outdoor exposure. The predominant clinical manifestations were fever, rash, and eschar. Laboratory findings revealed thrombocytopenia, elevated aspartate aminotransferase (AST) and creatine kinase (CK), as well as increased inflammatory markers including C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6). R. japonica nucleic acid was detected in all patients by metagenomic next-generation sequencing (mNGS) of blood samples. Three patients initially received empirical doxycycline therapy, which was subsequently adjusted to a standard regimen after diagnostic confirmation. Defervescence occurred at a median of two days (range, 1-7 days), followed by gradual resolution of rash and alleviation of systemic symptoms. All patients achieved complete clinical recovery and were discharged without complications.
CONCLUSION: This study highlights the importance of heightened clinical awareness of R. japonica infection, emphasizing the integration of epidemiological context with hallmark clinical features - particularly fever, rash, and eschar - during peak transmission seasons in endemic areas. Early recognition allows the timely initiation of doxycycline therapy, which is essential for achieving favorable outcomes. Moreover, metagenomic next-generation sequencing (mNGS) provides the definitive identification of pathogens and guides targeted antimicrobial therapy.}, }
@article {pmid41539854, year = {2026}, author = {Choi, S and Kwon, H and Kim, WK and Ko, G}, title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510017}, pmid = {41539854}, issn = {1738-8872}, mesh = {*Clostridium Infections/microbiology/therapy/prevention & control ; Animals ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; *Clostridioides difficile ; Disease Models, Animal ; Feces/microbiology ; Metagenomics ; }, abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.}, }
@article {pmid41539958, year = {2026}, author = {Chen, D and Luo, LL and Yang, M and Wang, Y and Zhang, HY and Liu, ZQ and Qiao, LN}, title = {[Clinical characteristics of Pneumocystis jirovecii pneumonia in non-human immunodeficiency virus infected children].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {64}, number = {2}, pages = {204-209}, doi = {10.3760/cma.j.cn112140-20250811-00740}, pmid = {41539958}, issn = {0578-1310}, support = {2021YFC2701704//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/mortality/drug therapy ; Male ; Female ; Retrospective Studies ; *Pneumocystis carinii/isolation & purification ; Infant ; Child, Preschool ; Child ; Respiration, Artificial/statistics & numerical data ; Prognosis ; Hospitalization/statistics & numerical data ; }, abstract = {Objective: To analyze the clinical characteristics of Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV) infected children, aiming to provide a basis for early diagnosis, timely treatment, and improved prognosis. Methods: A single-center retrospective case series study was conducted to analyze the general information, laboratory indicators, imaging features, treatment, and outcomes of 59 pediatric patients with non-HIV-infected PJP admitted to the Department of Pediatrics, West China Second Hospital, Sichuan University, from February 2022 to June 2025.These patients were categorized into two groups based on the presence or absence of underlying diseases.Comparative analysis was performed to assess differences in hospitalization duration, intensive care unit (ICU) admission rate, mechanical ventilation rate, mortality, and other relevant aspects between the 2 groups.The rank sum test, χ[2] test or Fisher exact test was employed for intergroup comparisons. Results: The age at presentation of 59 patients: 0.5 (0.3, 2.5) years, including 40 males and 19 females. Among the underlying diseases, there were 12 cases (20%) of primary immunodeficiency, 4 cases (11%) each of autoimmune diseases, hematologic malignancies, and organ transplantation 30 cases (51%) had received treatment with glucocorticoids and immunosuppressants before diagnosis. The main clinical symptoms were cough in 57 cases (97%), dyspnea in 51 cases (86%) and, fever in 35 cases (59%). The peripheral white blood cell count was 9.2 (6.3, 13.9)×10[9]/L, with neutrophils 4.4 (1.8, 7.4)×10[9]/L and lymphocytes 3.4 (2.0, 6.1)×10[9]/L. C-reactive protein (CRP) 1.4 (0.5, 11.6) mg/L, procalcitonin 0.2 (0.1, 0.6) μg/L, the lactate dehydrogenase was (582±49) U/L. Fifty-three percent (16/30) of fungal G-test results were positive, 27% (11/41) of the children had CD4[+] T-cell counts <0.5×10[9]/L, and 32% (13/41) had CD4[+]/CD8[+] ratios <1.0.The main imaging findings included consolidation or patchy opacities in 48 cases (81%), diffuse ground-glass opacities in 29 cases (49%), and decreased transparency in 20 cases (34%). Pneumocystis was detected via metagenomic next-generation sequencing (mNGS) in all cases. Co-infections were present in 57 cases (97%). Among the 59 pediatric patients, 34 cases (58%) were treated with trimethoprim-sulfamethoxazole monotherapy, 19 cases (32%) received combination therapy with micafungin, and 7 cases (12%) received combination therapy with clindamycin. Fifty-three cases (90%) required varying degrees of respiratory support. Concurrent glucocorticoid therapy was administered in 70% (41/59) of cases at anti-PJP treatment initiation. Fifty-five cases (93%) improved, and 4 cases (7%) died.There were 36 cases in the group with underlying diseases and 23 cases in the group without underlying diseases. No statistically significant differences were observed between the two groups in terms of length of hospital stay, ICU admission rate and length of ICU stay, mechanical ventilation rate, or mortality rate (all P>0.05). Conclusions: Non-HIV-infected children with PJP tend to occur in infants under 3 years old. It is often complicated by underlying diseases such as immunodeficiency, with most patients having a history of glucocorticoid or immunosuppressant use. Clinical manifestations and imaging findings lack specificity, and mNGS facilitates early diagnosis. The core treatment is trimethoprim-sulfamethoxazole, most children require respiratory support, and combination with low-dose glucocorticoids may improve prognosis.}, }
@article {pmid41540059, year = {2026}, author = {St John, E and Reysenbach, AL}, title = {Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {283}, pmid = {41540059}, issn = {2052-4463}, support = {DEB-2409507//National Science Foundation/ ; }, mesh = {*Metagenome ; *Hydrothermal Vents/microbiology ; *Archaea/genetics ; Bacteria/genetics/classification ; Microbiota ; *Genome, Archaeal ; }, abstract = {Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993-2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.}, }
@article {pmid41540332, year = {2026}, author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L}, title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41540332}, issn = {1471-2180}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; Metagenome ; *Drug Resistance, Microbial/genetics ; }, abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.}, }
@article {pmid41540749, year = {2026}, author = {Kong, L and Xu, H and Wang, Y and Tao, Y and Xiao, P and Wang, Z and Zhang, M and Zheng, X and Zhang, C and Cui, S and Xu, T and Pang, Z and Wang, A and Ren, N and Zheng, C}, title = {Single-Cell Profiling Reveals Hidden Drivers of Sediment Phosphorus Release.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {4830-4839}, doi = {10.1021/acs.est.5c15684}, pmid = {41540749}, issn = {1520-5851}, mesh = {*Phosphorus ; *Geologic Sediments/chemistry ; Eutrophication ; Bacteria/metabolism ; Single-Cell Analysis ; }, abstract = {As external phosphorus inputs are progressively brought under control, microbe-mediated release of legacy phosphorus from sediments to the overlying waters has become a primary contributor to persistent eutrophication and recurrent algal blooms in global freshwater ecosystems. However, inherent challenges exist in capturing the in situ metabolic activity of phosphorus-solubilizing bacteria (PSB) due to intrinsic cultivation biases and the disconnect between bulk metagenomic profiles and the functions of viable cells. Furthermore, a lack of research into the coupling the phenotypic activity and adaptive genetic strategies of PSB in heterogeneous sedimentary environments has led to limited understanding of the mechanisms underlying endogenous phosphorus release. Here, using single-cell Raman spectroscopy coupled with deuterium oxide labeling (Raman-D2O), distinct in situ phosphorus-solubilizing activities of PSB inhabiting eutrophic, mesotrophic, and oligotrophic sediments were quantified. Inorganic PSB dominated in all sediment types but exhibited the highest activity in nutrient-rich eutrophic sites. Their activities correlated strongly with phosphorus speciation and release fluxes at the sediment-water interface of their habits. In contrast, organic PSB prevailed in oligotrophic sediments. Raman-activated cell sorting conbined with metagenomic sequencing uncovered that low-abundance taxa (e.g., Bacillus and Acinetobacter) acted as disproportionate drivers of phosphorus mobilization. PSB from eutrophic sediments were enriched in genes encoding phosphatases and organic acid hydrolysis pathways, whereas their oligotrophic counterparts favored genes related to high-affinity transporters and polyphosphate storage. These findings elucidate how nutrient regimes shape PSB metabolic traits, advancing mechanistic insights into microbial phosphorus dynamics in aquatic ecosystems and providing a theoretical basis for optimizing lake management strategies to mitigate endogenous pollutant-driven eutrophication risks.}, }
@article {pmid41541065, year = {2025}, author = {Zhang, X and Liu, C and Han, Y and She, J and Wu, W and Wang, L and Song, J and Gao, GF and Xu, Z and Liang, H and Liu, J}, title = {Sustained circulation of Aedes albopictus-derived novel almendraviruses in the urban parks.}, journal = {Biosafety and health}, volume = {7}, number = {6}, pages = {369-376}, pmid = {41541065}, issn = {2590-0536}, abstract = {The Rhabdoviridae family comprises a diverse range of negative-sense single-stranded ribonucleic acid (RNA) viruses, including significant human and mammalian viruses transmitted by various arthropod species. Herein, using Aedes albopictus (Ae. albopictus) samples collected in two urban parks during 2023 and 2024, through metagenomics sequencing, 16 sequences were identified as putative novel viruses, showing closest homology to insect-specific viruses, mycoviruses, or plant-associated viruses. Notably, two novel viruses, Aedes albopictus almendravirus GCCDC15 (Aealb-AlmV GCCDC15) and Aedes albopictus almendravirus GCCDC16 (Aealb-AlmV GCCDC16) were identified and successfully isolated. Both of these viruses belong to the genus Almendravirus within the Rhabdoviridae family. Phylogenetic analysis revealed that Aealb-AlmV GCCDC15 and GCCDC16 are distantly related to Coot Bay virus (the United States of America, 2013) and Menghai rhabdovirus (Yunnan Province, China, 2017). The genetic distances between these two viruses and their most similar viruses are marked by 59.85 % and 87.20 % of amino acid identity in the L protein, respectively, supporting their classification as two new species in the Rhabdoviridae family. Cytopathic effects and rod-like virions were observed in mosquito cells (C6/36) after inoculating with supernatants from the Ae. albopictus samples. To investigate the natural distribution and persistence of the novel almendraviruses, we conducted a specific reverse transcription-polymerase chain reaction (RT-PCR) screening of Ae. albopictus mosquitoes collected from two urban parks across different time points. The assays confirmed the presence of both Aealb-AlmV GCCDC15 and GCCDC16 in mosquito populations. Critically, these viruses were detected repeatedly over successive sampling periods and in mosquitoes from geographically distinct sites within the urban environment. In summary, our study delineates the virome characteristics of Aedes mosquitoes in the urban ecosystem and successfully isolated two novel rhabdoviruses. The recurrent detection provides clear evidence for the sustained circulation of Ae. albopictus-derived almendraviruses in urban parks, highlighting their ongoing transmission and establishment in these habitats.}, }
@article {pmid41541500, year = {2025}, author = {Broedlow, CA and Swanson, E and Cherenack, EM and Basting, C and Nogueira, NF and France, M and Yue, P and Chakrawarti, A and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Ravel, J and Fein, LA and Holm, J and Alcaide, ML and Klatt, NR}, title = {Common cervicovaginal sequencing methods result in discordant molecular diagnoses of bacterial vaginosis and reveal strain level effects of Gardnerella vaginalis.}, journal = {npj women's health}, volume = {3}, number = {}, pages = {}, pmid = {41541500}, issn = {2948-1716}, support = {P30 AI073961/AI/NIAID NIH HHS/United States ; R01 AI138718/AI/NIAID NIH HHS/United States ; }, abstract = {Bacterial vaginosis (BV) is associated with HIV transmission and pre-term birth, yet the etiology of BV remains unknown. Our analysis addressed that knowledge gap by comparing diagnostic techniques and using Bayesian inference to find species-specific associations with clinical indicators. We also assessed the effect of sequencing methodology on the results of molecular BV profiling. We observed significant differences in microbial diversity within BV-associated CSTs based on clinical diagnosis. CST assignments were substantially influenced by sequencing methodology, with concordance between methods as low as 59% for metatranscriptomic and metataxonomic-based CST assignment. We also found that Gardnerella has a strain-dependent association with individual Amsel's criteria, and that Dialister micraerophilus and Parvimonas micra are positively associated with Amsel's criteria while Lactobacillus is negatively associated. These results highlight the challenge of characterizing a condition without a single etiological agent, reinforcing the need for more granular diagnoses and treatments that are sensitive to BV variability.}, }
@article {pmid41542073, year = {2025}, author = {Kapoor, S and Mehta, P and Patial, V and Pandey, R and Padwad, YS}, title = {Phloretin-induced modulation in gut microbiome, mitigates colonic inflammation and alleviates colitis-associated colorectal cancer in mice.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {2730-2746}, pmid = {41542073}, issn = {2001-0370}, abstract = {Colitis associated colorectal cancer (CAC) is the fourth common cancer known to cause significant mortalities worldwide. Phloretin is a dihydrochalcone naturally found in apple, pear and strawberry. It exhibited different biological activities, namely anti-inflammatory, anticancer and anti-microbial. In the present study, the role of phloretin towards alleviating colonic inflammation and regulating gut microbiota was explored. The treatment of phloretin led to the reduction in the intestinal inflammation and maintained colon length-weight ratio by decreasing the total number of tumor nodules. We registered reduction in the colonic inflammatory cytokines levels namely TNFα, IL1β, IFNγ, and IL6 as well as expression of HSP90, Cox2, and Src found decreased. Results highlighted the restoration in the levels of tight junction proteins and the expression of Muc2 and Muc3. Further, role of phloretin in inducing apoptosis of tumor cells and the deregulation β-catenin pathway was studied. The histopathological analysis revealed normal colonic structure by decreasing leukocyte infiltration, as well as, circumvention in the reduction of the numbers of goblet cell, crypt abscess and ulceration in phloretin and 5-ASA (5-aminosalicylic acid) treated animals, compared to the diseased group. Metagenomic analysis of the gut microbiome in CAC mice revealed that phloretin significantly increased the abundance of Lactobacillus species, which exert probiotic effects and inhibit synchronous colon tumor growth by modulating β-catenin signaling. The increased abundance of L. reuteri and L. murinus was associated with regulated cellular proliferation, reduced TNF-α production, and decreased expression of COX-2, cyclin D1, and Bcl-2. In conclusion, the results obtained signify the nutraceutical potential of phloretin in restoring the intestinal barrier, maintaining the beneficial gut microbial population, and amelioration of CAC in mice.}, }
@article {pmid41542089, year = {2025}, author = {Zhang, D and Hu, J and Gu, B and Cao, B and Lu, J and Chen, Q and Wang, L and Pei, G and Liu, ZX and Cheng, MG and Gao, S and Li, X}, title = {BodyMeta: A comprehensive database for microbes under various pathological and physiological conditions.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {3685-3692}, pmid = {41542089}, issn = {2001-0370}, abstract = {Microorganisms residing in the gut and other anatomical sites exhibit substantial alterations under both physiological and pathological conditions, which are intricately linked to human health. Consequently, the establishment of a comprehensive metagenomic database encompassing diverse body sites under both pathological and physiological conditions is highly important. In this study, we developed BodyMeta (Body Metagenome Database), an upgraded version of the gutMEGA (gut Metagenome Atlas database), and we expanded the included studies considerably from 182 to 1261. These studies were classified into two categories: 600 literature-based studies without raw data (comprising 107 whole-genome sequencing and 493 16S amplicon sequencing studies) and 661 studies containing 663 raw datasets. We systematically categorized 1842 conditions derived from the 1261 studies into 966 pathological and 879 physiological conditions spanning 31 body sites, with the pathological conditions organized according to MeSH (Medical Subject Headings) terms. We comprehensively annotated the microbial contents, diversities, biomarkers and functional differences of the curated raw 16S amplicon sequencing data. In total, 59010 microbial taxa from literature sources and 40657 from raw datasets were mapped to the NCBI Taxonomy database. Additionally, related information about literature and experiments were compiled within BodyMeta. Collectively, the BodyMeta database provides a comprehensive resource for metagenomic investigations related to both physiological and pathological conditions, which can be freely accessed at https://bodymeta.omicsbio.info/.}, }
@article {pmid41542367, year = {2026}, author = {Sladký, O and Veselý, P and Břinda, K}, title = {FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT).}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbaf290}, pmid = {41542367}, issn = {2635-0041}, abstract = {MOTIVATION: The growing volumes and heterogeneity of genomic data call for scalable and versatile k-mer-set indexes. However, state-of-the-art indexes such as SBWT and SSHash depend on long non-branching paths in de Bruijn graphs, which limits their efficiency for small k, sampled data, or high-diversity settings.
RESULTS: We introduce FMSI, a superstring-based index for arbitrary k-mer sets that supports efficient membership and compressed dictionary queries with strong theoretical guarantees. FMSI builds on recent advances in k-mer superstrings and uses the Masked Burrows-Wheeler Transform, a novel extension of the classical Burrows-Wheeler Transform that incorporates position masking. Across a range of k values and dataset types-including genomic, pangenomic, and metagenomic-FMSI consistently achieves superior query space efficiency, using up to 2-3× less memory than state-of-the-art methods, while maintaining competitive query times. Only a space-optimized version of SBWT can match the FMSI's footprint in some cases, but then FMSI is 2-3× faster. Our results establish superstring-based indexing as a robust, scalable, and versatile framework for arbitrary k-mer sets across diverse bioinformatics applications.
FMSI is developed in C++ and released under the MIT license, with source code provided at https://github.com/OndrejSladky/fmsi and an installable package available through Bioconda. The datasets used in the experiments are deposited at Zenodo (https://doi.org/10.5281/zenodo.14722244).}, }
@article {pmid41543189, year = {2026}, author = {Hasan, GM and Mohammad, T and Zaidi, S and Shamsi, A and Sohal, SS and Hassan, MI}, title = {<p>Klebsiella pneumoniae and pyogenic liver abscess: Emerging clinical threats, virulence mechanisms and therapeutic strategies (Review)</p>.}, journal = {Molecular medicine reports}, volume = {33}, number = {3}, pages = {}, pmid = {41543189}, issn = {1791-3004}, mesh = {Humans ; *Klebsiella pneumoniae/pathogenicity/drug effects/genetics ; *Liver Abscess, Pyogenic/microbiology/drug therapy/diagnosis/epidemiology/therapy ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Klebsiella Infections/drug therapy/microbiology/epidemiology/diagnosis ; Virulence ; Drug Resistance, Multiple, Bacterial ; Animals ; }, abstract = {Klebsiella pneumoniae has emerged as a leading cause of pyogenic liver abscess (PLA), driven by hypervirulent and multidrug‑resistant (MDR) strains that pose major diagnostic and therapeutic challenges. This organism exhibits extensive capsular diversity (K1‑K80), with serotypes K1, K2, K5, K20, K54 and K57 being the most associated with invasive infections and severe clinical outcomes. Increasing convergence between hypervirulence and MDR determinants threatens effective management worldwide. Pharmacological and safety limitations of current antibiotics, including nephrotoxicity of colistin, hepatotoxicity of tigecycline and poor drug penetration into abscess cavities, further complicate treatment and encourage exploration of non‑traditional strategies such as anti‑virulence or immunomodulatory approaches. Recent advancements in rapid diagnostic tools such as metagenomic sequencing, MALDI‑TOF and point‑of‑care PCR assays offer promising prospects for early detection and antimicrobial optimization. Pharmacokinetic challenges at the abscess site and the emergence of hybrid hvKp‑MDR strains emphasize the urgency of precision‑guided therapy and robust global surveillance. K. pneumoniae‑associated PLA thus represents an evolving global health threat and understanding serotype diversity, antibiotic limitations and diagnostic innovations is essential for developing more effective preventive and therapeutic strategies. The present review provides current insights into the epidemiology, pathogenesis and therapeutic challenges of K. pneumoniae‑associated PLA, while highlighting translational opportunities and research priorities to counter the escalating dual threat of hypervirulence and resistance.
.}, }
@article {pmid41543249, year = {2026}, author = {Beals, DG and Carper, DL and Hochanadel, LH and Jawdy, SS and Klingeman, DM and Piatkowski, BT and Weston, DJ and Doktycz, MJ and Pelletier, DA}, title = {Genomic signatures in Variovorax enabling colonization of the Populus endosphere.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0160525}, pmid = {41543249}, issn = {2379-5077}, mesh = {*Populus/microbiology ; Plant Roots/microbiology ; Rhizosphere ; *Comamonadaceae/genetics/classification ; *Genome, Bacterial ; Metagenomics ; Soil Microbiology ; Microbiota/genetics ; Genomics ; }, abstract = {Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.IMPORTANCEPlants often depend on diverse microbial partners to support their growth, resilience, and adaptation to changing environments. Among these microbes, some bacteria inhabit the rhizosphere (the narrow zone around roots where microbes interact with the plant) while others are able to enter and persist within root tissues. The traits that distinguish these two lifestyles remain poorly understood. In this study, we examined a group of related Variovorax strains from poplar tree root microbiomes to ask why some rhizosphere-associated strains also become successful endosphere colonizers. We found that strains appear to succeed through different strategies: some may benefit from rapid growth on plant-derived carbon sources, while others may rely on stress tolerance or fine-tuned regulation. These results suggest that there is no single path from the rhizosphere into the root interior, but rather multiple strategies shaped by the host environment. Understanding this diversity can inform efforts to design resilient plant-microbe communities.}, }
@article {pmid41543271, year = {2026}, author = {Yamazaki, K and Yamaguchi, T and Yokoyama, Y and Tonosaki, Y and Kursanbaeva, K and Motooka, D and Akeda, Y and Kashimoto, T}, title = {Nutrient acquisition drives Edwardsiella tarda pathogenesis in necrotizing soft tissue infection.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0165725}, pmid = {41543271}, issn = {2379-5077}, support = {19K15979//Japan Society for the Promotion of Science/ ; 22K14998//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Mice ; *Enterobacteriaceae Infections/microbiology/metabolism/pathology ; *Edwardsiella tarda/pathogenicity/genetics/metabolism ; *Soft Tissue Infections/microbiology/pathology/metabolism ; Virulence Factors/metabolism/genetics ; Virulence ; *Nutrients/metabolism ; Humans ; Disease Models, Animal ; Necrosis ; }, abstract = {Necrotizing soft tissue infections (NSTIs) are rapidly progressive and life-threatening diseases caused by diverse bacterial pathogens. While classical virulence factors, such as toxins and secretion systems, have been extensively characterized, the role of metabolic fitness in supporting bacterial survival within the nutrient-restricted host environment remains underexplored. Edwardsiella tarda, a human-pathogenic bacterium implicated in NSTIs, represents an emerging model for studying non-canonical pathogenic strategies. Here, we employed transposon-directed insertion site sequencing (TraDIS) to identify genes critical for E. tarda survival in a murine soft tissue infection model. A genome-wide screen revealed 41 genes significantly depleted during the infection, including those involved in iron and zinc acquisition (fetB, zupT), vitamin biosynthesis (pdxK, cobA), and polyamine metabolism (speB). Functional assays using defined minimal media demonstrated that supplementation with vitamin B6 or putrescine enhanced bacterial growth, validating their contribution to fitness under nutrient-limited conditions. Our findings indicate that E. tarda pathogenesis is driven not solely by classical virulence factors but also by its ability to acquire essential nutrients and adapt metabolically to host-imposed nutritional stress. This study provides the first genome-wide fitness map for E. tarda during soft tissue infection and reveals new targets for therapeutic intervention that disrupt nutrient acquisition systems. These results also emphasize the broader relevance of metabolic adaptation as a determinant of virulence in invasive bacterial infections.IMPORTANCENecrotizing soft tissue infections (NSTIs) are severe, rapidly progressing bacterial infections with high morbidity and mortality. Although classical virulence factors such as toxins have been widely studied, much less is known about how pathogens adapt metabolically to survive within the nutrient-restricted environment in host tissues. This study uses Edwardsiella tarda, an emerging NSTI pathogen, as a model to identify genes required for in vivo fitness using transposon insertion sequencing. By revealing the critical roles of nutrient acquisition and metabolic adaptation, rather than toxin production alone, this work challenges conventional paradigms of bacterial virulence. Our findings suggest that targeting bacterial nutrient acquisition pathways may offer a novel therapeutic approach to control invasive infections. Furthermore, this study provides the first genome-wide fitness map of E. tarda during soft tissue infection, offering a valuable resource for future research into polymicrobial wound infections and host-pathogen nutrient competition.}, }
@article {pmid41543328, year = {2026}, author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L}, title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.}, journal = {Molecular nutrition & food research}, volume = {70}, number = {1}, pages = {e70375}, doi = {10.1002/mnfr.70375}, pmid = {41543328}, issn = {1613-4133}, support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; }, abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.}, }
@article {pmid41544440, year = {2026}, author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X}, title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106373}, pmid = {41544440}, issn = {1525-3171}, mesh = {Animals ; *Chickens/virology ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Bacteriophages/drug effects/physiology/genetics ; Dietary Supplements/analysis ; *Virome/drug effects ; Animal Feed/analysis ; Diet/veterinary ; *Chlortetracycline/pharmacology/administration & dosage ; *Plant Extracts/pharmacology/administration & dosage ; }, abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.}, }
@article {pmid41544536, year = {2026}, author = {Chen, R and Li, Z and Li, D and Mao, X and Xu, Z}, title = {Clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in the etiological diagnosis of community-acquired pneumonia in children.}, journal = {International journal of medical microbiology : IJMM}, volume = {322}, number = {}, pages = {151701}, doi = {10.1016/j.ijmm.2026.151701}, pmid = {41544536}, issn = {1618-0607}, abstract = {CAP is a major cause of pediatric hospitalization on a global scale, particularly in developing countries where the morbidity and mortality rates remain high. The etiological diagnosis of CAP in children is challenging, particularly for children with severe and high-risk conditions, such as immunodeficiency. This is primarily due to the nonspecific distribution of the causative agent and the limitations of traditional detection methods. As an emerging molecular diagnostic technology, BALF mNGS has been shown to detect the nucleic acid sequences of bacterial, viral, fungal, and atypical pathogens directly from clinical samples. This is attributed to the technology's unbiased, high throughput, and high sensitivity, which significantly improves the detection rate of pathogens. Furthermore, BALF mNGS also improves the detection of mixed infections. This capacity for precise analysis is of significant value, as it facilitates the identification of drug-resistant genes and rare pathogens. Consequently, this enhanced diagnostic capability provides a reliable foundation for the precise treatment of childhood CAP. Nevertheless, its clinical application continues to encounter challenges, including high cost, invasive sampling methods, complex data analysis processes, and insufficient standardization of pre-analytical sample processing. The technical principles, clinical value and optimization strategies of BALF mNGS are systematically reviewed in this paper, with the aim of providing a reference for improving the pathogenetic diagnosis of CAP in children.}, }
@article {pmid41544592, year = {2026}, author = {Zheng, Z and Lyu, H and Li, Z and Tang, J and He, J}, title = {Unraveling water depth dependent microplastic aging driven by functional microbial community interaction in a real urban river.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141133}, doi = {10.1016/j.jhazmat.2026.141133}, pmid = {41544592}, issn = {1873-3336}, mesh = {*Microplastics/metabolism/analysis/chemistry ; *Rivers/microbiology/chemistry ; Biofilms ; *Water Pollutants, Chemical/metabolism/analysis ; Bacteria/genetics/metabolism ; Polyvinyl Chloride/chemistry ; *Microbiota ; Polyesters/chemistry ; Biodegradation, Environmental ; Water Microbiology ; Cities ; }, abstract = {Microplastic (MPs) biofilms are dynamic microhabitats that regulate substance transformation processes. However, the influence of natural urban water depth gradients on the biofilm functions and subsequent aging of MPs remains poorly understood. Herein, we characterized the aging process of MPs in different depths of a real urban river, and the biofilm driven aging mechanism was illustrated. Surface characterization of the MPs showed an increase in oxygen-containing functional groups (CO, C-O) and O/C in polylactic acid (PLA) during aging, which indicated oxidation and hydrolysis reactions, especially at 2.0 m deep water depth. In polyvinyl chloride (PVC) MPs, carbonyl index (CI) was 2 times higher at 2.0 m as compared to 0.1 m water depth and lower chlorine content was found, indicating higher oxidative degradation and dechlorination processes in deeper water. Moreover, biofilms may regulate the synergism between oxygenase and hydrolases in PLA biofilms and oxygenase and dehalogenase in PVC biofilms. Microorganisms with both denitrification and MPs degradation functions, such as Acidovorax, Comamonas, Dechloromonas, were enriched in MPs biofilm. In addition, a positive correlation was found between MPs degradation genes (TGL2, katG, ncd2) and denitrification genes (napA, nirS, norB) in PLA biofilms at deeper water depth, suggesting a potential effect of denitrification functions on MPs aging (45 d incubation). This research challenges the conventional thoughts of higher MPs aging in shallow water, emphasizing the significant role of moderate depth gradients water in regulating the ecological function of microplastic biofilm, which is essential for evaluating the fate of MPs in real urban rivers.}, }
@article {pmid41544844, year = {2026}, author = {Wei, Y and Hu, Y and Shi, Q and Su, N and Chen, X and Chong, L and Cui, X}, title = {Successful treatment of probable disseminated mucormycosis using liposomal amphotericin B and isavuconazole in myelodysplastic syndrome: A case report and literature review.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108394}, doi = {10.1016/j.ijid.2026.108394}, pmid = {41544844}, issn = {1878-3511}, mesh = {Humans ; Female ; Aged ; *Mucormycosis/drug therapy/complications/diagnosis ; *Antifungal Agents/therapeutic use/administration & dosage ; *Amphotericin B/therapeutic use ; *Pyridines/therapeutic use/administration & dosage ; *Triazoles/therapeutic use ; *Nitriles/therapeutic use ; *Myelodysplastic Syndromes/complications ; Fatal Outcome ; Immunocompromised Host ; Drug Therapy, Combination ; Treatment Outcome ; }, abstract = {BACKGROUND: Mucormycosis is a rare, aggressive, and life-threatening fungal infection that predominantly affects immunocompromised individuals and is associated with a high mortality rate.
CASE PRESENTATION: We treated a 72-year-old woman with myelodysplastic syndrome (MDS) who developed disseminated mucormycosis involving the lungs, skin, and central nervous system (CNS). Diagnosis was supported by metagenomic next-generation sequencing (mNGS), and she received combination antifungal therapy with liposomal amphotericin B and isavuconazole. Her clinical status stabilized after 4 weeks of treatment. She later died approximately 2 weeks after discharge because of carbapenem-resistant Pseudomonas aeruginosa bacteremia.
CONCLUSIONS: Our case highlights the importance of prompt diagnosis and timely initiation of therapy for mucormycosis and indicates that combination antifungal therapy may be an effective approach to managing severe disseminated mucormycosis in immunocompromised patients.}, }
@article {pmid41544986, year = {2026}, author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z}, title = {Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111205}, doi = {10.1016/j.ygeno.2026.111205}, pmid = {41544986}, issn = {1089-8646}, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Fermentation ; Female ; Cattle/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; Pregnancy ; *Microbiota ; Metagenome ; }, abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.}, }
@article {pmid41545429, year = {2026}, author = {Maharaj, SD and Nkuna, R and Matambo, TS}, title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5486}, pmid = {41545429}, issn = {2045-2322}, mesh = {*Sewage/microbiology/chemistry ; *Wastewater/microbiology/chemistry ; *Metagenomics/methods ; Bacteria/genetics/classification ; *Metagenome ; South Africa ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; High-Throughput Nucleotide Sequencing ; Biological Oxygen Demand Analysis ; Filtration ; Microbiota ; }, abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.}, }
@article {pmid41545588, year = {2026}, author = {Buddle, S and Brown, LK and Morfopoulou, S and Torres Montaguth, OE and Scoto, M and Herder, V and Dhawan, A and Brown, JR and Atkinson, L and Kopec, A and Davis, D and Storey, N and Campos, L and Sebire, N and Macpherson, H and Lee, J and Orton, R and Baranello, G and Asamaphan, P and Ilia, G and Karda, R and Belfield, H and , and Counsell, J and Waddington, SN and Thomson, EC and Muntoni, F and Breuer, J}, title = {Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy.}, journal = {Nature medicine}, volume = {32}, number = {2}, pages = {472-480}, pmid = {41545588}, issn = {1546-170X}, mesh = {Humans ; *Dependovirus/genetics ; *Genetic Therapy/adverse effects ; *Genetic Vectors/genetics/adverse effects ; *Liver/virology/pathology/metabolism ; *Plasmids/genetics ; Genome, Viral ; Male ; Child ; Biological Products ; Recombinant Fusion Proteins ; }, abstract = {Adeno-associated viruses (AAVs) are common vectors in gene therapy but can frequently cause liver complications in patients. The mechanisms underlying AAV-related liver toxicity remain poorly understood, posing challenges for effective prevention and intervention. Here we conducted a case study of a child with spinal muscular atrophy type 1 experiencing substantial hepatitis after receiving onasemnogene abeparvovec, undertaking long- and short-read metagenomic sequencing of liver tissue. We identified manufacturing plasmid sequences with complex structures and recombination. Vector genomes had extensive disruption and concatemerization as well as numerous vector-human fusion junctions. We also identified human betaherpesvirus 6B in the liver. Further work and investigation of more patients is needed to establish whether the presence of manufacturing plasmid sequences or helper viruses contribute to the formation of these complex concatemeric DNA structures in the liver, and whether these are a factor in the development of liver toxicity after AAV gene therapy.}, }
@article {pmid41545847, year = {2026}, author = {Xu, Z and Gao, L and Chen, Z and Tang, L and Wang, Y}, title = {Metagenomic next-generation sequencing for the diagnosis and evaluation of pediatric pleural effusion: a case series.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {69}, pmid = {41545847}, issn = {1471-2466}, support = {2023C03009//the "Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; }, abstract = {BACKGROUND: Pleural effusion is a common symptom in children with respiratory diseases, with infections being the leading cause. Currently, the use of metagenomic next-generation sequencing (mNGS) for pleural effusion has not been fully evaluated in pediatric lung disease patients.
METHODS: Patients who had undergone mNGS for pleural effusion were included in the study. Patients were categorized into a clinically useful group and a not clinically useful group on the basis of their clinical data, laboratory results, and mNGS results.
RESULTS: A total of 48 children were included in this study. The number of positive mNGS results was 32/48 (66.7%), which was greater than that of conventional tests (22/48 [45.8%]). The diagnostic concordance of mNGS for detecting bacterial infections was 62.5% (20/32) higher than that of conventional detection methods, which was 15.6% (5/32). However, the diagnostic concordance of mNGS in detecting mycoplasma infections (4/9 vs. 7/9) and tuberculosis infections (0/5 vs. 5/5) was lower than that of conventional detection methods. Compared with the not clinically useful group, the clinically useful group had a lower mean age (50.50 [IQR, 32.25, 102.50] vs. 98.00 [IQR, 60.00, 118.50] months, P = 0.019), a greater incidence of wheezing (n = 5/23 vs. n = 0/23, P = 0.018), a greater incidence of pulmonary consolidation (n = 15/23 vs. n = 8/23, P = 0.039), and a greater incidence of loculated pleural effusion (n = 5/23 vs. n = 0/23, P = 0.018). Additionally, the clinically useful group had a longer hospital stay (17.0 [IQR, 10.75, 25.0] vs. 12.0 [IQR, 6.75, 15.00] days, P = 0.011). Nevertheless, the rate of improvement after treatment was greater in the clinically useful group than in the not clinically useful group (100% vs. 73.9%, P = 0.009).
CONCLUSION: mNGS has distinct diagnostic advantages, with more accurate bacterial identification in pediatric pleural effusion. Negative results may prompt exploration of non-infectious causes. However, pathogen-specific limitations should be considered.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-026-04117-1.}, }
@article {pmid41546385, year = {2026}, author = {Chang, H and Qin, X}, title = {Red Complex Bacteria as a Hidden Cause of Chronic Lung Abscess: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e949102}, pmid = {41546385}, issn = {1941-5923}, mesh = {Humans ; *Lung Abscess/microbiology/diagnostic imaging/diagnosis/drug therapy ; Chronic Disease ; Male ; *Chronic Periodontitis/complications/microbiology ; Tomography, X-Ray Computed ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Hemoptysis/etiology ; }, abstract = {BACKGROUND Common oral pathogens such as Treponema denticola, Porphyromonas gingivalis, and Tannerella forsythia, which form biofilms in the periodontal pockets, are classified together as Red Complex bacteria in Socransky's subgingival cluster model and are key pathogenic bacteria in periodontitis. Oral pathogens play a critical role in pulmonary infections, particularly in the pathogenesis of lung abscesses. Lung abscesses caused by Red Complex bacteria have rarely been described; to our knowledge, few cases have been reported to date. CASE REPORT We present the first documented case of chronic lung abscess caused by Red Complex bacteria, with recurrent hemoptysis as the main symptom. The patient had chronic periodontitis and uncontrolled diabetes, and exhibited an indolent clinical course with consistently negative bacterial cultures. Chest computed tomography (CT) demonstrated a thick-walled cavity with minimal liquefactive changes in the right upper lobe. Red Complex bacteria in the bronchoalveolar lavage fluid and the lung tissue were identified by metagenomics next-generation sequencing (mNGS). The patient underwent intravenous penicillin therapy. The hemoptysis resolved completely coupled with improvement in clinical status and inflammatory markers. The chest CT demonstrated near-complete resolution of the lung abscess during follow-up. CONCLUSIONS Red Complex bacteria are rare pathogens in patients with periodontitis who develop culture-negative chronic lung abscesses accompanied by recurrent hemoptysis. This case report highlights this rare etiology and reveals a critical diagnostic limitation, as routine cultures frequently fail to detect these fastidious organisms. The incorporation of mNGS into the diagnostic algorithm for such cases can facilitate a definitive diagnosis and guide precise antimicrobial therapy.}, }
@article {pmid41546513, year = {2026}, author = {Yang, YY and Bueno de Mesquita, CP and Lawrence, CR and Weyman, PD and Dores, D and Timmermann, T and Fierer, N and Fuenzalida-Meriz, GA}, title = {Synergistic Effects of a Microbial Amendment and Crushed Basalt: Soil Geochemical and Microbial Responses.}, journal = {Global change biology}, volume = {32}, number = {1}, pages = {e70705}, pmid = {41546513}, issn = {1365-2486}, support = {//Andes Ag, Inc./ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacillus subtilis/physiology/metabolism ; *Silicates/chemistry/metabolism ; Carbon Dioxide/metabolism ; Glycine max ; }, abstract = {Over geologic timescales, the natural weathering of silicate minerals in soils and regolith regulates atmospheric CO2. Although this process is slow relative to anthropogenic emissions, several strategies have been proposed to accelerate this process for climate mitigation. These include the application of finely-ground silicate rock to increase mineral surface area (enhanced weathering, EW) and the use of microbes that catalyze mineral dissolution and CO2 biomineralization (microbial carbon dioxide mineralization, MCM). While both approaches show promise, their combined application has rarely been tested. Here, we examined how soil chemistry and bacterial communities respond to a basalt feedstock rich in silicate minerals, a Bacillus subtilis strain (MP1) previously shown to enhance weathering, and their combination. In a 91-day soybean mesocosm experiment with slightly acidic soil (pH 6.6), MP1 persisted where applied, indicating successful inoculation via seed treatment. Basalt amendments had the strongest effect on soil bacterial community composition, whereas inoculation with MP1 exerted a smaller but detectable influence. Biogeochemical indices of weathering indicated that co-application of basalt and MP1 enhanced carbonate alkalinity beyond basalt alone. Soil carbonate alkalinity increased with MP1 treatment both with and without basalt, while soil pH and cation exchange capacity (CEC) increased with basalt in both MP1 and non-MP1 treatments. Total carbon was highest in the combined MP1 + basalt treatment, suggesting that MP1 may mitigate short-term organic carbon losses associated with basalt-driven priming. Overall, these results provide new insights into interactions between biological and mineral-based carbon dioxide removal (CDR) strategies, suggesting that co-application of MP1 with basalt in slightly acidic soil may enhance carbonate alkalinity while reducing organic carbon losses relative to basalt alone. Thus, pairing B. subtilis MP1 with enhanced weathering deployments emerges as a promising strategy to improve CDR efficiency.}, }
@article {pmid41546695, year = {2026}, author = {Zhang, T and Liu, H and Huang, Z and Fan, Y and Liu, F and Su, E and Ming, Y and Zhu, W and Wang, C and Yu, X and Niu, M and Wu, K and Sun, X and Yang, Y and He, Z and Yan, Q}, title = {Microbially Driven Organic Carbon Degradation and Nutrient Cycling during Macroalgal Decomposition.}, journal = {Environmental science & technology}, volume = {60}, number = {4}, pages = {3216-3229}, doi = {10.1021/acs.est.5c09758}, pmid = {41546695}, issn = {1520-5851}, mesh = {*Carbon/metabolism ; *Seaweed/metabolism ; Nutrients ; }, abstract = {The release of labile organic carbon (OC) and nutrients during seasonal macroalgal blooms can undermine blue carbon sequestration in coastal ecosystems. Although marine microorganisms mediate OC degradation during macroalgal decay, the underlying mechanisms remain poorly defined. This study employed an integrated multiomics approach (amplicon sequencing, metagenomics, and metatranscriptomics) to investigate microbial regulation of OC degradation and coupled nutrient cycling in coastal sediments with and without decomposing Sargassaceae. Total carbon in sediments increased by over 33% in the Sargassaceae area. Microbial α-diversity in the Sargassaceae area decreased significantly (p < 0.05), while processes linked to OC degradation, carbohydrate metabolism, nitrate (NO3[-]) reduction, inorganic phosphorus utilization, and sulfur metabolism were significantly upregulated (p < 0.05). Accordingly, gene expression and extracellular hydrolase activities targeting key biopolymers (i.e., cellulose, hemicellulose, starch, and chitin) were significantly upregulated (p < 0.05) in the area with Sargassaceae. Metabolism reconstruction of metagenome-assembled genomes identified Vibrio, Pseudoalteromonas, Alteromonas, and Exiguobacterium_A as primary OC degraders, with genomic capacities enriched in NO3[-] reduction and assimilatory sulfate reduction. Key environmental drivers─including the C/N ratio, dissolved organic carbon, total dissolved nitrogen (DON), and NO3[-]─shaped microbial metabolic activities during macroalgal decomposition. Our finding demonstrates that microbially driven OC degradation is a pivotal process coupled with nutrients cycling, advancing the mechanistic understanding of microbial carbon processing and its biogeochemical linkages during macroalgal decomposition in coastal ecosystems.}, }
@article {pmid41546704, year = {2026}, author = {Ramadoss, R and Siddique, A and Rashid, N and Liberski, AR and Vincent, AS and Mackey, HR}, title = {Effects of nitrogen and phosphorous concentrations on PHA synthesis by PNSB enriched phototrophic mixed microbial culture.}, journal = {Bioprocess and biosystems engineering}, volume = {49}, number = {3}, pages = {621-636}, pmid = {41546704}, issn = {1615-7605}, support = {NPRP11-S-0110-180245//Qatar National Research Fund/ ; }, mesh = {*Phosphorus/metabolism/pharmacology ; *Nitrogen/metabolism ; *Polyhydroxyalkanoates/biosynthesis ; Wastewater/microbiology ; }, abstract = {Global economic burden due to plastic pollution is estimated to be over $3 trillion annually. Bioplastics derived from bacteria-synthesized biopolymers like polyhydroxyalkanoates (PHAs), are a remarkably versatile sustainable alternative. Research on optimal growth-conditions for microbial PHA-synthesis fed-on sustainable substrates, particularly by phototrophic-mixed-cultures (PMC) enriched with purple non-sulphur bacteria (PNSB) is essential. This study intends to understand the effect of nitrogen and phosphorus concentrations on PHA-production by PMC grown using fuel synthesis wastewater (FSW) (organic by-product of Fischer-Tropsch process) as substrate. Stoichiometric quantification and 16 S metagenomic sequencing followed by statistical and bioinformatic analysis were done. High PHA-production (65-82% of biomass) is observed to be induced by Low-Nitrogen conditions enriching Rhodopseudomonas, Paludibacter and Pleomorphomonas and a Low-Phosphorus condition enriching Rhodopseudomonas, Rhodoplanes and Lentimicrobium. Analysis of metabolic-potential revealed 16 enzymes (of 8 different PHA-synthesis-pathways) inherent within the genomes of bacteria enriched by these culture conditions. This study identifies optimal nitrogen and phosphorus concentrations and the corresponding microbial-composition of FSW substrate-grown PMC-system to maximize PHA-production in a laboratory-scale bioprocess.}, }
@article {pmid41547150, year = {2026}, author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W}, title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111622}, doi = {10.1016/j.ijfoodmicro.2026.111622}, pmid = {41547150}, issn = {1879-3460}, mesh = {Animals ; Horses ; *Milk/microbiology ; Metagenomics ; *Lactobacillales/genetics/physiology ; Fermentation ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/classification/isolation & purification/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Female ; Food Microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.}, }
@article {pmid41547203, year = {2026}, author = {Zhi, C and Wang, D and He, B and Hou, G and Gao, M and Mu, H and Wei, R and Wu, X and Bai, J and Jiao, Y and Hu, X}, title = {Metabolic coupling of arsenic, carbon, nitrogen, sulfur and iron in high-salinity groundwater in the Yellow River Delta: Insights from metagenomic analyses.}, journal = {Water research}, volume = {292}, number = {}, pages = {125368}, doi = {10.1016/j.watres.2026.125368}, pmid = {41547203}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; Sulfur/metabolism ; Arsenic/metabolism ; Iron/metabolism ; Nitrogen/metabolism ; Salinity ; Carbon/metabolism ; Metagenomics ; Rivers/chemistry ; Water Pollutants, Chemical ; }, abstract = {Arsenic (As) mobilization in deltaic aquifers is regulated by tightly linked C-N-S-Fe-As biogeochemical processes, yet the influence of salinity on these interactions remains poorly resolved. Here, we investigated high-salinity groundwater from the Yellow River Delta, where total dissolved solids range from 1 to 35 g/L and As concentrations reach 303 μg/L. By integrating metagenomic sequencing, metagenome-assembled genomes (MAGs), and nitrogen and sulfur isotopic measurements, we characterized how salinity and redox gradients restructure microbial functional potential and regulate As cycling. Functional-gene profiles show a transition from nitrate- and Fe(III)-coupled metabolisms in low-salinity groundwater to sulfate- and sulfite-driven anaerobic pathways under high-salinity conditions, consistent with δ[15]N-NH4[+], δ[15]N-NO3[-], and δ[34]S-SO4[2-] signatures. Genome-resolved analyses further reveal that Pseudomonadota and Desulfobacterota dominate carbon oxidation, nitrogen and iron reduction, and sulfur-intermediate reduction, while Muiribacteriota and Planctomycetota specialize in sulfite reduction and anammox/Feammox, respectively. Together, these results show that microbial communities reorganize along the salinity gradient, with arsenic mobilization associated with nitrogen- and iron-coupled reductive processes in low-salinity groundwater and with sulfur-driven reduction under high-salinity conditions. By linking microbial metabolic interactions to salinity-related redox environments, this study provides a process-based basis for anticipating how arsenic mobility may change as coastal aquifers undergo salinization.}, }
@article {pmid41547254, year = {2026}, author = {Li, C and Liu, Z and Zhao, N and Pan, H and Wang, H and Zhang, Y}, title = {Hidden oral-joint-lung axis: Porphyromonas gingivalis Infection promotes the EMyT of RA-ILD by inhibiting the JUN-regulated palmitoylation balance.}, journal = {International immunopharmacology}, volume = {172}, number = {}, pages = {116210}, doi = {10.1016/j.intimp.2026.116210}, pmid = {41547254}, issn = {1878-1705}, mesh = {Animals ; Humans ; *Porphyromonas gingivalis ; *Arthritis, Rheumatoid/complications/immunology/microbiology ; Mice ; Lipoylation ; *Bacteroidaceae Infections/immunology/complications ; *Lung Diseases, Interstitial/microbiology/immunology/pathology/etiology ; Male ; Lung/pathology ; Cell Line ; *Proto-Oncogene Proteins c-jun/metabolism ; Mice, Inbred DBA ; Arthritis, Experimental ; }, abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a major cause of mortality among patients with rheumatoid arthritis (RA), yet the pathological mechanism linking joint and lung involvement remains poorly understood. The pathogenic role of Porphyromonas gingivalis (P.g) in RA has been established. This study investigated how P.g infection drives RA-ILD through palmitoylation-mediated epithelial-myofibroblast transition (EMyT), thereby uncovering a mechanistic basis for the oral-joint-lung connection.
METHODS: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and 16S rRNA sequencing of fecal samples from patients with RA-ILD were analyzed to assess the association between P.g and RA-ILD. A collagen-induced arthritis (CIA) mouse model and human lung epithelial cell lines (A549 and BEAS-2B) infected with P.g were established. Palmitoylation dynamics, EMyT marker expression, and the function of the hub gene JUN were evaluated using immunopathology, qPCR, western blotting (WB), single-cell sequencing, and molecular docking. Mechanistic studies employed the JUN activator c2-ceramide, the JUN inhibitor pterostilbene, and the palmitoylation inhibitor 2-BP to determine how P.g regulates palmitoylation in promoting RA-ILD.
RESULTS: Both mNGS and 16S rRNA analyses revealed a strong association between Porphyromonas spp. infection and RA/RA-ILD. P.g infection significantly increased EMyT marker expression (collagen I, fibronectin, and vimentin) in vitro and induced pulmonary fibrosis in CIA-ILD mice, with palmitoylation playing a central role. Mechanistically, JUN was identified as a key regulator of palmitoylation. P.g suppressed JUN level, activated ZDHHC3, and inhibited PPT1, leading to palmitoylation imbalance. Activation of JUN by c2-ceramide, combined with inhibition of palmitoylation by 2-BP, effectively suppressed EMyT progression in RA-ILD.
CONCLUSION: This study identifies a novel "oral-joint-lung axis" in which P.g infection promotes EMyT and fibrosis in RA-ILD by disrupting JUN-regulated palmitoylation homeostasis. Modulation of this axis provides a promising therapeutic strategy for RA-ILD.}, }
@article {pmid41547817, year = {2026}, author = {Xiao, Y and Tang, Y and Yan, Y and Cheng, Q and Chen, X and Wang, L and Li, X}, title = {Targeted next-generation sequencing has comparable clinical value to metagenomic NGS for pulmonary infections in hematological malignancy patients: a real-world propensity score-matched study.}, journal = {European journal of medical research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40001-026-03893-0}, pmid = {41547817}, issn = {2047-783X}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is widely recognized in immunocompromised populations due to its unbiased ability to identify pathogens, while targeted next-generation sequencing (tNGS) combines PCR amplification with high-throughput sequencing technology, with advantages of lower costs and shorter turnaround times. However, it remains unclear whether tNGS can be applied in the same way as mNGS for immunodeficient patients with hematologic malignances (HM).
METHODS: This retrospective study analyzed clinical data from 245 HM patients suspected of pneumonia between April 2019 and April 2024. Bronchoalveolar lavage fluid (BALF) samples were tested using either tNGS or mNGS. Propensity score matching (PSM) (1:1) balanced the groups.
RESULTS: tNGS and mNGS showed comparable sensitivity, specificity, and accuracy for pathogen detection (97.3% vs 94.2%, 26.3% vs 26.1%, 82.6% vs 77.2%; all P > 0.05), with similar accuracy across immunodeficiency states (severe immunodeficiency: 80.0% vs 81.8%; non-severe immunodeficiency: 64.7% vs 86.7%; both P > 0.05). For non-severe pneumonia, tNGS was comparable to mNGS (accuracy: 77.9% vs 86.3%, P > 0.05), but mNGS was significantly superior in severe cases (accuracy: 50.0% vs 100.0%, P = 0.002). Both groups improved rate of correct antibiotic use (tNGS: 50.9% to 84.3%; mNGS: 57.1% to 77.8%, P < 0.01) and reduced overuse rates (tNGS: 25.9% to 2.8%; mNGS: 4.8% to 25.4%; P < 0.01), with no difference in chemotherapy intervals (37.5 ± 22.9 days vs 41.0 ± 38.4 days; P = 0.89).
CONCLUSION: In HM patients suspected of pulmonary infection, BALF-tNGS showed comparable diagnostic efficacy as BALF-mNGS, with similar clinical value across varying immunodeficiency states. tNGS is a viable alternative for non-severe pneumonia, while mNGS is superior in severe cases. Collectively, the findings of this study highlight tNGS as an alternative diagnostic approach for HM patients.}, }
@article {pmid41547860, year = {2026}, author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA}, title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {25}, pmid = {41547860}, issn = {2049-2618}, mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.
RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.
CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.}, }
@article {pmid41547908, year = {2026}, author = {Kim, YC and Won, SY and Jeong, BH}, title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {31}, pmid = {41547908}, issn = {1297-9716}, support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; }, mesh = {Animals ; *Prion Diseases/microbiology/prevention & control/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Catechin/analogs & derivatives/pharmacology ; Mice ; Mice, Inbred C57BL ; Biomarkers ; Male ; }, abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.}, }
@article {pmid41548304, year = {2026}, author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T}, title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141134}, doi = {10.1016/j.jhazmat.2026.141134}, pmid = {41548304}, issn = {1873-3336}, mesh = {*Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Microbial Interactions ; Bacteria/genetics ; Genes, Bacterial ; Microbiota ; China ; Water Microbiology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.}, }
@article {pmid41548597, year = {2026}, author = {Zhao, M and Yu, X and Zhao, M and Zhang, G}, title = {Structured framework for the application of metagenomic next-generation sequencing in the whole-process management of lower respiratory tract infections.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {32}, number = {2}, pages = {102910}, doi = {10.1016/j.jiac.2026.102910}, pmid = {41548597}, issn = {1437-7780}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Respiratory Tract Infections/drug therapy/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; Aged ; Adult ; China ; Young Adult ; Tomography, X-Ray Computed ; }, abstract = {OBJECTIVES: This study aims to assess the impact of metagenomic next-generation sequencing (mNGS) on optimizing diagnostic-therapeutic pathways for lower respiratory tract infections (LRTIs).
METHODS: This retrospective observational study analyzed 42 consecutive LRTI patients at Jiading Branch of Shanghai General Hospital (June 2023-October 2024). Comprehensive clinical data were evaluated including demographic features, laboratory result, radiological findings, mNGS interpretation, treatment modifications, and outcomes.
RESULTS: The mNGS detected pathogens in 37/42 patients (88.1 %), despite the fact that 38 patients (90.5 %) had received ineffective empirical antibiotic therapy prior to mNGS testing. More than half the patients (22/42, 52.4 %) had comorbidities and about half the cases were within the normal range in the level of inflammatory biomarker. Pathognomonic CT features suggesting specific pathogens were observed in 33.3 % (14/42) of cases. With regard to the interpretation of mNGS reports combaining the clinical characteristics, the results were consistent with the final diagnosis in 30 (30/42, 71.4 %) patients. Crucially, 92.9 % (39/42) underwent treatment modifications: 66.7 % (28/42) transitioned to targeted/narrower-spectrum antibiotics and 26.2 % (11/42) discontinued antimicrobial therapy following infection exclusion. Patients receiving targeted regimens demonstrated universal clinical improvement with radiological resolution, particularly in complex infections.
CONCLUSION: While mNGS provides robust pathogen detection, its clinical application requires integration with multidimensional patient data. The standardized protocol proposed in this study has the potential to enhances diagnostic efficiency and resource utilization in LRTI management.}, }
@article {pmid41548675, year = {2026}, author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A}, title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: Comparative performance of endogenous vs. exogenous consortia.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134038}, doi = {10.1016/j.biortech.2026.134038}, pmid = {41548675}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Fatty Acids/biosynthesis ; *Microbial Consortia/physiology ; *Microbiota ; Bioreactors/microbiology ; Bacteria/metabolism ; }, abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.}, }
@article {pmid41549250, year = {2026}, author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J}, title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.}, journal = {BMC gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12876-025-04582-8}, pmid = {41549250}, issn = {1471-230X}, support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; }, }
@article {pmid41549294, year = {2026}, author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC}, title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.}, journal = {Current microbiology}, volume = {83}, number = {2}, pages = {139}, pmid = {41549294}, issn = {1432-0991}, mesh = {*Lakes/virology ; *Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; India ; Phylogeny ; Ecosystem ; Biodiversity ; Fresh Water/virology ; Bacteriophages/genetics/classification/isolation & purification ; }, abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.}, }
@article {pmid41549319, year = {2026}, author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Chen, J and Fang, H}, title = {The impact of the timing of mNGS-guided antibiotic adjustment on clinical outcomes in ICU patients with severe community-acquired pneumonia: a retrospective study.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {25}, number = {1}, pages = {12}, pmid = {41549319}, issn = {1476-0711}, support = {No. 2023KY1296//Zhejiang Provincial Department of Health/ ; No. 2022K71//the Quzhou Bureau of Science and Technology/ ; }, mesh = {Humans ; *Community-Acquired Infections/drug therapy/microbiology/mortality/diagnosis ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Intensive Care Units ; Middle Aged ; Aged ; *High-Throughput Nucleotide Sequencing/methods ; Treatment Outcome ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics/methods ; *Pneumonia/drug therapy/microbiology/mortality ; Community-Acquired Pneumonia ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of intensive care unit (ICU) admission and mortality. Prompt pathogen identification and timely administration of appropriate antimicrobial therapy are essential for improving patient outcomes. Although metagenomic next-generation sequencing (mNGS) enables rapid pathogen detection, the prognostic impact of the timing of mNGS-guided antibiotic adjustment remains unclear.
METHODS: We conducted a multicenter retrospective study of ICU patients diagnosed with SCAP who underwent both bronchoalveolar lavage fluid (BALF) mNGS and conventional microbiological tests (CMTs). Patients were categorized into early (≤ 72 h) and late (> 72 h) antibiotic adjustment groups based on the interval from ICU admission to the time of antibiotic adjustment guided by mNGS results. Subgroup analyses were performed according to immune status.
RESULTS: In our study, mNGS significantly outperformed conventional microbiological tests (CMTs) in pathogen detection (92.70% vs. 57.18%, P < 0.001), with a particularly higher yield for mixed infections (51.63% vs. 19.14%, P < 0.001). Early mNGS-guided antibiotic adjustment was associated with a significantly reduced 28-day mortality compared to late adjustment (41.98% vs. 53.76%, P = 0.037). Furthermore, multivariate logistic regression analysis confirmed early adjustment as an independent protective factor for 28-day mortality (adjusted OR = 0.44, 95% CI: 0.23-0.83, P = 0.011). In the immunocompromised subgroup, early mNGS-guided adjustment was associated with significantly lower 28-day mortality than late adjustment (39.29% vs. 60.00%, P = 0.029), with a significant interaction observed between timing and immune status (P = 0.042).
CONCLUSION: Early mNGS-guided antibiotic adjustment is associated with improved survival among ICU patients with SCAP. This benefit is more pronounced in immunocompromised patients, underscoring the importance of early mNGS application to guide antimicrobial decision-making in this vulnerable population.}, }
@article {pmid41550372, year = {2025}, author = {Tenea, GN and Jarrin-V, P and Lin, L}, title = {Editorial: Trigger the microbiome changes in foods via metagenomic technologies: from diagnostic to potential changes in product safety or quality risk profiles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1766291}, doi = {10.3389/fbioe.2025.1766291}, pmid = {41550372}, issn = {2296-4185}, }
@article {pmid41550607, year = {2025}, author = {Zhang, W and Zhang, L and Liu, H}, title = {Correction: Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1760028}, doi = {10.3389/fped.2025.1760028}, pmid = {41550607}, issn = {2296-2360}, abstract = {[This corrects the article DOI: 10.3389/fped.2025.1594899.].}, }
@article {pmid41551013, year = {2025}, author = {Wang, C and Chang, K and Chen, M and Zou, X and Ni, Y and Zhang, Q and Zhao, L and Xing, B and Guo, L and Chen, W and Cao, B}, title = {Enrichment of the commensal microbiome in the lower respiratory tract is associated with improved outcomes following lung transplantation.}, journal = {Chinese medical journal pulmonary and critical care medicine}, volume = {3}, number = {4}, pages = {308-318}, pmid = {41551013}, issn = {2772-5588}, abstract = {BACKGROUND: Alterations in the respiratory microbiome are common following lung transplantation; however, the complex relationship between microbial composition and posttransplant clinical outcomes remains insufficiently characterized. This study aimed to delineate microbial signatures within the lower respiratory tract and to elucidate their associations with posttransplant outcomes in lung transplant recipients (LTRs).
METHODS: Metagenomic sequencing was performed on 138 bronchoalveolar lavage fluid (BALF) samples collected in 2023 from patients who had undergone lung transplantation between 2017 and 2023 at the China-Japan Friendship Hospital. Lung function indices, hematologic parameters, and serum cytokine levels were assessed, and patients were prospectively followed to record adverse clinical events.
RESULTS: The lung microbiome of stable LTRs formed four distinct clusters, exhibiting marked heterogeneity in both α- and β-diversity. The most prevalent cluster, enriched with oral-origin commensals, such as Neisseria subflava (N. subflava), Prevotella melaninogenica, and Streptococcus mitis (S. mitis), demonstrated the highest microbial diversity, and was associated with the lowest C-reactive protein levels, fewest adverse events, and the longest complication-free postoperative duration. In contrast, a virus-enriched cluster characterized by reduced diversity and high abundance of Torque teno virus and Cytomegalovirus human betaherpesvirus 5 was associated with poorer outcomes. BALF samples from infected LTRs exhibited more severe dysbiosis than those from immunocompetent individuals, with reduced diversity and pathogen dominance. Concurrent infections aggravated antibody-mediated rejection-related lung function decline, indicating complex microbiome-immune interactions. Integrative modeling of microbiome, hematologic, and pulmonary function data yielded superior diagnostic performance for infection detection (area under the receiver operating characteristic curve = 0.93).
CONCLUSION: The composition of the lung microbiome may serve as a prognostic biomarker for clinical outcomes after lung transplantation. The presence of diverse, commensal-dominated communities was associated with improved outcomes, whereas viral enrichment correlated with adverse events. These findings underscore the clinical importance of microbiome monitoring in posttransplant management and suggest that targeted modulation of microbial communities could improve long-term graft stability and patient prognosis.}, }
@article {pmid41551170, year = {2026}, author = {Chang, CC and Pak, J and Bae, S and Kim, GD and Son, HS}, title = {Impact of low aging temperature on the microbial and metabolic dynamics of rice wine during long-term storage.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101294}, pmid = {41551170}, issn = {2665-9271}, abstract = {This study investigated the effects of aging temperature and microbial inoculation on the physicochemical, microbiological, and metabolic properties of Korean rice wine (makgeolli) during long-term storage. Samples were aged at three different temperatures (4 °C, -1 °C, and -5 °C) for 180 days and were inoculated with Lactiplantibacillus plantarum or Saccharomyces cerevisiae to examine their respective influences on metabolite shifts during cold storage. Microbial communities were analyzed using amplicon (16S rRNA) and shotgun metagenomic sequencing, and metabolite profiles were determined by GC-MS to provide an integrative understanding of microbial and metabolic stability during long-term cold storage. Lower aging temperatures reduced fluctuations in metabolic and microbial activities, particularly among LAB, thereby contributing to a more stable physicochemical profile and extended shelf life. During rice wine aging, LAB exerted a more pronounced effect on metabolite dynamics than yeast, particularly for pyruvate, γ-aminobutyric acid, and lactic acid, underscoring their role in the aging process. Additionally, sub-zero aging temperatures preserved the initial microbial composition, limited enzymatic degradation, and stabilized organic acid profiles, reflecting enhanced chemical stability of the product during aging. While such chemical stability may have implications for sensory outcomes, this remains a hypothesis that requires direct sensory evaluation in future studies. Overall, the findings suggest that controlled storage temperatures and targeted microbial inoculation can improve the chemical and microbiological stability of rice wine during long-term storage.}, }
@article {pmid41551178, year = {2026}, author = {Esposito, A and Valentino, V and Tagliamonte, S and Sequino, G and Vitaglione, P and Ercolini, D and De Filippis, F}, title = {Development of a synbiotic dietary supplement containing potential Next Generation Probiotics for modulation of the gut microbiome and metabolome.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101289}, pmid = {41551178}, issn = {2665-9271}, abstract = {The term Next Generation Probiotics (NGPs) refers to microbial strains positively impacting on human health, but do not belong to common probiotic species (e.g., lactic acid bacteria, LAB). We characterized genomically and phenotypically 14 strains isolated from the gut microbiome of healthy individuals, to evaluate their ability to produce urolithins, equol and short-chain fatty acids (SCFA). The 4 most promising strains (namely Bacteroides uniformis A4, Bacteroides thetaiotaomicron A14, unclassified Bacteroidaceae A26 and unclassified Lachnospiraceae A49) were used for the production of a synbiotic formulation, containing the strains and the precursors of health-promoting molecules. This dietary supplement was administered for 2 weeks to a continuous mucosal-Simulator of the Human Intestinal Microbial Ecosystem (mSHIME) model inoculated with a faecal sample from a low fiber-consuming donor. We performed Shotgun Metagenome Sequencing on a total of 204 samples collected from lumen and mucosa compartments, and determined the concentration of SCFA, equol and urolithin. Our results highlighted that the potential NGP strains contained in the supplement persisted in the gut ecosystem during 2 weeks of washout (Wilcoxon's rank sum test, p-value <0.05). In addition, the treatment led to an enrichment in beneficial taxa and to an increase in the production of SCFAs (p-value <0.05). This study demonstrated that feeding the gut microbiota with NGPs and dietary prebiotics can modulate both the gut microbiome and metabolome, suggesting a potential beneficial impact on human health. However, further in vivo studies are needed to confirm these results.}, }
@article {pmid41551289, year = {2025}, author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP}, title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {}, pmid = {41551289}, issn = {2993-3935}, support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R35 GM155168/GM/NIGMS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK122042/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; }, abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.}, }
@article {pmid41551358, year = {2026}, author = {Wu, X and Yin, Y and Guo, Y and Sun, L and Shi, Q and Ji, T and Wang, H}, title = {A case of atypical cat scratch disease with bone and joint infection diagnosed through clinical metagenomics.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02482}, pmid = {41551358}, issn = {2214-2509}, abstract = {Cat scratch disease (CSD) is a common zoonotic infection caused by Bartonella henselae (B. henselae) and typically presents with fever and regional lymphadenopathy. However, skeletal involvement, including osteomyelitis and arthritis, is rare. We report a 28-year-old immunocompetent female who presented with a five‑month history of persistent right knee swelling without fever or lymphadenopathy. She had previously undergone distal femoral tumor resection with prosthetic joint replacement, and this episode of chronic knee swelling together with the imaging findings was highly suggestive of prosthetic joint infection. Approximately one month before the onset of knee swelling, she had sustained a scratch from a cat. Conventional microbiological tests, including joint effusion and drainage fluid cultures, were negative. Metagenomic next‑generation sequencing (mNGS) of joint effusion identified B. henselae with 27 specific sequence reads, 0.1 % genome coverage and an RPM ratio of 1.9. This result was subsequently confirmed by a quantitative PCR assay targeting the nuoG gene. The patient underwent surgical debridement followed by oral minocycline and rifampin for 8 weeks, resulting in marked clinical improvement. This case underscores that B. henselae infection should be considered in culture‑negative bone and joint, particularly prosthetic joint, infections with a history of cat exposure, and that mNGS can provide valuable etiological evidence in atypical CSD.}, }
@article {pmid41551517, year = {2025}, author = {Wang, Y and Zhang, X}, title = {Rapid diagnosis of Lemierre's syndrome by metagenomic next-generation sequencing: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1730031}, pmid = {41551517}, issn = {2296-858X}, abstract = {Lemierre's syndrome, also known as postopharyngeal septicaemia or necrobacillosis, is a rare, fatal opportunistic infection, often caused by Fusobacterium necrophorum invading the throat. Bacterial culture is a conventional method to establish a diagnosis, but is time-consuming and insensitive in some cases. Metagenomic next-generation sequencing (mNGS), as an emerging technique, has become an important supplementary detection method for infectious diseases. It greatly favors the rapid, precise diagnosis and treatment of Lemierre's syndrome through accurately obtaining etiological information. We reported a case of Lemierre's syndrome that was rapidly and accurately diagnosed by mNGS.}, }
@article {pmid41551583, year = {2026}, author = {Chen, T and Huang, R and Huang, Y and Wang, J and Wang, Z and Zhang, X}, title = {Shared signatures of alcohol-associated dysbiosis in humans and non-human primates.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100534}, pmid = {41551583}, issn = {2666-5174}, abstract = {Alcohol use disorder (AUD) is a chronic brain disease with limited therapeutic options. Increasing evidence suggests that the gut microbiome contributes to AUD via the microbiome-gut-brain axis. Here, we conducted a cross-species investigation of gut microbiota alterations in patients with clinically diagnosed AUD and in non-human primates (NHPs) subjected to long-term alcohol (ethanol) self-administration, using metagenomic sequencing. Both cohorts showed reduced microbial diversity and conserved dysbiosis, with consistent depletion of Verrucomicrobia, Actinobacteria, Faecalibacterium, Akkermansia, Intestinibacter, Phascolarctobacterium, and Ruminococcus, alongside increased Blautia and Coprococcus. These microbial shifts correlated with liver function indices, notably positive associations between Ruminococcus and bilirubin levels in both species, suggesting a potential role in liver injury. Functional analyses revealed conserved microbial adaptations, including upregulated DNA repair pathways, fermentative energy metabolism, and downregulated glutamate/glutamine biosynthesis. Together, these results identify evolutionarily conserved microbial and metabolic alterations linking alcohol consumption, gut dysbiosis, and hepatic dysfunction. Our cross-species evidence highlights the gut microbiome as a potential biomarker and therapeutic target for AUD.}, }
@article {pmid41551588, year = {2026}, author = {Arnold, CB and Kelder, A and Woltemate, S and Geffers, R and von Felde, A and Knudsen, KEB and Visscher, C and Vital, M}, title = {Uncovering differences in rye and wheat degradation by human gut microbiota applying a quantitative multi-metaOmics in vitro approach.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100532}, pmid = {41551588}, issn = {2666-5174}, abstract = {While wheat is the most common grain used in bread-making worldwide, rye is popular in many European countries too. Rye is associated with several health benefits, which is attributed to its comparatively higher dietary fiber content (primarily fructans and arabinoxylans) that promote production of short chain fatty acids (SCFA) by gut microbiota, in particular butyrate. Intervention studies revealed bacterial alterations upon rye administration, however, the detailed mechanisms involved in its degradation are not understood. We grew fecal communities (n = 20) on pre-digested rye and wheat, respectively, demonstrating that rye was yielding higher cell and SCFA concentrations in almost all samples along with distinct abundances of many taxa. A multi metaOmics (metagenomics/metatranscriptomics) approach (n = 5 donors) showed higher bacterial growth rates for most taxa on rye compared to wheat. The higher growth rate of rye was accompanied by increased expression of genes involved in growth and energy generation suggesting higher carbon substrate accessibility. The carbohydrate active enzyme repertoire was greatly distinct between communities growing on the two substrates with several specific glycoside hydrolases increasingly expressed in rye containing cultures. Agathobacter faecis was revealed as the key butyrogenic species for rye degradation and its expression pattern based on metagenome assembled genomes showed adaptation to growth on rye via expression of genes involved in arabinoxylan degradation and fructose (major monomer of fructans) uptake. Our study verifies higher SCFA production from rye over wheat and gives detailed insights into molecular mechanisms involved. It suggests that the observed health benefits of rye are mediated by gut microbiota.}, }
@article {pmid41551788, year = {2026}, author = {Song, Q and Li, J and Liu, Y and Li, W and Li, M and Zhang, B and Guo, B}, title = {Metagenomics and volatile metabolomics reveal microbial succession and its correlations with fruity flavor volatile compounds during Mianhua industrial processing.}, journal = {Food chemistry: X}, volume = {33}, number = {}, pages = {103446}, pmid = {41551788}, issn = {2590-1575}, abstract = {Mianhua, a traditional fermentation-type staple food popular in northern China, undergoes dynamic microbial and volatile compound changes during industrial processing. 848 volatile compounds were identified using volatile metabolomics dominated by esters (18.51 %), notably hexanoic acid ethyl ester and octanoic acid ethyl ester, which confer fruity flavors. Metagenomics analysis revealed Proteus (25.93 %), Fructilactobacillus (16.63 %), Lactobacillus (10.16 %) and Companilactobacillus (7.14 %) as dominant genera. Mixing with traditional starters was critical for flavor development, driven by microbial succession and synergistic interactions between Lactobacillaceae (e.g., Fructilactobacillus sanfranciscensis and Lactobacillus helveticus) and Kazachstania during fermentation. Notably, F. sanfranciscensis and L. helveticus were significantly correlated with the formation of key esters with fruity characteristics, elucidating their roles in substrate conversion via carbohydrate metabolism and the esterification pathways. This study clarifies the microbial contributions to fruity flavor and provides insights into volatile-microbiota correlations, laying a foundation for future flavor-oriented research and industrial applications of microbiota regulation in Mianhua production.}, }
@article {pmid41551812, year = {2026}, author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Zhang, Z and Xie, F and Ai, L}, title = {Docynia delavayi polyphenols enhance short-chain fatty acid synthesis via the chlorogenic acid-caffeic acid-protocatechuic acid pathway: insights from in vitro digestion-fermentation.}, journal = {Food chemistry: X}, volume = {33}, number = {}, pages = {103416}, pmid = {41551812}, issn = {2590-1575}, abstract = {Docynia delavayi fruit polyphenols (DDP) demonstrate potential for enhancing short-chain fatty acid (SCFA) synthesis; however, underlying mechanisms remain poorly understood. This study utilized an in vitro digestion-fermentation model combined with multi-omics analyses to explore these mechanisms. The in vitro model revealed notable alterations in both 1,1'-diphenyl-2-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical-scavenging capacities, as well as in total phenolic and flavonoid content, accompanied by increased production of acetic, propionic, and butyric acids. Metagenomic indicated that DDP stimulated Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Bifidobacterium longum, and Bifidobacterium bifidum growth. Metabolomics demonstrated enrichment of SCFA-associated metabolic pathways, including propanoate and butyrate metabolism, and identified caffeic acid and protocatechuic acid as primary bioactive metabolites produced from DDP. Multi-omics analysis suggested that DDP modulated gut microbiota by enriching the chlorogenic acid-caffeic acid-protocatechuic acid metabolic pathway (r > 0.95, p < 0.01), ultimately boosting SCFA biosynthesis. This study offers new insights into the mechanisms by which polyphenols regulate health.}, }
@article {pmid41551931, year = {2026}, author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I}, title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {1}, pages = {lqaf172}, pmid = {41551931}, issn = {2631-9268}, support = {R01 AI151059/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; }, abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.}, }
@article {pmid41552431, year = {2026}, author = {Buonaccorsi, A and McMullen, BN and Builder, B and Drummond, K and Halteman, S and See, JC and Thomas, E and Viands, A and Worley, S and Wright, JR and Keeney, J and Lamendella, R}, title = {Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101305}, pmid = {41552431}, issn = {2352-7714}, abstract = {The rise in tick populations across the United States has contributed to a surge in tick-borne diseases, with Pennsylvania ranking among the highest in reported cases. To better understand local pathogen prevalence and microbial community structure, an integrative study of ticks collected from ten recreational trails in Huntingdon County, Pennsylvania during the summer of 2023 was conducted. A total of 96 ticks were sampled, with 33 PCR-positive specimens selected for shotgun metagenomic sequencing. Pathogen screening via qPCR detected Borreliella burgdorferi, Borrelia miyamotoi, Babesia spp., and Anaplasma phagocytophilum. Shotgun metagenomics revealed a broader diversity of tick-borne pathogens, including Rickettsia and Ehrlichia spp., and demonstrated increased sensitivity by detecting low-abundance pathogens in samples that were PCR-negative. Co-infections were common, and multivariate statistical analysis identified significant associations between environmental variables (e.g., humidity, time of day, land cover) and microbial diversity and predicted gene function. Notably, diversity was higher in ticks collected during early afternoon and from northern sites. Co-occurrence network analysis showed Rickettsia as a central taxon with multiple significant positive associations with other microbes while other pathogens were largely absent or peripheral. These findings underscore the enhanced resolution of metagenomic approaches for pathogen detection and the value of combining molecular surveillance with ecological metadata. Our study provides critical insights into local tick microbiomes and pathogen prevalence, which may inform public health interventions and vector management strategies in central Pennsylvania.}, }
@article {pmid41552860, year = {2026}, author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A}, title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.}, journal = {Molecular ecology resources}, volume = {26}, number = {2}, pages = {e70102}, pmid = {41552860}, issn = {1755-0998}, support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; }, mesh = {*DNA, Environmental/isolation & purification/genetics ; *Biodiversity ; *Deoxyribonucleases/metabolism ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/classification/genetics ; Rivers/chemistry ; *Metagenomics/methods ; }, abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.}, }
@article {pmid41552936, year = {2026}, author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y}, title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.}, journal = {Food & function}, volume = {17}, number = {3}, pages = {1451-1464}, doi = {10.1039/d5fo04604a}, pmid = {41552936}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Rutin/pharmacology/administration & dosage ; Male ; *Insulin Resistance ; *Glycation End Products, Advanced/adverse effects/metabolism ; Mice ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dietary Advanced Glycation End Products ; }, abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.}, }
@article {pmid41552949, year = {2026}, author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B}, title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.}, journal = {Journal of phycology}, volume = {62}, number = {1}, pages = {25-43}, pmid = {41552949}, issn = {1529-8817}, support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; }, mesh = {*Diatoms/classification/genetics/growth & development/physiology/ultrastructure ; Phylogeny ; Germany ; Sweden ; Algal Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.}, }
@article {pmid41554738, year = {2026}, author = {Zheng, J and Zhang, C and Xiang, S and Li, M and Wang, H and Shi, K and Tondrob, D and Han, Y}, title = {Integrated metabolomics and metagenomics uncover pathogenic mechanisms of Fusarium wilt and faba bean defense responses.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {25}, pmid = {41554738}, issn = {2396-8370}, support = {31901929//National Natural Science Foundation of China/ ; cstc2021jcyj-msxmX1021//Natural Science Foundation of Chongqing Municipality/ ; }, abstract = {Fusarium wilt diseases pose a huge threat to faba bean (Vicia faba L.) production globally, with significant outbreaks in Chongqing, China. Symptomatic plants showed wilting leaves and rotten roots, ultimately perishing in the advanced stage. Morphological features, multilocus phylogenetic analyses, and pathogenicity tests demonstrated that the primary causal agent was Fusarium oxysporum. Untargeted metabolomics of faba beans revealed substantial metabolic differences in the infected faba bean roots. Plants responded to fungal biotic stress by reprogramming key metabolic pathways, including alanine, aspartate, and glutamate metabolism, the citrate cycle, arginine biosynthesis, and jasmonic acid metabolism, which collectively underscore activated defense responses. Metagenome sequencing showed that Fusarium wilt significantly reshaped the structure of the rhizosphere microbiota and affected the abundance of genes encoding element cycling in soil. This work elucidates the pathogenic mechanisms of F. oxysporum by integrating pathogen identification, host metabolism, and microbiome ecology. Our findings offer biomarkers for disease diagnosis and targets for biocontrol, advancing sustainable management of Fusarium wilt diseases in legumes.}, }
@article {pmid41554846, year = {2026}, author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A}, title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5761}, pmid = {41554846}, issn = {2045-2322}, support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; }, mesh = {Animals ; Larva/microbiology/drug effects/growth & development ; *Disinfection/methods ; *Microbiota/drug effects ; *Ovum/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology/growth & development ; Disinfectants/pharmacology ; Bacteria/genetics/classification/drug effects ; }, abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.}, }
@article {pmid41555276, year = {2026}, author = {Zhang, J and Feng, S and Liu, Z and Xie, K and Gu, C and Shen, J and Zhang, Y and Zhou, Y}, title = {Surgical treatment of Emphysematous Osteomyelitis of the spine in malnutrition and anemia patient: a rare case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {82}, pmid = {41555276}, issn = {1471-2334}, abstract = {BACKGROUND: Emphysematous Osteomyelitis is a rare and potentially fatal form of severe osteomyelitis. It is characterized by gas produced by pathogenic bacteria accumulating in bone structures and surrounding soft tissues. Its rarity and severe nature pose significant challenges for diagnosis and treatment. This case report describes the diagnosis and treatment of Emphysematous Osteomyelitis of the spine in a patient with long-term malnutrition and anemia.
CASE PRESENTATION: A 72-year-old agricultural worker presented with persistent low back pain accompanied by radiating pain in both lower limbs for one month. The patient reported continuous dull pain that worsened with postural changes and improved when lying flat. Based on clinical presentation, biochemical indicators, and imaging studies, spinal infection was initially suspected. Empirical antimicrobial therapy administered for two weeks after admission proved ineffective and was complicated by an epidural abscess, leading to the decision for surgical intervention in the third week. Intraoperative tissue samples were identified through culture identification and high-throughput culture and metagenomic pathogen detection, identifying Citrobacter koseri and Staphylococcus aureus as causative pathogens. Postoperatively, based on antimicrobial susceptibility testing results, treatment was switched to intravenous meropenem and levofloxacin. One month postoperatively, the patient showed good recovery with normalized infection markers, no fever, and significant pain relief.
DISCUSSION AND CONCLUSION: In summary, this rare and severe form of Emphysematous Osteomyelitis requires prompt diagnosis and treatment in clinical practice. The diagnosis of Emphysematous Osteomyelitis of the spine relies on imaging studies. Failure to achieve accurate and timely diagnosis may lead to misdiagnosis or delayed treatment, which not only compromises therapeutic efficacy but may also result in catastrophic consequences. Timely antibiotic therapy, early detection, and aggressive surgical intervention when necessary are key to the successful management of Emphysematous Osteomyelitis of the spine.}, }
@article {pmid41555453, year = {2026}, author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M}, title = {Spatial and temporal patterns of public transit aerobiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {64}, pmid = {41555453}, issn = {2049-2618}, mesh = {*Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Humans ; *Air Microbiology ; Metagenomics/methods ; *Microbiota/genetics ; Cities ; Seasons ; Biodiversity ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.
RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.
CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.}, }
@article {pmid41556085, year = {2026}, author = {Chen, J and Ling, D and Wang, F and Liu, L and Ren, Y and Chen, C and Su, N}, title = {Septic Shock Caused by Coinfection of Shewanella algae Bloodstream Infection and Epstein-Barr Virus: Clinical Characteristics and Genomic Analysis.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70221}, pmid = {41556085}, issn = {2045-8827}, support = {2023170//Chengdu Medical Research Project/ ; Q22080//Youth Innovation Project of Sichuan Medical Association/ ; 2024001//Youth Innovation Medical Research Project of Chongzhou People's Hospital/ ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Bacteremia/microbiology/complications ; China ; *Coinfection/diagnosis/microbiology/virology ; *Epstein-Barr Virus Infections/complications/virology/diagnosis ; Genome, Bacterial ; Genomics ; *Gram-Negative Bacterial Infections/microbiology/complications/diagnosis ; *Herpesvirus 4, Human/isolation & purification/genetics ; Microbial Sensitivity Tests ; Phylogeny ; *Shewanella/genetics/isolation & purification/classification/pathogenicity ; *Shock, Septic/microbiology/diagnosis/virology ; Virulence Factors/genetics ; }, abstract = {Shewanella algae, a marine-origin opportunistic pathogen, has shown a significant increase in non-coastal infections, yet its environmental adaptability and synergistic pathogenic mechanisms with Epstein-Barr virus (EBV) coinfection remain unclear. This study reports a clinical case of S. algae bloodstream infection complicated by EBV reactivation leading to septic shock in Sichuan Province, China, and elucidates the molecular mechanisms through genomic analysis. Pathogen identification was performed via blood culture, antibiotic susceptibility testing, and genomic annotation. The strain harbored resistance genes (acrB, tolC, tet(35), golS) and virulence factors (bplL/bplF, clpC/clpP, tonB). Phylogenetic analysis indicated the highest genetic affinity to freshwater-derived Shewanella chilikensis, while pan-genome analysis identified 1412 unique genes, including transmembrane transporters and carbohydrate-active enzyme genes, suggesting freshwater adaptive evolution. Metagenomic next-generation sequencing (mNGS) detected a high EBV load. The patient succumbed to multi-organ failure. This study reveals that S. algae may evolve freshwater adaptability to cause inland infections, and EBV coinfection accelerates septic shock through immunosuppression and inflammatory cascades. Genomic analysis provides critical insights for precision diagnosis and treatment of polymicrobial infections.}, }
@article {pmid41556347, year = {2026}, author = {}, title = {Correction to: HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.}, journal = {Nucleic acids research}, volume = {54}, number = {2}, pages = {}, doi = {10.1093/nar/gkag014}, pmid = {41556347}, issn = {1362-4962}, }
@article {pmid41556498, year = {2026}, author = {Becsei, Á and Munk, P and Fuschi, A and Otani, S and Stéger, J and Visontai, D and Papp, K and Brinch, C and Kant, R and Weinstein, I and Vapalahti, O and de Graaf, M and Schapendonk, CME and Roelfsema, J and van den Beld, M and Pijnacker, R and Franz, E and Alba, P and Battisti, A and De Cesare, A and Indio, V and Troja, F and Sironen, T and Oliveri, C and Pasquali, F and Liachko, I and Auch, B and O'Cathail, C and Bányai, K and Makó, M and Pollner, P and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM}, title = {A comprehensive database for biological data derived from sewage in five European cities.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {41556498}, issn = {1758-0463}, support = {NNF16OC0021856//Novo Nordisk Foundation/ ; NNF24SA0094147//Novo Nordisk Foundation/ ; 874735//Horizon 2020/ ; INV-044643/GATES/Gates Foundation/United States ; NKKP-153428//National Research, Development and Innovation Office of Hungary/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office of Hungary/ ; }, mesh = {Cities ; *Databases, Genetic ; Europe ; *Metagenome ; *Metagenomics ; *Sewage/microbiology ; Datasets as Topic ; }, abstract = {Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.}, }
@article {pmid41556507, year = {2026}, author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M}, title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.}, journal = {Global change biology}, volume = {32}, number = {1}, pages = {e70704}, doi = {10.1111/gcb.70704}, pmid = {41556507}, issn = {1365-2486}, support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Metagenomics ; *Metagenome ; *Stress, Physiological ; Biodiversity ; *Climate Change ; Ecosystem ; Bacteria/genetics/classification ; }, abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.}, }
@article {pmid41556662, year = {2026}, author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H}, title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0142725}, pmid = {41556662}, issn = {2379-5077}, support = {2022YFC2302700, 2023YFC2305900//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Kenya ; *Microbiota/genetics ; *Aedes/microbiology/virology ; *Culex/microbiology/virology ; *Transcriptome ; Phylogeny ; Bacteria/genetics/classification/isolation & purification ; Geography ; Virome ; Mosquito Vectors/microbiology/virology ; }, abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.}, }
@article {pmid41556741, year = {2026}, author = {Cao, L and Wang, X and Zhou, Y and Qiu, J and Zeng, Q and Zhang, C and Pan, L}, title = {Diagnosis of Paralytic Rabies by Metagenomics Next-Generation Sequencing: A Case Report and Review of the Literature.}, journal = {Veterinary medicine and science}, volume = {12}, number = {1}, pages = {e70748}, pmid = {41556741}, issn = {2053-1095}, mesh = {Animals ; Dogs ; *Dog Diseases/diagnosis/virology ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics ; *Rabies/diagnosis/veterinary/virology ; *Rabies virus/genetics/isolation & purification ; }, abstract = {Paralytic rabies is an atypical form of the disease that is notoriously difficult to diagnose early due to the absence of classic features like hydrophobia. The case being discussed presents a patient who has altered mental status, for whom the initial diagnosis was difficult due to an absent clear bite history and typical symptoms. The final diagnosis of the case was confirmed by metagenomic next-generation sequencing (mNGS) of directly from cerebrospinal fluid, which led to the detection of the rabies virus. This case underscores the critical diagnostic value of mNGS in identifying elusive neurotropic infections.}, }
@article {pmid41557465, year = {2026}, author = {Ivanov, A and Popov, V and Morozov, M and Olekhnovich, E and Ulyantsev, V}, title = {MetaFX: feature extraction from whole-genome metagenomic sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {2}, pages = {}, pmid = {41557465}, issn = {1367-4811}, support = {23-75-10125//Russian Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Software ; *Whole Genome Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Metagenome ; Machine Learning ; Inflammatory Bowel Diseases/microbiology ; Databases, Genetic ; }, abstract = {MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers.
RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average.
MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.}, }
@article {pmid41557799, year = {2026}, author = {Liao, T and Chen, S and Wang, S and Huang, Y and Tsui, SKW and Stüeken, EE and Cao, Q and Luo, H}, title = {Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth's history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {4}, pages = {e2515709123}, pmid = {41557799}, issn = {1091-6490}, mesh = {*Bacteria, Aerobic/genetics/metabolism/classification ; Earth, Planet ; Genome, Bacterial ; Genetic Markers ; Oxygen/metabolism ; Phylogeny ; Evolution, Molecular ; Machine Learning ; Aerobiosis ; }, abstract = {The transition from anaerobic to aerobic life was a pivotal adaptation in Earth's history, yet the timing and genomic drivers remain poorly resolved. Traditional approaches relying on oxygen-utilizing genes need improvement for obligate anaerobes and fragmentary environmental genomes, where gene absence may reflect poor assembly rather than phenotype. We developed a machine learning model (GBDT40-LR) to predict microbial oxygen requirements using 40 broadly conserved genes, 35 without direct oxygen roles. This approach overcomes incompleteness biases in environmental genomes. Applied to 80,787 bacterial genomes [including metagenome-derived assemblies (MAGs)], the model classified 42,014 aerobes and 38,775 anaerobes, enabling large-scale ancestral reconstruction. Molecular clock dating indicates an emergence of aerobic bacterium prior to the Great Oxidation Event (GOE, 2.5 to 2.3 Ga), likely around ~2.7 Ga. Aerobic lineages subsequently diversified during the GOE and Neoproterozoic Oxygenation Event (NOE, 0.8 to 0.55 Ga), with persistent anaerobe diversity across Earth's oxygenation. This establishes that aerobic bacteria originated planetary oxygenation, potentially by 200 to 400 My, providing insights into phenotypic evolution and prolonged anaerobe-aerobe coexistence.}, }
@article {pmid41558030, year = {2026}, author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, A and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E}, title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.}, journal = {Blood advances}, volume = {10}, number = {6}, pages = {1979-1991}, pmid = {41558030}, issn = {2473-9537}, mesh = {Humans ; *Graft vs Host Disease/etiology/epidemiology/microbiology ; Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Female ; Male ; Incidence ; Middle Aged ; *Bacteria/metabolism ; Adult ; *Carbohydrate Metabolism ; Retrospective Studies ; *Gastrointestinal Diseases/etiology/epidemiology/microbiology ; Metagenomics ; }, abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of stool from patients with allo-HSCT (N = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate-degrading functionality of these bacteria, we investigated gene abundances for carbohydrate-active enzymes (CAZymes) and found that Parabacteroides merdae, P distasonis, and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared with those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with a reduced risk of LGI-GVHD. All these findings show the importance of the carbohydrate-degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.}, }
@article {pmid41558076, year = {2026}, author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S}, title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106427}, pmid = {41558076}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Chickens/immunology/microbiology/physiology ; *T-Lymphocytes, Regulatory/drug effects/immunology ; *Triterpenes/administration & dosage/metabolism/pharmacology ; Ursolic Acid ; Dietary Supplements/analysis ; Diet/veterinary ; *Intestines/drug effects/physiology/microbiology ; Animal Feed/analysis ; *Th17 Cells/drug effects/immunology ; Random Allocation ; Dose-Response Relationship, Drug ; Male ; }, abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.}, }
@article {pmid41558305, year = {2026}, author = {Gu, X and Yu, P and Duan, X and Chen, J and Zhou, Y and Jian, Q and Huang, M and Xue, G and Li, X}, title = {Metatranscriptomics reveals system-specific viral adaptive strategies and prokaryotic defense trade-offs across anaerobic digestion systems.}, journal = {Water research}, volume = {292}, number = {}, pages = {125401}, doi = {10.1016/j.watres.2026.125401}, pmid = {41558305}, issn = {1879-2448}, mesh = {Anaerobiosis ; Transcriptome ; Metagenomics ; Viruses/genetics ; }, abstract = {Viruses are increasingly recognized as critical modulators of microbial community dynamics in anaerobic digestion (AD) systems, yet their ecological roles across distinct AD process types remain poorly understood. Here, we investigated viral ecology in three full-scale food waste treatment systems representing three predominant process types-dry AD (Dry-AD), wet AD (Wet-AD), and two-stage wet AD (2St-wet-AD)-through integrated metatranscriptomics and metagenomics. We recovered 4404 viral operational taxonomic units (vOTUs) and 206 metagenome-assembled genomes (MAGs). Dry-AD exhibited unique viral-prokaryotic diversity decoupling, elevated lysogeny (48.7% vs. 22.1%-26.5% in wet systems), and reduced transcriptionally active communities (viruses: 65.5% vs. 89.4% and 80.7% in wet systems; prokaryotes: 76.9% vs. 94.5% and 86.3% in wet systems). Comparative analyses revealed stronger viral endemism (55.4% system-specific vOTUs) than prokaryotes (30.6% MAGs). Virus-host networks demonstrated highly centralized infection patterns in Dry-AD with uneven transcript-based virus-host ratios (VHR) (Clostridia: 18.28 vs. Methanomicrobia: 0.15) compared to more uniform ratios (≈1.0) in wet systems. Transcriptomic profiling provided the first quantitative evidence of system-specific antiviral defense strategies: Wet-AD exhibited the highest defense gene transcriptional activity (3833 TPM), Dry-AD reduced defenses transcription (2614 TPM), while 2St-wet-AD displayed the lowest defense transcriptional activity (2455 TPM). Functional annotation revealed viral auxiliary metabolic genes exhibited distinct transcriptional patterns: enhancing host stress resilience in Dry-AD, promoting nutrient acquisition in Wet-AD, and improving metabolic efficiency in 2St-wet-AD. These findings reveal that viruses adopt distinct ecological roles across different AD process types, providing mechanistic insights for developing system-specific strategies to optimize stability and efficiency.}, }
@article {pmid41558352, year = {2026}, author = {Xia, J and Li, C and Zhen, Y and Liu, M and Guo, J and Jiang, F}, title = {Bell-shaped response of mercury methylation to sulfate loading in urban sewer systems: Implications for source-level control.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141191}, doi = {10.1016/j.jhazmat.2026.141191}, pmid = {41558352}, issn = {1873-3336}, mesh = {*Sulfates/chemistry/metabolism ; Methylation ; *Sewage/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; Bioreactors ; *Mercury/metabolism/chemistry ; *Methylmercury Compounds/metabolism ; Cities ; }, abstract = {Urban sewer systems act as incubators for mercury-methylating (hgcA) microorganisms, yet how sulfate-an abundant and variable sewage constituent-drives this process remains unclear. Here, we combined controlled bioreactor experiments, batch incubations, and genome-resolved metagenomics to demonstrate that Hg methylation potential follows a nonlinear, bell-shaped response to sulfate loading. The MeHg production rate peaked at moderate sulfate concentrations (75-150 mg/L), reaching levels 1.2-5.4 times higher than those observed under low sulfate conditions (6-30 mg/L). This enhancement arose from distinct community responses: at 75 mg/L, a phylogenetically diverse hgcA consortium emerged, with methanogens and fermenters complementing SRB, whereas at 150 mg/L, SRB-methylators such as Desulfobulbus dominated, indicating functional specialization. Outside this range, low sulfate (<30 mg/L) suppressed most hgcA populations due to electron acceptor scarcity, while high sulfate (>300 mg/L) favored non-methylating SRB like Desulfobacter postgatei, thereby reducing overall methylation potential. Importantly, by integrating our findings with reported sewage data, we show that sulfate concentrations in most domestic sewage fall within the optimal range for hgcA proliferation, explaining their consistently high abundances worldwide. Our results also highlight the potential basis for source-level interventions, such as substituting sulfate-free coagulants or restricting sulfate-rich industrial discharges, to reduce hgcA proliferation and mitigate downstream MeHg risks in urban water systems.}, }
@article {pmid41558437, year = {2026}, author = {Wang, S and Zhang, T and Shi, Y and Zhang, Y and Fan, J and Shen, Z}, title = {Immobilized exogenous proteinase K enhances mesophilic anaerobic co-digestion of polylactic acid and food waste.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128634}, doi = {10.1016/j.jenvman.2026.128634}, pmid = {41558437}, issn = {1095-8630}, mesh = {*Polyesters/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; Methane ; Hydrolysis ; Food Loss and Waste ; }, abstract = {Hydrolysis efficiency constraints impede anaerobic biodegradation of plastics, inducing kinetic imbalance during co-digestion with organic substrates. To address this limitation in food waste (FW) and commercial polylactic acid (PLA) biodegradable plastics (BPs), protease K (Pro K) was embedded onto BPs to leverage PLA-specific depolymerization activity. Regulatory mechanisms of enzymatic action on anaerobic microbial degradation were investigated through integration of classical model equations with metagenomic analysis. Results demonstrate that during hydrolysis, enzymatic reinforcement augmented hydrolysis rates, elevating BPs degradation from 7.3 % to 19.3 %. Throughout hydrogen/acidogenesis, microbial cascade responses were activated, enabling directional enhancement of the 'lactate-propionate-acetate' metabolic pathway. During methanogenesis, methyl oxidation was inhibited while concurrent reinforcement of hydrogenotrophic methanogenesis occurred, yielding 23.32 % (311.37 mL/g·VSadded[-1]) methane elevation. Metagenomic analysis revealed Pro K-mediated regulation of anaerobic metabolic gene pathways, establishing a novel strategy for accelerated BPs degradation and methane yield.}, }
@article {pmid41558447, year = {2026}, author = {Han, Y and Wang, A and Zhang, Z and Liu, L and Chen, Q and Fan, W and Tan, E and Tang, K}, title = {Multi-omics reveal the prevalence of Thaumarchaeota and their biogeochemical roles in coastal low oxygen zones.}, journal = {Marine pollution bulletin}, volume = {225}, number = {}, pages = {119293}, doi = {10.1016/j.marpolbul.2026.119293}, pmid = {41558447}, issn = {1879-3363}, mesh = {*Archaea ; *Oxygen/analysis ; China ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Eutrophication ; Microbiota ; Bacteria ; Proteomics ; Multiomics ; }, abstract = {The intensification of coastal hypoxia under anthropogenic eutrophication and climate change necessitates understanding microbial adaptive mechanisms. However, the composition of microbial communities and their biogeochemical roles in response to oxygen gradients remain poorly understood. Here, we employed integrated multi-omics approaches to analyze microbial communities and their biogeochemical functions across oxic to low oxygen gradients off the Yangtze River Estuary in East China Sea. Results revealed that surface oxic waters hosted phytoplankton (Synechococcus) and opportunistic bacteria (Flavobacteriia, Pelagibacterales), while bottom layers enriched chemolithoautotrophs (Thaumarchaeota, Nitrospina) and facultative anaerobes (Planctomycetes, Marine Group II), with sediment resuspension further amplified particle-attached taxa. Meanwhile, a remarkable shift in microbial nitrogen metabolism was observed between oxic and low oxygen waters, with dissolved nitrogen assimilation dominated in oxic waters. Despite genomic potential for complete nitrogen reduction in low oxygen waters, our metaproteomics revealed only a significant expression of nitrate reductases. This decoupling between genomic potential and proteomic expression implies that ambient oxygen levels remain above thresholds for full pathway activation, showcasing microbial metabolic plasticity. Both metagenomic and metaproteomic have confirmed that Thaumarchaeota, particularly the genus Nitrosopumilus, emerged as keystone taxa, contributing to nitrification and dark carbon fixation, thereby coupling nitrogen‑carbon biogeochemical cycling in coastal hypoxic zones. These findings highlight redox-driven microbial niche differentiation and metabolic adaptation, providing predictive insights into biogeochemical feedbacks under expanding coastal deoxygenation.}, }
@article {pmid41558481, year = {2026}, author = {Keller, V and Calchera, A and Otte, J and Tuovinen Nogerius, V and Schmitt, I}, title = {Ubiquitous occurrence of the black fungus Melanina gundecimermaniae in the lichen Umbilicaria pustulata.}, journal = {Current biology : CB}, volume = {36}, number = {3}, pages = {748-759.e5}, doi = {10.1016/j.cub.2025.12.046}, pmid = {41558481}, issn = {1879-0445}, mesh = {*Lichens/microbiology/physiology ; *Symbiosis ; *Ascomycota/physiology/genetics ; Metagenome ; Europe ; North America ; Genome, Fungal ; }, abstract = {Lichen symbioses frequently include additional fungal associates beyond the canonical mycobiont (fungus) and photobiont (alga/cyanobacterium). Despite the prevalence and diversity of these lichen cohabitants, their geographic distribution and role within the lichen consortium remain poorly understood. Combining genomics, metagenomics, and advanced microscopy, we identified the black fungus Melanina gundecimermaniae as a constant cohabitant in the lichen Umbilicaria pustulata. We analyzed metagenomes from 149 individuals across 15 populations, spanning the Europe-wide range of U. pustulata. Additionally, we screened pooled metagenomes of U. pustulata and Umbilicaria phaea along five elevation gradients (Europe and North America). Genome mapping, using a near-complete reference genome of M. gundecimermaniae, revealed that the black fungus was present in 100% of the screened lichen metagenomes, with 0.85%-3.78% of reads mapping against the reference. Among all lichen-associated fungi, it was one of the most common. These findings indicate that the black fungus is widely distributed and associated with different lichen species, underscoring its potential ecological significance. Using fluorescence in situ hybridization coupled with confocal laser scanning microscopy, we confirmed the presence of M. gundecimermaniae within various structures of U. pustulata, including vegetative symbiotic propagules involved in dispersal. Elucidating its widespread occurrence across continents, consistent presence in U. pustulata, and ability to be dispersed together with the lichens' canonical partners, our findings suggest a potential interaction of M. gundecimermaniae that extends beyond incidental colonization. Our study contributes to the growing body of evidence that organismal complexity within lichens is a prevalent and largely unexplored dimension of the lichen symbiosis.}, }
@article {pmid41558536, year = {2026}, author = {Kasuma, N and Fitri, H and Wulandari, RW and Ernesto, G and Juwita, DR and Effendi, MDS and Wirza, TR}, title = {Salivary Microbiome Differences in Stunted and Healthy Children: A Metagenomic Analysis.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0045-1814094}, pmid = {41558536}, issn = {1305-7456}, abstract = {This study aimed to compare the composition and diversity of the salivary microbiome in stunted and nonstunted children using 16S rRNA gene sequencing to explore the relationship between nutritional status and oral microbiota.A total of 20 saliva samples were collected from children aged 6 to 10 years, comprising two groups: stunted (n = 10) and healthy controls (n = 10). Deoxyribonucleic acid was extracted, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Bioinformatics analysis included taxonomic assignment, calculation of relative abundance, α diversity (using Shannon and Simpson indices), β diversity (UniFrac-based principal coordinate analysis and permutational multivariate analysis of variance [PERMANOVA]), and differential abundance testing using the Mann-Whitney U test.The dominant phyla in both groups were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being more prevalent in the stunted group. At the genus level, Neisseria and Veillonella were more abundant in stunted children. Notably, Veillonella was significantly elevated in the stunted group (28.6%) compared with controls (14.9%, p = 0.0376). Alpha diversity indices revealed a higher diversity trend in the stunted group, although this difference was not statistically significant (Shannon, p = 0.130; Simpson, p = 0.762). Beta diversity analysis revealed no considerable clustering between groups (PERMANOVA p > 0.05), indicating moderate interindividual variability but no clear group separation.Children with stunted growth demonstrated distinct microbial signatures in their salivary microbiota, particularly in the increased abundance of Proteobacteria and Veillonella, suggesting a potential link between chronic undernutrition and oral microbial dysbiosis. These findings underscore the need for additional studies to investigate the impact of nutritional status on oral and systemic health through the microbiome axis.}, }
@article {pmid41559018, year = {2026}, author = {Liu, J and Li, D and Wang, S and Gao, S and Xu, B and Zhao, J and Liu, Q and Chen, M and Zhou, X and Cai, Y and He, L}, title = {Congenital babesiosis in China: first molecularly confirmed case of vertical transmission of Babesia microti.}, journal = {Emerging microbes & infections}, volume = {15}, number = {1}, pages = {2608389}, pmid = {41559018}, issn = {2222-1751}, mesh = {Female ; Humans ; Infant ; Male ; Antiprotozoal Agents/therapeutic use ; *Atovaquone/therapeutic use ; Azithromycin/therapeutic use ; *Babesia microti/genetics/isolation & purification/classification ; *Babesiosis/transmission/drug therapy/diagnosis/parasitology ; China ; *Infectious Disease Transmission, Vertical ; *Proguanil/therapeutic use ; Drug Combinations ; }, abstract = {Congenital babesiosis is rarely reported globally. We report a 74-day-old male infant presented with fever, pallor, and severe, life-threatening haemolytic anaemia (haemoglobin: 45 g/L). The infant had 16% parasitemia with ring forms evident on peripheral blood smear. Babesia microti infection was confirmed in both the mother and infant by PCR and metagenomic next- generation sequencing. Genetic analysis revealed an identical strain in bot. Treatment with intravenous azithromycin and oral atovaquone/proguanil resulted in rapid clearance of parasitemia and resolution of anaemia. This first molecularly confirmed case of congenital B. microti transmission in China demonstrates vertical transmission from an asymptomatic mother. It underscores the need for heightened clinical suspicion in neonates with unexplained haemolytic anaemia in endemic regions and highlights critical gaps in access to essential anti-babesia therapies.}, }
@article {pmid41559060, year = {2026}, author = {Ding, Z and Wen, T and Teng, X and Yang, W and Yuan, X and Liu, X and Xie, P and Zhao, X and Shen, Q and Yuan, J}, title = {Enhancing soil citrulline degrading function to mitigate soil-borne Fusarium wilt.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41559060}, issn = {2041-1723}, support = {42322708//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Fusarium/metabolism/pathogenicity ; *Soil Microbiology ; *Citrulline/metabolism ; Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Soil/chemistry ; Pseudomonas putida/genetics/metabolism ; Metagenomics ; Fusaric Acid/metabolism ; }, abstract = {Continuous cropping often exacerbates soil-borne diseases, particularly Fusarium wilt, yet the intricate rhizosphere relationships among phyto-derived metabolites, pathogens, and particular microbial functions remain poorly understood. Here, we observe that citrulline accumulation during continuous cropping is positively correlated with Fusarium wilt severity by enhancing fusaric acid production in Fusarium oxysporum. Metagenomic analyses reveal that citrulline turnover-related functions, represented by functional modules including M00978, are significantly enriched in healthy rhizosphere soils but are notably reduced in Fusarium-conducive soils. The functional genes, arcB and argH, are identified in Pseudomonas putida YDTA3, with arcB being essential for citrulline-degradation via knockout experiments. The inoculation of an arcB-expressing indigenous Escherichia consortium (EO-arcB) in three independent continuous cropping systems of cucurbit crops demonstrates that enhancing and maintaining the soil citrulline-degrading function mitigates soil-borne Fusarium wilt. In summary, this study advances our understanding of rhizosphere interactions underlying Fusarium wilt disease occurrence and offers a promising biocontrol strategy.}, }
@article {pmid41559596, year = {2026}, author = {Liu, Y and Zhang, Q and Li, J and Wu, X and Zang, Q and Wang, Q and Huang, P and Wang, Y and Zhang, S and Liu, S and Zhu, C and Zhao, Y and Yan, T and He, Y}, title = {mNGS improves the efficiency of infection diagnosis and treatment in acute-on-chronic liver failure.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {129}, pmid = {41559596}, issn = {1471-230X}, mesh = {Humans ; *Acute-On-Chronic Liver Failure/complications/microbiology ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Propensity Score ; Liver Transplantation ; Early Diagnosis ; }, abstract = {INTRODUCTION: The early diagnosis of infections in acute-on-chronic liver failure (ACLF) is still difficult. mNGS(metagenomic next-generation sequencing) is a no-bias, sensitive pathogen diagnosis method, and further research on mNGS in ACLF is needed.
METHODS: A total of 275 ACLF patients with suspected or confirmed infections were recruited and divided into the mNGS group and the non-mNGS group. Differences between the two groups were assessed.
RESULTS: The 1:1 Propensity score matching (PSM) for balancing the baseline variables produced 86 patients in each group. From these 86 patients in the mNGS group, 134 samples were collected and analyzed. The overall microbiological positive rate (103/134, 76.9%) detected by mNGS was higher than that detected by culture (24/134, 17.9%), particularly for fungi (14.9% vs. 2.2%). The etiological diagnosis rates for pulmonary and thoracoabdominal infections detected by the mNGS method were higher than those of the culture method (47.9% vs. 11.4%; 52.0% vs. 18.4%, respectively). The etiological diagnosis can be confirmed 22.83 ± 26.27 h ahead of time. mNGS testing did not significantly improve 90-day transplant-free survival in the overall cohort (sHR 0.96, 95% CI 0.72-1.27; P = 0.76). In the subgroup where mNGS guided therapy, numerically higher resolution rates were observed for pulmonary (53.8% vs 37.1%), abdominal (63.2% vs 52.6%), and bloodstream infections (66.7% vs 50.0%), though these differences were not statistically significant.
CONCLUSIONS: mNGS is a valuable diagnostic tool for ACLF with infections, especially for viruses and fungi. mNGS allows for precise and earlier pathogen diagnosis, enabling timely and targeted anti-infective therapy. mNGS may be associated with improved clinical outcomes in ACLF patients with co-infections, though this potential association requires further validation.
TRIAL REGISTRATION: The study was registered on Clinicaltrials.gov (registration number: NCT05740696, release date: February22,2023). Accessible at: https://classic.
CLINICALTRIALS: gov/ct2/show/NCT05740696.}, }
@article {pmid41559772, year = {2026}, author = {Gómez-Martínez, S and Pérez-Pérez, L and Ucero-Carrretón, A and López-García, Á and Galisteo, C and Carvajal, A and Argüello, H}, title = {Exploring the potential for competitive exclusion of commensal probiotic candidates against the insidious swine pathogen Brachyspira hyodysenteriae.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {19}, pmid = {41559772}, issn = {2524-4671}, support = {EDU/1868/2022//Junta de Castilla y León/ ; EDU 1009/2024//Junta de Castilla y León/ ; CNS2022-136066//Junta de Castilla y León/ ; PRE-2020-093762//Ministerio de Ciencia e Innovación/ ; Predoc grant 2025//Universidad de León/ ; }, abstract = {BACKGROUND: Research into animal microbiota reveals the intricate relationships between commensal bacteria and enteric pathogens. Metagenomics and culturomics offer novel opportunities in probiotic research, which is particularly interesting for diseases where treatment alternatives are limited, such as swine dysentery (SD), which is caused by Brachyspira hyodysenteriae (B. hyo). This study evaluates the potential ability of a collection of 28 isolates from species of interest to outcompete the anaerobic pathogen B. hyo by an array of in vitro assays designed to characterize their competitive exclusion capacity in co-cultures, alongside assessing the antimicrobial activity of the isolates cell-free supernatants (CFS) and the mechanisms by which they inhibit B. hyo growth.
RESULTS: 20 of the 28 isolates tested were able to reduce the growth of B. hyo by more than one log10 bacteria/mL after 96 h of co-culture, with different inhibitory dynamics observed. Notably, Intestinibaculum porci (J1/23 CM6), Dorea longicatena (J1/23 YB16), Bifidobacterium thermoacidophilum (J1/23 YB69), Mobilitalea sibirica (J1/23 YB21), Clostridium butyricum (CECT 361), and Parabacteroides goldsteinii (DSMZ 29187) reduced B. hyo growth in more than 2 log10 units (bacteria/mL). The anti-B. hyo activity of the tested CFS demonstrated that the mechanisms involved went beyond nutrient competition, with a CFS concentration-dependent reduction. CFS from 11 isolates achieved a reduction of over 2 log10 bacteria/mL, with C. butyricum and Paraprevotella clara (DSMZ 19731) CFS standing out with values of 2–3 log10 bacteria/mL. A pH-dependent effect was disclosed for part of the isolates tested, while C. butyricum, Limosilactobacillus mucosae, B. thermoacidophilum and Lactiplantibacillus plantarum maintained part of their anti-B. hyo activity at fixed pH (7.0). A combined analysis of the short chain fatty acid profile and pH on B. hyo growth inhibition revealed differences between isolates, with similar effect for CFS of isolates with similar production of lactic and acetic acids and no clear effect of the pH.
CONCLUSIONS: This study demonstrates the potential of pig gut commensals to outcompete B. hyo and discloses part of the mechanisms involved in the growth inhibition, providing a foundation into future research in competitive exclusion as strategy to control SD.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00511-y.}, }
@article {pmid41559841, year = {2026}, author = {Galgano, S and Faruk, MU and Eising, I and Houdijk, JGM and Khattak, F}, title = {Dietary muramidase leads to the downregulation of peptidoglycan biosynthesis and to caecal microbial modulation in laying hens.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {7}, pmid = {41559841}, issn = {2524-4671}, abstract = {BACKGROUND: In-feed muramidase enzyme has been linked to numerous advantages in several animal species. In the past years, muramidase has been shown to be effective in hydrolyzing peptidoglycan fragments, especially at small-intestine level in broilers, and to improve digestibility and performance. Moreover, previous studies also showed a possible anti-inflammatory effect of some secondary metabolites derived from the hydrolysis of peptidoglycan. Although a major effort has been carried out to unravel the in vivo mechanism of action of muramidase, there is currently little information on its metabolic interactions in laying hens, especially considering the fundamental differences with broilers in terms of microbiota and host genetics. Therefore, we conducted a 20-week study, testing five different levels of inclusion of muramidase, from 0 mg/kg to 600 mg/kg. We analyzed dry matter and nitrogen digestibility, apparent metabolizable energy, body weight gain, caecal microbiota and microbiome.
RESULTS: The intervention with muramidase (Balancius[®], DSM Nutritional Products Ltd., Basel, Switzerland) led to a drop in α-diversity (Shannon index; P < 0.05) and to microbial composition changes, with a decrease in Lactobacillus and an increase in Collinsella, amongst others (Q < 0.05), at all the muramidase concentrations compared to 0 mg/kg. In parallel, we found that muramidase led to an increased protein digestibility as revealed by the increased nitrogen retention, together with a dose-dependent amelioration of body weight, dry matter digestibility and metabolizable energy (P < 0.05). At functional gene level, we observed a net decrease in the microbial potential to metabolize amino acids, likely as a direct consequence of the lower amino acid availability at caecal level, as linked to the increased nitrogen retention. Moreover, muramidase also led to a decreased microbial functional potential to synthesize peptidoglycan.
CONCLUSION: This study is the first to investigate the effects of dietary muramidase supplementation on nutrient digestibility and metagenomics in laying hens. Our findings align perfectly with the previous studies in broilers, especially in terms of increased protein digestibility. Moreover, for the first time, a direct correlation between the observed phenotype and both microbiota and microbiome has allowed us to gain further insights into the mechanism of action of muramidase in laying hens.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00506-9.}, }
@article {pmid41559953, year = {2026}, author = {Wu, J and Sun, D and Pan, Y and Liu, DF and Zhang, H and Zhou, JH and Gao, T and Wu, J and He, RL and Chen, YG and Li, WW}, title = {Overlooked Roles of Pharmaceutical Metabolic Products in Stimulating Microbial Metabolism and Antibiotic Resistance Gene Dissemination of Anaerobic Sludge.}, journal = {Environmental microbiology}, volume = {28}, number = {1}, pages = {e70247}, doi = {10.1111/1462-2920.70247}, pmid = {41559953}, issn = {1462-2920}, support = {51878638//National Natural Science Foundation of China/ ; 52192681//National Natural Science Foundation of China/ ; 22106160//National Natural Science Foundation of China/ ; U21A20160//National Natural Science Foundation of China/ ; 202423110050028//Key R&D Project of Anhui Province, China/ ; SYG2024111//Science and Technology Program of Suzhou/ ; WK2060000099//Fundamental Research Funds for the Central Universities/ ; //Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education/ ; JYB2025XDXM909//State Key Laboratory of Advanced Environmental Technology/ ; SKLAET2025-LH01//State Key Laboratory of Advanced Environmental Technology/ ; }, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Metformin/metabolism/pharmacology ; *Bacteria/genetics/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Biotransformation ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {The roles of non-antibiotic pharmaceuticals in shaping the dissemination behaviours of antibiotic resistance genes (ARGs) in wastewater treatment systems remain poorly understood, and the influences of their transformation products have been overlooked. Here, we unveil more profound impacts of the metformin (MET) biotransformation product than the parent pollutant on the microbial community structure and ARG propagation of wastewater anaerobic sludge. The exposure to MET and its metabolic products guanylurea (GUA) at environmentally relevant concentrations both raised the methane production and resulted in up to 52.5% higher sludge ARGs abundance relative to the unexposed control. Especially, the GUA group showed up to 188-fold upregulation in several ARGs including bcrA, PmrF, acrB and mexF, enabled 3218-fold enrichment of plasmids from several bacteria. The underlying mechanisms were elucidated by integrated metagenomics, molecular dynamics simulations, and metabolic profiling analyses. MET and GUA were found to trigger coordinated cellular responses including disrupted glycerophospholipid metabolism, increased membrane permeability and broad metabolic reprogramming, which collectively boosted the ARGs dissemination. Overall, this work establishes a mechanistic link between micropollutant-induced microbial stress and ARGs propagation in anaerobic sludge, and advocates for re-evaluating the environmental risks of non-antibiotic pharmaceuticals and integrating resistance control into wastewater management framework.}, }
@article {pmid41560107, year = {2026}, author = {Duan, JX and Jian, H and Chang, L and Teng, J and Lai, SY and Yang, QX and Che, GL and Luo, LL and Liu, F}, title = {mNGS facilitates the diagnosis of pediatric murine typhus: A case report.}, journal = {Medicine}, volume = {105}, number = {3}, pages = {e47253}, pmid = {41560107}, issn = {1536-5964}, mesh = {Child ; Humans ; Anti-Bacterial Agents/therapeutic use ; Dexamethasone/therapeutic use ; Doxycycline/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/drug therapy/microbiology ; *Rickettsia typhi/genetics/isolation & purification ; *Typhus, Endemic Flea-Borne/complications/diagnosis/drug therapy/microbiology ; }, abstract = {RATIONALE: Murine typhus, caused by Rickettsia typhi, is a globally distributed flea-borne rickettsiosis. Although rarely recognized, it can trigger hemophagocytic lymphohistiocytosis (HLH), a life-threatening hyperinflammatory syndrome. Nonspecific febrile illness and atypical petechial eruptions frequently lead to delayed or missed diagnoses. This report aims to illustrate the diagnostic process and clinical implications of murine typhus-associated HLH in a pediatric patient, and to evaluate the utility of metagenomic next-generation sequencing (mNGS) as an unbiased detection tool for occult pathogens.
PATIENT CONCERNS: A 10-year-old child was admitted with unexplained recurrent fever and generalized petechiae, refractory to treatment at outside hospitals.
DIAGNOSES: The patient was ultimately diagnosed with murine typhus-associated HLH caused by R typhi, based on a comprehensive diagnostic work-up.
INTERVENTIONS: Empirical dexamethasone was initiated promptly to control hyperinflammation. After mNGS confirmation, oral doxycycline was added for targeted anti-rickettsial therapy.
OUTCOMES: The patient's clinical status continued to improve, culminating in discharge.
LESSONS: Murine typhus-associated HLH should be considered in febrile children with unexplained cytopenias and petechiae. Early empiric HLH-directed immunosuppression followed by pathogen-specific therapy improves prognosis. mNGS provides a rapid, unbiased method to detect rare, overlooked pathogens and guide definitive treatment when conventional tests are negative.}, }
@article {pmid41560354, year = {2026}, author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S}, title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {17}, pages = {e17596}, doi = {10.1002/advs.202517596}, pmid = {41560354}, issn = {2198-3844}, support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science & Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Thiamine/metabolism ; Male ; Mice, Inbred C57BL ; *Fatty Liver/metabolism/microbiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Liver/metabolism ; Prebiotics/administration & dosage ; *Eubacteriales/metabolism ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.}, }
@article {pmid41560360, year = {2026}, author = {Zhang, J and Wang, Z and Li, S and Luo, C and Li, H and Ma, S and Wang, P and Liu, H and Sun, L and Yin, Y and Zhang, W and Wang, Q}, title = {Phocaeicola coprophilus-Derived 6-Methyluracil Attenuates Radiation-Induced Intestinal Fibrosis by Suppressing the IDO1-Kynurenine-AHR Axis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {18}, pages = {e18502}, doi = {10.1002/advs.202518502}, pmid = {41560360}, issn = {2198-3844}, support = {JDYY15202429//Youth Development Fund of the First Hospital of Jilin University/ ; JDYY-DEP-2022006//Doctor of Excellence Program (DEP), The First Hospital of Jilin University/ ; YDZJ202402012CXJD//Department of Science and Technology of Jilin Province/ ; 82330017//National Natural Science Foundation of China/ ; 82270610//National Natural Science Foundation of China/ ; 20240484505//Beijing Nova Program/ ; 2024ZD0530100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, mesh = {Animals ; Mice ; *Kynurenine/metabolism ; *Fibrosis/metabolism ; *Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Gastrointestinal Microbiome ; *Receptors, Aryl Hydrocarbon/metabolism ; Humans ; *Uracil/analogs & derivatives/metabolism/pharmacology ; Male ; *Intestines/pathology/radiation effects ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Therapeutic options for radiation-induced intestinal fibrosis (RIF) remain limited. This study reveals that intestinal kynurenine (Kyn) is persistently elevated after radiation and correlates with fibrosis severity in both murine models and human rectal cancer samples. Exogenous Kyn exacerbated RIF, whereas inhibition of indoleamine 2,3-dioxygenase 1 (IDO1) attenuated fibrotic progression. Mechanistically, Kyn activates the aryl hydrocarbon receptor (AHR) to promote fibroblast activation and fibrosis. Antibiotic depletion of gut microbiota abrogates radiation-induced IDO1-Kyn upregulation and protects against RIF. Conversely, fecal microbiota transplantation from irradiated mice recapitulates the elevated IDO1-Kyn phenotype. Metagenomic analysis identify radiation-induced depletion of Phocaeicola coprophilus (P. coprophilus), whose abundance inversely correlates with Kyn levels. Supplementation with live P. coprophilus suppresses IDO1-Kyn signaling and ameliorates RIF. Untargeted metabolomics further show that radiation reduces 6-methyluracil, a metabolite derived from P. coprophilus. Exogenous 6-methyluracil replenishment inhibits repression of the IDO1-Kyn axis and mitigates fibrosis. Together, these findings define a microbiota-metabolite-host pathway in which radiation depletes P. coprophilus, leading to loss of 6-methyluracil and derepression of the IDO1-Kyn-AHR axis, thereby driving fibrogenesis. Restoration of either P. coprophilus or its metabolite 6-methyluracil represents a promising therapeutic strategy against RIF.}, }
@article {pmid41560914, year = {2025}, author = {Chevokina, E and Sibiryakina, D and Sobolev, A and Slonova, D and Demkina, A and Yurikova, D and Galivondzhyan, A and Konovalova, O and Sutormin, D and Isaev, A}, title = {Efficient recovery and DNA extraction for algae-associated microbial communities.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1693747}, pmid = {41560914}, issn = {1664-462X}, abstract = {The extraction of high-quality microbial DNA from environmental samples is critical for many downstream applications, including short- and long-read metagenomic sequencing. However, environmental DNA is prone to low recovery, degradation, and contamination by enzymatic inhibitors, with the extent of these issues largely dependent on the DNA purification method. The embedding of bacterial cells in a mucoid matrix within biofilms further complicates the process, making the study of algal symbionts particularly challenging. This study benchmarked five methods to recover microbial cells from biofilms associated with three major groups of marine macroalgae, namely: red (Palmaria stenogona), brown (Saccharina japonica), and green (Ulva lactuca). This was followed by a systematic evaluation of six widely used commercial DNA purification kits for their ability to extract high-quality DNA suitable for 16S rRNA gene and shotgun sequencing. A universal trade-off was observed between the quantity and quality of the extracted DNA. While whole-sample homogenization and manual collection of biofilms resulted in high levels of chloroplast contamination, washing microbial cells with a buffer led to low DNA recovery; however, the use of a detergent improved DNA yields. A comparison of the DNA extraction kits revealed that their efficiency varied significantly among algal species, with the GeneJET Genomic DNA Purification Kit (Thermo Scientific) identified as the most versatile. The present findings provide a comparative benchmark of methods to recover algae-associated microbial communities and extract their DNA, offering guidance in selecting procedures suited for metagenomic sequencing.}, }
@article {pmid41561024, year = {2025}, author = {Chen, YX and Xuan, YS and Wang, MH and Li, Y and Shi, SM and Zhao, HY and Niu, YH and Chen, M and Li, SY}, title = {Research on the regulation of gut microbiota homeostasis and immune function in asthmatic mice by Huanglong Zhixiao Formula.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1726388}, pmid = {41561024}, issn = {1664-302X}, abstract = {BACKGROUND: Asthma affects approximately 334 million people worldwide. Accumulating evidence indicates that gut dysbiosis exacerbates airway inflammation through the gut-lung axis. In the present study, using an OVA-induced murine model of asthma, we investigated whether Huanglong Zhixiao Formula (HLZXF) restores gut lung homeostasis by reshaping the gut microbiota and enhancing intestinal barrier function, thereby attenuating pulmonary pathological changes.
METHODS: Female BALB/c mice were randomly assigned to three groups (n = 15 per group): Control (C), Asthma Model (MX), and HLZXF-treated (ZG) groups. Asthma was induced by OVA sensitization and challenge over a 6-week period. The ZG group received daily oral gavage of HLZXF, 1 h prior to each OVA challenge. Fecal samples were collected for metagenomic sequencing. Lung and intestinal tissues were excised for HE and IHC staining of tight junction proteins, including Claudin, Occludin, and ZO-1. Alpha and beta diversity analyses were conducted to evaluate the composition and structure of the gut microbiota.
RESULTS: We analyzed the structure of the gut microbiota, detected the expression levels of intestinal barrier-related proteins, and assessed inflammatory injury in the lungs and intestines. Results demonstrated that HLZXF significantly ameliorated gut microbiota dysbiosis in asthmatic mice, as evidenced by the significant enrichment of Heminiphilus faecis and Paramuribaculum intestinale. Additionally, certain fungal taxa, such as Piromyces finnis and Rhizopus arrhizus, were significantly enriched in the ZG group. HLZXF also significantly upregulated the expression levels of the tight junction proteins Claudin, Occludin, and ZO-1 in intestinal tissues, thereby promoting the repair of the intestinal mucosal barrier. Furthermore, HLZXF significantly attenuated inflammatory cell infiltration and tissue injury in the lungs and intestines, alleviated alveolar septal thickening, and enhanced the integrity of the intestinal mucosal barrier.
CONCLUSION: This study elucidates the potential therapeutic mechanisms of HLZXF in the treatment of asthma from the perspective of gut microbiota and intestinal barrier function. It highlights that HLZXF can attenuate pulmonary inflammation by regulating the balance of gut microbiota and enhancing intestinal barrier function.}, }
@article {pmid41561026, year = {2025}, author = {Li, F and Qiu, Z and Pei, Z and Zhu, Q and Shen, S and Fan, L and Xu, L and Huang, C and Wang, J and Huang, B and Huang, L and Liu, X and Han, Q}, title = {Effects of pesticides on soil microbial community structure and nitrogen transformation in tobacco fields affected by root rot.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1733977}, pmid = {41561026}, issn = {1664-302X}, abstract = {INTRODUCTION: In tobacco planting soil infected with root rot disease, the potential impacts of prothioconazole (T1), pyrisoxazole (T2), kasugamycin combined with Paenibacillus polymyxa (T3), and cyclobutrifluram (T4) on soil microecology remain unclear. This study examined their effects on soil microbial communities and nitrogen transformation processes.
METHODS: By measuring soil nitrogen forms and enzyme activities, combined with metagenomic sequencing, we conducted a comprehensive assessment of the soil microecology, focusing on shifts in microbial community composition, xenobiotic degradation potential, and nitrogen cycling processes.
RESULTS AND DISCUSSION: The results revealed that pesticide application significantly changed the content of nitrogen forms and their transformation rate. T1 and T2 treatments significantly increased the accumulation of ammonium nitrogen (NH4 [+]-N), while T2 and T4 markedly promoted the accumulation of nitrate nitrogen (NO3 [-]-N). Microbial community analysis indicated that the T2 and T4 treatments significantly affected the microbial structure. Analysis of xenobiotic degradation pathways showed that multiple pathways were suppressed by the four pesticide treatments, with the T2 treatment exhibiting the broadest suppressive effect. Metagenomic analysis further revealed that the T2 treatment promoted the accumulation of both NH4 [+]-N and NO3 [-]-N by up-regulating the mineralization gene (gdh) and nitrification genes (hao and nxrAB), while the T4 treatment facilitated NO3 [-]-N accumulation by up-regulating nitrification genes (hao and nxrAB). Correlation network analysis uncovered relationships between key nitrogen cycle genes and microbial genera, showing that nitrification genes (hao and nxrAB) in the T2 and T4 treatment groups exhibited positive correlations with Nitrobacter and Nitrosovibrio. This research clarifies the pathways through which these four pesticides influence the soil nitrogen cycle, providing an important theoretical basis for their ecological risk assessment and rational application.}, }
@article {pmid41561037, year = {2025}, author = {Zhang, S and Mo, Y and Yang, J and Chen, X and Gao, M and Su, Y and Qiu, Q and He, Q}, title = {Vertical stratification of P pools in subtropical plantation soils under fertilization and dry-season irrigation: multiomics regulatory strategies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1714023}, pmid = {41561037}, issn = {1664-302X}, abstract = {The rapid expansion of fast-growing plantations in subtropical regions is closely linked to silvicultural practices, however, improper practices often lead to soil acidification and reduced nutrient bioavailability. Phosphorus (P), one of the most critical elements for plantation tree growth, shows complex spatial distribution patterns in soil that are influenced by multiple factors, directly affecting plantation productivity. This study investigated the effects of long-term fertilization and dry-season irrigation on the vertical distribution of phosphorus in an 8-year-old subtropical Eucalyptus plantation. This study employed stratified sampling (0-30 cm topsoil, 30-60 cm subsoil, 60-90 cm substratum) during dry seasons, coupled with metagenomics, metabolomics, and environmental factor analysis, to reveal vertical phosphorus cycling patterns and multiomics regulatory networks. Key findings: (1) Fertilization and dry-season irrigation had a limited influence on labile phosphorus and the diversity of P-cycling microorganisms. The topsoil presented significantly greater P availability than did the subsoil, manifested as elevated acid phosphatase activity (ACP), significant enrichment of the tryptophan metabolic pathway, and greater microbial diversity. (2) pH and the C:P ratio represent critical factors of vertical stratification in soil P cycling. Under acidic conditions, topsoil microorganisms facilitate P release via diverse metabolic pathways, whereas oligotrophic constraints in the substratum limit enzymatic activities. (3) Potential cross-stratum microbial functional coordination exists in acidic soil P cycling, with linkages to tryptophan metabolism and polyphosphate, synthesis/degradation. Our study provides theoretical multiomics insights for optimizing the management of soil P pools in subtropical plantations under fertilization and dry-season irrigation.}, }
@article {pmid41561086, year = {2025}, author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX}, title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1740322}, pmid = {41561086}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Gastrointestinal Diseases/therapy/microbiology ; Probiotics/therapeutic use ; Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Phage Therapy ; Dysbiosis/therapy ; }, abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.}, }
@article {pmid41561096, year = {2025}, author = {Wan, L and Huang, C and Kong, W and Li, M and Lu, C}, title = {The analysis of gut microbiota characteristics in children with global developmental delay.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1606453}, pmid = {41561096}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Female ; Feces/microbiology ; Male ; *Developmental Disabilities/microbiology ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Child ; DNA, Bacterial/genetics ; Infant ; Biodiversity ; China ; }, abstract = {OBJECTIVE: To explore the composition and functional changes of gut microbiota in children with Global Developmental Delay(GDD),and to explore the role of gut microbiota in the pathogenesis of GDD using high-throughput sequencing.
METHODS: A prospective study was conducted to select 26 children diagnosed with GDD at Longgang District Maternal and Child HealthCare Hospital of Shenzhen City from January 2024 to December 2024 as the disease group(GDD), and 59 healthy children of the same age were selected as the healthy group(HC).General information of the children was collected through a questionnaire survey, and fecal samples from all participants were collected. Total DNA was extracted and amplified, and high-throughput sequencing of the 16S rRNA gene was performed for biological analysis of the sequencing results.
RESULTS: The alpha diversity analysis revealed a significant reduction in microbial diversity in the GDD group (Chao1 index, P = 0.007), while the beta diversity showed significant segregation between groups (R² = 0.067, P = 0.001);At the phylum level, the relative abundance of Actinobacteria was significantly increased (P < 0.01), while the abundance of Bacteroidetes was significantly decreased (P < 0.05) in the GDD group;At the genus level, the abundance of Bifidobacterium, Fusicatenibacter, and Erysipelatoclostridium were significantly increased in the GDD group (all P < 0.001), while the abundance of Faecalibacterium, Phascolarctobacterium, and Alistipes were significantly reduced (all P < 0.001);Functional prediction based on 16S rRNA data suggested potential differences in microbial metabolic pathways, including mRNA surveillance, proteasome, and atrazine degradation, in the GDD group. These findings hypothesize a functional shift in the gut microbiome associated with GDD, which requires validation by direct metagenomic or metabolomic methods.
CONCLUSION: Children with GDD have significant differences in gut microbiota composition and diversity compared to HC,and the abundance and abnormal metabolic pathway may be closely related to the neuroinflammatory process, suggesting that intestinal microecological regulation may become a new intervention target for GDD.}, }
@article {pmid41561308, year = {2026}, author = {Mei, Z and He, C and Balcazar, JL and Fu, Y and Dou, Q and Liu, Y and Dercon, G and Jiang, X and Elsner, M and Wang, F}, title = {Antibiotic-degrading bacteria shape resistome dynamics and horizontal gene transfer potential in soils with contrasting properties.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf246}, pmid = {41561308}, issn = {2730-6151}, abstract = {Soils act as both reservoirs and filters of antimicrobial resistance genes (ARGs); however, the ecological and genetic traits of antibiotic-degrading bacteria (ADB) and their interactions with nondegrading bacteria (NADB) across soil types remain poorly understood. In particular, the role of ADB in ARG dynamics and their potential contribution to horizontal gene transfer (HGT) are still underexplored. Here, we applied [13]C-DNA stable isotope probing (DNA-SIP) combined with metagenomic sequencing to resolve active ADB from NADB in two contrasting soils: Ultisol and Mollisol. ADB harbored significantly more abundant and diverse chromosomal ARGs - especially multidrug and tetracycline resistance genes - often co-localized with mobile genetic elements (MGEs) and degradation genes, suggesting robust and regulated resistance strategies. In contrast, NADB relied more on plasmid-borne ARGs, reflecting flexible but potentially transient adaptation. Soil properties shaped both resistome composition and host taxa. Mollisol enriched enzymatic degraders such as Lysobacter and Nocardioides, while Ultisol favored stress-tolerant Burkholderia, which carried up to 34 ARGs and exhibited membrane-associated resistance. Notably, 89 ARGs or MGEs were found co-localized with degradation genes on assembled contigs, highlighting a strong potential for HGT. In addition, 24 high-potential ARG hosts were identified, including Ralstonia pickettii and Saccharomonospora viridis. These findings reveal that antibiotic degradation is embedded within complex, soil-specific resistome networks. This work enhances our understanding of ARG ecology and supports targeted mitigation strategies based on soil microbiome characteristics.}, }
@article {pmid41561899, year = {2026}, author = {Labbancz, J and Birnbaum, A and Dhingra, A}, title = {Long-read metagenomic dataset from domestic rabbit manure and domestic rabbit manure-derived vermicompost.}, journal = {Data in brief}, volume = {64}, number = {}, pages = {112425}, pmid = {41561899}, issn = {2352-3409}, abstract = {This dataset describes samples collected from two Domestic Rabbit manure sources and three Domestic Rabbit manure-derived vermicompost bins. Three samples were taken from each and total DNA was isolated. Nanopore sequencing was used to collect data from all isolated DNA samples. After length and quality filtering, 181.5 gigabases (Gb) of sequencing data was collected across 15 samples. Streptomyces, Bradyrhizobium, Mesorhizobium, and Microbacterium were in the top 5 genera for all vermicompost samples, but two vermicompost samples had very high proportions of Escherichia and Mycobacterium. Vermicomposting can enable the development of beneficial microbial communities, but often lacking a thermophilic phase, may also allow for the growth of potentially pathogenic microbes. The vermicomposts described by this dataset contains both beneficial and potentially harmful microbial communities and may be used to support comparisons between composts and vermicomposts of different backgrounds for safety and utility.}, }
@article {pmid41562034, year = {2026}, author = {Sanchez-Cid, C and Vrchovecká, S and Dehon, E and Wacławek, S and Vogel, TM}, title = {Environmental Consequences of Anthropogenic Pollution: Non-antibiotic-Drug-Driven Antibiotic Resistance Selection in a Model Aquatic Ecosystem.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {1}, pages = {132-143}, pmid = {41562034}, issn = {2833-8278}, abstract = {Non-antibiotic drugs (NADs) used in human therapy may induce antibiotic resistance selection and dissemination in vitro. However, the potential risks of antibiotic resistance emergence associated with environmental NAD pollution have not been addressed. Here, we conducted a multidisciplinary study on river water microcosms using growth kinetics, qPCR, metagenomics, 16S rRNA sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether NADs alter river bacterial ecology and select for antibiotic resistance genes (ARGs). Four NADs with different mechanisms of action were included at a high (mg/L) and low (μg/L) dose to establish dose-response relationships: chlorpromazine (antipsychotic), diclofenac (anti-inflammatory), diphenhydramine (antihistamine), and fluoxetine (antidepressant). Although the community response to NAD pollution was compound-specific and dose-dependent, all NADs and doses were stable in the environment, altered the composition and activity of bacterial communities, and selected for several ARGs, mostly β-lactamases and aminoglycoside resistance genes, some of which were associated with horizontal gene transfer genes. Pseudomonas (including some ARG-harboring subpopulations) was identified as a key player in the response to NAD pollution. Here, we demonstrate NAD-driven antibiotic resistance selection in complex aquatic communities, raising concerns about the collateral effects on human and environmental health due to the extensive anthropocentric use of NADs.}, }
@article {pmid41562094, year = {2025}, author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P}, title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1717935}, pmid = {41562094}, issn = {1664-3224}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Phlebotomus/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Leishmaniasis/parasitology ; *Insect Vectors/microbiology/parasitology ; Bacteria/genetics/classification ; }, abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.
METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.
RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).
DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.}, }
@article {pmid41562140, year = {2026}, author = {Assenmacher, CA and Mou, K and Li, G and Hsu, K and Sahin, O and Cole, SD}, title = {Actinomyces sp. detected by next-generation sequencing in paraffin-embedded, formalin-fixed tissues of a dog with severe panophthalmitis and periocular cellulitis.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {38}, number = {2}, pages = {288-292}, pmid = {41562140}, issn = {1943-4936}, support = {S10 OD023465/OD/NIH HHS/United States ; }, mesh = {Dogs ; Animals ; *Dog Diseases/microbiology/diagnosis/pathology ; Male ; *Actinomyces/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing/veterinary ; *Actinomycosis/veterinary/microbiology/diagnosis ; *Cellulitis/veterinary/microbiology ; Paraffin Embedding/veterinary ; }, abstract = {A 9-mo-old, castrated male Saint Bernard dog was presented for evaluation of periorbital swelling, severe uveitis, and secondary glaucoma. Concurrently, chest radiographs had evidence of pneumonia. Enucleation was performed after failure of aggressive medical management. Histopathology of the globe confirmed severe necrosuppurative panophthalmitis and periocular cellulitis with myriad intra- and extracellular bacteria forming long filamentous chains. The bacteria were gram-positive and GMS-positive but acid-fast-negative. Next-generation sequencing (NGS) was performed on formalin-fixed, paraffin-embedded (FFPE) tissue from the eye. We identified a bacterium in the Actinomycetaceae family with a 100% BLAST match, suggestive of the previously described Actinomyces catuli strain (CCUG 41709). Clinical improvement followed enucleation and continued medical management, leading to reduction of the periocular swelling and resolution of the lung disease. Uveitis is common in dogs and is the most common cause of glaucoma. In many cases of bacterial uveitis, the exact bacterial organisms remain unknown if culture is not performed before fixation. Actinomyces sp. should be considered in patients with severe endophthalmitis or panophthalmitis, especially with evidence of systemic disease. NGS on FFPE samples may be a useful tool for identifying infectious organisms, especially in cases in which culture is not an option.}, }
@article {pmid41562259, year = {2026}, author = {Stuart, KC and Oomen, RA and Tigano, A and Wellenreuther, M and Wold, J and Field, DL and Mérot, C}, title = {A Beginner's Guide to Structural Variants in Eco-Evolutionary Population Genomics.}, journal = {Molecular ecology}, volume = {35}, number = {2}, pages = {e70216}, doi = {10.1111/mec.70216}, pmid = {41562259}, issn = {1365-294X}, support = {UOA1911//Royal Society Te Apārangi/ ; MFP-PAF2301//Royal Society Te Apārangi/ ; //Genomics Aotearoa ECR Grant/ ; RGPIN-2024-06892//Natural Sciences and Engineering Research Council of Canada Discovery Grant/ ; TRF-0000000175//New Brunswick Innovation Foundation/ ; 2021-05580//Swedish Research Council Starting Grant/ ; CAWX2304//New Zealand Ministry of Business, Innovation and Employment, Smart Ideas Grant/ ; PFR2430//New Zealand Ministry of Business, Innovation and Employment, Smart Ideas Grant/ ; //Fisheries and Oceans Canada/ ; 101115983(EVOL-SV)/ERC_/European Research Council/International ; }, mesh = {*Genetics, Population/methods ; *Genomics/methods ; *Evolution, Molecular ; DNA Transposable Elements ; Animals ; Genetic Variation ; Whole Genome Sequencing ; *Genomic Structural Variation ; *Metagenomics/methods ; *Biological Evolution ; Humans ; }, abstract = {Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. This has paved the way to study the eco-evolutionary dynamics of SVs across the tree of life and within a population genomics framework. In this review, we provide the necessary fundamentals to help researchers generate and analyse population-level SV data. We discuss the unique properties of different SV groups and how these fundamental differences interact with important biological and evolutionary processes using both empirical results and theory. This includes discussion of unresolved issues around SVs, such as technical difficulties in identification, accounting for diversity and evaluating functional effects. We explicitly integrate into this discussion transposable elements, which are an important component of SVs often identified in population-level variant data. Finally, we focus on the practical side of SV analysis, offering a framework for SV identification and data analysis. In particular, we examine the heterogeneous nature of SV properties (type, length, sequence identity) that should be considered when studying them in ecology and evolution. This review aims to provide resources and guidelines to help researchers navigate the complexities of a relatively new field of eco-evolutionary genomics research.}, }
@article {pmid41562342, year = {2026}, author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J}, title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.}, journal = {Clinical and experimental rheumatology}, volume = {44}, number = {2}, pages = {186-193}, doi = {10.55563/clinexprheumatol/1b8sv1}, pmid = {41562342}, issn = {0392-856X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; Middle Aged ; *Myositis, Inclusion Body/microbiology/diagnosis ; Feces/microbiology ; Case-Control Studies ; *Bacteria/genetics/classification ; Severity of Illness Index ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Aged, 80 and over ; }, abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.
METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.
RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (≥ 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).
CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.}, }
@article {pmid41562434, year = {2026}, author = {Jasilionis, A and Sivakumar, P and Dobruchowska, JM and Fjermedal, S and Guðmundsson, H and Adalsteinsson, BT and Hreggviðsson, GÓ and Meyer, AS and Nordberg Karlsson, E}, title = {Characterisation of a phylogenetically distinct PL25 family ulvan lyase from a seaweed biomass enriched metagenome.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.70390}, pmid = {41562434}, issn = {1742-4658}, support = {//European Commision/ ; }, abstract = {Ulvan is a polysaccharide most abundant in green macroalgae biomass. Investigation of ulvan confirmed the potential of the polysaccharide for food, pharmaceutical and chemistry applications, emphasising the beneficial properties of ulvan oligosaccharides. Efficient production of oligosaccharides requires action of ulvan lyases capable of ensuring polysaccharide enzymatic depolymerisation. The armoury of available ulvan lyases was expanded by characterisation of SH2L_Ulv3 ulvan lyase, which was found to be phylogenetically distinct from previously characterised lyases attributed to PL25 family. A gene encoding a novel ulvan lyase was identified among sequences from a seaweed biomass metagenome enriched in an intertidal coastal hot spring. Identified ulvan lyase was most similar to a hypothetical protein from a Bacteroidales bacterium. Recombinant SH2L_Ulv3 was heterologously (over)produced in Escherichia coli at a high yield, remaining soluble in the expression host as well as after affinity purification. Ulvan lyase active as a 48.6 kDa monomer with evaluated activity optimum pH 7.5 and 200 mm NaCl at 25 °C demonstrated broad substrate specificity. SH2L_Ulv3 degraded ulvan from blade-thallus as well as tubular-thallus morphology algae species, efficiently producing three different DP4 and DP2 unsaturated oligosaccharides. The kinetic parameters of SH2L_Ulv3 were KM 3.63 ± 0.12 mg·mL[-1], Vmax 1.78 ± 0.04 μmol·min[-1]·mL[-1] and kcat 1.46 ± 0.04 s[-1]. Magnesium ion stimulated SH2L_Ulv3 activity. The characterised enzyme was not thermostable, displaying Tm 42 °C. The computationally modelled structure of SH2L_Ulv3 revealed structural organisation and active site architecture as well as ligand substrate binding and zinc ion coordinating residues typical for PL25 lyases; however, with a larger central active site cleft facilitating ulvan polysaccharide degradation.}, }
@article {pmid41562608, year = {2026}, author = {Kos, D and Warr, B and Suchan, DM and Wadt, D and Russell, JN and Norfield, M and Liang, J and Jelinski, M and Cameron, ADS and Ruzzini, A}, title = {Survey of bacteria associated with septic arthritis in beef feedlot cattle.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0167525}, pmid = {41562608}, issn = {1098-5336}, support = {20210572//Saskatchewan Agriculture Development Fund/ ; 2021-088//Saskatchewan Cattle Association/ ; //Natural Sciences and Engineering Research Council of Canada/ ; POC.35.23//Beef Cattle Research Council of Canada/ ; }, mesh = {Animals ; Cattle ; *Arthritis, Infectious/microbiology/veterinary ; *Cattle Diseases/microbiology ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Canada/epidemiology ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; }, abstract = {Septic arthritis (SA) is a cause of lameness in cattle attributed to bacterial infections. Mycoplasmopsis bovis is the best known and characterized etiological agent of SA; however, cases caused by diverse bacteria have been reported. Accordingly, we surveyed bacteria associated with septic and healthy joints from animals in western Canadian feedlots. Microbial community profiling showed that M. bovis was the most frequently detected pathogen in septic joints, followed by Metamycoplasma alkalescens and Trueperella pyogenes. In most cases, disease was ostensibly caused by a single pathogen, though polymicrobial infections and complex communities were also observed in DNA isolated from septic joints. The application of enhanced metagenomics by target DNA hybridization capture sequencing (CapSeq) provided more robust pathogen detection and characterization. CapSeq revealed resistance determinants that escaped detection using a conventional shotgun metagenomic approach. Notably, a series of nucleotide polymorphisms to M. bovis rrs, rrl, gyrA, and parC gene sequences were observed that confer resistance to macrolides and oxytetracycline-resistant T. pyogenes were also apparent in the CapSeq data. Complementary pathogen isolation, whole-genome sequencing, and phenotyping efforts were focused on the two most prominent pathogens, M. bovis and M. alkalescens, and corroborated metagenomic data sets.IMPORTANCEInformed antimicrobial use for the treatment of septic arthritis (SA) has been limited by overlooking the potential diversity of causative agents and our knowledge of their antimicrobial resistance (AMR) profiles. This survey begins to provide epidemiological insights, offering renewed appreciation of Metamycoplasma alkalescens as an etiological agent of SA and highlighting the prominence of important AMR determinants. Finally, the survey suggests that our knowledge of even the identities of the causative agents of SA is incomplete.}, }
@article {pmid41563008, year = {2026}, author = {Karatzas, E and Beracochea, M and Baltoumas, FA and Aplakidou, E and Richardson, L and Fellows Yates, JA and Lundin, D and , and Buluç, A and Kyrpides, NC and Georgakopoulos-Soares, I and Pavlopoulos, GA and Finn, RD}, title = {nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41563008}, issn = {2047-217X}, support = {//European Union/ ; DE-AC02-05CH11231//Hellenic Foundation for Research and Innovation/ ; }, mesh = {*Proteins/chemistry/genetics/classification ; *Software ; *Computational Biology/methods ; Databases, Protein ; Metagenomics/methods ; Sequence Alignment ; Molecular Sequence Annotation ; }, abstract = {The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.}, }
@article {pmid41563943, year = {2026}, author = {Xiong, HF and Zhang, WT and Liu, Y and Hou, F and Liu, B and Cui, TT and He, ZY and Zhang, X and Zhao, R and Sun, LY}, title = {Successful Use of Sulbactam-Durlobactam in Treating Carbapenem-Resistant Acinetobacter baumannii Pneumonia and Sepsis After Liver Transplantation: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e949738}, pmid = {41563943}, issn = {1941-5923}, mesh = {Humans ; Female ; *Liver Transplantation/adverse effects ; *Acinetobacter Infections/drug therapy ; *Acinetobacter baumannii/drug effects ; *Sulbactam/therapeutic use ; *Sepsis/drug therapy/microbiology ; Young Adult ; Carbapenems/pharmacology ; *Postoperative Complications/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/drug therapy/microbiology ; }, abstract = {BACKGROUND Orthotopic liver transplantation is the primary treatment for end-stage liver disease; however, postoperative infections, especially those caused by carbapenem-resistant Acinetobacter baumannii (CRAB), remain a major cause of mortality due to limited therapeutic options. Sulbactam-durlobactam (SUL-DUR), a novel b-lactam/b-lactamase inhibitor combination, has shown potent activity against CRAB. This report describes the first reported use of SUL-DUR in a liver transplant recipient with CRAB pneumonia and sepsis. CASE REPORT A 22-year-old woman with acute liver failure underwent auxiliary liver transplantation. Postoperatively, she developed CRAB pneumonia and septicemia confirmed by imaging, bronchoscopy, and metagenomic next-generation sequencing. She received combination therapy with SUL-DUR (1 g/1 g every 8 h), meropenem, eravacycline, and neutralized polymyxin B. Blood and sputum cultures confirmed CRAB susceptibility to SUL-DUR. Following treatment, inflammatory markers (CRP, IL-6, PCT) and pathogen loads markedly decreased, leading to complete clinical resolution without significant adverse effects. The patient was successfully discharged after rehabilitation. CONCLUSIONS SUL-DUR demonstrated excellent efficacy and safety in treating CRAB pneumonia and sepsis after liver transplantation. This case supports Phase III trial data and suggests the potential for use in high-risk, immunocompromised populations. Further studies are warranted to validate its clinical role and inform future guidelines for multidrug-resistant infections.}, }
@article {pmid41564488, year = {2026}, author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X}, title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128688}, doi = {10.1016/j.jenvman.2026.128688}, pmid = {41564488}, issn = {1095-8630}, mesh = {*Lakes/chemistry ; Seasons ; *Geologic Sediments/chemistry ; Microbiota ; Carbon ; }, abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.}, }
@article {pmid41564537, year = {2026}, author = {Asokan, S and Damilare, II and Kumar, S and Pandey, RK and Verma, G and Banerjee, N and Radhamanalan, G and Vijayan, S and Jacob, T and Rajeswary, D}, title = {From pandemic influenza to novel coronaviruses: emerging infectious diseases of the 21st century.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {4}, pages = {117277}, doi = {10.1016/j.diagmicrobio.2026.117277}, pmid = {41564537}, issn = {1879-0070}, mesh = {Humans ; *Communicable Diseases, Emerging/epidemiology/history/virology ; Pandemics ; Animals ; *Influenza, Human/epidemiology/history/virology ; COVID-19/epidemiology ; SARS-CoV-2 ; *Coronavirus Infections/epidemiology ; History, 21st Century ; }, abstract = {Emerging infectious diseases have risen significantly in the twenty-first century as ecological disruption, climate change, expanding human-animal interfaces, and global mobility intensify opportunities for pathogen transmission. This review synthesizes historical and contemporary evidence across viral, bacterial, fungal, and parasitic threats to characterize how diverse pathogens emerge and spread. Foundational events such as the 1918 influenza pandemic, mid-century influenza pandemics, the emergence of HIV/AIDS, and the eradication of smallpox provide context for understanding modern disease dynamics. In recent decades, coronaviruses including SARS, MERS, and SARS-CoV-2, pandemic H1N1, avian influenza subtypes, and major arboviruses such as dengue, chikungunya, Zika, West Nile virus, and yellow fever have demonstrated the rapidity with which zoonotic pathogens can disseminate globally. Viral hemorrhagic fevers including Ebola, Marburg, Lassa, and Crimean-Congo hemorrhagic fever remain critical threats, especially in regions with limited health-care capacity. Concurrently, antimicrobial resistance, the emergence of Candida auris, and the climate-driven expansion of endemic mycoses involving Histoplasma, Coccidioides, and Blastomyces highlight the increasing importance of fungal pathogens. Parasitic diseases such as artemisinin-resistant malaria, zoonotic trypanosomiasis, and expanding Leishmania transmission reflect shifting ecological conditions. These patterns are shaped by intersecting drivers including deforestation, wildlife trade, agricultural intensification, urban crowding, conflict, and rapid microbial evolution that enable spillover and sustained transmission. Although advances in genomic surveillance, metagenomic diagnostics, mRNA vaccines, monoclonal antibodies, and broad-spectrum antivirals have strengthened global response capacity, substantial gaps persist in equity, surveillance, and access to countermeasures. Strengthening One Health systems and resilient public health infrastructures is essential to anticipate and mitigate emerging infectious threats.}, }
@article {pmid41564676, year = {2026}, author = {Liu, J and Zhang, W and Wang, R and Wu, S and Bai, X and Wang, X and Zhu, W and Ding, C}, title = {Functional decoupling between plant remediation efficacy and microbial metal resistance in iron tailings: A Robinia pseudoacacia-driven paradox.}, journal = {Ecotoxicology and environmental safety}, volume = {310}, number = {}, pages = {119760}, doi = {10.1016/j.ecoenv.2026.119760}, pmid = {41564676}, issn = {1090-2414}, mesh = {*Robinia/metabolism ; *Mining ; *Soil Pollutants/metabolism/toxicity ; *Metals, Heavy/toxicity/metabolism ; Biodegradation, Environmental ; *Iron ; Soil Microbiology ; Soil/chemistry ; China ; *Environmental Restoration and Remediation/methods ; }, abstract = {Mining-derived iron tailings pose severe ecotoxicological risks through soil degradation and persistent heavy metal contamination. This study evaluates the ecorestoration potential of three tree species-Populus davidiana, Robinia pseudoacacia, and Rhus typhina-in iron tailings from China's Huluyu Iron Mine. Using an integrated assessment combining soil quality index (SQI), enzymatic activities, metagenomics, and partial least squares path modeling (PLS-PM), we demonstrate that Robinia pseudoacacia achieved the highest SQI (0.68) by significantly mitigating metal stress, which was associated with a marked reduction in soil pH (to 6.29). This acidification is consistent with the well-documented role of root exudates in legumes, alongside enhancing nutrient accumulation (total carbon: 24.8 g/kg; total nitrogen: 1.5 g/kg), and stimulating sucrase and phosphatase activities. Paradoxically, Robinia pseudoacacia soils exhibited minimal enrichment of microbial metal resistance genes, challenging the prevailing "Rhizosphere Synergy Hypothesis." Instead, Robinia pseudoacacia's efficacy relied on functional decoupling from microbial metal detoxification pathways, favoring metabolic optimization of carbon/nitrogen cycling and organic acid-driven pH regulation. PLS-PM confirmed soil chemical properties (pH, total carbon, nitrogen) and enzymatic activities as direct positive drivers of SQI (p < 0.05), while heavy metal content exerted significant negative effects (r = -0.55, p < 0.001). These findings establish RP as an optimal species for iron tailings restoration, reconciling soil fertility enhancement with a potential reduction in metal bioavailability mediated by soil acidification. We propose a predictive SQI framework for selecting remediation species in metalliferous environments, offering critical insights into sustainable management of mining-associated ecotoxicological risks.}, }
@article {pmid41564978, year = {2026}, author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z}, title = {Maxing Shigan decoction serves as a key component of Lianhua Qingwen in alleviating lung and gut injury by restoring gut microbiota homeostasis and inhibiting inflammation via TLR4/NF-κB and JAK2/STAT3 dual regulation.}, journal = {Microbial pathogenesis}, volume = {212}, number = {}, pages = {108285}, doi = {10.1016/j.micpath.2026.108285}, pmid = {41564978}, issn = {1096-1208}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Toll-Like Receptor 4/metabolism ; *Drugs, Chinese Herbal/pharmacology ; NF-kappa B/metabolism ; STAT3 Transcription Factor/metabolism ; Mice ; *Acute Lung Injury/drug therapy ; Janus Kinase 2/metabolism ; Inflammation/drug therapy ; Lung/drug effects/pathology ; Male ; Lipopolysaccharides ; Colitis, Ulcerative/drug therapy/chemically induced ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; }, abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and Western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.}, }
@article {pmid41565402, year = {2026}, author = {Zhou, Y and Wang, H and Guo, L and Liu, X and Wang, X and Liu, Y and Shang, M and Zheng, B and Li, K and Liu, L and Li, J and Ding, G}, title = {Human umbilical cord MSC-derived exosomes attenuate radiation-induced pulmonary fibrosis via remodeling the gut-lung axis in mice.}, journal = {Life sciences in space research}, volume = {48}, number = {}, pages = {204-215}, doi = {10.1016/j.lssr.2025.11.011}, pmid = {41565402}, issn = {2214-5532}, mesh = {*Exosomes/metabolism ; Humans ; Animals ; Mice ; *Mesenchymal Stem Cells/cytology/metabolism ; *Pulmonary Fibrosis/etiology/therapy ; *Umbilical Cord/cytology ; Gastrointestinal Microbiome ; *Lung/radiation effects/metabolism/pathology ; Male ; Mice, Inbred C57BL ; }, abstract = {OBJECTIVE: To investigate whether human umbilical cord mesenchymal stem cell-derived exosomes (hUC-MSC-Exos) attenuate radiation-induced pulmonary fibrosis (RIPF) through modulation of the gut-lung axis.
METHODS: The therapeutic efficacy of hUC-MSC-Exos was evaluated in a mouse model of RIPF through histopathology and western blot analysis of fibrosis markers (α-SMA, Vimentin, and E-cadherin). Gut barrier integrity (ZO-1, Occludin) and intestinal inflammation (IL-6, IL-1β) were examined using immunohistochemistry, RT-qPCR, and ELISA. Gut microbial composition and metabolic profiles were characterized via metagenomics and untargeted metabolomics, followed by integrated bioinformatics analyses to identify key pathways and metabolites.
RESULTS: hUC-MSC-Exos significantly reduced pulmonary collagen deposition and restored fibrosis markers expression, concomitant with enhanced gut barrier function and attenuated intestinal inflammation. Multi-omics analysis revealed restoration of gut microbiota homeostasis and metabolic reprogramming, with the alanine, aspartate, and glutamate pathway being notably co-regulated. L-Glutamic acid was the most significantly altered metabolite and correlated significantly positively with the severity of pulmonary fibrosis and gut dysfunction. Gut microbiota associated with L-Glutamic acid (e.g., Duncaniella, Ruminococcus) were also significantly restructured.
CONCLUSIONS: hUC-MSC-Exos attenuate RIPF through a comprehensive remodeling of the gut-lung axis, in which L-Glutamic acid and its associated microbiota serve as potential mediators. These findings highlight the gut-lung axis as a promising therapeutic target for RIPF.}, }
@article {pmid41565669, year = {2026}, author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J}, title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {45}, pmid = {41565669}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Trichuriasis/microbiology/parasitology/epidemiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Trichuris ; Tanzania/epidemiology ; Animals ; Laos/epidemiology ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; Female ; Feces/microbiology ; Male ; Adult ; Mucins/metabolism ; }, abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.}, }
@article {pmid41565819, year = {2026}, author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N}, title = {Baby-to-baby strain transmission shapes the developing gut microbiome.}, journal = {Nature}, volume = {651}, number = {8104}, pages = {191-200}, pmid = {41565819}, issn = {1476-4687}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Infant ; Female ; Feces/microbiology ; Male ; Infant, Newborn ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Siblings ; Adult ; Bacteria/classification/genetics/isolation & purification/drug effects ; Metagenomics ; }, abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.}, }
@article {pmid41566339, year = {2026}, author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A}, title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {67}, pmid = {41566339}, issn = {2049-2618}, support = {FPU21/03421//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; No 818368//European Commission under the European Union´s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Animals ; *Microbiota/genetics ; Swine/microbiology ; Abattoirs ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Pork Meat/microbiology ; Metagenome ; Food Microbiology ; *Drug Resistance, Bacterial/genetics ; *Red Meat/microbiology ; *Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.
RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.
CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.}, }
@article {pmid41567008, year = {2026}, author = {Zhao, S and Rogers, MJ and Ding, C and He, J}, title = {Stable Function, Dynamic Phylotypes: Microdiversity as a Reservoir for Resilience in Dehalococcoides.}, journal = {Environmental science & technology}, volume = {60}, number = {4}, pages = {3364-3373}, doi = {10.1021/acs.est.5c14525}, pmid = {41567008}, issn = {1520-5851}, mesh = {*Chloroflexi/genetics ; Biodegradation, Environmental ; Halogenation ; Phylogeny ; }, abstract = {Organohalide-respiring bacteria (OHRB) are key contributors to global halogen cycling and mitigation of anthropogenic halogenated pollutants, yet their persistence is challenged by slow growth and restricted metabolic capacity. The mechanisms supporting long-term functional stability remain unclear. As a key OHRB, Dehalococcoides faces similar constraints, including declining abundance and loss or divergence of functional genes in bioaugmentation. Here we demonstrate that strain-level microdiversity within Dehalococcoides supports the resilience of community-scale dehalogenation. In AEDhc, a reconstructed consortium derived from eight Dehalococcoides-containing enrichment cultures, sequencing of a Dehalococcoides-specific marker gene revealed 30 distinct Dehalococcoides phylotypes coexisting within the community. Despite fluctuations in phylotype abundance over successive transfers, AEDhc consistently debrominated tetra- and pentabrominated diphenyl ethers (0.39 ± 0.06 - 0.45 ± 0.05 μM Br[-]/d), producing no detectable accumulation of intermediates. Proteomics analyses revealed that among 71 putative reductive dehalogenase (RDase) genes identified in metagenomic analysis, expression was consistently dominated by PcbA1-like and TceA-like RDases across transfers. These findings demonstrated that Dehalococcoides phylotypes can coexist and fluctuate dynamically even under constant cultivation conditions, with genetic variation serving as a reservoir of metabolic potential. Such microdiversity enhances functional stability and ecological resilience, highlighting the need to consider strain-level heterogeneity in bioremediation strategies.}, }
@article {pmid41567631, year = {2025}, author = {Wang, S and Hu, Y and Li, X and Ou, Y and Chen, J and Chen, Y and Chen, J and Bai, K and Xu, F and Wang, X and Du, H and Yuan, D and Yang, Z and Yuan, J and Niu, H}, title = {Gut microbiota-dependent anti-inflammatory mechanisms of berberine in ameliorating hypertension: role of SCFAs, LPS reduction, and STAT3 signaling.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1696934}, pmid = {41567631}, issn = {1663-9812}, abstract = {BACKGROUND: Hypertension is a chronic disease closely related to vascular remodeling, inflammatory response and intestinal flora disorders. Traditional Chinese medicines, especially Rhizoma Coptidis, are becoming increasingly popular as a possible cardioprotective drug. Berberine, the main active ingredient of Rhizoma Coptidis, has various pharmacological activities, but its specific mechanism of regulating blood pressure through intestinal flora is not clear.
METHODS: In this study, the potential targets of berberine were predicted using network pharmacology, and its antihypertensive mechanism was validated in spontaneously hypertensive rats (SHR). A comprehensive evaluation integrating non-invasive blood pressure measurement, echocardiography, histological analyses (H&E and Masson staining), immunohistochemistry, qPCR, metagenomic sequencing, and untargeted metabolomics was performed to investigate the effects of berberine on cardiovascular remodeling, intestinal barrier integrity, gut microbial composition, and metabolic profiles.
RESULTS: Network pharmacology screened 160 common targets of berberine and hypertension, among which STAT3 may play a key role. Animal experiments confirmed that berberine significantly reduced SHR blood pressure and improved aortic fibrosis and cardiac function. In addition, berberine repaired intestinal barrier damage, upregulated ZO-1 and Occludin expression, and significantly altered the structure of the intestinal flora, increasing the abundance of Short-chain fatty acids (SCFAs) - producing bacteria (e.g., Marvinbryantia, Bacteroides), while decreasing pro-inflammatory bacteria (e.g., Mycoplasma, Treponema). Metabolomics analysis showed that berberine increased fecal SCFAs levels and decreased serum Lipopolysaccharide (LPS). Molecular docking and experimental validation showed that berberine attenuated the inflammatory response by inhibiting STAT3 activation and decreasing colonic IL-6 expression.
CONCLUSION: Berberine exerts antihypertensive effects by regulating the gut flora-SCFAs-LPS-IL6-STAT3 axis, improving intestinal barrier function, and reducing systemic inflammation. This study provides a new mechanistic basis for berberine treatment of hypertension.}, }
@article {pmid41568034, year = {2025}, author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS}, title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1660973}, pmid = {41568034}, issn = {1664-302X}, abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.}, }
@article {pmid41568044, year = {2025}, author = {Kan, Y and Ma, XY and Wang, YL and Sun, B and Wang, S}, title = {A comprehensive comparison of web-based tools for amplicon-metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1711000}, pmid = {41568044}, issn = {1664-302X}, abstract = {Amplicon sequencing provides a suitable approach for microbiome profiling, supported by a variety of R-based and web-based tools. In this review, we systematically evaluated eight freely accessible web-based tools suitable for users without scripting experience, comparing their performance across modules including alpha and beta diversity, taxonomic composition, differential comparison, network and correlation analysis, functional profiling, machine learning, tree-plot and user experience. While all tools exhibit limited data filtering and normalization options, performance varied considerably across modules. Mian and MicrobiomeAnalyst 2.0 excelled in alpha diversity analysis and taxonomic composition analysis, METAGENassist outperformed others in beta diversity, and MicrobiomeAnalyst 2.0 achieved the highest score in differential comparison and functional analysis. Namco and Mian outperform in network analysis and correlation analysis, respectively. Machine-learning functions were comparable across animalcules, MicrobiomeAnalyst 2.0 and METAGENassist, with the best treeplot visualization in animalcules and MicrobiomeAnalyst 2.0. And, user experience was highest for animalcules and Mian. Overall, MicrobiomeAnalyst 2.0 achieving the highest overall performance, followed by Mian and Namco. Several limitations among evaluated tools include inconsistent accessibility, diverse input data formats, restricted feature sets, and incomplete retention of key information in exported figures. Future development should integrate preprocessing, interactive visualization and figure export, alongside advanced statistical methods, multi-omics integration and meta-analytical capabilities, to enhance flexibility, reproducibility and interpretability. This comprehensive assessment provides a practical reference for researchers in selecting the most suitable web-based tools for specific microbiome analysis tasks, highlighting the importance of both module-specific performance and overall tool capabilities.}, }
@article {pmid41568321, year = {2026}, author = {Yahyapour, A and Najafi, A and Ahmadi, A and Salarizadeh, N}, title = {Immunoprotective and neuroprotective properties of gut microbiome in psoriasis.}, journal = {Journal of translational autoimmunity}, volume = {12}, number = {}, pages = {100348}, pmid = {41568321}, issn = {2589-9090}, abstract = {Psoriasis impacts nearly 100 million people globally and is associated with neuropsychiatric comorbidities such as depression and anxiety. With gut microbiome dysbiosis serving as a primary pathophysiological factor, the gut-brain-skin axis provides a crucial framework for understanding this relationship. This review evaluates the mechanisms of the gut-brain-skin axis in psoriasis pathophysiology and assesses the therapeutic potential of microbiome-based treatments, combining preclinical, clinical, and multi-omics data. Patients with psoriasis show specific gut dysbiosis patterns, including reduced microbial diversity, lower SCFA-producing bacteria (especially Faecalibacterium and Akkermansia), and increased pro-inflammatory bacteria. This microbial imbalance damages intestinal barrier integrity, triggers systemic inflammation, activates cutaneous Th17 pathways, and induces neuroinflammation through blood-brain barrier disruption. Axis communication occurs through immune-inflammatory mechanisms mediated by SCFAs and neuroendocrine pathways involving microbially-derived neurotransmitters (GABA, serotonin, dopamine). Metagenomic research indicates functional deficiencies in neurotransmitter and SCFA synthesis pathways are more significant than taxonomic alterations. Machine learning models can utilize these functional features to identify patients at risk for neuropsychiatric comorbidities and predict treatment response. Recent randomized controlled trials demonstrate that targeted interventions (probiotics, prebiotics, postbiotics, fecal microbiota transplantation) significantly improve Psoriasis Area and Severity Index scores, inflammatory markers, and microbiota composition. The evidence supports a shift toward integrated microbiome strategies, emphasizing functional approaches including mitochondrial therapies, psychobiotics, precision nutrition, and multi-omics-guided therapies.}, }
@article {pmid41568738, year = {2026}, author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA}, title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {22}, number = {1}, pages = {e71023}, pmid = {41568738}, issn = {1552-5279}, support = {//TMCity/ ; }, mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; }, abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.}, }
@article {pmid41569097, year = {2026}, author = {Ayala-Montaño, S and Afolayan, AO and Kociurzynski, R and Loeber, U and Reuter, S}, title = {Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41569097}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; Computational Biology/methods ; *DNA Contamination ; *Metagenome ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Infant, Newborn ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; }, abstract = {Metagenomic sequencing of clinical samples has significantly enhanced our understanding of microbial communities. However, microbial contamination and host-derived DNA remain a major obstacle to accurate data interpretation. Here, we present a methodology called 'Stop-Check-Go' for detecting and mitigating contaminants in metagenomic datasets obtained from neonatal patient samples (nasal and rectal swabs). This method incorporates laboratory and bioinformatics work combining a prevalence method, coverage estimation and microbiological reports. We compared the 'Stop-Check-Go' decontamination system with other published decontamination tools and commonly found poor performance in decontaminating microbiologically negative patients (false positives). We emphasize that host DNA decreased by an average of 76% per sample using a lysis method and was further reduced during post-sequencing analysis. Microbial species were classified as putative contaminants and assigned to 'Stop' in nearly 60% of the dataset. The 'Stop-Check-Go' system was developed to address the specific need of decontaminating low-biomass samples, where existing tools primarily designed for short-read metagenomic data showed limited performance.}, }
@article {pmid41569365, year = {2026}, author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L}, title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).}, journal = {Environmental science and pollution research international}, volume = {33}, number = {4}, pages = {1447-1458}, pmid = {41569365}, issn = {1614-7499}, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Portugal ; *Soil Microbiology ; *Microplastics/analysis ; Soil/chemistry ; *Soil Pollutants/analysis ; Environmental Monitoring ; Microbiota ; Bacteria ; }, abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.}, }
@article {pmid41570020, year = {2026}, author = {Beuker, C and Schulte-Mecklenbeck, A and Wirth, T and Kleffner, I and Thomas, C and Strunk, D and Schmidt-Pogoda, A and Gross, CC and Klotz, L and Minnerup, J}, title = {Spontaneous cervical artery dissection is associated with a distinct peripheral immune cell signature.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0340592}, pmid = {41570020}, issn = {1932-6203}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; *Leukocytes, Mononuclear/immunology ; Case-Control Studies ; *Vertebral Artery Dissection/immunology ; Killer Cells, Natural/immunology ; }, abstract = {OBJECTIVES: Despite being a major cause of ischemic stroke in young adults, the biological underpinnings of cervical artery dissection (CeAD) remain poorly defined. Recent data implicate immune activation as a potential contributor. We aimed to determine whether patients with CeAD display a distinct peripheral immune signature, which may provide insights into pathogenic inflammatory processes.
METHODS: Peripheral blood mononuclear cells (PBMCs) from patients with spontaneous CeAD (n = 7 without and n = 11 with ischemic stroke) and ten age-matched healthy controls were analyzed via multi-color flow cytometry. Immune cell composition and activation markers were assessed, and sparse partial least squares discriminant analysis (sPLS-DA) was employed to identify CeAD-associated immune features. A secondary comparison with ischemic stroke controls was included to assess the specificity of identified immune alterations.
RESULTS: Compared to healthy controls, CeAD patients displayed increased frequencies of CD4 ⁺ T cells and decreased natural killer T (NKT) cells. sPLS-DA demonstrated clear separation of CeAD and control immune profiles, driven by increased CD28 expression on naïve CD8 ⁺ T cells, NKp46 on NK cells, and IL-2Rα (CD25) on myeloid dendritic cells (mDC2). Elevated granzyme K in naïve CD8 ⁺ T cells indicated enhanced cytotoxic potential, while regulatory T cells were diminished. These alterations were largely preserved when compared to ischemic stroke controls, suggesting CeAD-specific immune activation. No microbial pathogens were detected by untargeted metagenomic sequencing.
DISCUSSION: CeAD is associated with a distinct peripheral immune signature characterized by enhanced cytotoxic activity and reduced regulatory features. These alterations may reflect a post-infectious autoimmune mechanism triggering CeAD or a secondary immune-inflammatory response to vascular injury. Larger, longitudinal studies are needed to clarify causality and assess whether immune modulation could serve as a therapeutic target in CeAD.}, }
@article {pmid41570402, year = {2026}, author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL}, title = {Gut microbiota is different before the development of preeclampsia.}, journal = {Pregnancy hypertension}, volume = {43}, number = {}, pages = {101415}, doi = {10.1016/j.preghy.2026.101415}, pmid = {41570402}, issn = {2210-7797}, mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology/physiopathology/diagnosis ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Blood Pressure ; Case-Control Studies ; }, abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.
STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28 weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.
MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.
RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.
CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.}, }
@article {pmid41570486, year = {2026}, author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K}, title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.}, journal = {Journal of neuroimmunology}, volume = {413}, number = {}, pages = {578870}, doi = {10.1016/j.jneuroim.2026.578870}, pmid = {41570486}, issn = {1872-8421}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; Animals ; *Neuroinflammatory Diseases/metabolism ; *Probiotics/administration & dosage ; *Cognitive Aging/physiology ; *Brain-Gut Axis/physiology/drug effects ; *Brain/metabolism ; *Dysbiosis/metabolism ; *Aging ; }, abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.}, }
@article {pmid41570514, year = {2026}, author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T}, title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.}, journal = {Marine pollution bulletin}, volume = {225}, number = {}, pages = {119288}, doi = {10.1016/j.marpolbul.2026.119288}, pmid = {41570514}, issn = {1879-3363}, mesh = {*Lakes/microbiology ; *Microbiota ; *Nitrogen Cycle ; Metagenomics ; *Metagenome ; Nitrogen/metabolism ; Denitrification ; Bacteria ; Ecosystem ; }, abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.}, }
@article {pmid41570646, year = {2026}, author = {Sidikjan, N and Li, Y and Chen, Y and Guo, XP and Liu, M and Huang, Y}, title = {Multimedia profiling of metal resistance genes in the Yangtze Estuary: Biofilm dominance and community-driven regulatory pathways.}, journal = {Ecotoxicology and environmental safety}, volume = {310}, number = {}, pages = {119769}, doi = {10.1016/j.ecoenv.2026.119769}, pmid = {41570646}, issn = {1090-2414}, mesh = {*Biofilms/drug effects ; *Estuaries ; *Metals, Heavy/toxicity/analysis ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Genes, Bacterial ; Geologic Sediments/microbiology ; Drug Resistance, Microbial/genetics ; Microbiota ; }, abstract = {Biofilms are critical microbial assemblages that function as sinks and potential reservoirs of metal resistance genes (MRGs) in contaminated aquatic systems. In this study, metagenomic sequencing and environmental profiling were employed to characterize MRGs distribution, heavy metal contamination, and microbial community structure across water, sediment, and biofilm samples in the Yangtze Estuary. Biofilms exhibited significantly higher concentrations of heavy metals and MRGs than other matrices, particularly for key genes such as corS (Cu-resistance), nrsS (Ni-resistance), and pbrA (Pb-resistance). Ecological risk assessment identified cadmium as the primary risk contributor, especially in biofilms. Partial redundancy analysis revealed that microbial community composition was the dominant factor shaping MRGs distribution, rather than metal concentrations alone. Network and canonical correspondence analyses further demonstrated strong co-occurrence patterns between MRGs and antibiotic resistance genes (ARGs), regulated by eutrophication (TN, Chl-a) and heavy metals (Pb, Cd, Cu). Notably, Pb-resistance genes in biofilm communities were significantly enriched and closely associated with Cyanobacteria and Proteobacteria, reflecting a multi-stage co-occurrence pattern potentially involving pbrT, pbrA, cadD, and czcD. These findings highlight the ecological significance of biofilms in MRGs enrichment, dissemination, and risk propagation in estuarine ecosystems under combined pollution stress.}, }
@article {pmid41570777, year = {2026}, author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J}, title = {Long-term pet ownership promotes resistome similarity between cats and their owners.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110074}, doi = {10.1016/j.envint.2026.110074}, pmid = {41570777}, issn = {1873-6750}, mesh = {Animals ; Cats ; *Pets/microbiology ; *Ownership ; Humans ; *Gastrointestinal Microbiome ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; }, abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.}, }
@article {pmid41572158, year = {2026}, author = {Wijaya, SC and Richi, M and Waturangi, DE and Yulandi, A}, title = {Linking metagenomic insight to cultivable microbes: isolation of a vitamin B12-producing Sphingomonad from Indonesian tempeh.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {127}, pmid = {41572158}, issn = {1471-2180}, abstract = {BACKGROUND: Tempeh, a famous traditional Indonesian fermented soybean product, reportedly contains vitamin B12. Although Enterobacteriaceae have been previously implicated in vitamin B12 production in tempeh, the function of Sphingomonadaceae, which is abundant in some tempeh samples, remains unknown. This study aimed to identify and characterize vitamin B12-producing bacteria from Empang (EMP) tempeh, with a focus on the understudied Sphingomonad.
RESULTS: Metagenomic analysis focusing on vitamin B12 biosynthesis genes revealed that Sphingomonad genes had a complete set gene that required for producing the vitamin. A total of 44 yellow-pigmented isolates, characteristic of Sphingomonas, were screened via a vitamin B12 assay, three of which demonstrated potential for de novo biosynthesis. On the basis of 16S rRNA gene analysis, all three isolates were identified as Sphingomonas paucimobilis. Whole-genome sequencing and annotation of the EMP5-4 isolate revealed a complete gene set for the aerobic vitamin B12 biosynthesis pathway, including hem genes, cob genes and cobalamin riboswitches. Vitamin B12 production was confirmed through fermentation in a TSB medium with cobalt and DMBI supplementation and quantified at 0.949 µg/mL via HPLC. A genome-based safety assessment identified only low confidence antibiotic resistance and virulence genes, and a hemolysis assay revealed no red blood cell lysis, suggesting minimal pathogenicity.
CONCLUSION: These findings demonstrate that S. paucimobilis from tempeh may serve as a novel microbial source of vitamin B12, supporting its potential application in functional foods for individuals who avoid animal-derived products.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04681-2.}, }
@article {pmid41572308, year = {2026}, author = {Natalia, Z and Aleksandra, S and Egor, S and Ksenia, K}, title = {Bacteriophages in gut metagenomes: from analysis to application.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {40}, pmid = {41572308}, issn = {1743-422X}, support = {23-75-10125//Russian Science Foundation/ ; }, mesh = {*Bacteriophages/genetics/classification/isolation & purification/physiology ; Humans ; *Gastrointestinal Microbiome ; *Metagenome ; Metagenomics/methods ; Computational Biology/methods ; Genome, Viral ; *Virome ; }, abstract = {Bacteriophages constitute a major component of the human gut virome, playing very important roles in shaping of the structure and function of the gut microbiota. Moreover, bacteriophages interact with the human immune system, thereby influencing various disease processes. Recent advancements in metagenomic sequencing and computational analysis have substantially expanded our understanding of gut phage diversity and the scale of the so-called 'viral dark matter'. In this review, we summarize current bioinformatic approaches for identifying and annotating bacteriophage sequences in metagenomic data, discuss key challenges in taxonomic classification and host prediction of phages, as well as the limitations associated with the assembly and analysis of viral metagenome-assembled genomes (vMAGs). We also analyze the therapeutic potential of bacteriophages, including their application in cancer immunotherapy, inflammatory diseases, and liver diseases, and their promise as diagnostic and prognostic biomarkers.}, }
@article {pmid41572348, year = {2026}, author = {He, W and Yu, Z and Wu, Z and Olesen, AK and Madsen, JS and Dechesne, A and Smets, BF and Nesme, J and Sørensen, SJ}, title = {Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {39}, pmid = {41572348}, issn = {2049-2618}, support = {NNF 200C0062223//Novo Nordisk Foundation Data Science Collaborative Research Programme 2020/ ; DARWIN project #7044-00004B//Joint Programming Initiative-Antimicrobial Resistance grant/ ; }, mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Spain ; Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Denmark ; *Drug Resistance, Bacterial/genetics ; Europe ; Whole Genome Sequencing ; Humans ; }, abstract = {BACKGROUND: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored.
RESULTS: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes.
CONCLUSIONS: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.}, }
@article {pmid41572438, year = {2026}, author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chanchaem, P and Klomkliew, P and Payungporn, S and Zhang, Y}, title = {Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.}, journal = {Acta neuropsychiatrica}, volume = {38}, number = {}, pages = {e16}, doi = {10.1017/neu.2026.10056}, pmid = {41572438}, issn = {1601-5215}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Major Depressive Disorder/microbiology/metabolism/psychology ; Metagenomics ; Male ; Female ; Adult ; *Suicidal Ideation ; Middle Aged ; Dysbiosis/microbiology ; Cognition/physiology ; Affect/physiology ; }, abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.
AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune–metabolic biomarkers of MDD.
METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).
RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, that is, Ruminococcus gnavus, Veillonella rogosaem, and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, that is, Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants, and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.
CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.}, }
@article {pmid41572814, year = {2026}, author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V}, title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.}, journal = {Journal of orthodontics}, volume = {53}, number = {1}, pages = {34-44}, doi = {10.1177/14653125251408048}, pmid = {41572814}, issn = {1465-3133}, mesh = {Humans ; Longitudinal Studies ; *Orthodontic Appliances, Fixed/microbiology/adverse effects ; Male ; Female ; Metagenomics ; *Dysbiosis/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Adolescent ; DNA, Bacterial ; *Mouth/microbiology ; Young Adult ; Bacteria/classification ; }, abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to understand the relationship between orthodontic therapy and oral health better.
METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.
RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).
CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.}, }
@article {pmid41572827, year = {2025}, author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y}, title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.}, journal = {Immunotherapy}, volume = {17}, number = {17-18}, pages = {1231-1239}, pmid = {41572827}, issn = {1750-7448}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Dysbiosis/metabolism ; *Immune Checkpoint Inhibitors/adverse effects ; Proteomics/methods ; Male ; Female ; Metabolomics/methods ; *Thrombocytopenia/chemically induced/metabolism/etiology ; Middle Aged ; Aged ; *Neoplasms/drug therapy/immunology ; Multiomics ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.
METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n = 8) and without ICIs-TCP (n = 8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.
RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.
CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.}, }
@article {pmid41572901, year = {2026}, author = {Hock, L and Luiken, R and Valério, E and Vargha, M and Vierheilig, J and Börjesson, S and Pitkänen, T and Schmitt, H}, title = {Integrating AMR surveillance into wastewater monitoring systems in 2025: a position on the implementation of Article 17 of the Urban Wastewater Treatment Directive (UWWTD).}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {31}, number = {3}, pages = {}, pmid = {41572901}, issn = {1560-7917}, mesh = {*Wastewater/microbiology ; Humans ; *Water Purification/legislation & jurisprudence/methods ; European Union ; *Environmental Monitoring/methods ; Europe ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Public Health ; Water Microbiology ; }, abstract = {The recast Urban Wastewater Treatment Directive (UWWTD) calls for monitoring antimicrobial resistance (AMR) in wastewater of large European agglomerations (≥ 100,000 person equivalents). Guidance on scope and methods is currently in development. Two European Joint Actions share a goal to harmonise procedures and indicators: the European Union (EU)-Wastewater Integrated Surveillance for Public Health (EU-WISH), aiming to strengthen wastewater-based surveillance (WBS) for public health and the EU-Joint Action Antimicrobial Resistance and Healthcare Associated Infections (EU-JAMRAI) 2, providing among others, approaches for environmental surveillance of AMR. An EU-WISH survey in 2024, mapping WBS AMR-related activities across Europe, revealed that of 27 countries surveyed, 11 had an operative AMR WBS system and mainly employed WBS to determine AMR trends, primarily through culture-based analyses, in-depth characterisation of specific bacteria, and quantitative PCR for specific resistance genes. Occasionally metagenomics was used. We argue that prioritising AMR WBS targets should consider the intended objectives of surveillance, which could include uncovering AMR trends and emerging AMR determinants in humans, the assessment of antimicrobial/AMR environmental release, and wastewater treatment efficiency. Targets should be assessed for their public health relevance and the usefulness of complementary information they provide, while integrating measurability, resource efficiency, and expertise from different One Health domains.}, }
@article {pmid41574048, year = {2026}, author = {Ru, SS and Li, W and Hao, J and Cao, CY and Ma, L and Zhang, X}, title = {Evaluation of the diagnostic value of metagenomic next-generation sequencing for zoonotic cestode Spirometra mansoni infection.}, journal = {Food and waterborne parasitology}, volume = {42}, number = {}, pages = {e00316}, pmid = {41574048}, issn = {2405-6766}, abstract = {Metagenomic next-generation sequencing (mNGS) technology offers substantial advantages in parasite detection; however, we still know very little about its diagnostic value for Spirometra mansoni infection. In this study, mNGS technology was used to analyse faecal samples and blood samples from cats infected with S. mansoni, as well as tissue samples and blood samples from mice infected with the plerocercoid larvae of S. mansoni. Moreover, polymerase chain reaction (PCR) was employed to validate the mNGS results. The diagnostic value of mNGS for S. mansoni infection was systematically evaluated. The mNGS results revealed that the read counts of S. mansoni in the cat faeces (CF) samples were 301,497 (CF1), 1,330,549 (CF2), 1,181,162 (CF3), and 0 (CF0), with relative abundances of 3.17%, 16.64%, 13.14%, and 0%, respectively. In the mouse tissue (MT) samples, the read counts of S. mansoni were 10,791 (MT1), 438 (MT2), 3697 (MT3), and 10 (MT0), with relative abundances of 67.21%, 3.65%, 21.12%, and 0.16%, respectively. No sequences of S. mansoni were detected in the cat blood samples or mouse blood samples. The PCR results were consistent with the mNGS results, confirming the accuracy of the mNGS analysis. In addition, during the detection process, the assembly-based analysis did not detect sequences of S. mansoni in all samples. In contrast, the read-based analysis successfully detected the target sequences without fail. Finally, the analysis of microbiota diversity in the definitive host faecal samples revealed that compared with those in the control group, the elevated microbial taxa in the infected group mainly were probiotics, such as Prevotella copri and Bifidobacterium adolescentis. Conversely, the decreased microbial populations were primarily associated with certain diseases, such as Collinsella stercoris and Catenibacterium sp. In this study, the diagnostic value of mNGS for S. mansoni infection was systematically evaluated. These findings establish a foundation for the more precise application of mNGS technology in the detection of S. mansoni and related cestode infections.}, }
@article {pmid41574217, year = {2026}, author = {Rulhania, A and Panigrahi, S and Swami, S and Singh, Y and Balyan, P and Singh, KP and Mir, RR and Kumar, U}, title = {Identification and expression analysis of putative genomic regions disseminating biotic stress tolerance in chickpea (Cicer arietinum).}, journal = {3 Biotech}, volume = {16}, number = {2}, pages = {81}, pmid = {41574217}, issn = {2190-572X}, abstract = {UNLABELLED: Chickpea (Cicer arietinum L.) productivity is heavily constrained by major biotic stresses, particularly Fusarium wilt, Ascochyta blight and Botrytis gray mold, which collectively cause significant annual yield losses worldwide. To develop a refined understanding of the genetic architecture underlying resistance to these pathogens, a comprehensive meta-analysis was conducted using 113 QTLs taken from 24 independent studies, including diverse mapping populations. This analysis led to the identification of 27 MQTLs, which represent both novel genomic regions and, crucially, refined positions of previously known QTLs with reduced confidence intervals. Four robust Breeders' MQTLs were identified on the basis of high phenotypic variance (PVE ≥ 10%), a low confidence interval (CI ≤ 2 cM) and the involvement of multiple initial QTLs. Among these breeder MQTLs, 229 candidate genes, including key players in plant defense, such as receptor-like kinases (RLKs), resistance gene analogues (RGAs) and genes for RML1A, HSPRO2 and endochitinase A, were identified. These genes were validated through qRT‒PCR expression profiling in contrasting genotypes (WR-315 and JG-62). These refined genomic regions and their associated markers provide a direct pathway for pyramiding multiple resistance QTLs through marker-assisted selection and provide a direct pathway to breed chickpea varieties with durable, broad-spectrum resistance to key fungal diseases. The integrated meta-genomic framework significantly enhances precision and utility and paves the way for the functional characterization of the underlying resistance mechanisms.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04698-y.}, }
@article {pmid41574290, year = {2025}, author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1719300}, pmid = {41574290}, issn = {2235-2988}, mesh = {*Feces/virology ; Animals ; Phylogeny ; *Metagenomics ; *DNA Viruses/genetics/classification/isolation & purification ; Tibet ; Cattle/virology ; *Virome ; *Picornaviridae/genetics/classification/isolation & purification ; Genome, Viral ; China ; }, abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.
METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.
RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.
DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.}, }
@article {pmid41574306, year = {2025}, author = {Guo, S and Wang, L and Sai, X and Tang, S and Wang, J and Wang, A and Qiu, D and Han, S and Wu, Y and Chen, C}, title = {Effect of BALF-based mNGS on clinical outcomes of immunocompromised subjects with opportunistic pulmonary infections: a multicenter propensity score-matched study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1724935}, pmid = {41574306}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Immunocompromised Host ; Aged ; Propensity Score ; *Opportunistic Infections/diagnosis/microbiology/drug therapy/mortality ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Treatment Outcome ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising tool for pathogen detection. However, its clinical utility in detecting opportunistic pulmonary infections of immunocompromised patients remains controversial.
METHODS: This multicenter retrospective study involving 162 immunocompromised patients with opportunistic pulmonary infections was conducted across four respiratory centers. The enrolled patients were divided into the conventional microbiological tests (CMT) group and the mNGS group based on whether mNGS of BALF was performed after admission. Propensity score-matching (PSM) was adopted to minimize selection bias, and sensitivity analysis confirmed the robustness. The primary outcomes were >30% improvement in oxygenation index (OI) at 7 days post-admission and clinical improvement by day 14 as assessed with the WHO 7-category ordinal scale. Secondary outcomes included 21-day mortality, incidence of septic shock during hospitalization, and pathogen detection rate.
RESULTS: Among the 110 patients who underwent mNGS, the results prompted modifications to the antibiotic therapy in 89 patients (80.9%), encompassing both escalation and de-escalation of therapy. The remaining 52 patients received only CMT. After the PSM, 41 matched pairs were further analyzed. Compared to the CMT group, OI improvement >30% on day 7 was more frequent in the mNGS group (41.5% vs. 9.8%, P = 0.001). Clinical improvement on day 14 in the mNGS group was higher than in the CMT group (36.6% vs. 9.8%, P = 0.004). Additionally, BALF mNGS was associated with decreased 21-day mortality (7.3% vs. 34.1%; P = 0.003) in patients with opportunistic pulmonary infections, while showing no significant association with reduced incidence of septic shock during hospitalization. Moreover, the causative pathogen detection rate was significantly higher in the mNGS group compared to the CMT group (97.6% vs. 22.0%, P<0.001), demonstrating the superior diagnostic yield of mNGS.
CONCLUSION: Our study indicated that early BALF mNGS testing upon admission was associated with improved OI up to day 7, clinical improvement on day 14, and decreased 21-day mortality. These benefits are likely facilitated by the higher diagnostic yield of mNGS and its direct impact on guiding targeted antibiotic therapy.}, }
@article {pmid41574341, year = {2025}, author = {Destras, G and Sabatier, M and Bal, A and Simon, B and Semanas, Q and Regue, H and Boyer, T and Ploin, D and Gillet, Y and Lina, B and Anani, H and Josset, L}, title = {Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1685035}, pmid = {41574341}, issn = {1664-302X}, abstract = {INTRODUCTION: Omics-based studies focusing on a single kingdom, such as bacterial 16S gene sequencing, viral metagenomics, and human mRNA sequencing, are commonly used to explore the microbiome and its association with host responses. But combining these approaches is often expensive and time-consuming. Metatranscriptomics provides a snapshot of the entire active microbiome through bulk RNA sequencing in a single test, yet its performance relative to kingdom-specific methods has not been systematically assessed.
METHODS: We compared metatranscriptomics with three kingdom-specific sequencing approaches in 20 nasopharyngeal aspirates from infants 7 months of age hospitalized for bronchiolitis at the Hospices Civils de Lyon.
RESULTS: Applying specific sequencing depth thresholds (≥1,000 bacterial reads, ≥100,000 human reads, and detection of an internal RNA control), metatranscriptomics showed high detection concordance and correlated abundance for RNA viruses and human coding genes. Metatranscriptomics also detected RNA from both eukaryotic and prokaryotic DNA viruses, suggesting potential for identifying transcriptional activity. For the bacteriome, 82% of genera exceeding 0.5% relative abundance were captured, revealing distinct transcriptional profiles at the species level. Metatranscriptomics reproduced multi-omics-derived host-microbiome endotypes and revealed stronger key microbial associations, particularly for transcriptionally active microorganisms.
DISCUSSION: These findings indicate that a single metatranscriptomics run can complement or replace kingdom-specific approaches for profiling RNA viruses and the host transcriptome, while also identifying transcriptionally active bacteria and DNA viruses. Low-abundance or latent microorganisms may still require targeted assays. Metatranscriptomics thus provides a cost- and time-efficient strategy for integrated microbiome research and holds promise for clinical applications in acute infections and cases of diagnostic uncertainty.}, }
@article {pmid41574342, year = {2025}, author = {Feng, Q and Liu, B and Liu, H and Fan, Y and Gao, S and Zhang, J and Kuang, Y and Wang, W and Liang, H and Qiu, Y and Wen, H and Feng, Z and Huang, Y and Zuo, W and Zhang, X and Zeng, J and Wu, J and Liang, Y and Gu, J}, title = {The application value and limitations of metagenomic detection technology based on cerebrospinal fluid samples in suspected central nervous system infection: a retrospective study.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1689253}, pmid = {41574342}, issn = {1664-302X}, abstract = {BACKGROUND: Accurately diagnosing central nervous system (CNS) infections remains challenging. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) in diagnosing suspected CNS infections and its role in facilitating rapid and accurate pathogen identification.
METHODS: This retrospective study enrolled cerebrospinal fluid specimens from 246 patients with suspected CNS infections and 20 controls with definitively ruled-out infections. Using clinical diagnoses established by an expert panel based on comprehensive criteria as the reference standard, we evaluated the diagnostic performance of mNGS relative to culture and conventional tests. Additionally, we analyzed the therapeutic guidance value of positive mNGS results and risk factors for false negatives.
RESULTS: mNGS showed 73.2% (180/246) agreement with clinical diagnosis, superior to culture (54.1%, 133/246) and conventional methods (61.4%, 151/246). For general bacteria and fungi, mNGS showed 61.9% (26/42) concordance with culture. False negatives in mNGS predominantly involved viral missed detection. Age, presence of systemic infection, headache, and cerebrospinal fluid glucose levels were likely key determinants of mNGS performance. mNGS detection of Epstein-Barr virus, Streptococcus spp., Mycobacterium tuberculosis complex, herpes simplex virus type 1, and Staphylococcus spp. suggested high pathogenic potential, whereas Torque teno virus detection more likely indicated carriage or experimental contamination.
CONCLUSION: mNGS holds significant value for the diagnosis, therapeutic management, and prognostic assessment of suspected CNS infections.}, }
@article {pmid41574343, year = {2025}, author = {Saba Villarroel, PM and Piorkowski, G and Laojun, S and Liégeois, F and Gumpangset, N and Missé, D and Chaiphongpachara, T and Wichit, S}, title = {Metagenomic exploration of the virome of Rhipicephalus sanguineus ticks from Chachoengsao, Thailand.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1736178}, pmid = {41574343}, issn = {1664-302X}, abstract = {Ticks are obligate blood-feeding ectoparasites that harbor a wide diversity of microorganisms. Rhipicephalus sanguineus, the brown dog tick, is globally distributed and poses significant veterinary and public health concerns due to its close association with companion animals and its occasional infestation of humans. However, the virome of this species in Thailand remains poorly characterized. In this study, we employed DNA Nanoball sequencing to investigate the virome of 80 R. sanguineus ticks, grouped into five pools, collected from dogs in Chachoengsao Province, Thailand, in 2023. Three viruses were identified: Brown dog tick phlebovirus 2 (BDTPV2), Changping tick virus 2 (CpTV-2), and Bole tick virus 4 (BLTV4), all detected in male ticks. These results highlight the need for further investigation into the ecological roles and biological significance of these viruses. Overall, our findings provide an updated perspective on the R. sanguineus virome in Thailand and underscore the importance of continued surveillance of tick-associated viruses within the One Health framework.}, }
@article {pmid41574363, year = {2025}, author = {Xiao, J and Pu, C and Zhou, X and Zhang, X and Zhang, S and Yang, P and Zhang, Y and Xiong, L}, title = {Solving the diagnostic dilemma in bone infections: metagenomic next generation sequencing enhances pathogen identification accuracy.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1699607}, pmid = {41574363}, issn = {2296-858X}, abstract = {OBJECTIVE: Metagenomic Next Generation Sequencing (mNGS) offers a rapid, unbiased, and culture-independent approach to pathogen identification by analyzing all nucleic acids present in clinical samples. Despite its growing use, the diagnostic utility of mNGS in bone infections remains inadequately characterized. This study aimed to assess the diagnostic accuracy of mNGS compared to conventional microbial cultures and to explore its associations with clinical severity and patient outcomes.
METHODS: We retrospectively enrolled 135 adult patients treated for suspected bone infections between October 2023 to January 2025 at Union Hospital, Tongji Medical College. Among these, 101 patients were classified as the infection group (IG) based on clinical and laboratory criteria, encompassing osteomyelitis, post-traumatic limb infections, and diabetic foot infections. mNGS results were compared to traditional cultures in terms of sensitivity, specificity, predictive values, and discordant cases. The IG was further stratified into mNGS-positive (n = 95) and mNGS-negative (n = 6) subgroups. Clinical parameters-including leukocyte differentials, C-reactive protein (CRP), procalcitonin (PCT), albumin, length of hospital stay, and mortality-were analyzed in relation to mNGS findings.
RESULTS: Among all patients, 74.81% were confirmed to have infections. mNGS demonstrated a markedly higher sensitivity than culture (94.06% vs. 47.52%, p = 0.000) while maintaining comparable specificity (85.29% vs. 76.47%, p = 0.549). Age showed a potential trend in influencing mNGS positivity (p = 0.092). Although not statistically significant, mNGS-positive patients tended to have longer hospitalizations (p = 0.098), suggesting possible associations with infection complexity or pathogen load.
CONCLUSION: mNGS substantially enhances the diagnostic yield for bone infections, particularly in polymicrobial, low-abundance, or culture-negative scenarios. mNGS-negative patients had significantly shorter hospital stays and a lower rehospitalization rate. Its rapid and comprehensive pathogen detection may enable more timely and targeted antimicrobial therapy, potentially improving patient outcomes and reducing healthcare burden. These findings support the integration of mNGS as a valuable adjunct to conventional diagnostic workflows in orthopedic infectious diseases.}, }
@article {pmid41574538, year = {2026}, author = {Thakur, M and Dolker, S and Ghosh, A and Wangmo, LK and Singh, VK and Hasan, M and Acharya, AP and Biswas, A and Sarkar, S and Sharma, LK and Banerjee, D}, title = {Metagenomic Surveillance of Blood-Fed Mosquitoes for Assessing Zoonotic Risk in Managed Animal Settings.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {26}, number = {4}, pages = {201-210}, doi = {10.1177/15303667261417424}, pmid = {41574538}, issn = {1557-7759}, mesh = {Animals ; *Zoonoses/epidemiology/transmission ; *Culicidae/microbiology/genetics/physiology/classification ; Metagenomics ; Female ; India/epidemiology ; *Mosquito Vectors/microbiology ; Humans ; Livestock ; Buffaloes ; }, abstract = {BACKGROUND: Vector-borne zoonotic diseases remain a major global public health concern, particularly at interfaces where humans, domestic animals, and wildlife interact closely. Conventional surveillance approaches often fail to detect early zoonotic spillover events, especially in farm and zoological settings. Blood-fed mosquitoes, which feed on diverse vertebrate hosts, offer a unique opportunity for non-invasive environmental surveillance through xenosurveillance. This study evaluates the feasibility of using blood-fed mosquitoes as biological samplers to assess zoonotic risk in managed animal settings in eastern India.
METHODS: A total of 185 blood-fed female mosquitoes were collected from livestock farms and zoological enclosures in West Bengal, India, and grouped based on host association (cattle, buffalo, goat, poultry, zebra, and deer). Mosquito species were identified using mitochondrial cytochrome c oxidase I (COI) gene sequencing. Host-group-wise pooled DNA from mosquito heads and abdomens was subjected to shotgun metagenomic sequencing using Oxford Nanopore MinION technology. Taxonomic classification was performed using Kraken 2, and microbial diversity was analyzed through alpha and beta diversity metrics using phyloseq.
RESULTS: Six mosquito species were identified, including Culex tritaeniorhynchus, Culex vishnui, and Mansonia uniformis, known vectors of zoonotic pathogens. Metagenomic analysis revealed diverse microbial communities dominated by Actinobacteria, Proteobacteria, and Firmicutes, with significant host-associated variation in microbial composition. Buffalo- and zebra-associated mosquitoes exhibited the highest microbial richness, while cattle-associated mosquitoes showed comparatively lower diversity. Genomic fragments corresponding to potential zoonotic and veterinary pathogens-including Plasmodium relictum, Babesia bigemina, and Clostridium botulinum-were detected across multiple host groups. Beta diversity analysis demonstrated clear host-driven clustering of mosquito-associated microbiomes.
CONCLUSION: This pilot study demonstrates that blood-fed mosquitoes can serve as effective non-invasive biological samplers for detecting environmental DNA signatures of potential zoonotic pathogens in managed animal settings. While the detection of pathogen-associated genomic fragments does not confirm active infection or transmission, the findings highlight the utility of mosquito-based metagenomic surveillance as an early warning and risk-detection tool within a One Health framework. Integrating such approaches with targeted diagnostics and epidemiological surveillance may strengthen preparedness for emerging vector-borne zoonotic threats.}, }
@article {pmid41575223, year = {2026}, author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W}, title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41575223}, issn = {1751-7370}, support = {//The National Key Research and Development Program of China/ ; Project32098//National Science and Technology Major Project/ ; }, mesh = {Humans ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Bacteria/genetics/drug effects/classification ; Healthy Volunteers ; Genome, Bacterial ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.}, }
@article {pmid41575959, year = {2026}, author = {Duan, Z and Lian, D and Wang, K and Hu, Y and Fu, H and Wen, R and Zhao, Y and Hu, X and Pan, P and Xu, J and Chen, J and Xiao, L and Wang, L and Yu, X and Han, X and Xie, W and Xie, F and Xie, L and Han, Z}, title = {Multi-modal data to identify key factors influencing lung injury in ARDS patients undergoing invasive mechanical ventilation: A prospective multi-center observational study protocol.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0332985}, pmid = {41575959}, issn = {1932-6203}, mesh = {Humans ; *Respiratory Distress Syndrome/therapy ; *Respiration, Artificial/adverse effects ; Prospective Studies ; Biomarkers ; *Lung Injury/etiology ; Multicenter Studies as Topic ; Female ; Male ; }, abstract = {BACKGROUND: Patients with moderate to severe acute respiratory distress syndrome (ARDS) exhibit extremely poor prognoses following mechanical ventilation, with mortality rates as high as 40% to 55%. Despite extensive research into ARDS classification and prognostic assessment, the disease's pathogenesis remains incompletely understood, and there remains a critical lack of specific biomarkers and effective therapeutic targets for its prevention and management. The core challenges lie in two key areas. First, ARDS demonstrates marked heterogeneity in etiology, pathophysiology, and pathogenesis. Existing research, predominantly reliant on population-level average data, fails to capture inter-individual variability, hindering the precise identification of patient subgroups responsive to specific therapeutic regimens. Second, current definitions of ARDS phenotypes are often confined to clinical symptoms and routine diagnostic indices, lacking integrated analysis of deeper mechanistic indicators, such as key biomarkers and respiratory mechanics parameters, thereby limiting the stability and clinical utility of existing classification systems.
METHODS/DESIGN: We designed a prospective multicenter cohort study incorporating multi-omics analyses. This research aims to investigate the mechanisms underlying the development and progression of ARDS during mechanical ventilation, providing a theoretical foundation and practical guidance for future ARDS therapies. The study plans to enroll over 165 patients with moderate to severe ARDS receiving mechanical ventilation across 10 medical centers. Peripheral blood and bronchoalveolar lavage fluid (BALF) samples will be collected on the first 24 hours after enrollment and at extubation for metagenomic/meta-transcriptomic sequencing, bulk RNA sequencing, single-cell RNA sequencing, proteomics detection, and metabolomics analyses. Concurrently, comprehensive monitoring of physiological indices, electrical impedance tomography, transpulmonary pressure, pulmonary ultrasound findings, and other relevant parameters will be conducted during the enrollment. Study participants will be stratified by survival and mortality outcomes to analyze the dynamic trends of all measured indices and their underlying molecular mechanisms. Biomarkers derived from multi-omics data and clinical baseline characteristics will be evaluated and integrated, followed by multidimensional dimensionality reduction. Predictive models will be subsequently constructed via early or late fusion to identify core prognostic markers, with performance validated using standardized metrics.
DISCUSSION: Through comparative analysis of multi-omics data, we aim to identify specific markers and risk factors associated with distinct clinical trajectories of ARDS, further clarifying the key determinants of lung injury. Ultimately, this research will reveal critical immune cell subtypes that govern ARDS onset and prognosis, offering novel insights and therapeutic targets to advance precision medicine for ARDS.
STUDY PROTOCOL REGISTRATION: ClinicalTrials.gov NCT05922826.}, }
@article {pmid41576448, year = {2026}, author = {Ding, Y and Liu, BW and Wu, D and Li, HZ and Du, S and Zhu, D}, title = {Effects of earthworms on soil virus-associated ARGs and resistance phenotypes in long-term field cropping systems.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141205}, doi = {10.1016/j.jhazmat.2026.141205}, pmid = {41576448}, issn = {1873-3336}, mesh = {*Oligochaeta/physiology ; Animals ; *Soil Microbiology ; Phenotype ; Rhizosphere ; Triticum/growth & development ; Virulence Factors/genetics ; Zea mays/growth & development ; }, abstract = {Long-term effects of earthworms on soil resistomes under realistic field conditions remain poorly understood. Here, we conducted a two-year corn-wheat rotation study within a long-term field experiment established in 2018 to systematically investigate how a one-time earthworm addition durably modulates resistomes. Integrated metagenomics and viromics analyses revealed that diverse ARGs and virulence factor genes (VFGs) were consistently higher in rhizosphere than bulk soils, identifying the rhizosphere as a hotspot for resistance dissemination. Despite limited metagenomic shifts, long-term earthworm activity suppressed virus-associated ARGs and VFGs, as well as high-risk ARGs, especially in bulk soils. Notably, early phenotypic resistance in the rhizosphere increased markedly in Year 1 (ciprofloxacin + 38.9 %, meropenem + 31.3 %) without concurrent genotypic changes, whereas significant genotypic shifts emerged only in Year 2, indicating that phenotypic resistance preceded genotypic changes. Long-term earthworm addition reshaped microbial life-history strategies from R- to K-strategist traits, enhanced lysogeny proportions that dominated 72.73-85.05 % of the viromes throughout the 2-year crop rotation, and stabilized virus-host networks. Caudovirales infecting Streptomyces and Pseudomonas acted as hubs linking ARGs to nutrient-cycling taxa, with earthworms reinforcing cooperative cross-kingdom interactions. These findings highlight earthworms' long-term regulatory role in microbial adaptation and resistome dynamics, informing resistance risk management under the One Health framework.}, }
@article {pmid41576514, year = {2026}, author = {Hao, Y and Li, Y and Liu, F and Long, J and Yang, H}, title = {Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106487}, pmid = {41576514}, issn = {1525-3171}, abstract = {Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.}, }
@article {pmid41576635, year = {2026}, author = {Quan, M and Zhang, X and Chen, C and Feng, Y and Lv, X and Wang, X and Ye, H}, title = {Perinephritic and psoas abscess by an unusual coinfection with Trichomonas vaginalis and Lactobacillus johnsonii.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {4}, pages = {117276}, doi = {10.1016/j.diagmicrobio.2026.117276}, pmid = {41576635}, issn = {1879-0070}, mesh = {Humans ; Middle Aged ; Female ; *Coinfection/diagnosis/microbiology/parasitology ; *Trichomonas vaginalis/isolation & purification/genetics ; *Psoas Abscess/microbiology/diagnosis/parasitology/therapy ; *Lactobacillus/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Trichomonas Infections/diagnosis/complications ; Metronidazole/therapeutic use ; High-Throughput Nucleotide Sequencing ; *Gram-Positive Bacterial Infections/diagnosis/microbiology ; }, abstract = {Trichomoniasis, caused by Trichomonas vaginalis, is a common nonviral sexually transmitted infection that presents with vaginitis, urethritis, cystitis, prostatitis, and rarely perinephric abscess. Here we presented a 49-year-old female with fever and lumbago diagnosed with a coinfection of perinephric and psoas abscess caused by Lactobacillus johnsonii and T. vaginalis, with the etiological diagnosis established using pus culture and metagenomic next-generation sequencing (mNGS). The patient achieved complete recovery following abscess drainage, incision, and combined therapy with metronidazole and piperacillin/tazobactam. Rare manifestations of trichomoniasis are easily misdiagnosed, and mNGS can help identify T. vaginalis quickly and accurately without prediction.}, }
@article {pmid41576748, year = {2026}, author = {Maza-Márquez, P and González-López, J and Rodelas, B}, title = {Metagenomic profiling of bacterial resistomes in full-scale wastewater treatment plants in Spain.}, journal = {Journal of environmental management}, volume = {400}, number = {}, pages = {128695}, doi = {10.1016/j.jenvman.2026.128695}, pmid = {41576748}, issn = {1095-8630}, mesh = {*Wastewater/microbiology ; Spain ; Sewage/microbiology ; *Bacteria/genetics ; Bioreactors/microbiology ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; }, abstract = {Investigating the resistome of activated sludge communities is critical to understand the spread of antimicrobial resistances. Here, the resistomes of five full-scale wastewater treatment plants (WWTPs) in Spain were analyzed using a metagenomic approach. 888, 1361 and 1062 unique antibiotic resistance genes (ARGs) were identified in the aerated bioreactors, the anoxic/anaerobic bioreactors, and the treated effluents, respectively. The core resistome comprised 25 ARGs conferring resistance to betalactams (penP, blaI), fosmidomycin (fsr), tetracycline (tetA), thiopeptides (tipA), and vancomycin (vanJ, vanR, vanW, vanX, vanY). The cumulative coverages of ARGs for betalactams, cationic antimicrobial peptides (CAMPs), mercury, lincomycin, quaternary ammonia, and multidrug resistance mechanisms decreased in the effluents. In contrast, the ARGs for ethionamide, methylenomycin, thiopeptides, and vancomycin increased their relative abundances in the effluents of some WWTPs. Proteobacteria were the major putative hosts of ARGs in all samples, followed by Bacteroidetes in the bioreactors and Actinobacteria in the effluents. The genera making bigger contributions to the cumulative coverage of ARGs shifted across the different WWTPs and sample types, showing that different groups of bacteria hosting the resistome were enriched in each case. Many genera identified as putative hosts of ARGs are key players of biological wastewater treatment, including filamentous bacteria, nitrifiers, denitrifiers, and polyphosphate-accumulating organisms. These findings point to the optimization of the tertiary treatment of effluents and management of sludge as the most suitable approaches to mitigate the dissemination of ARGs from WWTPs globally.}, }
@article {pmid41576933, year = {2026}, author = {Hernandez-Leyva, AJ and Berna, AZ and Bui, MH and Liu, Y and Rosen, AL and Lint, MA and Whiteside, SA and Jaeger, N and McDonough, RT and Joardar, N and Santiago-Borges, J and Tomera, CP and Luo, W and Odom John, AR and Kau, AL}, title = {The gut microbiota shapes the human and murine breath volatilome.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, pmid = {41576933}, issn = {1932-7420}, support = {F30 DK127584/DK/NIDDK NIH HHS/United States ; R01 HD109963/HD/NICHD NIH HHS/United States ; R21 AI154370/AI/NIAID NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; }, abstract = {The gut microbiota is crucial to health, yet implementation of microbiota-based therapeutics is limited by the lack of rapid diagnostics. We hypothesize that breath contains gut microbe-derived volatile organic compounds (VOCs) reflecting microbiota composition and metabolism. In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function. By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome. VOCs from cultured gut microbes were identified in vivo in monocolonized gnotobiotic colonized mice. As a proof of principle, we demonstrated that exhaled breath predicts the abundance of a disease-associated bacterium, Eubacterium siraeum, in children with asthma. Altogether, our studies identify microbe-derived VOCs in breath, show that gut bacterial metabolism directly contributes to mammalian breath VOC profiles, and inform the development of non-invasive microbiome diagnostics.}, }
@article {pmid41576939, year = {2026}, author = {Nalapareddy, K and Haslam, DB and Kissmann, AK and Alenghat, T and Stahl, S and Rosenau, F and Zheng, Y and Geiger, H}, title = {Microbiota from young mice restore the function of aged ISCs.}, journal = {Stem cell reports}, volume = {21}, number = {2}, pages = {102788}, pmid = {41576939}, issn = {2213-6711}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Aging ; *Stem Cells/metabolism/cytology ; Wnt Signaling Pathway ; *Intestinal Mucosa/microbiology/metabolism/cytology ; Mice, Inbred C57BL ; Basic Helix-Loop-Helix Proteins/metabolism/genetics ; Regeneration ; *Microbiota ; Akkermansia ; }, abstract = {Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.}, }
@article {pmid41576942, year = {2026}, author = {Masi, D and Watanabe, M and Clément, K}, title = {Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions.}, journal = {Cell reports. Medicine}, volume = {7}, number = {2}, pages = {102573}, pmid = {41576942}, issn = {2666-3791}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/therapy/diet therapy ; Animals ; *Diet ; Mice ; }, abstract = {In the mid-2000s, mouse studies suggested that the gut microbiome might influence energy harvest, fat storage, appetite, insulin sensitivity, and inflammation. Since then, our understanding of the gut microbiome's role in obesity has advanced significantly. Mechanistic studies identified microbial metabolites, such as short-chain fatty acids, bile acids, branched-chain amino acids, tryptophan catabolites, and imidazole propionate, as key modulators of metabolism, inflammation, and gut-brain communication. Metagenomic and multi-omics technologies now provide deeper insights into the intricate interactions between microbes, metabolites, and host factors, reshaping obesity research and reinforcing the need for phenotype stratification by recognizing microbiome-driven metabolic profiles. Integrating gut microbiome data into clinical strategies may enable targeted interventions for specific obesity subtypes, advancing prevention and personalized care. However, as new anti-obesity medications emerge, it is imperative to determine how microbiome-based therapies can complement them, considering efficacy, cost, and patient-specific variability.}, }
@article {pmid41576946, year = {2026}, author = {Lan, X and Liang, Q and He, J and Wu, J and Zhang, X and Li, F and Li, L and Zhao, G and Guo, R and Jia, H}, title = {Microbial single-cell omics in situ.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {101128}, doi = {10.1016/j.xgen.2025.101128}, pmid = {41576946}, issn = {2666-979X}, abstract = {Metagenomics has enabled the understanding of the microbial composition and functional potential in various environments. Using laser-induced forward transfer (LIFT) technology, we report high-quality microbial single-cell genomes or transcriptomes in complex samples such as mouse gut, human saliva, and tumor sections. Bacterial cells in close proximity to each other or to host cells could be directly analyzed using this single-cell approach. Bacterial cells in mice or human samples could be fluorescently labeled for single-cell visualization before collection. The high-quality single-cell transcriptome results allow us to delineate cell-fate commitment in Bacillus sporulation and preliminarily characterize gene expression from Bacteroides in a colorectal cancer sample. The method is scalable and precise and empowers insights about microbial populations and single-cell interactions with the host.}, }
@article {pmid41577053, year = {2026}, author = {Wang, Z and Luo, Z and You, J and Zhu, X and Sui, X and Ji, G}, title = {Synergistic application of biochar with organic fertilizer enhances soil carbon sequestration by optimizing mineral-associated organic matter formation pathway contributions.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134063}, doi = {10.1016/j.biortech.2026.134063}, pmid = {41577053}, issn = {1873-2976}, mesh = {*Charcoal/chemistry/pharmacology ; *Soil/chemistry ; *Fertilizers ; *Carbon Sequestration ; Soil Microbiology ; *Carbon ; *Minerals/chemistry ; *Organic Chemicals ; }, abstract = {Mineral-associated organic matter (MAOM) constitutes the dominant long-term carbon pool for soil organic carbon (SOC) sequestration, yet how MAOM formation pathways respond to soil management strategies remains unclear. We conducted a field experiment with four treatments: no addition (Control), biochar (BC) applied alone, or combined with low-dose (BC + LF) and high-dose (BC + HF) organic fertilizer (OF). Enzyme activity and metagenomic analyses revealed that different amendments enhanced MAOM formation by facilitating microbial carbon pump (MCP)-mediated turnover pathway. BC + LF appropriately improved MCP by elevating multiple enzyme activities (57.7%-198.8%), enriching r-strategists (e.g., Pseudomonadota), and shifting microbial communities toward resource acquisition, while simultaneously preserving microbial community structure to maximize MAOM formation (37.3%). In contrast, BC alone marginally promoted recalcitrant carbon turnover, whereas BC + HF overstimulated labile carbon turnover. Both treatments limited MAOM accumulation, resulting in only 18.6% and 22.2% increases, respectively. Given the dual role of dissolved organic matter (DOM) as microbial substrate and MAOM precursor, we analyzed DOM characteristics and DOM-microbial interactions to reveal two pathways for MAOM formation: direct sorption of aromatic compounds and microbial transformation of DOM molecules to highly unsaturated compounds (HUCs). A DOM "abundance-transformation" indicator-based approach was applied to estimate the proportional contributions of these two pathways. The amendments increased microbial contributions from 24.3% to 77.1%, with peak MAOM accumulation occurring when microbial contributions reached a critical threshold of 56.2%. Overall, our findings advance mechanistic understanding of how organic amendments regulate microbial turnover to enhance stable carbon pools and highlight that optimizing the balance of MAOM formation pathways can maximize SOC sequestration.}, }
@article {pmid41577432, year = {2026}, author = {Shen, J and Tigabu, A and Mishra, SK and Urmi, U and Ozkan, J and Stapleton, F and Yasir, M and Willcox, M}, title = {Antimicrobial resistance surveillance: lessons learnt from large databases of antimicrobial resistance genes.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2025-328620}, pmid = {41577432}, issn = {1468-2079}, abstract = {Ocular infections, caused by a variety of microbes, are likely to become more difficult to treat due to the global increase in antimicrobial resistance (AMR). Traditional assays for resistance only analyse a small proportion of the possible resistance capability of microbes. This review discusses the use of genomic datasets for predicting AMR and their current applications in investigating ocular infections. The use of whole genome sequencing coupled with several large databases on antimicrobial resistance genes (ARGs) can predict phenotypic resistance and multidrug resistance in bacteria. Use of this technology for viral and fungal infections is less advanced and would be a useful area for future research. Metagenomic analysis of the ocular surface microbiome for ARGs could be a sensitive and rapid method for tracking resistance in ocular infections, and monitoring commensal reservoirs of transferable ARGs. Applications of these newer technologies to ocular infections also have the potential to assess the long-term impact of topical antibiotics, disinfectants and preservative use on the ocular microbiome, as well as being used in epidemiological studies to study acquisition and transmission of ARGs.}, }
@article {pmid41577947, year = {2026}, author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE}, title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6583}, pmid = {41577947}, issn = {2045-2322}, support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; }, abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.}, }
@article {pmid41578124, year = {2026}, author = {Candeliere, F and Sola, L and Busi, E and Pedroni, S and Raimondi, S and Amaretti, A and Greco, S and Dominici, M and Rossi, M}, title = {Altered abundance in cancer patients gut of diadenylate cyclase-encoding bacteria.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6070}, pmid = {41578124}, issn = {2045-2322}, support = {Progetto identificato con codice PE00000019, Titolo "HEAL ITALIA" - Spoke 5 - CUP E93C22001860006//PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR) - MISSIONE 4 COMPONENTE 2/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics ; *Neoplasms/microbiology ; *Phosphorus-Oxygen Lyases/metabolism/genetics ; Female ; Male ; }, abstract = {c-di-AMP is a bacterial second messenger recognized by host immune sensors such as the STING pathway, linking gut microbiota activity to tumor immunity. This interaction holds significant therapeutic potential particularly for oncologic patients, given the increasingly recognized relationship between gut microbiota and tumor immunity. Recent evidence shows that microbial c-di-AMP can enhance anti-tumor responses and improve the efficacy of PD-1/PD-L1 blockade and radiotherapy. This study identified gut microbial species capable of synthesizing c-di-AMP by mining the Unified Human Gastrointestinal Protein catalogue for diadenylate cyclases (DACs), generating a database of 4,228 DACs across 3,901 species out of 4,744 presents in the Unified Human Gastrointestinal Genome catalogue. Analysis of metagenomic data from 190 healthy subjects and 569 cancer patients (melanoma, NSCLC, renal carcinoma) revealed a significantly higher abundance of DAC-encoding species in healthy microbiota, with no differences between responders and non-responders to immunotherapy. These findings indicate that c-di-AMP-producing bacteria are depleted in cancer-associated microbiota, supporting further studies on their role in modulating anti-tumor immunity.}, }
@article {pmid41578762, year = {2025}, author = {Shen, F and Xu, C and Wang, C}, title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.}, journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology}, volume = {37}, number = {1}, pages = {62-74}, pmid = {41578762}, issn = {2148-5607}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; Female ; Middle Aged ; *Biomarkers, Tumor/analysis ; Aged ; *Adenoma/microbiology/diagnosis ; Case-Control Studies ; Disease Progression ; Early Detection of Cancer/methods ; Fusobacterium nucleatum/isolation & purification ; Adult ; }, abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.
MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.
RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.
CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression. Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.}, }
@article {pmid41578951, year = {2026}, author = {Yang, Q and Wei, X and Wang, DP and Lai, Y and Luo, H and Liu, AF}, title = {Unraveling the taxonomic novelty and functional significance of viruses in anammox granular sludges.}, journal = {FEMS microbiology letters}, volume = {373}, number = {}, pages = {}, doi = {10.1093/femsle/fnag008}, pmid = {41578951}, issn = {1574-6968}, support = {2025A1515010753//Natural Science Foundation of Guangdong Province/ ; XBY-K1-2023-19//Key Science and Technology Project of PowerChina Northwest Engineering Corporation Limited/ ; 230225176275072//Science and Technology Planning Project of Shaoguan City/ ; }, mesh = {Oxidation-Reduction ; Metagenomics ; Anaerobiosis ; *Sewage/virology/microbiology ; *Ammonium Compounds/metabolism ; Bioreactors/microbiology/virology ; *Viruses/classification/genetics/isolation & purification ; *Bacteria/virology/metabolism/genetics ; Phylogeny ; Genome, Viral ; }, abstract = {The microbial communities in anaerobic ammonium oxidation (anammox) bioreactors have been extensively studied to unveil their diversity and roles in nitrogen removal. Yet, the viruses infecting the key functional microorganisms in these systems remain unexplored. Here, we utilize genome-resolved metagenomics to systematically assess viral diversity, functions and interaction with microbial hosts in granular sludges of different sizes from three laboratory-scale (LS) and full-scale (FS) anammox reactors. Analysis of the 190 microbial genomes recovered through bulk metagenomics revealed the predominance (FS 29%-54% and LS 31%-45%) of anammox species exclusively from the Brocadiae in all sludges examined. Viral metagenomics identified 5210 candidate viral species, 61.1∼97.3% of which were novel. Members of six genera from the Caudovirales order constitute the majority of the taxonomically assigned viral species. Between-group variance analysis revealed that both environment (reactor type) and granule size had a significant influence on the metabolic potential of viruses. In silico predictions showed that many of the important functional microbes were frequent targets of previously unrecognized viruses, including six viral populations infecting the anammox bacteria. Our results suggest that viruses actively infect microbial hosts and thus may have a major impact on the microbial metabolic processes and biogeochemical cycling in the anammox reactors.}, }
@article {pmid41579151, year = {2026}, author = {Gan, T and Zhang, N and Liu, L and Li, W and Ding, M and Chen, J and Zhou, T and Mao, A}, title = {Lactobacillus plantarum CCFM639 Alleviates Hypertension by Reshaping Gut Microbiota and Regulating Key Metabolites.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41579151}, issn = {1867-1314}, support = {82400481//National Natural Science Foundation of China/ ; }, abstract = {A strong association between the gut microbiome and hypertension has emerged. Our previous work demonstrated that supplementation with L. plantarum CCFM639 (CCFM639) reduced blood pressure (BP) in hypertensive mice involving inhibiting the growth of S. aureofaciens Tü117 and conducted an exploratory randomized trial in adults with prehypertension or stage 1 hypertension. Here, we evaluate the effects of CCFM639 supplementation (10[9] CFU/day for 8 weeks) on the gut microbiome and serum metabolome in a subset of these participants (n = 20). Untargeted metabolomic analysis was performed on serum samples, and stool microbiome composition was assessed via metagenomic sequencing. Mono-CCFM639 supplementation altered the metabolomic profile without affecting gut microbiota diversity but reshaped microbial composition. CCFM639 supplementation modulated both the gut microbiome and serum metabolome. Circulating gut-derived metabolites are likely to account for the improvements in BP, suggesting that CCFM639 supplementation could be a key component of nutritional interventions targeting the gut microbiota for hypertension management.}, }
@article {pmid41579934, year = {2026}, author = {Yu, Y and Che, L and Sun, L and Wang, S and Du, N}, title = {A Rare Case of Disseminated Mycoplasma pneumoniae Infection Spreading from a Pelvic Lesion to a Psoas Muscle Abscess.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108420}, doi = {10.1016/j.ijid.2026.108420}, pmid = {41579934}, issn = {1878-3511}, abstract = {This study reports a case of extrapulmonary infection caused by Mycoplasma pneumoniae manifesting as soft tissue abscesses in an immunocompromised host. A 17-year-old female with a history of aplastic anemia and haploidentical hematopoietic stem cell transplantation presented with recurrent fever and pelvic/psoas abscesses. mNGS of abscess drainage identified M. pneumoniae as the dominant pathogen and revealed a macrolide-resistant 23S rRNA A2063G mutation. Targeted therapy with tigecycline and omadacycline led to clinical resolution. This case underscores the critical role of mNGS in diagnosing culture-negative extrapulmonary infections and guiding antimicrobial therapy based on resistance profiling in immunocompromised patients.}, }
@article {pmid41579937, year = {2026}, author = {Wu, Y and Yu, X and Qi, J and Chen, Y and Wang, R and Liu, J and Zhang, Y and Zhang, W}, title = {Metagenomic next-generation sequencing enables early detection and outcome improvement in perioperative mucormycosis after liver transplantation: A single-center experience.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108419}, doi = {10.1016/j.ijid.2026.108419}, pmid = {41579937}, issn = {1878-3511}, mesh = {Humans ; *Liver Transplantation/adverse effects ; Male ; *Mucormycosis/diagnosis/drug therapy/microbiology ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Antifungal Agents/therapeutic use ; *Metagenomics/methods ; Adult ; Early Diagnosis ; Aged ; Female ; Treatment Outcome ; }, abstract = {OBJECTIVES: Mucormycosis is a rapidly progressive and highly lethal fungal infection in liver transplant recipients, with early diagnosis remaining a major challenge. This study aimed to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for early detection and management of perioperative mucormycosis in adult liver transplant patients.
METHODS: A retrospective analysis was conducted on 539 adult patients who underwent liver transplantation between June 2022 and August 2025 at a single tertiary center. Nine patients with clinically confirmed perioperative mucormycosis, in whom mNGS was the first positive diagnostic tool, were included. Clinical characteristics, diagnostic modalities, antifungal strategies, and outcomes were systematically reviewed.
RESULTS: Mucormycosis was identified in 1.67% (9/539) of liver transplant recipients. All patients were male with a median age of 51 years. Pulmonary mucormycosis was the most common presentation (n = 5), followed by disseminated (n = 3) and cutaneous infection (n = 1). In all cases, mNGS provided the earliest microbiological evidence, preceding culture and histopathology. Species detected included Cunninghamella spp., Rhizopus microsporus, and Rhizomucor pusillus. The mortality rate of disseminated disease was 100%, whereas localized pulmonary and cutaneous infections had a combined cure or improvement rate of 66.7%. Early targeted antifungal therapy guided by mNGS (amphotericin B formulations combined with posaconazole or isavuconazole) was associated with improved outcomes in nondisseminated cases.
CONCLUSION: mNGS enables earlier detection of perioperative mucormycosis compared to conventional diagnostic methods and supports timely initiation of targeted therapy. Rapid mNGS-guided intervention may prevent progression to disseminated disease and improve prognosis in liver transplant recipients. Integration of mNGS into the diagnostic workflow is recommended for high-risk patients with unexplained pulmonary or cutaneous lesions.}, }
@article {pmid41579975, year = {2026}, author = {Ferrero, G and Mastrocola, R and Tarallo, S and Pardini, B and Scheijen, J and van de Waarenburg, M and Gallo, G and Chatziioannou, AC and Robinot, N and Keski-Rahkonen, P and Piccinno, G and Segata, N and Aglago, EK and Hughes, DJ and Jenab, M and Schalkwijk, CG and Naccarati, A}, title = {Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.}, journal = {Free radical biology & medicine}, volume = {246}, number = {}, pages = {518-530}, pmid = {41579975}, issn = {1873-4596}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; *Pyruvaldehyde/metabolism/blood ; *Glycation End Products, Advanced/metabolism/blood ; *Colonic Neoplasms/metabolism/pathology/genetics/blood/microbiology ; Male ; Female ; Feces/chemistry/microbiology ; Middle Aged ; Glyoxal/metabolism ; Aged ; Lactoylglutathione Lyase/genetics/metabolism ; Gastrointestinal Microbiome ; Deoxyglucose/analogs & derivatives/metabolism ; Metabolomics ; Receptor for Advanced Glycation End Products/genetics/metabolism ; }, abstract = {Advanced Glycation Endproducts (AGEs) arise from the reaction of proteins with highly reactive dicarbonyl compounds such as methylglyoxal (MGO), glyoxal (GO) and 3-deoxyglucosone (3-DG), which have been implicated in inflammation and carcinogenesis. How dicarbonyls and AGEs are distributed across tumor tissue and surrogate specimens, and how they relate to systemic metabolism, AGE-related pathways, and alterations in gut microbiota in colon cancer, remains poorly understood. An integrative multi-specimen analysis of MGO, GO, 3-DG and major AGEs was performed using targeted tandem mass spectrometry in matched tumor tissue, adjacent normal mucosa, plasma, and stool from 26 sporadic colon cancer patients. These measurements were combined with tumor RNA-sequencing, untargeted plasma metabolomics, and stool shotgun metagenomics generated from the same individuals. A marked accumulation of MGO was observed in tumor tissue when compared with adjacent mucosa, accompanied by higher levels of the MGO-derived AGE Nδ-[5-hydro-5-methyl-4-imidazolon-2-yl]-ornithine (MG-H1). Tissue MG-H1 concentrations significantly correlated with corresponding plasma levels. Elevated tumor MGO levels were associated with up-regulation of GLO1 (encoding for the detoxifying enzyme glyoxalase-1), DDOST (coding for the AGE-clearance receptor AGE-R1), and the glycolytic flux marker triose phosphate isomerase (TPI), alongside down-regulation of the AGE-scavenger receptor CD36. These findings suggest a candidate remodeling of dicarbonyl-handling pathways. The MGO/GO ratio in tumors was positively associated with the relative abundances of Fusobacterium nucleatum and Parvimonas micra, two bacterial species related to colorectal carcinogenesis, and with metagenomic signatures of oral-derived taxa colonizing the gut. This pilot integrative analysis highlighted novel coherent associations among tissue, circulating, and stool levels of MGO-derived AGEs, the expression of AGE-related metabolic pathways, and microbial signatures in colon cancer. If confirmed in larger studies, these candidate molecular and microbial interactions may provide novel insights into the dicarbonyl stress involvement in tumor biology.}, }
@article {pmid41581053, year = {2026}, author = {Li, X and Ma, R and Gan, L and Zhang, R and Qian, J}, title = {Metagenomic sequencing provides evidence of the nasal microbiota's influence on idiopathic orbital myositis: A case-control study.}, journal = {Indian journal of ophthalmology}, volume = {74}, number = {2}, pages = {307-309}, pmid = {41581053}, issn = {1998-3689}, }
@article {pmid41581112, year = {2026}, author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P}, title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.}, journal = {Archives of virology}, volume = {171}, number = {2}, pages = {62}, pmid = {41581112}, issn = {1432-8798}, mesh = {*Plant Diseases/virology ; *Solanum lycopersicum/virology ; *Hemiptera/virology ; Animals ; Phylogeny ; *Virome/genetics ; Reunion ; Metagenomics ; *Luteoviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; }, abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.}, }
@article {pmid41581292, year = {2026}, author = {Diehl, C and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Pastore, J and da Silveira Nicoloso, R and Dorn, M and Kich, JD and Siqueira, FM}, title = {Shaping soil fungal communities: How swine waste treatment systems and geography drive fungal community shifts.}, journal = {The Science of the total environment}, volume = {1015}, number = {}, pages = {181376}, doi = {10.1016/j.scitotenv.2026.181376}, pmid = {41581292}, issn = {1879-1026}, mesh = {Animals ; *Soil Microbiology ; Swine ; *Fungi/classification ; Brazil ; Fertilizers ; *Mycobiome ; Soil/chemistry ; Manure ; }, abstract = {The use of swine waste as an organic fertilizer is an important practice in sustainable agriculture. This study aims to evaluate the effects of two common swine waste treatment systems, Covered Lagoon Biodigesters (CLB) and Waste Stabilization Ponds (WSP), on fungal community structure in soil. Soil and waste samples were collected from swine farms across five Brazilian states, representing different geographical regions with distinct climate, soil types, and vegetation. A metagenomic approach was employed to analyze the fungal communities present in the samples. Our results revealed that fertilization with swine waste did not significantly affect the overall diversity of fungal communities, although distinct shifts in community composition were observed between fertilized and non-fertilized soils. Notably, reads assigned to Sugiyamaella lignohabitans were detected only in samples from waste stabilization ponds, suggesting that this environment may favor fungal taxa associated with lignocellulose degradation. Furthermore, the fungal genera Fusarium and Rhizophagus exhibited contrasting responses to fertilization, with Fusarium being more abundant in fertilized soils and Rhizophagus decreasing in abundance. Geographic variation in fungal community composition was also observed, correlating with the physicochemical properties of the soil. These findings indicate that, in our dataset, the waste treatment systems had little influence on the fungal diversity of waste samples, whereas soil fertilization with swine waste was associated with marked shifts in fungal community composition, particularly in terms of taxonomic structure.}, }
@article {pmid41581397, year = {2026}, author = {Fan, Y and Wang, Y and Liu, D and Yao, Y and Liu, J and Zhao, J and Dong, L and Wang, C and Liu, W}, title = {Exposure evidence and transmission characteristics of biological aerosols in a high-rise building.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141221}, doi = {10.1016/j.jhazmat.2026.141221}, pmid = {41581397}, issn = {1873-3336}, mesh = {Aerosols/analysis ; *Air Pollution, Indoor/analysis ; Humans ; *Air Microbiology ; Sewage/microbiology ; Environmental Monitoring ; Housing ; }, abstract = {Indoor bioaerosols originating from residential drainage systems have the potential to migrate into living spaces, possibly posing a respiratory concern. By coupling the technology of metagenomic shotgun sequencing with fluorescein tracers, the residents living on the same drainage riser of a 17-story residence and their associated sewage wells were studied to analyse the microbial spectrum of indoor bioaerosols and the spatiotemporal distribution characteristics of their lateral and longitudinal propagation. The air samples collected from these apartments and the sewage samples collected from corresponding sewage wells revealed that the relative abundances of P. aeruginosa and A. baumannii of the bacterial community in the air reached 30% and 10 % respectively. Moreover, the fecal indicator bacterium S. enterica could be detected, confirming the presence of the "fecal-water-air"" chain. Tracer experiments further revealed that a breach in water seals allowed aerosols of less than 0.5 µm cross-floor to diffuse over three layers within 19 min through the stack effect, with upwards deposition 2.5-3.1 times greater than downwards deposition. Even though the water seals remained intact, a single toilet flush could horizontally spread 0.3 µm biological aerosols into adjacent rooms within 6 min. In summary, the contribution of the drainage system to indoor bioaerosols was confirmed for the first time in both genetic sequencing and aerosol transport dimensions, providing a reference basis for the biosafety design of high-rise residential buildings.}, }
@article {pmid41581442, year = {2026}, author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W}, title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.}, journal = {Virology}, volume = {617}, number = {}, pages = {110814}, doi = {10.1016/j.virol.2026.110814}, pmid = {41581442}, issn = {1096-0341}, mesh = {Animals ; *Metagenomics ; *Animals, Wild/virology ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; Feces/virology ; Tibet ; *Virome ; Genome, Viral ; Genetic Variation ; Mammals/virology ; RNA, Viral/genetics ; }, abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.}, }
@article {pmid41581464, year = {2026}, author = {Trinh, HP and Lee, SH and Park, HD}, title = {Nitrogen loading fluctuations impact microbial community assembly and functional redundancy in anammox reactors.}, journal = {Water research}, volume = {293}, number = {}, pages = {125434}, doi = {10.1016/j.watres.2026.125434}, pmid = {41581464}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; *Nitrogen/metabolism ; Bacteria/metabolism ; }, abstract = {Nitrogen loading rate (NLR) fluctuations are common in full-scale anammox systems and can compromise process stability, yet the ecological mechanisms underlying system resilience under disturbed conditions remain insufficiently understood. This study investigated how different intensities of NLR disturbances influence microbial community assembly processes and functional redundancy, and how these ecological responses shape nitrogen removal performance. Two anammox sequencing batch reactors were operated for 180 days under either stable (R1) or fluctuating (R2) NLR conditions. Moderate NLR fluctuations (1.4-fold, Phase A) enhanced nitrogen removal efficiency (up to 99.7%) and increased the relative abundance of anammox bacteria to 26.4%, whereas severe fluctuations (2.0-fold, Phase B) caused deterioration in nitrogen removal efficiency (to 72.2%) and a decline in anammox bacteria abundance (7.1%). Metagenome-assembled genome analysis revealed pathway-level reorganization of nitrogen metabolism under fluctuating conditions, with increases in anammox-associated genes (hzsABC and hdh/hao-like) and the DNRA gene (nrfAH) during Phase A, followed by partial declines in Phase B. Neutral community modeling showed that stochastic processes dominated microbial assembly under moderate fluctuations (R[2] = 0.77), promoting coexistence and community adaptability, while deterministic selection prevailed under severe fluctuations (R[2] = 0.56). Functional redundancy exhibited a similar non-linear response, increasing under moderate disturbance (0.73) and declining sharply under severe disturbance (0.48), indicating reduced buffering capacity. These findings provide quantitative insight into the mechanistic link between loading disturbances and ecosystem resilience, offering a foundation for developing operational strategies that enhance the robustness of anammox-based nitrogen removal systems.}, }
@article {pmid41581489, year = {2026}, author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J}, title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.}, journal = {Food chemistry}, volume = {505}, number = {}, pages = {147984}, doi = {10.1016/j.foodchem.2026.147984}, pmid = {41581489}, issn = {1873-7072}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Insulin Resistance ; *Indoles/metabolism ; *Tryptophan/metabolism ; Mice ; *Ellagic Acid/metabolism/pharmacology ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Humans ; Multiomics ; }, abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.}, }
@article {pmid41581932, year = {2026}, author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK}, title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.}, journal = {Advances in protein chemistry and structural biology}, volume = {149}, number = {}, pages = {171-201}, doi = {10.1016/bs.apcsb.2025.08.002}, pmid = {41581932}, issn = {1876-1631}, mesh = {*Biotechnology/economics ; *Antimicrobial Peptides/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; Humans ; Animals ; Delivery of Health Care/economics ; *Anti-Bacterial Agents/pharmacology/chemistry ; }, abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.}, }
@article {pmid41582156, year = {2026}, author = {Shi, LD and Ercoli, MF and Kim, J and de Araujo Junior, AT and Estera-Molina, K and Soni, S and Weitz, TS and Shigenaga, AM and Dukovski, I and Sachdeva, R and Turumtay, H and Louie, KB and Bowen, BP and Kosina, SM and Scheller, HV and Pett-Ridge, J and Segrè, D and Northen, TR and Ronald, PC and Banfield, JF}, title = {Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41582156}, issn = {2041-1723}, support = {INV-037174/GATES/Gates Foundation/United States ; INV-037174/GATES/Gates Foundation/United States ; //Chan Zuckerberg Initiative Foundation/ ; }, mesh = {*Oryza/genetics/metabolism ; *Rhizosphere ; *Methane/metabolism ; *Hydrogen/metabolism ; Genotype ; Soil Microbiology ; Plants, Genetically Modified/metabolism/genetics ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Plant Roots/metabolism/microbiology ; Tyrosine/metabolism/genetics ; Plant Proteins/genetics/metabolism ; }, abstract = {Rice paddies significantly contribute to atmospheric methane (CH4). Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduce cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over 70 days of growth compared with controls. Genome-resolved metatranscriptomic data from PSY rhizosphere soils reveal lower ratios of gene activities for (mostly hydrogenotrophic) CH4 production versus consumption, decreased activity of H2-producing genes, and increased activity of bacterial H2 oxidation pathways. Metabolic modeling using metagenomic and metabolomic data predicts elevated H2 oxidation and suppressed H2 production in the PSY rhizosphere. Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in genes utilizing gluconeogenic acids compared with H2-producing counterparts, and their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates. Overall, our study indicates that decreased CH4 emissions are due to a lower amount of H2 available for hydrogenotrophic methanogenesis and provides a powerful strategy to mitigate CH4 emissions from increasingly widespread rice cultivation.}, }
@article {pmid41582242, year = {2026}, author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM}, title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5348}, pmid = {41582242}, issn = {2045-2322}, mesh = {*Solanum lycopersicum/virology/genetics/microbiology/growth & development ; *Endophytes/genetics/isolation & purification/classification ; *Begomovirus/pathogenicity ; *Plant Diseases/virology/genetics/microbiology ; *Disease Resistance/genetics ; Genotype ; Biodiversity ; Bacteria/isolation & purification/genetics/classification ; }, abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.}, }
@article {pmid41582543, year = {2026}, author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF}, title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {1}, pages = {26-35}, doi = {10.3967/bes2025.089}, pmid = {41582543}, issn = {2214-0190}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Blood Pressure ; *Hypertension/microbiology ; Prospective Studies ; Aged ; Blood Pressure Monitoring, Ambulatory ; China ; Adult ; }, abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).
METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.
RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).
CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.}, }
@article {pmid41582602, year = {2026}, author = {Hernani, R and Albert, E and Hernani-Morales, C and Zúñiga, S and Benzaquén, A and González-Castillo, L and Colomer, E and Morell, J and Català-Senent, JF and Piñana, JL and Giménez, E and Pérez, A and Hernández-Boluda, JC and Arroyo, I and Rivada, M and Barber, T and Alemany, T and Santacatalina, E and Rentero-Garrido, P and Terol, MJ and Díaz, R and Navarro, D and Solano, C}, title = {Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing.}, journal = {European journal of haematology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ejh.70121}, pmid = {41582602}, issn = {1600-0609}, support = {//Fundación FERO and the Fundación para la Promoción de Acciones Solidarias/ ; //European Union through the Operational Program of the European Regional Development Fund/ ; CA23/00007//bioinformatics technician/ ; //2023 Strategic Action in Health/ ; //Instituto de Salud Carlos III/ ; //European Union/ ; }, abstract = {The interplay between the commensal microbiota and the mammalian immune system may influence the outcomes of T cell-driven cancer immunotherapies. However, clinical studies supporting microbiota-based interventions in chimeric antigen receptor T-cell (CAR-T) therapy remain scarce. This study included 30 adult patients with B-cell lymphoma treated with axicabtagene ciloleucel (axi-cel) or 4-1BB investigational product. Shotgun metagenomics sequencing (SMS) of fecal samples, collected before lymphodepletion and 1 month post infusion, enabled species-level resolution. We also trained 25 microbiome-based machine-learning (ML) models for response prediction. Neither prior "high-risk" antibiotics exposure nor alpha diversity influenced toxicity, response, or survival. However, dysbiosis was observed between 11 healthy controls and patients, particularly in those treated with axi-cel. SMS identified species associated with clinical outcomes. Increased abundance of Alistipes senegalensis and Alistipes onderdonkii correlated with lower neurotoxicity and improved survival, respectively. Bifidobacterium longum was associated with reduced cytokine release syndrome, whereas Bifidobacterium adolescentis, Bifidobacterium bifidum, and Bifidobacterium breve correlated with poorer survival. ML models demonstrated strong predictive performance, with some identifying non-responders using only six species selected by the Boruta method (Bacteroides xylanisolvens, Bifidobacterium bifidum, Bifidobacterium breve, Eubacteriaceae bacterium Marseille-Q4139, Negativibacillus massiliensis, and Sellimonas intestinalis). These findings deepen current knowledge and support prospective microbiota-based strategies in CAR-T therapy.}, }
@article {pmid41582618, year = {2026}, author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J}, title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {1}, pages = {e70212}, pmid = {41582618}, issn = {2190-6009}, mesh = {Humans ; Male ; Female ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Soybean Proteins/administration & dosage/pharmacology ; Aged, 80 and over ; *Muscle, Skeletal/physiology ; *Meals ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; *Sarcopenia/diet therapy ; }, abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.
METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).
RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.
CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.}, }
@article {pmid41582887, year = {2026}, author = {Zhang, C and Atashgahi, S and Bosma, TNP and Smidt, H}, title = {Organohalide respiration by a Desulforhopalus-dominated community.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41582887}, issn = {1751-7370}, support = {NRGWI.obrug.2018.005/NWO_/Dutch Research Council/Netherlands ; //Innovation Program Microbiology/ ; }, mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; Phenols/metabolism ; Oxidoreductases/genetics/metabolism ; Phenol/metabolism ; }, abstract = {Marine sediments harbor diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (>85% complete, <3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.}, }
@article {pmid41584315, year = {2026}, author = {Ibrahim, O and Aboushaala, R and Ahmed, N and Savoia, A and Ward, SO and Patel, SN and Lopez, G and Sansom, SE and Williams, B and Singh, K and Al-Harthi, L and Aboushaala, K}, title = {The diagnostic value of metagenomic next-generation sequencing versus traditional microbiological testing in native pyogenic spinal infections: A systematic review and meta-analysis.}, journal = {North American Spine Society journal}, volume = {25}, number = {}, pages = {100840}, pmid = {41584315}, issn = {2666-5484}, support = {KL2 TR002387/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Native pyogenic spinal infections (PSIs), including spondylodiscitis and vertebral osteomyelitis, are challenging to diagnose due to low culture sensitivity and delayed results. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool, but its comparative clinical utility remains uncertain. The purpose of this study is to systematically compare the diagnostic performance and clinical impact of mNGS versus conventional microbial culture in detecting pathogens responsible for native PSIs.
METHODS: The current systematic review and meta-analysis was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive literature search was performed across 6 major databases. Eligible studies directly compared mNGS with standard culture for native PSIs and reported diagnostic performance metrics. Data were extracted and analyzed using a random-effects model to produce pooled estimates. Study quality was assessed using the Newcastle-Ottawa Scale. Primary outcomes included pooled sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Secondary outcomes assessed diagnostic yield, time to diagnosis, treatment modification, and false-positive or contamination events.
RESULTS: A total of 1,227 patients from 12 studies were included, encompassing those with suspected or confirmed native PSIs. Pooled sensitivity and specificity of mNGS were 89.7% (95% CI: 85.6-93.1%) and 86.2% (95% CI: 80.5-91.0%), respectively. mNGS demonstrated a significantly higher diagnostic yield (69-90%) compared to culture (27.2-44.7%) and enabled faster diagnosis (range, 17.7-48 hours). mNGS informed antimicrobial selection in up to 70.3% of cases and detected a broader pathogen spectrum. The incidence of false positives was low (range, 1-5) but non-negligible, emphasizing the need for careful interpretation.
CONCLUSIONS: mNGS outperforms conventional culture in sensitivity, speed, and breadth of pathogen detection in native PSIs and supports more tailored antimicrobial therapy. However, careful interpretation is necessary due to potential false positives. These findings support the integration of mNGS into clinical workflows, particularly in complex or culture-negative infections.}, }
@article {pmid41585260, year = {2025}, author = {Gao, Y and Wang, X and Cheng, Y and Ye, S and Dong, X and Zhu, C}, title = {Case Report: NGS-guided rapid diagnosis of tuberculous otitis media-a rare case of dual-site Mycobacterium tuberculosis infection.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1734666}, pmid = {41585260}, issn = {2296-858X}, abstract = {BACKGROUND: Tuberculous otitis media (TOM) is an exceptionally rare form of extrapulmonary tuberculosis that was usually diagnosed only after long-standing ear discharge or profound hearing loss. This case reported a young man in whom deafness was the sentinel event leading to the discovery of pulmonary tuberculosis and molecular confirmation of concurrent TOM.
CASE PRESENTATION: A 23-year-old male presented with bilateral, progressive hearing loss that had been labeled "chronic suppurative otitis media" by local clinics. Persistent constitutional symptoms prompted chest imaging that revealed bilateral cavitary infiltrates. Broncho-alveolar lavage metagenomic next-generation sequencing identified Mycobacterium tuberculosis complex (MTBC). After transfer to our tuberculosis center, targeted NGS of serous middle-ear fluid detected MTBC; the isolate carried an rpsL K43R mutation conferring streptomycin resistance, identical to the pulmonary strain. Standard four-drug anti-tuberculosis therapy was initiated; within 4 weeks, cough and fever resolved, inflammatory markers normalized, and the pulmonary cavity showed reduction in size compared to baseline.
CONCLUSION: This case highlights that unexplained hearing loss may serve as an early indicator of disseminated tuberculosis. High-throughput sequencing of aural discharge enables rapid diagnosis of TOM, facilitates resistance-guided treatment, and helps trace the pathways of pathogen transmission.}, }
@article {pmid41585377, year = {2026}, author = {Tollenaar, SL and Khorasaniha, R and Jovel, J and Ba, I and Voisin, A and Miller, R and Olof, H and Mahmood, R and Marrie, RA and Strachan, E and Soares, LP and Cheng, C and Janveaux, J and Zaidi, D and Bernstein, CN and Bonner, C and Bar-Or, A and Waubant, E and Yeh, EA and Graham, M and Arnold, DL and O'Mahony, J and Banwell, BL and Zhu, F and Mirza, AI and Karimi-Abdolrezaee, S and Tsai, S and Tremlett, H and McGregor, K and Willing, BP and Armstrong, H}, title = {Reduced fibre-fermenting capacity of gut microbes in multiple sclerosis may result in prebiotic dietary fibre β-fructan promoting inflammation and CNS damage.}, journal = {eGastroenterology}, volume = {4}, number = {1}, pages = {e100296}, pmid = {41585377}, issn = {2976-7296}, abstract = {BACKGROUND: Some people with multiple sclerosis display changes in their gut microbiota with separate evidence suggesting that symptoms may worsen following a high-fibre diet. We hypothesised that in people with multiple sclerosis whose gut microbiota are less able to efficiently ferment dietary fibres, unfermented β-fructans induce inflammation.
METHODS: Diet data (n=48 individuals with multiple sclerosis, n=78 unaffected controls) and stool microbiome data (n=31 individuals with multiple sclerosis, n=61 unaffected controls) were previously collected from participants. Daily fibre subtype intakes were calculated and compared with faecal shotgun metagenomic sequencing in paediatric onset multiple sclerosis and unaffected persons. Response to unfermented β-fructans was examined in a germ-free experimental autoimmune encephalomyelitis (EAE) mouse model (unable to ferment fibres). Mice were fed β-fructans or control fibre diet beginning at symptom onset (day 14). EAE scores and weights were recorded daily. Intestinal and central nervous system tissues were collected at two endpoints to examine inflammatory responses and demyelinating lesions.
RESULTS: Individuals with paediatric onset multiple sclerosis consumed less β-fructans (2.4 g/day±0.3 SD; p<0.05) than unaffected participants (3.6 g/day±0.4), which coincided with differences in the gut microbiota including lower fibre fermenting enzymes. Mice exposed to unfermented β-fructans sustained worsened EAE symptoms (day 20-28; p<0.05), immune activation in the gut and immune activation plus demyelinating lesions in the spinal cord compared with mice on control diet.
CONCLUSIONS: The gut microbiota of individuals with paediatric-onset multiple sclerosis showed reduced fibre fermenting properties, and our animal findings suggest that unfermented β-fructans can worsen demyelination and promote gut-brain axis immune activation. Lower β-fructan consumption was observed among participants with paediatric-onset multiple sclerosis. Future longitudinal studies are warranted to confirm the findings uncovered in this manuscript.}, }
@article {pmid41585407, year = {2025}, author = {Marcatti, R and Franco, LAM and Rocha, EC and Nardi, MS and Summa, JL and da Silva, ETBC and da Rosa, AR and de Oliveira, DC and Graciolli, G and Sabino, EC}, title = {Metagenomics enables the first detection of Trypanosoma sp. in Streblidae (Diptera: Hippoboscoidea) parasitizing bats in São Paulo, Brazil.}, journal = {Frontiers in systems biology}, volume = {5}, number = {}, pages = {1721019}, pmid = {41585407}, issn = {2674-0702}, abstract = {INTRODUCTION: Bats play important ecological roles but can also harbor a wide diversity of pathogens, including trypanosomatids. Knowledge about the circulation of Trypanosoma spp. in bat ectoparasites remains limited, particularly in peri-urban environments.
METHODS: In this study, we used shotgun metagenomic sequencing to investigate the presence of Trypanosoma spp. in streblid flies parasitizing Carollia perspicillata bats collected in a peri-urban fragment of the Atlantic Forest in São Paulo, Brazil. A small, preliminary set of pooled samples was analyzed, followed by phylogenetic reconstruction.
RESULTS: Trypanosoma sequences were detected in flies from the family Streblidae. Phylogenetic analysis showed that these sequences cluster within the Neobat 4 clade, which has previously been reported in Carollia spp. bats. This represents the first detection of Trypanosoma sp. in streblid flies parasitizing bats in São Paulo.
DISCUSSION: Although the vector competence of streblid flies for Trypanosoma transmission is still unknown, their close ecological association with bats suggests that they may serve as a non-invasive tool for pathogen surveillance when direct bat sampling is limited. This study expands the known geographic distribution of the Neobat 4 clade and contributes to understanding parasite circulation among bats and their ectoparasites.}, }
@article {pmid41585514, year = {2025}, author = {Wei, C and Chen, Z}, title = {Comprehensive genome analysis uncovers the diversity of jumbo phages in the pig gut microbiome.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1697229}, pmid = {41585514}, issn = {2297-1769}, abstract = {Gut microbiome research has historically focused on bacterial communities. In contrast, the roles of viruses, especially jumbo phages, remain poorly understood. Jumbo phages are of major interest because their large genomes encode unique functions that can influence host metabolism and ecosystem dynamics. This study bridges this gap by identifying 1,545 jumbo phage genomes from 450 pig gut metagenomes. Using CRISPR spacer analysis, we predicted archaeal or bacterial hosts and reconstructed competitive phage networks within this ecosystem. Phylogenetic divergence combined with orthologous protein comparisons supported establishing 14 novel jumbo phage families. Functionally, 10 of these novel families encode auxiliary metabolic genes (AMGs) that enhance host metabolism alongside anti-defense systems including DNA methyltransferases, HNH endonucleases, and glycosyltransferases. Ecological interactions were further elucidated through co-abundance networks (n = 857 pairs) and CRISPR spacer matching (n = 425 pairs), revealing relationships between novel jumbo phages and other jumbo phages. Collectively, this work expands genomic resources for pig gut viromes and delivers new insights into jumbo phages' functional capabilities, host associations, and global prevalence.}, }
@article {pmid41585543, year = {2026}, author = {Li, T and Wang, Q and Lin, Y and Li, Y and Luo, Z and Zhang, W and Sun, N and Dong, H and Zhang, W and Meng, Y}, title = {Mycobacterium avium complex causing transverse pericardial sinus infection: A case report.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02479}, pmid = {41585543}, issn = {2214-2509}, abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as significant opportunistic pathogens in humans, yet they remain rarely implicated in cardiac conditions. Here, we report a rare case of Mycobacterium avium complex (MAC) infection in the transverse pericardial sinus, an unusual site previously undocumented for NTM infection. The patient, a 68-year-old male with prior cardiac surgery, presented with recurrent fever lasting for over 10 days. Positron emission tomography/computed tomography demonstrated a hypermetabolic mass-like lesion within the transverse pericardial sinus, radiologically suggestive of an infectious process. Empirical broad-spectrum antimicrobial therapy failed to achieve clinical response. Following surgical intervention to remove lesion tissue from the transverse pericardial sinus, histopathological analysis revealed granulomatous inflammation and acid-fast bacilli, indicating NTM infection. Metagenomic next-generation sequencing (mNGS) identified MAC in the tissue sample. After starting antimycobacterial therapy, the patient's body temperature gradually returned to normal, and no recurrence was noted during a 7-month follow-up via serial surveillance imaging. This case suggests that, in patients with a history of cardiac surgery who present with unexplained pericardial or mediastinal lesions and non-diagnostic routine cultures and examinations, atypical pathogens such as NTM may warrant consideration within a broad differential diagnosis. It also illustrates the potential value of surgical intervention and mNGS in diagnosing and managing such rare infections.}, }
@article {pmid41585813, year = {2025}, author = {Rong, F and Mingying, Z and Ying, B and Yiyun, H and Ying, Q and Zheng, X and Xiaolei, C}, title = {Pulmonary mucormycosis with bacterial coinfection in an adolescent with poorly controlled type 1 diabetes: a case report.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1724850}, pmid = {41585813}, issn = {1664-2392}, mesh = {Humans ; Female ; *Mucormycosis/complications/microbiology/drug therapy ; Child ; *Diabetes Mellitus, Type 1/complications/microbiology ; *Coinfection/microbiology/complications ; *Lung Diseases, Fungal/complications/microbiology/drug therapy ; Rhizopus/isolation & purification ; *Bacterial Infections/complications/microbiology ; }, abstract = {BACKGROUND: Pulmonary Mucormycosis (PM), a severe fungal infection affecting mainly immunocompromised individuals, is often caused by fungi like Rhizopus and Mucor. This report details a 12-year-old diabetic girl with pulmonary mucormycosis from an unusual Rhizopus species. Successful treatment involved stabilizing her blood glucose and managing multiple co-infections. This case provides important insights into diagnosing and treating rare fungal infections in diabetic children.
CASE SUMMARY: A 12-year-old girl with a two-year history of type 1 diabetes, inconsistently monitored, was hospitalized. She had a persistent cough for over ten days and a six-day high fever. Previous treatments with dexamethasone and antibiotics were ineffective. She showed symptoms of a productive cough, right-sided pleuritic chest pain, and a fever of 40°C. Examination revealed reduced breath sounds and moist rales in the right lung. Tests confirmed a severe infection, and imaging showed inflammatory consolidation, multiple cavitations, and pleural effusion in the right lung.
DIAGNOSIS: Metagenomic next-generation sequencing (mNGS) analyzes all nucleic acids from a patient's bronchoalveolar lavage fluid to identify various pathogens without traditional cultures. The analysis identified Rhizopus species and Streptococcus pneumoniae, confirming pulmonary mucormycosis with a bacterial infection. Additionally, the glycated hemoglobin (HbA1c) level was 14.3%, indicating poorly controlled diabetes.
TREATMENT: A comprehensive treatment regimen was employed. The bacterial co-infection was addressed with intravenous administration of meropenem and linezolid, while nebulized amphotericin B was utilized to treat the pulmonary mucormycosis. To mitigate the underlying risk factor, intensive glycemic control was achieved through the use of an insulin pump. Furthermore, bronchoscopy was conducted to clear respiratory secretions.
OUTCOME: After 11 days in the hospital, the patient stabilized and was discharged. At a follow-up 1.5 months later, infection markers and blood glucose levels were normal.
CONCLUSION: This case highlights the high risk of severe infections like pulmonary mucormycosis in adolescents with poorly managed type 1 diabetes. Metagenomic sequencing was crucial for quickly identifying co-infections. Successful treatment required a comprehensive approach, including targeted antimicrobial therapy, strict glycemic control, and bronchoscopic support, leading to a positive outcome.}, }
@article {pmid41585896, year = {2025}, author = {Jiang, H and Hu, XW and Deng, X and Huang, XJ and Chen, YL and Yang, YF and Du, Y and Ji, S and Tang, DQ}, title = {Liuwei Dihuang pills ameliorate renal injury in experimental type 2 diabetes mellitus rat by regulating host-gut microbiota interaction.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1715600}, pmid = {41585896}, issn = {1663-9812}, abstract = {BACKGROUND: Liuwei Dihuang pills (LW) are widely used as the traditional tonic prescription for the treatment of diabetes and diabetic kidney disease (DKD). This study aimed to investigate the potential mechanism underlying LW-mediated prevention and treatment of DKD from the perspective of host-gut microbiome co-metabolism.
METHODS: A rat model of DKD was established using high-fat diet and streptozotocin. Levels of type IV collagen (Col IV), fibronectin (FN), laminin (Lam), transforming growth factor-β (TGF-β), SMAD family member 7 (SMAD7), and SMAD3 in the kidneys were determined by real time-polymerase chain reaction and Western blot. Fecal metabolites were profiled using ultra-high-performance liquid chromatography-tandem mass spectrometry. Metagenomic sequencing of the feces was performed using high-throughput sequencing.
RESULTS: When combined with metformin (MET)-based therapy, LW significantly improved serum creatinine and blood urea nitrogen levels, kidney index, 24-h urine volume, urine protein content and excretion rate, and urinary creatinine and cystatin C levels. It also attenuated morphological changes. Correspondingly, LW intervention reduced the renal expression of TGF-β, SMAD3, Col IV, LAM, FN, interleukin (IL)-6, and IL-1β, while increasing SMAD7 expression. Additionally, it normalized metabolic pathway abnormalities in galactose, butyric acid, fructose, mannose, amino sugar, and nucleotide sugar metabolism. Moreover, LW regulated bacterial imbalances, notably in specific species such as Allobaculum unclassified, Escherichia coli, Pseudoflavonifractor capillosus, Desulfovibrio porci, Oscillibacter sp. CU971, Parablautia muri, Phocaeicola dorei, Phocaeicola faecalis, Phocaeicola vulgatus, and Raoultella unclassified.
CONCLUSION: The combination of LW and MET ameliorated renal impairment in DKD rats by regulating the TGF-β/SMAD signaling pathway, metabolic disturbances in endogenous metabolites, and gut microbiota dysbiosis.}, }
@article {pmid41586308, year = {2025}, author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L}, title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1695928}, pmid = {41586308}, issn = {2235-2988}, mesh = {Humans ; Cross-Sectional Studies ; *Metagenomics ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Microbiota/genetics ; Aged ; Severity of Illness Index ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Inflammation/microbiology ; *Abscess/microbiology ; }, abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.
METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.
RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.
CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.}, }
@article {pmid41586357, year = {2025}, author = {Wuyunsiqin, and Bai, T and Yang, D and Hashentuya, and Namila, and Jin, C and Tana, and Zhao, P and Wang, M and Menggenduxi, }, title = {Mongolian medicine Wulanwendusu-11 alleviates myocardial ischemia-reperfusion injury by modulating the intestinal microbiota and associated metabolic pathways.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1693472}, pmid = {41586357}, issn = {1664-302X}, abstract = {OBJECTIVE: Wulanwendusu-11 (WLWDS-11) is a commonly used Mongolian medicine for treating cardiovascular diseases. However, its regulating effect on intestinal flora-host metabolism in relieving chronic myocardial ischemia-reperfusion injury (MIRI) is still unclear. Therefore, this study aims to systematically explore the cardioprotective mechanism of WLWDS-11 from the perspective of metabolic interaction between intestinal microbiota and host.
METHODS: C57BL/6J mice were randomized into six experimental groups: MIRI model, sham surgery, and treatment groups for compound Danshen dripping pills (CDDP) plus three dosages of WLWDS-11 (denoted WLWDS-11-L, WLWDS-11-M, and WLWDS-11-H). General physiological indicators of mice in each group were observed, body weight, myocardial structure and pathological features were assessed by electrocardiogram, plasma cardiac enzyme levels. The cardiac function of mice was obtained by echocardiography. Immunohistochemical staining was used to detect the pathological changes in the heart. Immunofluorescence assay was used to detect the degree of apoptosis. Metabolomics and metagenomics were used to analyze treatment effects on intestinal microbiota and metabolites. Integrated analysis of the enriched oxidative phosphorylation and necrosis and apoptosis pathways. qRT-PCR and western blot were used to detect the expression of COX4I1, NDUFB8, SDHA, TFAM, RIPK1, RIPK3, MLKL and TNF-α.
RESULTS: WLWDS-11 (especially in high dose) can significantly improve the cardiac function, reduce the area of myocardial infarction and weaken apoptosis and fibrosis in MIRI mice. Metabolomic profiling revealed extensive metabolic alterations, pathway analysis implicated arginine/proline and unsaturated fatty acid metabolism, and hierarchical clustering identified specific correlations between differential flora (e.g., Kosakonia, Helicobacter spp.) and key metabolites. Integrated multi-omics analysis demonstrated that MIRI induces gut microbiota dysbiosis and systemic metabolic disturbances, characterized by the accumulation of oxidized lipids/lysophospholipids and disruption of critical metabolic pathways. The intervention of WLWDS-11 effectively reshaped the intestinal microbial community and made the metabolic spectrum return to normal. More importantly, correlation and network analysis confirmed the correlation between specific intestinal bacteria (such as Prevost, Kosakonia and Helicobacter) and host metabolites, and formed a flora-metabolite axis regulated by WLWDS-11. KEGG pathway analysis further confirmed the effects of the treatment on key pathways, including necrotizing apoptosis and oxidative phosphorylation. From the point of view of mechanism, WLWDS-11 reversed the mitochondrial dysfunction induced by MIRI by up-regulating the expressions of COX4I1, NDUFB8, SDHA and TFAM. By inhibiting the RIPK 1/RIPK 3/MLKL pathway and TNF-α, necrotizing apoptosis and inflammatory response are inhibited. These results suggest that WLWDS-11 may protect MIRI's heart by regulating the metabolic pathway of flora.
CONCLUSION: WLWDS-11 positively reshaped the gut microbial environment by suppressing pathogenic bacteria and promoting beneficial strains, thereby fostering eubiosis, attenuating cardiac pathology, and ultimately conferring cardio protection. These findings identify WLWDS-11 as a potential candidate drug and provide a molecular mechanistic basis for the clinical treatment of MIRI.}, }
@article {pmid41586370, year = {2025}, author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L}, title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1718782}, pmid = {41586370}, issn = {1664-302X}, abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.
METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.
RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.
DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.}, }
@article {pmid41586495, year = {2026}, author = {Carroll, AC and Mortimer, L and Ghosh, H and Reuter, S and Grundmann, H and Brinda, K and Hanage, WP and Li, A and Paterson, A and Purssell, A and Rooney, AM and Yee, NR and Coburn, B and Able-Thomas, S and Antonio, M and McGeer, A and MacFadden, DR}, title = {Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection.}, journal = {Antimicrobial agents and chemotherapy}, volume = {70}, number = {3}, pages = {e0107125}, pmid = {41586495}, issn = {1098-6596}, mesh = {*Escherichia coli/genetics/classification/drug effects ; *Escherichia coli Infections/microbiology/epidemiology ; Disease Outbreaks ; Humans ; Phylogeny ; Genome, Bacterial/genetics ; Bacterial Typing Techniques/methods ; }, abstract = {Identifying the genetic relatedness of resistant bacterial pathogens in healthcare settings can help identify undetected transmission events and outbreaks. However, current methods are time- and resource-intensive. We evaluated a rapid neighbor typing method paired with long-read sequencing for assessment of genetic relatedness. Utilizing a data set of primary clinical samples and published isolate data from two outbreaks of Escherichia coli, we applied genomic neighbor typing of long-read sequence data to rapidly estimate genetic relatedness. We assessed the correlation between neighbor typing predicted genetic distance and pairwise genetic distance from short-read draft whole genomes for all sample pairs. Predicted genetic trees using neighbor typing were compared to reference genetic trees generated using mash distances and maximum-likelihood (ML) methods to assess the extent of agreement, along with metrics of cluster similarity (cluster comparability and Baker's gamma index [BGI]) and tree topology similarity (generalized Robinson-Foulds [GRF] metric). For all three data sets, we found strong correlations between the reference methods and predicted genetic distances (Spearman's rho = 0.75-0.95, P < 0.001), which improved when using a lineage score-informed approach (Spearman's rho = 0.93-0.94, P < 0.001). Predicted genetic trees and clusters from neighbor typing were comparable to those generated using either mashtree or an ML method, with a range of cluster comparability of 85.8-99.5%, BGIs of 0.8-0.95, and GRF values of 0.34-0.8. Pairing the neighbor typing method with long-read sequencing can enable accurate predictions of the relatedness of E. coli samples and isolates, and could potentially be used as a rapid outbreak surveillance tool.}, }
@article {pmid41586524, year = {2026}, author = {Bloemen, B and Delvoye, M and Hoffman, S and Marchal, K and Vanneste, K and Fraiture, M-A and Roosens, NHC and De Keersmaecker, SCJ}, title = {Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0128225}, pmid = {41586524}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/genetics ; DNA Methylation ; *Interspersed Repetitive Sequences/genetics ; Humans ; Plasmids/genetics ; *Bacillus/genetics ; Bacteriophages/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Bioreactors/microbiology ; }, abstract = {UNLABELLED: Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike a niche-aspecific Bacillus velezensis strain carrying a plasmid and linear phage-plasmid into a batch bioreactor simulating the human gut, and use it as a spike-in control to assess the performance of Hi-C sequencing and Oxford Nanopore Technologies (ONT)-enabled DNA methylation detection to identify MGE-host pairs. To improve recovery of low-abundance genomes, we used a novel ONT adaptive sampling (AS) strategy that depletes de novo assembled, sample-specific high-abundance contigs, rather than relying on reference genomes. This approach led to an approximately twofold enrichment of low-abundance replicons, including the spike-in strain. Methylation-based host assignment failed for the B. velezensis MGEs, likely due to the absence of DNA methylation. In contrast, Hi-C successfully linked the phage-plasmid to its host, but not the plasmid, likely due to non-intact cells, and only after removing artefactual signals through bioinformatic processing. For a native Escherichia coli strain, Hi-C and methylation data linked it to two plasmids. Selective isolation and whole-genome sequencing of both the native E. coli and spike-in B. velezensis then confirmed the metagenomic observations. Our results highlight that Hi-C and methylation data can provide powerful insights into MGE-host associations, but their interpretation requires careful computational analysis and biological validation. Moreover, our AS strategy offers a cost-efficient method to boost coverage of low-abundance genomes, improving metagenomic investigation of MGEs in complex microbiomes.
IMPORTANCE: Mobile genetic elements are important contributors to horizontal gene transfer, including of antimicrobial resistance genes. Understanding which microbes carry these mobile elements is vital to assess the spread of resistance. Here, we use a nanopore adaptive sampling approach to increase detection of low-abundance bacteria and mobile elements and use DNA methylation detection and Hi-C sequencing to determine mobile element hosts. By introducing a known bacterium and isolating a native strain, we could evaluate the performance of these methods, indicating that although powerful, they require careful experimental design, interpretation, and validation. However, when combined, these approaches enable a comprehensive investigation of mobile elements and gene transfer dynamics in complex environments.}, }
@article {pmid41586525, year = {2026}, author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R}, title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0148825}, pmid = {41586525}, issn = {2379-5077}, support = {ANID/BASAL FB210008//Agencia Nacional de Investigación y Desarrollo/ ; ANID/FONDECYT 1221035//Agencia Nacional de Investigación y Desarrollo/ ; ANID/FONDECYT 3230527//Agencia Nacional de Investigación y Desarrollo/ ; ANID/BECAS 21241467//Agencia Nacional de Investigación y Desarrollo/ ; ANID/Becas 21241350//Agencia Nacional de Investigación y Desarrollo/ ; Beca 10202955//Vicerrectoria de Investigacion y Doctorados Universidad San Sebastian/ ; }, mesh = {Oxidation-Reduction ; *Iron/metabolism ; *Bacteria/metabolism/classification/genetics ; Phylogeny ; Microbiota ; }, abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.
IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.}, }
@article {pmid41587207, year = {2026}, author = {Krzynowek, A and Snoeks, J and Faust, K}, title = {PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013892}, pmid = {41587207}, issn = {1553-7358}, mesh = {*Machine Learning ; *Plastics/metabolism/chemistry ; *Metagenomics/methods ; Metagenome ; Computational Biology/methods ; *Software ; Databases, Genetic ; Markov Chains ; }, abstract = {PlasticEnz is a new open-source tool for detecting plastic-degrading enzymes (plastizymes) in metagenomic data by combining sequence homology-based search with machine learning techniques. It integrates custom Hidden Markov Models, DIAMOND alignments, and polymer-specific classifiers trained on ProtBERT embeddings to identify candidate depolymerases from user-provided contigs, genomes, or protein sequences. PlasticEnz supports 11 plastic polymers with ML classifiers for PET and PHB, achieving F1 > 0.7 on an independent test set. Applied to plastic-exposed microcosms and field metagenomes, the tool recovered known PETases and PHBases, distinguished plastic-contaminated from pristine environments, and clustered predictions with validated reference enzymes. PlasticEnz is fast, scalable, and user-friendly, providing a robust framework for exploring microbial plastic degradation potential in complex communities.}, }
@article {pmid41587575, year = {2026}, author = {Kongor, B and Chatterjee, R}, title = {Saliva Speaks: A Critical Analysis of Salivary Biomarkers as an Early Oral Cancer Diagnostic Tool.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {584}, number = {}, pages = {120853}, doi = {10.1016/j.cca.2026.120853}, pmid = {41587575}, issn = {1873-3492}, mesh = {Humans ; *Mouth Neoplasms/diagnosis/metabolism ; *Saliva/chemistry/metabolism ; *Biomarkers, Tumor/analysis/metabolism ; *Early Detection of Cancer ; }, abstract = {Saliva is an easily accessible bio-fluid which consists of various diagnostic components that can reflect any tumor-related changes, offering a promising non-invasive approach for more accurate and early detection of oral cancer. The primary aim of this review is to provide an integrative evaluation of salivary biomarkers for oral cancer by combining qualitative synthesis with a semi-quantitative analysis of various diagnostic parameters. The work highlights biomarker trends by understanding their diagnostic potential across molecular categories through the visual representation of these quantitative data in bar graphs and heatmaps. Comprehensive literature evaluation was performed by using search engines like Pubmed, Science Direct, Google Scholar etc. on the topic of using salivary biomarkers as an oral cancer detection tool. Relevant data on study design, demographic information, sample type, analytical method, biomarker significance etc. were qualitatively summarized. Quantitative parameters including sensitivity, specificity, accuracy and p-values were either extracted or calculated from selected studies and visualized through bar graphs and heatmaps to facilitate comparative interpretation of diagnostic performance. Multiple salivary biomarkers were identified across genomic, transcriptomic, proteomic, metabolomic, and metagenomic levels, each showing significant involvement in molecular alterations and metabolic pathway dysregulation linked to oral malignancies. This review offers a novel semi-quantitative approach that bridges comprehensive literature summarization with diagnostic data interpretation. By integrating quantitative indices into bar graphs and heatmaps, it enables rapid visual comparison of salivary biomarker performance by revealing high-performing candidates of early oral cancer detection. Thus, saliva-based diagnostics hold great potential as a non-invasive, cost-effective reliable alternative to the conventional oral cancer detection methods.}, }
@article {pmid41587576, year = {2026}, author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA}, title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {584}, number = {}, pages = {120852}, doi = {10.1016/j.cca.2026.120852}, pmid = {41587576}, issn = {1873-3492}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Oxalates/metabolism ; *Kidney/metabolism ; Hyperoxaluria/metabolism ; Disease Management ; }, abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.}, }
@article {pmid41587649, year = {2026}, author = {Shi, J and Li, LK and Lin, LH and Li, DK and Lu, J and Saleh, SM and Zhang, TY and He, H and Dong, ZY and Xiao, Q and Xu, B and Zeng, C}, title = {Magnetic properties driving nitrogen removal improvement in magnetite-enhanced activated sludge: Mechanistic insights and process validation.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123870}, doi = {10.1016/j.envres.2026.123870}, pmid = {41587649}, issn = {1096-0953}, mesh = {*Sewage/microbiology/chemistry ; *Nitrogen ; *Ferrosoferric Oxide/chemistry ; *Waste Disposal, Fluid/methods ; Denitrification ; Bioreactors ; }, abstract = {The magnetite-enhanced activated sludge (MEAS) process offers a promising in situ strategy for upgrading wastewater treatment plants (WWTPs) to meet increasing treatment demands and stricter discharge regulations. Unlike conventional materials, magnetite possesses intrinsic magnetic properties, yet their influence on biological treatment efficiency and microbial ecology remains underexplored. This study systematically evaluated three types of magnetite particles with varying properties, focusing on their roles in denitrification, sludge settling, and microbial responses. Batch experiments under low carbon-to-nitrogen conditions (C/N = 4.4) demonstrated that magnetite with high saturation magnetization (65.9 emu/g) achieved 79.3 ± 10.2 % nitrate removal, 3.3 times higher than the control. It reduced the sludge volume index (SVI) from 84.7 to 28.4 mL/g by promoting compact floc formation through extracellular polymeric substance (EPS) protein conformational changes and enhanced microbe-particle interactions. It also increased bio-capacitance of the sludge and achieved a 77.0 % increase in electron transport system activity (ETSA). Surface analysis confirmed that magnetite served as a passive electron mediator rather than actively participating in redox cycling. Metagenomic sequencing further demonstrated the selective enrichment of denitrifying and magnetotactic bacteria and enrichment of key nitrogen metabolism genes (narG, nirK, narK, narH). Validation in an anaerobic-anoxic-aerobic (AAO) reactor treating real municipal wastewater achieved NH4[+]-N and total nitrogen removal efficiencies of 98.7 % and 73.6 %, respectively, meeting stringent discharge limits. These results identify saturation magnetization as a critical parameter for selecting or engineering magnetite materials and provide mechanistic insights and engineering guidance for deploying MEAS as an efficient, retrofit-friendly technology for WWTP upgrading.}, }
@article {pmid41587907, year = {2026}, author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M}, title = {Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {4}, pages = {3879-3891}, doi = {10.1021/acs.jafc.5c14362}, pmid = {41587907}, issn = {1520-5118}, mesh = {Molecular Dynamics Simulation ; *Peptides/chemistry/metabolism ; Taste ; Neural Networks, Computer ; Humans ; Animals ; *Fish Products/analysis/microbiology ; Metagenomics ; Fermentation ; *Flavoring Agents/chemistry/metabolism ; Molecular Docking Simulation ; Fishes ; *Receptors, G-Protein-Coupled/chemistry/metabolism ; Protein Binding ; Graph Neural Networks ; }, abstract = {Fermented fish products are vital sources of umami peptides. In this study, a hierarchical graph attention network-based model was developed to identify candidate umami peptides. Via an integrated approach combining metagenomics, molecular docking, attention weight analysis, molecular dynamics simulations, and experimental validation, three novel umami peptides (GYSSYK, LYSDSK, and TRTKASY) were identified from the Suanyu system, a traditional fermented fish product. It was revealed that T1R1 and T1R3 could form stable complexes with these peptides involving critical residues: GLU301, ARG277, LYS328, SER384, ASP147, GLN278, and HIS71. In sensory evaluation, candidate peptides showed high umami properties with umami threshold values of 0.28 (±0.14) mg/mL. Overall, this study presents a hierarchical graph attention network-based screening methodology for the rapid screening and in-depth study of umami peptides.}, }
@article {pmid41587946, year = {2026}, author = {Quraishi, MN and Moakes, CA and Yalchin, M and Blackwell, C and Segal, J and Ives, NJ and Magill, L and Manzoor, SE and Gerasimidis, K and McMullan, C and Mathers, J and Horniblow, R and Loi, S and Kaur, M and Loman, NJ and Sharma, N and Hawkey, P and McCune, V and Quick, J and Nicholls, S and McMurray, C and Nichols, B and Svolos, V and Raguideau, S and Kerbiriou, C and Oo, YH and Beggs, AD and Crees, N and Hansen, R and Hart, AL and Gaya, DR and Quince, C and Iqbal, TH}, title = {Mechanistic insights into fecal microbiota transplantation for the treatment of ulcerative colitis: analysis of the STOP-Colitis trial.}, journal = {Journal of Crohn's & colitis}, volume = {20}, number = {3}, pages = {}, pmid = {41587946}, issn = {1876-4479}, support = {13/179/01//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Colitis, Ulcerative/therapy/microbiology/immunology ; Male ; Adult ; Female ; Middle Aged ; Prospective Studies ; Feces/microbiology/chemistry ; Pilot Projects ; Gastrointestinal Microbiome ; Colonoscopy ; Treatment Outcome ; Intubation, Gastrointestinal ; Fatty Acids, Volatile/metabolism ; }, abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising therapy for ulcerative colitis, but variable responses and unclear mechanisms limit its efficacy. We aimed to compare nasogastric versus colonic FMT delivery and define the microbial and immunological changes associated with clinical response.
METHODS: In this prospective, open-label, randomized pilot trial (STOP-Colitis), 30 adults with active ulcerative colitis were randomized to receive multidose FMT via nasogastric tube or colonoscopy with subsequent enemas. Key endpoints were clinical outcomes at week 8 and longitudinal multi-omic analyses of stool and biopsies to define changes in microbial composition (16S rRNA and shotgun metagenomics), short-chain fatty acids (SCFAs), mucosal T-cells, and host gene expression.
RESULTS: Colonic FMT was superior to nasogastric delivery, with a higher clinical response rate at week 8 (75% [9/12] vs 25% [2/8]; risk ratio 2.94, 95% CI 0.84-10.30-per protocol analysis). Response was underpinned by successful microbial engraftment, leading to significantly increased fecal microbial diversity and enrichment of SCFA-producing taxa, including Oscillospiraceae and Christensenellaceae. This correlated with reduced fecal calprotectin. Responders showed a significant increase in mucosal regulatory T cells (P = .01), with a concurrent decrease in Th17 (P = 0.03) and CD8+ T cells. This anti-inflammatory shift was confirmed by mucosal transcriptomics, which revealed upregulation of metabolic pathways and downregulation of proinflammatory defense pathways in responders. (Trial registration: ISRCTN74072945).
CONCLUSION: Colonic FMT is a more effective delivery route than nasogastric administration. Clinical response is driven by the engraftment of immunomodulatory bacteria that restore a healthy host-microbe dialogue, providing rationale for developing targeted microbial therapeutics.}, }
@article {pmid41588069, year = {2026}, author = {Muñoz-Hisado, V and Bartolomé, M and Osácar, MC and Giménez, R and Cazenave, G and Garcia-Lopez, E and Moreno, A and Cid, C}, title = {Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6232}, pmid = {41588069}, issn = {2045-2322}, support = {HORIZON-MSCA-2022-PF-01 (01107943)//European Union/ ; PTA2022-021737-I//the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/ ; }, mesh = {*Permafrost/microbiology ; *Caves/microbiology ; *Biomineralization ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/metabolism ; Phylogeny ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored from a microbiological point of view. The Devaux cave, in the Central Pyrenees, still hosts perennial ice. To test whether this ice contained microbial communities, prokaryotic and eukaryotic microorganisms were searched by sequencing their 16S and 18S rRNA genes. From the taxonomic information, the potential functional pathways of these communities were predicted using bioinformatic techniques. In addition, the genome of the microorganisms housed in the perennial ice samples was investigated, and through metagenomic studies their metabolic capacity was elucidated. The cryogenic mineralization of the Devaux cave leads to the production of various Ca and Mg carbonates: calcite, aragonite, vaterite, Mg-rich calcite, and nesquehonite, whose formation may have been favored by the microorganisms in the cave. Among the genes encoding enzymes that enable reactions involved in biomineralization, those belonging to the nitrate and sulfate reduction dissimilatory pathways as well as ureases, ammonia lyases, and carbonic anhydrases were identified. This research takes a further step in the investigation of biomineralization, using the Devaux cave as a model.}, }
@article {pmid41588163, year = {2026}, author = {Young, V and Dohai, B and Halder, H and Fernandez-Macgregor, J and van Heusden, NS and Hitch, TCA and Weller, B and Hyden, P and Saha, D and Pieren, DKJ and Rittchen, S and Lambourne, L and Maseko, SB and Lin, CW and Tun, YM and Bibus, J and Pletschacher, L and Boujeant, M and Choteau, SA and Bergogne, L and Perrin, J and Ober, F and Schwehn, P and Rothballer, ST and Altmann, M and Altmann, S and Strobel, A and Rothballer, M and Tofaute, M and Kotlarz, D and Heinig, M and Clavel, T and Calderwood, MA and Vidal, M and Twizere, JC and Vincentelli, R and Krappmann, D and Boes, M and Falter, C and Rattei, T and Brun, C and Zanzoni, A and Falter-Braun, P}, title = {Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {442-460}, pmid = {41588163}, issn = {2058-5276}, support = {01EA1803//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 101003633//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 210592381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 11819559//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-HDIM-000//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Type III Secretion Systems/genetics/metabolism/immunology ; Bacterial Proteins/metabolism/genetics ; NF-kappa B/metabolism ; *Host-Pathogen Interactions/immunology ; Metagenomics ; *Host Microbial Interactions/immunology ; Cytokines/metabolism ; Protein Interaction Maps ; }, abstract = {Pseudomonadota (formerly Proteobacteria) are prevalent in the commensal human gut microbiota, but also include many pathogens that rely on secretion systems to support pathogenicity by injecting proteins into host cells. Here we show that 80% of Pseudomonadota from healthy gut microbiomes also have intact type III secretion systems (T3SS). Candidate effectors predicted by machine learning display sequence and structural features that are distinct from those of pathogen effectors. Towards a systems-level functional understanding, we experimentally constructed a protein-protein meta-interactome map between human proteins and commensal effectors. Network analyses uncovered that effector-targeted neighbourhoods are enriched for genetic variation linked to microbiome-associated conditions, including autoimmune and metabolic diseases. Metagenomic analysis revealed effector enrichment in Crohn's disease but depletion in ulcerative colitis. Functionally, commensal effectors can translocate into human cells and modulate NF-κB signalling and cytokine secretion in vitro. Our findings indicate that T3SS contribute to microorganism-host cohabitation and that effector-host protein interactions may represent an underappreciated route by which commensal gut microbiota influences health.}, }
@article {pmid41588320, year = {2026}, author = {Guo, W and Yu, J and Wang, W and Wang, J and Ni, M and Zhou, M and Chen, X}, title = {Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41588320}, issn = {1471-2180}, support = {32402705//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, n = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing.
RESULTS: The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of Alistipes shahii, Alistipes onderdonkii, Bifidobacterium thermophilum, Akkermansia glycaniphila, and Methanobrevibacter sp. AbM4 in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as Prevotella and Succinivibrio, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with Methanobrevibacter sp017652345 exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups.
CONCLUSIONS: These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04631-y.}, }
@article {pmid41588461, year = {2026}, author = {Zheng, H and Payne, L and He, W and Mestre, MR and Yang, L and Dechesne, A and Pinilla-Redondo, R and Nesme, J and Sørensen, SJ}, title = {Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {50}, pmid = {41588461}, issn = {2049-2618}, mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; *Bacteria/genetics/virology/classification ; Bacteriophages/genetics ; Metagenomics/methods ; Interspersed Repetitive Sequences ; Europe ; Water Purification ; Metagenome ; }, abstract = {BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.
RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.
CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.}, }
@article {pmid41588512, year = {2026}, author = {Yu, S and Wu, Q and Ma, Y and Bano, S and Zhang, X}, title = {Keystone bacterial taxa drive denitrification and N2O emission via adaptive genomic and metabolic strategies in contrasting agricultural soils.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41588512}, issn = {2524-6372}, support = {42577128 and 31971526//National Natural Science Foundation of China/ ; (2017YFD0200102)//Key R&D project of the Ministry of Science and Technology/ ; }, abstract = {BACKGROUND: Soil denitrification mediated by microbial communities is a major source of nitrous oxide (N2O), a potent greenhouse gas. However, the regulatory roles of keystone taxa in this process remain poorly understood, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, offering an ideal model for exploring microbial mechanisms driving soil-specific denitrification dynamics.
RESULTS: We integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the two soil types. Structural equation modeling (SEM) and correlation analyses revealed strong associations between keystone taxa and denitrification rates and N2O emission patterns. Ensifer ASV205 was identified as a conserved keystone taxon in both soils and exhibited strain-level niche specialization. Comparative genomic analysis revealed that variations in denitrification gene composition and carbon-nitrogen metabolic pathways enabled Ensifer strains to act either as N2O producers or reducers, depending on environmental conditions.
CONCLUSIONS: Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study provides new insights into the microbial mechanisms regulating N2O emissions and lays the groundwork for developing microbiome-informed strategies to mitigate greenhouse gas emissions in agricultural soils.}, }
@article {pmid41589071, year = {2026}, author = {Caserta, MT and Mariani, TJ and Walsh, EE and Gill, SR and Gill, AL and Corbett, A and Harrington, D and Chu, C and Qiu, X}, title = {Nasal Biomarkers of Acute Illness Severity and Predictors of Recurrent Wheeze in Respiratory Syncytial Virus (RSV) Infected Infants.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag049}, pmid = {41589071}, issn = {1537-6613}, abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of hospitalization in infants and those with RSV disease appear more likely to develop recurrent wheeze. We examined nasal airway gene expression and microbiome composition during acute primary RSV infection to test associations with illness severity and identify infants with recurrent wheeze.
METHODS: Previously healthy infants with confirmed RSV infection were enrolled (Dec 2019 to Dec 2023). Clinical, demographic data, 2 anterior nasal swabs and a nasal wash were collected for metagenome and transcriptome sequencing. Disease severity was measured by the improved Global Respiratory Severity Score (iGRSS). Participants were followed for approximately 1 year after enrollment to identify recurrent wheeze. Multivariate regression models were developed to identify correlates and predictors of disease severity and recurrent wheeze, respectively.
RESULTS: 100 (90 hospitalized) infants were enrolled (mean age 3.2±2.3 months; 61% male). 405 genes (false discovery rate 0.10) were significantly and consistently associated with illness severity (iGRSS), implicating Innate Immune and Interleukin Signaling pathways. An abundance of Dolosigranulum in the nares was inversely associated with iGRSS while the abundance of Haemophilus was directly associated with iGRSS. Predictive models using nasal gene expression during acute infection had the power to classify recurrent wheeze (in-sample AUC=0.992; cross-validated AUC=0.882) while metagenomic features did not improve predictive performance.
CONCLUSIONS: We prospectively followed infants with primary RSV infection and identified associations between nasal gene expression, microbiome composition/function and acute disease severity and recurrent wheeze. Host transcriptional profiles during infection were predictive of recurrent wheeze within the following year.}, }
@article {pmid41589125, year = {2026}, author = {Panyako, PM and Ogada, S and Kuria, SN and Musina, J and Lichoti, JK and Ommeh, SC}, title = {Metagenomic Profiling of Fecal and Cecal Microbiota and Their Antimicrobial Resistance Genes in Indigenous Backyard Poultry.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {7306065}, pmid = {41589125}, issn = {1687-918X}, abstract = {Indigenous backyard poultry is the predominant type of poultry in developing countries. Rural smallholder farmers in these regions usually adopt the free-range (backyard) production system, which exposes the poultry to diverse environments and a broad spectrum of microorganisms that influence their diet and gut microbiota. In this cross-sectional purposive study, we evaluated the microbial community profiles of indigenous backyard poultry and their antimicrobial resistance genes (ARGs) using both cecal samples, which provide a more accurate representation of the core gut microbiota, and fecal samples, which allow for noninvasive monitoring and pathogen screening. We analyzed 32 pooled fecal and cecal samples using shotgun metagenomics, followed by functional and antimicrobial resistance (AMR) analyses to identify genes and metabolic pathways associated with poultry gut health and production. We report the presence of many commensal microorganisms in indigenous backyard poultry, with the most abundant being Bacteroidetes, Firmicutes, and Proteobacteria. The most dominant genera in the feces were Bacteroides, Methanobrevibacter, and Phocaeicola, while Bacteroides, Methanobrevibacter, and Chlamydia dominated in the ceca. No marked differences in microbial diversity were observed between the fecal and cecal samples. KEGG and COG database analyses revealed significantly enriched pathways associated with metabolism, cellular processes, and information storage and processing. Genes that confer resistance to tetracycline were the most abundant, raising concerns about the risks associated with inappropriate and excessive use of this antibiotic in poultry treatment. These findings deepen our understanding of the poultry gut microbiome, particularly regarding indigenous backyard poultry. Furthermore, the information about ARGs is a valuable indicator of antimicrobial use by rural smallholder farmers who have adopted the free-range production system in Kenya and other developing countries. These insights are crucial for farmers and the national livestock sector to monitor AMR in poultry, thereby enabling improved poultry management practices and informed policy decisions.}, }
@article {pmid41589836, year = {2026}, author = {Darlenski, R and Manuelyan, K and Dimova, I and Menzel, P and Schwarzer, R and Fluhr, JW and Bogdanov, I}, title = {Skin surface microbiome dynamics in the extremes: Learnings from Antarctica distinct community.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70324}, pmid = {41589836}, issn = {1468-3083}, support = {80-25-69/3.8.2021//Bulgarian National Program for Polar Research 2017-2021/ ; }, }
@article {pmid41589896, year = {2026}, author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT}, title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0258925}, pmid = {41589896}, issn = {1098-5336}, support = {ECOGIG Consortium//Gulf of Mexico Research Initiative/ ; 1831582//National Science Foundation/ ; 2129823//National Science Foundation/ ; }, mesh = {Gulf of America ; *Metagenome ; *Fresh Water/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Seawater/microbiology ; *Microbiota ; Metagenomics ; }, abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.}, }
@article {pmid41589901, year = {2026}, author = {Engl, T and Jakubova, L and Skrob, Z and Campeggi, S and Skala, R and Folkmanova, M and Pajer, P and Chmel, M and Cajthaml, T and Strejcek, M and Suman, J and Uhlik, O}, title = {Catabolism of acetosyringone and co-metabolic transformation of 2,4,6-trichlorophenol by a novel FAD-dependent monooxygenase.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0124225}, pmid = {41589901}, issn = {2379-5077}, support = {22-00132S//Grantová Agentura České Republiky/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, mesh = {*Chlorophenols/metabolism ; *Mixed Function Oxygenases/metabolism/genetics ; Biodegradation, Environmental ; Lignin/metabolism ; *Acetophenones/metabolism ; Pseudomonas/metabolism/genetics/enzymology ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Acetosyringone (AS), a prototypical syringyl-type monomer of lignin, functions as a model compound for the study of microbial catabolism of S-lignin-derived aromatics. In this study, we present the discovery of a novel metabolic pathway for AS catabolism, initiated by a previously uncharacterized FAD-dependent oxidoreductase, designated AsdA. In contrast to the sole previously documented AS funneling route, which entails side chain modification and conversion to syringic acid, AsdA catalyzes direct hydroxylation of the aromatic core. This represents a mechanistically distinct entry into central metabolism. The identification of this enzyme was achieved through metagenomic and functional analyses of a bacterial consortium enriched on AS as the sole carbon source. The consortium, predominantly comprising Pseudomonas rhizophila, exhibited co-metabolic transformation of the chlorinated pollutants 2,4,6-trichlorophenol (2,4,6-TCP) and 2,6-dichlorophenol. Subsequent functional assays substantiated the hypothesis that AsdA facilitates the transformation of both AS and 2,4,6-TCP. Induction assays employing a biosensor strain derived from the bacterial isolate Pseudomonas rhizophila AS1 confirmed AS-specific upregulation of the asd gene cluster. A survey of publicly available metagenomes has revealed that asdA is narrowly distributed but enriched in rhizosphere environments, pointing to its ecological significance. In summary, the present study unveils a hitherto unrecognized route for AS transformation and identifies an enzyme that exhibits dual functions in lignin-derived aromatic catabolism and environmental pollutant transformation. While the mechanisms underlying TCP degradation are well-established, the specific enzyme responsible for the conversion to 2,6-dichloro-p-hydroquinone had remained elusive-a knowledge gap that has now been addressed by AsdA.IMPORTANCEThe microbial conversion of lignin monomers is central to the global carbon cycle, yet pathways for syringyl-derived aromatics remain poorly resolved. Here, we identify AsdA, an enzyme initiating a previously unrecognized route for acetosyringone catabolism, providing new insight into how this abundant plant-derived compound is integrated into microbial metabolism. Beyond expanding the mechanistic diversity of lignin degradation, AsdA also catalyzes a key step in the transformation of the chlorinated pollutant 2,4,6-trichlorophenol, linking natural and anthropogenic compounds within a shared metabolic framework. The restricted yet rhizosphere-enriched distribution of asdA underscores its specialized role in plant-microbe interactions. By integrating enzyme function, microbial community context, and metagenomic distribution, we demonstrate how a single catalytic activity connects metabolic pathways and ecosystem processes, illustrating a multi-scale systems biology perspective on aromatic compound turnover.}, }
@article {pmid41590413, year = {2025}, author = {Ansari, RA and Egamberdievich, KE and Raximovna, MT and Sa'dinovna, YD and Enverovna, BL and Abbasovich, AS and Muqumovich, AD and Kurbonovich, TM}, title = {Phytomycobiomes and Ecosystem Services: Mechanisms, Evidence and Routes to Application.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {41590413}, issn = {2309-608X}, abstract = {Phytomycobiomes refer to the fungal consortia that inhabit plant tissues and the rhizosphere. Their documented functions include nutrient mobilization, carbon retention, stress mitigation and pathogen suppression, although measurable effects often depend on plant and soil conditions. In this review, we examine the current evidence for their ecological relevance and assess the molecular approaches most commonly used to characterize them. Arbuscular Mycorrhizal (AM) fungi, endophytes and saprotrophic taxa indicate measurable gains in nutrient acquisition, disease resistance and soil aggregation, although long-term consistency is rarely evaluated. Each function appears to have an explicit mechanistic attribution, with direct links between fungal groups, enzymatic pathways and measurable ecosystem outcomes. Several sequencing-based techniques are available, yet none offer complete accuracy. Internal Transcribed Spacer (ITS) amplicon surveys provide rapid taxonomic coverage but suffer from primer bias; shotgun metagenomics offers functional insight but at significant financial cost; and quantitative polymerase chain reaction (qPCR) assays remain useful for targeted quantification, whereas long-read technologies show promise but still lack widespread adoption. The field faces a number of unresolved constraints, including limited knowledge of host range, inconsistent performance under fluctuating environmental conditions and the absence of a standardized bioinformatic pipeline. Despite these limitations, we regard phytomycobiomes as viable candidates for replacing or reducing synthetic inputs, provided their application is guided by context-specific evidence rather than broad generalization.}, }
@article {pmid41590723, year = {2026}, author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A}, title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.}, journal = {Marine drugs}, volume = {24}, number = {1}, pages = {}, pmid = {41590723}, issn = {1660-3397}, support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; }, mesh = {*Cyanobacteria/isolation & purification/genetics/metabolism ; *Microalgae/isolation & purification/genetics ; Salinity ; Slovenia ; Metagenomics/methods ; Biodiversity ; Biotechnology/methods ; Ecosystem ; }, abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.}, }
@article {pmid41591393, year = {2026}, author = {Walden, N and Kiefer, C and Koch, MA}, title = {Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of homologous gene copies from target enrichment data.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syag007}, pmid = {41591393}, issn = {1076-836X}, abstract = {Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.}, }
@article {pmid41591576, year = {2026}, author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ}, title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {2}, pages = {62}, pmid = {41591576}, issn = {1573-0972}, support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG Nº 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Mycobiome/genetics ; Soil/chemistry ; Islands ; Phylogeny ; Biodiversity ; Nitrogen/analysis ; }, abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.}, }
@article {pmid41591600, year = {2026}, author = {Bilecen Şen, D and Ertürkmen, P and Alp Baltakesmez, D}, title = {Microbiota and quality profiling of fermented goat meat sausages (sucuk) under nitrite-reduced and mixed-culture strategies.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {2}, pages = {64}, pmid = {41591600}, issn = {1573-0972}, abstract = {The bioprotective activity of lactic acid bacteria (LAB) to modulate the microbiota and quality of nitrite-reduced fermented goat meat sucuk was investigated. Antagonistic activity of LAB strains against foodborne pathogens was evaluated using agar well diffusion, spot-on lawn, and cross-streak assays. Three LAB isolates affiliated with the genera Weissella, Limosilactobacillus, and Lactiplantibacillus, exhibiting inhibition zones > 18 mm, were selected and applied as a mixed culture (MC; 2:1:1). Sucuk formulations with 150, 75, and 0 ppm sodium nitrite were produced in the presence or absence of a MC and analyzed during fermentation (days 0 and 7) and refrigerated storage (days 7 and 14). Among the treatments, 75 ppm nitrite combined with MC (75-MC) exhibited the highest LAB counts, enhanced acidification (pH 4.7 on fermentation day 7), inhibited pathogens and spoilage microorganisms, and improved moisture and color stability (> 90% of initial L[*] and a[*]), with a significant treatment × day interaction (P < 0.05). Metagenomic analysis of the 16 S rRNA (V3–V4) and ITS2 regions revealed a LAB-dominated sucuk microbiota, characterized by Levilactobacillus (69.5%), Lactiplantibacillus (12.1%), Psychrobacter (8.8%), and Lacticaseibacillus (3.0%) among bacteria, and Yarrowia (46%), Kurtzmaniella (11.8%), Geotrichum (6.7%), and Cladosporium (5.5%) among fungi. This microbial composition was associated with enhanced microbial stability and technological quality, while mixed-culture strategies under nitrite-reduced conditions promoted a Lactobacillaceae-enriched microbiota, highlighting their potential role in bioprotection and product quality.}, }
@article {pmid41591867, year = {2026}, author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C}, title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70215}, doi = {10.1002/mbo3.70215}, pmid = {41591867}, issn = {2045-8827}, support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; }, mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; }, abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.}, }
@article {pmid41592401, year = {2026}, author = {Sandes, S and Figueiredo, N and Pires, S and Assis, D and Pedroso, S and Paiva, MJ and Neumann, E and Alvarenga, VO and Contreras-Castillo, CJ and Sant'Ana, AS}, title = {Lactic acid spraying on split carcasses reshapes microbial succession and reduces the occurrence of blown pack spoilage in vacuum-packaged beef stored at different temperatures over extended shelf life.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111659}, doi = {10.1016/j.ijfoodmicro.2026.111659}, pmid = {41592401}, issn = {1879-3460}, mesh = {Animals ; Food Packaging/methods ; Cattle ; Vacuum ; *Bacteria/drug effects/genetics/isolation & purification/classification/growth & development ; *Lactic Acid/pharmacology ; Temperature ; Food Storage ; Food Microbiology ; *Food Preservation/methods ; *Red Meat/microbiology ; Hydrogen-Ion Concentration ; Volatile Organic Compounds/analysis ; Microbiota/drug effects ; }, abstract = {Beef is a highly perishable product due to its high moisture content, neutral pH, and rich nutrient profile, which favor microbial growth and spoilage. While vacuum packaging extends shelf life by limiting aerobic bacteria, it may promote the proliferation of anaerobic and facultative anaerobic spoilage organisms, leading to blown pack spoilage. This study investigated the effects of lactic acid spraying on split carcasses categorized by two pH levels (high or ideal) on microbial succession and volatile organic compound (VOC) production in vacuum-packaged sirloins, stored at 0 °C, 4 °C, and 7 °C for up to 120 days. Using culture-based methods, 16S rRNA gene sequencing, and VOC profiling, it has been found that lactic acid treatment significantly reduced initial bacterial loads, especially in high-pH split carcasses (P < 0,05), and modulated microbial communities over time. Treated samples exhibited a lower incidence of blown pack spoilage (BPS) under specific storage time-temperature conditions. Nevertheless, bacterial changes under specific time-temperature storage conditions were characterized by a microbiota dominated by Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Carnobacterium, Hafnia-Obesumbacterium, and Serratia, regardless type of treatment. Overall microbial diversity was not significantly affected; however, the composition of dominant bacterial genera and VOC profiles differed between treated and non-treated groups, suggesting that specific bacterial taxa and compounds may serve as indicators of spoilage progression in vacuum-packed meat under defined storage conditions.}, }
@article {pmid41592403, year = {2026}, author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C}, title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111660}, doi = {10.1016/j.ijfoodmicro.2026.111660}, pmid = {41592403}, issn = {1879-3460}, mesh = {Fermentation ; Metagenomics ; Metabolomics ; *Pichia/metabolism/genetics/classification ; China ; *Microbiota ; *Wine/microbiology/analysis ; Species Specificity ; }, abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.}, }
@article {pmid41592660, year = {2026}, author = {Anburajan, P and Lee, SH and Maulana, DD and Park, HD}, title = {Functional genes and microbial interactions governing methanogenesis via direct interspecies electron transfer: Functions and emerging concepts.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134086}, doi = {10.1016/j.biortech.2026.134086}, pmid = {41592660}, issn = {1873-2976}, mesh = {*Methane/biosynthesis/metabolism ; Electron Transport/genetics ; *Microbial Interactions/genetics ; Anaerobiosis ; Bacteria/metabolism/genetics ; }, abstract = {Direct interspecies electron transfer (DIET) has emerged as an electron-exchange mechanism that enhances methane production in anaerobic digestion (AD) systems. Although the concept of direct electron exchange in syntrophic microbial communities was proposed in the early 2010 s, experimental validation and systematic recognition of methanogenesis via DIET have advanced primarily in the past decade. Significant progress has been made in identifying DIET-active microbial consortia; however, the functional genes and metabolic pathways governing these processes remain unclear. Recent advances in multi-omics approaches, including metagenomics, metatranscriptomics, and proteomics, have provided deeper insights into microbial community organization and gene-level functions underlying electron transfer in AD systems. This review synthesizes current knowledge on functional genes directly mediating DIET (e.g., pilA, omcS), as well as genes that indirectly support DIET, including hydrogenases, extracellular polymeric substance (EPS)-related genes, and methanogenesis-associated enzymes. Understanding of these functional genes is essential for optimizing AD processes and advancing bioenergy production.}, }
@article {pmid41592665, year = {2026}, author = {Yu, X and Lei, Z and Xu, L and Chen, S and Zeng, G and Wang, N and Lai, X and Liu, J}, title = {Disseminated Mycobacterium abscessus lymphadenopathy in an anti-interferon-γ autoantibody syndrome patient treated with anti-NTM therapy combined with hemoadsorption: A case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108438}, doi = {10.1016/j.ijid.2026.108438}, pmid = {41592665}, issn = {1878-3511}, mesh = {Humans ; Female ; Aged ; *Mycobacterium Infections, Nontuberculous/drug therapy/immunology/therapy/complications ; *Interferon-gamma/immunology ; *Lymphadenopathy/microbiology/therapy/immunology/diagnostic imaging ; *Autoantibodies/immunology/blood ; *Mycobacterium abscessus/isolation & purification ; *Autoimmune Diseases/immunology/complications/therapy ; Positron Emission Tomography Computed Tomography ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Anti-interferon-γ autoantibody syndrome (AIGAs) is a primary immunodeficiency disorder characterized by neutralizing autoantibodies blocking interferon-γ signaling, predisposing patients to severe opportunistic infections. No definitive treatment protocol exists, and conventional therapies carry infection risks. Hemoadsorption (HA) is effective for autoimmune diseases but has not been specifically investigated for AIGAs.
CASE PRESENTATION: A 65-year-old Chinese female was admitted with 10-month painless disseminated lymphadenopathy. 18F-fluorodeoxyglucose positron emission tomography/computed tomography showed multiple hypermetabolic lymph nodes, and ultrasound-guided biopsy revealed necrotizing granulomatous inflammation. Metagenomic next-generation sequencing identified Mycobacterium abscessus, and enzyme-linked immunosorbent assay confirmed high AIGA levels (88.05% at 1:3200 dilution). She received anti-nontuberculous mycobacteria therapy (clarithromycin, minocycline, contezolid) combined with one HA session using a cytokine adsorption column. Post-treatment, AIGA levels normalized to 0% at 24 weeks and remained stable. 72-week follow-up showed resolved lymphadenopathy and reduced lymph node size/metabolic activity on PET/CT.
CONCLUSION: This is the first report of single-session HA for AIGAs complicated by disseminated M. abscessus infection. HA effectively reduced AIGA levels, controlled infection, and avoided global immunosuppression, providing a promising adjunctive therapy for AIGA patients with severe disseminated infections.}, }
@article {pmid41592677, year = {2026}, author = {Si, M and Xiong, X and Yun, C and Chen, Y and Niu, H and Qu, Y and Liu, M and Wang, Y and Huang, L and Long, X and Wang, W and Yang, R and Liu, R and Pang, Y and Zhen, X and Li, R and Tian, T and Qi, X and Qiao, J}, title = {Microplastics and nanoplastics in follicular fluid are associated with diminished ovarian reserve: clinical and molecular insights.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.074}, pmid = {41592677}, issn = {2090-1224}, abstract = {INTRODUCTION: Ovarian aging is a significant concern, yet the influencing factors remain unclear. Environmental factors are crucial determinants of diminished ovarian reserve (DOR). Microplastics and nanoplastics (MNPs) are widespread in the environment and pose health risks. The effect of MNPs on ovarian function remains uncertain.
OBJECTIVES: The study aims to investigate whether exposure to MNPs negatively affects ovarian function. In particular, the research focuses on elucidating the association between MNPs-especially polyamide 66-and DOR, and validating Parabacteroides goldsteinii (P. goldsteinii) as a potential intervention.
METHODS: We conducted a case-control study analyzing MNPs in follicular fluid from 110 DOR patients and 110 age-matched controls. A mouse MNPs-exposure model assessed ovarian function and intestinal barrier integrity. Gut microbiota alterations were analyzed by metagenomic sequencing of fecal samples from MNPs-exposed mice. P. goldsteinii was identified and selected for microbial intervention, administered via oral gavage. The human granulosa cell line was treated with MNPs for 48 h, followed by transcriptomic sequencing to examine PI3K/AKT/mTOR pathway alterations.
RESULTS: Human follicular fluid contained multiple MNPs, with polyamide 66 levels significantly linked to DOR. Polystyrene and polyvinyl chloride concentrations were also higher in the DOR group. MNPs induced DOR-like phenotypes in mice, causing hormonal imbalances, disrupted estrous cycles, and increased atretic follicles, alongside intestinal barrier damage and gut microbiota dysbiosis. Notably, the abundance of P. goldsteinii and its key metabolite 7-keto-lithocholic acid (LCA) was significantly reduced following MNPs exposure. Supplementation with P. goldsteinii effectively reversed MNPs-induced DOR-like phenotypes, restored hormonal homeostasis, normalized estrous cyclicity, reduced follicular atresia, and elevated 7-keto-LCA levels. Mechanistically, MNPs triggered the PI3K/AKT/mTOR pathway, impairing granulosa cell function and ovarian reserve.
CONCLUSION: These findings elucidate how exposure to MNPs may harm female ovarian function and provide potential new strategies for ameliorating reproductive disorders through the environment‒gut‒ovarian axis.}, }
@article {pmid41592952, year = {2026}, author = {Iacucci, M and Zammarchi, I and Pugliano, CL and Santacroce, G and Capobianco, I and Majumder, S and Ruffa, A and Naranjo, V and Grisan, E and Nardone, OM and Ghosh, S}, title = {Shaping the future of postoperative recurrence in Crohn's disease: personalised approaches with AI-enabled imaging and multi-omics.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337171}, pmid = {41592952}, issn = {1468-3288}, abstract = {Postoperative recurrence (POR) is a major challenge in the long-term management of Crohn's disease (CD), affecting up to 70% of patients within the first year after surgical resection. The multifactorial pathogenesis of POR complicates prevention, while evolving surgical techniques and different anastomotic configurations further hinder accurate prediction and monitoring.Current surveillance strategies, including standard ileocolonoscopy and faecal calprotectin, remain limited by suboptimal accuracy, the absence of validated scoring systems and the lack of standardised monitoring intervals. Recent advances in high-resolution endoscopic imaging, such as confocal laser endomicroscopy and endocytoscopy, enable real-time, in vivo microstructural assessment of the anastomosis, offering opportunities for earlier and more precise detection of recurrence. In parallel, developments in intestinal ultrasound and cross-sectional imaging are reshaping non-invasive monitoring by providing transmural evaluation. Beyond imaging, multiomics approaches, spanning genomics, transcriptomics, proteomics, metabolomics and metagenomics, are uncovering novel biological pathways linked to POR, providing new mechanistic insights.Artificial intelligence (AI) has the potential to integrate clinical, endoscopic, imaging and omics data into predictive multimodal models for POR, supporting individualised risk stratification, early detection and personalised treatment strategies. While promising, these innovations require prospective validation, methodological standardisation and integration into clinical workflows before translation into routine practice.This review summarises the current understanding of POR, highlights emerging diagnostic and monitoring technologies and explores how AI-enabled endoscopy and multi-omics approaches may transform future management, paving the way towards precision medicine for POR in CD.}, }
@article {pmid41593136, year = {2026}, author = {Menke, S and Fackelmann, G and Vucetich, LM and Vucetich, JA and Forbey, JS and Sommer, S}, title = {Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3724}, pmid = {41593136}, issn = {2045-2322}, abstract = {UNLABELLED: Plant secondary compounds (PSCs) impose physiological and nutritional constraints on herbivores, yet many species continue to rely on PSC-rich forage during critical periods of the year. Moose (Alces alces) on Isle Royale National Park depend heavily on balsam fir (Abies balsamea) during winter, exposing them to a chemically defended and nutritionally limited diet. To investigate how this foraging strategy shapes both physiological responses and gut microbial communities, we integrated fecal diet composition, urinary markers of detoxification and nutritional status, 16S rRNA gene sequencing, and shotgun metagenomic profiling from free ranging moose of two separated populations from the western and eastern region of the island. Balsam fir consumption varied strongly by region and was positively associated with glucuronic acid to creatinine (GA:C) and urea nitrogen to creatinine (UN:C) ratios, indicating increased detoxification activity and reduced nutritional condition. Microbial alpha diversity declined with higher fir intake in nutritionally limited individuals, while beta diversity differed by region, balsam fir consumption, and UN:C. Several bacterial genera responded to PSC exposure, including increases in the butyrate-producing genus Roseburia and shifts in network prominence of Phascolarctobacterium. Metagenomic data revealed pathways involved in the degradation of aromatic and terpenoid PSCs, although pathway abundances did not differ significantly with balsam fir consumption after multiple testing correction. These results show that winter foraging on balsam fir produces coordinated dietary, physiological, and microbial patterns, with both host and gut microbial detoxification capacities interacting to accommodate the chemical and nutritional challenges of a PSC-rich winter diet.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-35555-w.}, }
@article {pmid41593326, year = {2026}, author = {Kotay, SM and Parikh, HI and Gweon, HS and Barry, K and Stoesser, N and Sarah Walker, A and Crook, DW and Vegesana, K and Mathers, AJ}, title = {Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {5}, pmid = {41593326}, issn = {2731-8745}, support = {BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; }, abstract = {The prevalence and proliferation of antimicrobial-resistant bacteria is considered one of the critical issues of our time. Wastewater is a habitat for complex microbial communities where bacteria share antimicrobial-resistance genes through horizontal gene transfer. Hospital wastewater plumbing systems are an ideal reservoir for environmental and pathogenic bacteria to interface and exchange antimicrobial-resistance genes. Replacement of contaminated plumbing may be the most intuitive and widely deployed response to the detection and colonization of highly-resistant potentially pathogenic bacteria in hospital sink drains. In this study, we analyzed sink-drain biofilms from six intensive-care patient rooms using shotgun metagenomic sequencing and microbial culture. We show an evident shift in biofilm community structure toward increased abundance of Enterobacteriaceae following plumbing replacement. Higher resistome load and abundance of clinically relevant resistance and typically encountered mobile genes in the newly replaced plumbing was also observed. Taken together, these finding suggest that exchanging contaminated plumbing for new plumbing may actually have the unexpected consequence of increased abundance of Enterobacterales and antimicrobial-resistance genes in the sink drains. Disruption of preexisting complex environmental biofilms may result in an unintended microbial population shifts and a potential subsequent increase in the amount of antimicrobial-resistant Enterobacterales which are targeted for elimination.}, }
@article {pmid41593363, year = {2026}, author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL}, title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {359-374}, pmid = {41593363}, issn = {2058-5276}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; }, mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; }, abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.}, }
@article {pmid41593438, year = {2026}, author = {Wang, X and Tian, D and Han, B and Zhao, K and Hao, W and Du, K and Li, X and Duan, Z}, title = {Exploring the impact of rumen microbiome on ovine flavor-related compounds and comparing flavor profiles between Tibetan sheep and Small-tail Han sheep.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41593438}, issn = {1471-2180}, support = {2024YFF0728800//National Key Research and Development Program of China/ ; 2024-ZJ-949//the Natural Science Foundation of Qinghai Province/ ; XDA26040305//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/analysis/metabolism ; Metagenomics ; Tibet ; *Flavoring Agents/metabolism/analysis ; Taste ; Tandem Mass Spectrometry ; }, abstract = {The characteristic 'mutton flavor', primarily attributed to branched-chain fatty acids (BCFAs), is influenced by various factors including rumen microbes. This study aims to elucidate the disparities in meat flavor compounds and their underlying regulatory mechanisms mediated by rumen microbes between two important sheep breeds on the Qinghai-Tibetan Plateau. We used LC-MS/MS to analyze BCFAs and rumen short-chain fatty acids (SCFAs), along with metagenomic sequencing to characterize the rumen microbiome. Compared to Tibetan sheep, Small Tail Han sheep exhibited significantly higher concentrations of BCFAs, including 4-ethyloctanoic acid (EOA) and 4-methyloctanoic acid (MOA), as well as SCFAs such as pentanoate, glutarate, and propionate. In contrast, acetate levels were inversely correlated with these fatty acids. Metagenomics revealed a predominance of Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes) in sheep. Furthermore, random forest and LEfSe analyses identified seven bacterial biomarkers, including Lactobacillus, Ligilactobacillus, Blautia, Anaerovibrio, Selenomonas, Phocaeicola, Sodaliphilus. Functional analysis indicated differences in carbohydrate degradation capabilities of two breeds. Likewise, strong positive correlations of propionate with MOA, and glutarate with EOA were observed, respectively. The findings are expected to provide critical insights into the potential for modulating meat flavor through nutritional strategies targeting rumen microbes.}, }
@article {pmid41593440, year = {2026}, author = {Lv, J and Liu, R and Sun, Z and Zhang, J and Zhang, Y and Zhao, X and Liu, J and Zhou, X and Zhang, M and Liu, Q and Gao, F}, title = {Gut Microbiota as Neuroimmune Modulators in Myasthenia Gravis: Mechanistic Insights from the Gut-Brain Axis to Therapeutic Innovations.}, journal = {The American journal of Chinese medicine}, volume = {54}, number = {1}, pages = {65-85}, doi = {10.1142/S0192415X26500023}, pmid = {41593440}, issn = {1793-6853}, mesh = {*Gastrointestinal Microbiome/immunology/physiology ; Humans ; *Myasthenia Gravis/immunology/therapy/microbiology ; *Neuroimmunomodulation ; Dysbiosis/immunology ; Probiotics ; *Brain/immunology ; Fecal Microbiota Transplantation ; Animals ; *Brain-Gut Axis/immunology ; }, abstract = {Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by an immune-mediated attack on neuromuscular junction acetylcholine receptors (AChRs), and its pathogenesis is closely linked to immune dysregulation. Emerging evidence has highlighted the pivotal role of the gut microbiota in the pathophysiology of MG through immunomodulation, microbial metabolite signaling, and gut-brain axis interactions. This review combines 16S rRNA sequencing, metagenomic, and metabolomic data to reveal distinct gut microbial signatures in patients with MG. These signatures include reduced α-diversity, depletion of beneficial taxa like Bacteroides and Bifidobacterium, enrichment of pathobionts such as Escherichia and Enterococcus, and diminished levels of the short-chain fatty acids (SCFA), which were inversely correlated with disease severity. Experimental models have demonstrated that fecal microbiota transplantation (FMT) and probiotic supplementation with strains like Bifidobacterium ameliorate symptoms by restoring Th17/Treg equilibrium, suppressing the expression of pro-inflammatory cytokines including IL-6 and TNF-α, and enhancing intestinal barrier integrity. Mechanistically, gut dysbiosis exacerbates autoimmunity via NF-αB pathway activation, disrupts tryptophan metabolism and impairs gut-brain signaling. While existing studies have established microbiota-MG associations, further causal validation, personalized therapeutic strategies, and multi-omics integration remain critical priorities. Microbiota-targeted interventions, including precision FMT and metabolite delivery, hold translational potential, but their validation via large-scale randomized controlled trials and interdisciplinary approaches like AI-driven microbiota profiling is essential if they are to advance precision medicine for MG management.}, }
@article {pmid41593479, year = {2026}, author = {Cheng, Z and Ye, Y and Gou, L and Chen, X and Zhang, L and Cao, W and Zhang, Q and Yin, H and Gao, F}, title = {Comprehensive analysis of microorganisms in severe septic patients in the intensive care unit by mNGS and microbial culture.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41593479}, issn = {1471-2180}, support = {21624318//Fundamental Research Funds for the Central Universities/ ; A2024458//the Guangdong Medical Research Foundation/ ; 2021TQ0126//the China Postdoctoral Science Foundation/ ; 2021ZT09Y552//the Program for Guangdong Introducing Innovative and Entrepreneurial Teams/ ; }, mesh = {Humans ; *Sepsis/microbiology ; Intensive Care Units ; Male ; Female ; Middle Aged ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Aged ; *Fungi/isolation & purification/genetics/classification/drug effects ; *High-Throughput Nucleotide Sequencing/methods ; Bronchoalveolar Lavage Fluid/microbiology ; *Metagenomics/methods ; Adult ; Viruses/isolation & purification/genetics/classification ; Aged, 80 and over ; Sputum/microbiology ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Severe sepsis is a life-threatening condition involving dysregulated systemic inflammatory responses and acute organ dysfunctions. Timely and accurate pathogen identification is critical for the effective treatment of severe septic patients in the intensive care unit (ICU). Although metagenomic next-generation sequencing (mNGS) enables the sensitive and unbiased detection of pathogens, its clinical implications in identification of causative pathogens, the association with the outcomes and the development of treatment regimens in such patients remain underexplored.
METHODS: 184 clinical samples were collected from 81 severe septic patients and subjected to mNGS analysis. Blood and bronchoalveolar lavage fluid (BAL) samples were collected from the majority of patients, while sputum, cerebrospinal fluid (CSF), pleural effusion (PE), ascites, urine, hydropericardium (HPC) and blister effusion (BE) samples were also collected from select patients. Microorganisms were detected by DNA and RNA mNGS and the top 5 microorganisms detected by mNGS in each sample were used for analysis. Microbes were isolated from most patients and the isolates were tested for drug susceptibility.
RESULTS: mNGS identified 183 top 5 microorganisms, with bacteria (92.3%), viruses (3.3%) and fungi (2.7%) as the major detected microbes. Among them, 40, 98 and 45 were pathogenic (21.9%), opportunistic (53.6%) and non-pathogenic (24.6%), respectively. Significantly more pathogenic microbes were detected in the sputum (83.3%) and the bronchoalveolar lavage fluid (BAL; 75.0%) than the blood (36.1%) by RNA mNGS (87.4%) than DNA mNGS (58.2%). Patients having the top-1 pathogenic microorganism detected by DNA mNGS or 4-5 pathogenic microorganisms detected by RNA mNGS had a poor association with clinical outcomes. Moreover, detection of R. pickettii, C. difficile and S. enterica were significantly associated with high mortality. The majority of patients (89.5%) were positive for microbial cultures. Each of these patients had at least one drug-resistant organism and nearly half (45.1%) were infected with two or more drug-resistant strains.
CONCLUSIONS: Detection of predominant pathogenic microorganisms or particular bacteria in the sputum or BAL samples by mNGS are associated with poor clinical outcomes among severe septic patients in ICU in this cohort. The high prevalence of multidrug-resistant bacteria among these patients underscores the importance of integration of mNGS with antimicrobial susceptibility assessment in the clinical practice to develop the most effective treatment regimens.}, }
@article {pmid41593721, year = {2026}, author = {Xi, J and Tao, H and Zhang, Z and Lian, B and Sun, W and Zhang, Y and Bu, S and Yang, X and Qian, X}, title = {Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41593721}, issn = {1751-7370}, mesh = {Animals ; Feces/microbiology ; *Deer/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Breeding ; Animals, Wild/microbiology ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; }, abstract = {Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife-human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal-human interface.}, }
@article {pmid41593747, year = {2026}, author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S}, title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {44}, pmid = {41593747}, issn = {1474-760X}, support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; }, mesh = {Animals ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Rumen/microbiology ; Metagenome ; }, abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.
RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves > 90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.
CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.}, }
@article {pmid41593761, year = {2026}, author = {Tigabu, A and Leung, PHM}, title = {Broad-spectrum antibiotic treatment reshapes the gut microbiome, resistome, and colonization potential of opportunistic pathogens: a metagenomics study.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41593761}, issn = {1757-4749}, abstract = {BACKGROUND: The gut microbiota (GM) harbors diverse antibiotic resistance genes (ARGs), which are primarily disseminated through horizontal gene transfer (HGT), contributing to the emergence and spread of multidrug-resistant (MDR) pathogens. Broad-spectrum antibiotics are commonly used to treat a wide range of bacterial infections; however, they also exert collateral effects on non-target microbes. A comprehensive understanding of the impact of broad-spectrum antibiotic treatment on GM composition and the resistome is essential for the effective management of dysbiosis-related complications.
METHODS: Twenty-one fecal samples were collected from randomly selected study participants. Metagenomic sequencing was performed using the Illumina NovaSeq 6000 platform. FastQC v0.12.1, Trimmomatic v0.39, and Bowtie2 were used for quality control, removal of low-quality reads and adapter sequences, and host DNA removal, respectively. Metagenome assembly, gene prediction, and taxonomic annotation were conducted using MEGAHIT v1.2.9, MetaGeneMark-2, and the NCBI non-redundant protein database (nr), respectively. Resistome profiling was performed using the Comprehensive Antibiotic Resistance Database (CARD) v3.3.4. Functional annotation of protein-coding genes was carried out against the KEGG v112.0, eggNOG v5.0, and CAZy databases.
RESULTS: An enrichment of the phylum Bacillota and a depletion of Bacteroidota were observed in fecal samples from antibiotic-treated patients. Specifically, the genus Enterococcus and Streptococcus were the most prominent genera in antibiotic-treated patients, whereas Prevotella, Bacteroides, and Faecalibacterium were more abundant in healthy controls. Notably, the opportunistic pathogen E. faecium was elevated in antibiotic-treated patients. In longitudinal patients receiving augmentin treatment, the genera Escherichia and Enterococcus predominated, with E. coli and E. faecium showing increased prevalence compared with baseline in the first and second longitudinal patients, respectively. Antimicrobial resistance genes associated with antibiotic target alteration and protection were strongly linked to Bacillota, whereas efflux pump-mediated resistance mechanisms were positively associated with Bacteroidota and Pseudomonadota. The genes tetM, tet45, vanHM, vanYM, and vanRM were enriched in antibiotic-treated patients, whereas tetQ, tetW, cfxA6, adeF, vanTG, vanYB, and vanWI were more abundant in controls. Furthermore, pmrF, vanM, and cfxA were identified as principal biomarker genes in the first, second, and third augmentin-treated longitudinal patients, respectively.
CONCLUSIONS: Dysbiosis of the gut microbiota and alterations in the resistome were detected in antibiotic-treated patients. Notably, the opportunistic pathogens E. faecium and E. coli were enriched in antibiotic-treated individuals, suggesting that broad-spectrum antibiotic therapy may facilitate their proliferation and colonization, thereby contributing to dysbiosis-related complications. These findings warrant validation in larger cohorts to better elucidate the dynamics of antibiotic-induced dysbiosis and the dissemination of resistance genes.}, }
@article {pmid41594066, year = {2025}, author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T}, title = {Clinical and Environmental Plasmids: Antibiotic Resistance, Virulence, Mobility, and ESKAPEE Pathogens.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594066}, issn = {2079-6382}, support = {UI/BD/153078/2022//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/04631/2021//Fundação para a Ciência e Tecnologia/ ; UIDP/00329/2025//Fundação para a Ciência e Tecnologia/ ; }, abstract = {BACKGROUND/OBJECTIVES: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates and environmental/metagenomes.
METHODS: We compare three distinct plasmid genome datasets-the NCBI Reference Sequence Database (RefSeq), the Integrated Microbial Genomes & Microbiomes system (IMG/PR) from bacterial isolates (I) and microbiomes (M)-to assess how plasmid origin shapes their characteristics, including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs) and host taxonomy.
RESULTS: We show that plasmids originating from bacterial isolates, more enriched in clinical samples, are fundamentally distinct from recovered from metagenomic data. Plasmids from isolates are larger, enriched in conjugative plasmids and display a higher frequency of ARGs and VGs than the ones assembled from metagenomes. Furthermore, ARGs are more frequently associated with highly mobile plasmids, particularly pCONJ.
CONCLUSIONS: These findings highlight the importance of plasmid origins in studies of plasmid epidemiology, functional potential and mobility.}, }
@article {pmid41594081, year = {2026}, author = {Mohamed, FA and Al-Bulushi, M and Melegh, S and Timmer, B and Meszéna, R and Freytag, C and Laczkó, L and Miló, L and Urbán, P and Bőkényné-Tóth, R and Gyenesei, A and Kardos, G and Nyul, A and Urbán, E and Pál, T and Sonnevend, Á}, title = {Emergence of OXA-48-like Carbapenemase-Producing Escherichia coli in Baranya County, Hungary.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594081}, issn = {2079-6382}, support = {300852//University of Pécs Medical School, Hungary/ ; }, abstract = {Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022-2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of blaOXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The blaOXA-48 and blaOXA-244 genes were chromosomally located, while blaOXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the blaOXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all blaOXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored blaCTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried blaOXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far.}, }
@article {pmid41594088, year = {2026}, author = {Soto-López, JD and Velásquez-González, O and Barrios-Izás, MA and Belhassen-García, M and Muñoz-Bellido, JL and Fernández-Soto, P and Muro, A}, title = {Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594088}, issn = {2079-6382}, abstract = {BACKGROUND/OBJECTIVES: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear.
METHODS: To characterize ARG diversity in wildlife exposed to contrasting levels of human influence, we analyzed homologs of resistance mechanisms from the Comprehensive Antibiotic Resistance Database in shotgun metagenomes of bat guano. Samples were collected from a colony exposed to continuous anthropogenic activity in Spain (Salamanca) and from a wild, non-impacted bat community in China (Guangdong). Metagenomic analyses revealed marked differences in taxonomic and resistome composition between sites.
RESULTS: Salamanca samples contained numerous hospital-associated genera (e.g., Mycobacterium, Staphylococcus, Corynebacterium), while Guangdong was dominated by Lactococcus, Aeromonas, and Stenotrophomonas. β-lactamases and MurA transferase homologs were the most abundant ARGs in both datasets, yet Salamanca exhibited higher richness and functional diversity (median Shannon index = 1.5; Simpson = 0.8) than Guangdong (Shannon = 1.1; Simpson = 0.66). Salamanca also showed enrichment of clinically relevant ARGs, including qacG, emrR, bacA, and acrB, conferring resistance to antibiotics critical for human medicine. In contrast, Guangdong exhibited a more restricted resistome dominated by β-lactamase and MurA homologs. Beta diversity analysis confirmed significant compositional differences between resistomes (PERMANOVA, R[2] = 0.019, F = 1.33, p = 0.001), indicating ecological rather than stochastic structuring.
CONCLUSIONS: These findings suggest that anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, potentially increasing their role as reservoirs of antimicrobial resistance.}, }
@article {pmid41594136, year = {2026}, author = {Kitano, T and Matsunaga, N and Akiyama, T and Azuma, T and Fujii, N and Tsukada, A and Hibino, H and Kuroda, M and Ohmagari, N}, title = {Environmental Dissemination of Antimicrobial Resistance: A Resistome-Based Comparison of Hospital and Community Wastewater Sources.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594136}, issn = {2079-6382}, support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; JP25fk0108666//Japan Agency for Medical Research and Development/ ; }, abstract = {Background/Objectives: Comparative analysis of antimicrobial resistomes in hospital and community wastewater can provide valuable insights into the diversity and distribution of antimicrobial resistance genes (ARGs), contributing to the advancement of the One Health approach. This study aimed to characterize and compare the resistome profiles of wastewater sources from a hospital and community. Methods: Longitudinal metagenomic analysis was conducted on wastewater samples collected from the National Center for Global Health and Medicine (hospital) and a shopping mall (community) in Tokyo, Japan, between December 2019 and September 2023. ARG abundance was quantified using reads per kilobase per million mapped reads (RPKM) values, and comparative analyses were performed to identify the significantly enriched ARGs in the two sources. Results: A total of 46 monthly wastewater samples from the hospital yielded 825 unique ARGs, with a mean RPKM of 2.5 across all detected genes. In contrast, 333 ARGs were identified in the three shopping mall wastewater samples, with a mean RPKM of 2.1. Among the ARGs significantly enriched in the hospital samples, 23, including genes conferring resistance to aminoglycosides (nine groups) and β-lactam antibiotics (eight groups), exhibited significantly high RPKM values. No ARGs were found to be significantly enriched in the community wastewater samples. Conclusions: This study highlights the higher diversity and abundance of ARGs, particularly those conferring resistance to aminoglycosides and β-lactam antibiotics including carbapenems, in hospital wastewater than in community wastewater. These findings underscore the importance of continuous resistome monitoring of hospital wastewater as part of the integrated One Health surveillance strategy.}, }
@article {pmid41594301, year = {2026}, author = {Camatti, J and Bonasoni, MP and Santunione, AL and Cecchi, R and Radheshi, E and Carretto, E}, title = {Postmortem Microbiology in Forensic Diagnostics: Interpretation of Infectious Causes of Death and Emerging Applications.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, pmid = {41594301}, issn = {2075-4418}, abstract = {Background/Objectives: Postmortem microbiology has traditionally been regarded with caution in forensic practice due to concerns related to contamination, bacterial translocation, and postmortem microbial overgrowth. As a result, microbiological findings obtained after death have often been considered unreliable or of limited diagnostic value. However, growing evidence indicates that, when appropriately interpreted and integrated with autopsy findings, histopathology, and circumstantial information, postmortem microbiology can provide crucial support for cause-of-death determination. This narrative review critically examines the current role of postmortem microbiology in forensic diagnostics, with a focus on its diagnostic applications, interpretative challenges, and future perspectives. Methods/Results: The transition from conventional culture-based techniques to molecular approaches-including polymerase chain reaction, microbiome analysis, and metagenomic methods-is discussed, highlighting both their potential advantages and inherent limitations within the forensic setting. Particular attention is devoted to key interpretative issues such as postmortem interval, sampling strategies, contamination, and bacterial translocation. In addition to cause-of-death attribution, emerging applications-including postmortem interval estimation, trace evidence analysis, and artificial intelligence-based models-are reviewed. Although these approaches show promising research potential, their routine forensic applicability remains limited by methodological heterogeneity, lack of standardization, and interpretative complexity. Conclusions: In conclusion, postmortem microbiology represents a valuable diagnostic tool when applied within a multidisciplinary forensic framework. Its effective use requires cautious interpretation and integration with pathological and contextual evidence, avoiding standalone or automated conclusions. Future progress will depend on standardized methodologies, multidisciplinary collaboration, and a clear distinction between experimental research and routine forensic practice.}, }
@article {pmid41594560, year = {2025}, author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB}, title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.}, journal = {Biomolecules}, volume = {16}, number = {1}, pages = {}, pmid = {41594560}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Amyloid beta-Peptides/metabolism ; Aged ; Feces/microbiology/chemistry ; Middle Aged ; Alzheimer Disease/metabolism ; Cognition ; }, abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.}, }
@article {pmid41594852, year = {2026}, author = {Zhao, Q and Li, B and Ma, J and Wei, J and Qin, W}, title = {The Gut Microbiome of the Goitered Gazelle Enables Plasticity by Responding to Environmental Factors in the Qaidam Basin.}, journal = {Biology}, volume = {15}, number = {2}, pages = {}, pmid = {41594852}, issn = {2079-7737}, support = {32160316//National Natural Science Foundation of China/ ; }, abstract = {The Qaidam Basin on the Qinghai-Tibet Plateau is an extreme arid environment, posing severe survival challenges. The goitered gazelle (Gazella subgutturosa) is a keystone species in this fragile ecosystem, yet the ecological role of its gut microbiota and its associations with environmental drivers remain poorly understood. We collected fecal samples from gazelles across seven regions of the basin. Metagenomic sequencing was employed to characterize the gut microbiome. Statistical analyses (Mantel tests, multiple regression on matrices, co-occurrence networks) were used to link microbial composition and function with key environmental factors. The gut microbiota was dominated by fiber-degrading phyla (Firmicutes, Bacteroidota) and enriched in metabolic pathways, aligning with a high-fiber diet. Regarding environmental drivers of gut microbial composition variations, isothermality and soil organic carbon were significant predictors, likely via vegetation and environmental inoculation. Regarding environmental drivers of gut microbial function variations, winter solar radiation was uniquely associated with metabolic function without altering microbial composition, suggesting a functional plasticity-the capacity to shift metabolic profiles independently of taxonomic turnover-in response to environmental variation. The gut microbiota of the goitered gazelle exhibits a stable core composition alongside environmentally responsive functional modules. This suggests the microbiome may serve as a significant mediator of host resilience, highlighting adaptation as a dynamic interplay between host, microbiome, and environment. These insights are crucial for microbiome-assisted conservation.}, }
@article {pmid41594879, year = {2026}, author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L}, title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).}, journal = {Biology}, volume = {15}, number = {2}, pages = {}, pmid = {41594879}, issn = {2079-7737}, support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; }, abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.}, }
@article {pmid41595429, year = {2025}, author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F}, title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, pmid = {41595429}, issn = {2073-4425}, support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen Cycle/genetics ; Metagenomics/methods ; Nitrogen/metabolism ; China ; Zea mays/growth & development ; Fertilizers ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification ; Charcoal ; }, abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.
METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.
RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.
CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.}, }
@article {pmid41595438, year = {2025}, author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D}, title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, pmid = {41595438}, issn = {2073-4425}, mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pilot Projects ; *Cervix Uteri/microbiology ; Greece ; *Lactobacillus/genetics/isolation & purification/classification ; Adult ; Middle Aged ; Vagina/microbiology ; }, abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.}, }
@article {pmid41595535, year = {2026}, author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y}, title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, pmid = {41595535}, issn = {2073-4425}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; Animals ; Genomics/methods ; Probiotics ; }, abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.}, }
@article {pmid41596119, year = {2026}, author = {Patanè, GT and Moreira, RJ and Almeida-Santos, M and Putaggio, S and Barreca, D and Oliveira, PF and Alves, MG}, title = {Anthocyanins and Metabolic Disease: A New Frontier in Precision Nutrition.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41596119}, issn = {2076-3921}, support = {2024.03012.BD//Fundação para a Ciência e Tecnologia/ ; UIDB/50006/2020//Laboratório Associado para a Química Verde/ ; CEECINST/00026/2018//Fundação para a Ciência e Tecnologia/ ; CDL-CTTRI-267-SGRH/2022//Fundação para a Ciência e Tecnologia/ ; UIDB/04501/2020-DOI 10.54499/UIDB/04501/2020 and UIDP/04501/2020-DOI 10.54499/UIDP/04501/2020//iBiMED/ ; }, abstract = {Metabolic syndrome (MetS) represents a global health challenge mainly driven by chronic low-grade inflammation and persistent oxidative stress (OS). Current therapeutic and nutritional strategies often fail to resolve these interconnected core pathologies due to the multifactorial nature of MetS. Anthocyanins (ACNs), a class of potent dietary flavonoids, offer significant promise due to their established pleiotropic effects, including robust antioxidant activity through modulation of the Nrf2/ARE pathway, anti-inflammatory effects via NF-κB suppression, and overall support for glucose and lipid homeostasis. However, the therapeutic efficacy of ACNs is characterized by interindividual variability, which is intrinsically linked to their low systemic bioavailability. This heterogeneity in the response is due to the complex interplay between genetic polymorphisms affecting absorption, distribution, metabolism, and excretion (ADME), as well as the specific biotransformation capacity of the gut microbiome. This review proposes that achieving the full clinical potential of ACNs requires moving beyond conventional nutritional advice. We propose that precision nutrition, which integrates multi-omics data (e.g., genomics, metagenomics, and metabolomics), can determine the individual phenotype, predict functional metabolic response, and tailor safer and effective ACN-rich interventions. This integrated, multifactorial approach is essential for optimizing the antioxidant and metabolic benefits of ACNs for the prevention and management of MetS and its associated pathologies.}, }
@article {pmid41596486, year = {2026}, author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C}, title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596486}, issn = {1422-0067}, support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; }, mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; }, abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.}, }
@article {pmid41596633, year = {2026}, author = {Tamayo-Ordóñez, YJ and Rosas-García, NM and Bello-López, JM and Tamayo-Ordóñez, MC and Tamayo-Ordóñez, FA and Calzada-Mendoza, CC and Ayil-Gutiérrez, BA}, title = {A Possible Recently Identified Evolutionary Strategy Using Membrane-Bound Vesicle Transfer of Genetic Material to Induce Bacterial Resistance, Virulence and Pathogenicity in Klebsiella oxytoca.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596633}, issn = {1422-0067}, mesh = {Gene Transfer, Horizontal ; *Klebsiella oxytoca/genetics/pathogenicity ; Virulence/genetics ; Phylogeny ; Evolution, Molecular ; Virulence Factors/genetics ; Genome, Bacterial ; Klebsiella Infections/microbiology ; *Drug Resistance, Bacterial/genetics ; Humans ; COVID-19 ; }, abstract = {Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism.}, }
@article {pmid41596659, year = {2026}, author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA}, title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596659}, issn = {1422-0067}, support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; }, abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.}, }
@article {pmid41596857, year = {2026}, author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K}, title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41596857}, issn = {2304-8158}, abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.}, }
@article {pmid41596861, year = {2026}, author = {Iturritxa, E and Mesanza, N and Torija, MJ}, title = {Wild Yeasts as Reservoirs of Bacterial Diversity: Biotechnological Insights from 16S rRNA Metabarcoding.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41596861}, issn = {2304-8158}, abstract = {Recently acquired evidence indicates that bacteria can utilise yeasts as survival niches. This study investigated the presence of hidden, intracellular bacteria (endobacteria) within wild yeasts collected from natural ecosystems and evaluated whether biotechnological processes influenced these bacterial communities. We examined the microbiotas of 28 axenic cultures of wild yeasts; these were selected due to their potential brewing and biocontrol uses and were isolated from habitats associated with Quercus and Vitis. We also analysed the microbiotas present after these strains were used to ferment beer wort. Bacterial communities were characterised using 16S rRNA gene amplicon metagenomics. The results indicate that yeast strains and their endobacterial partners have coevolved, and their compositions are shaped by the environmental conditions. Substantial bacterial diversity was detected across strains in both axenic cultures and post-fermentation samples. The ecological origin of the yeast (oak- or grape-associated) did not significantly affect the endobacterial community structure. Across all samples, the dominant phyla were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, with Proteobacteria representing over 90% of sequences. Most bacterial genera were shared between axenic and fermentation conditions. However, Escherichia and Comamonas predominated in axenic cultures, while Parvibaculum dominated after fermentation. These findings suggest that yeasts constitute stable microhabitats for bacterial communities, and their relative abundances can shift during fermentation processes.}, }
@article {pmid41597216, year = {2026}, author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP}, title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.}, journal = {Cells}, volume = {15}, number = {2}, pages = {}, pmid = {41597216}, issn = {2073-4409}, support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Homeostasis/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Azoxymethane ; Dextran Sulfate ; *Antineoplastic Agents/pharmacology ; Male ; Humans ; }, abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.}, }
@article {pmid41597231, year = {2026}, author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y}, title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.}, journal = {Cells}, volume = {15}, number = {2}, pages = {}, pmid = {41597231}, issn = {2073-4409}, support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; }, mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; }, abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.}, }
@article {pmid41597535, year = {2025}, author = {Wang, Y and Liu, S and Zheng, Z and Ma, J and Xiang, Y and Wu, L and Ding, C and Shi, Y}, title = {Deciphering the Structure and Genetic Basis of Adaptive Mechanism of Soil Microbial Communities in a Manganese Electrolysis Plant.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597535}, issn = {2076-2607}, support = {QKHJCZK [2021] 224//Science and Technology Program of Guizhou Province/ ; QKHCG [2023] ZD008//Guizhou Provincial Science and Technology Projects/ ; No. [2023] 026//Guizhou Key Laboratory of Green Metallurgy and Process Strengthening/ ; No. [2023] 70//Science and Technology Major Project of Tongren/ ; }, abstract = {The development of China's manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms in Mn production areas remains limited. In order to address this, soil properties and microbial structural characteristics across different functional zones in a typical Mn electrolysis plant in China's "Manganese Triangle" were investigated via metagenomic sequencing. Results showed soil Mn levels significantly exceeded background values, indicating high environmental risk. Acidobacteria and Proteobacteria were dominant phyla. Microbial abundance was lowest in the adjacent natural reservoir, whereas diversity was highest in the sewage treatment plant. Correlation analyses identified Mn, nitrate nitrogen, ammonium nitrogen, pH, and moisture as key environmental drivers, with Mn being the primary one. Metagenomic analysis revealed abundant Mn resistance genes, enabling microbial survival under high Mn stress. This study demonstrated that excessive Mn exposure enriched Mn-resistant genes, thereby shaping unique microbial communities dominated by Mn-resistant bacteria. These findings clarified the structural characteristics and adaptive mechanisms of soil microbial communities in Mn-contaminated areas, providing a theoretical basis for ecological risk management and bioremediation.}, }
@article {pmid41597576, year = {2025}, author = {Wang, L and Zhao, Y}, title = {The Response of Substrate Microbial Communities to the Addition of Mineral Nutrients During the Growth Period of Straw Mushroom Volvariella volvacea.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597576}, issn = {2076-2607}, support = {No. 2024YFD1200204//National Key R&D Program of China/ ; No. 21N51900500//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; KFKT2023-03//the Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; }, abstract = {Volvariella volvacea were grown on an abandoned cotton-based substrate, which was divided into two conditions: a group with added nutrients (N3P3) and a control group (CK). Using metagenomic sequencing technology, the study investigated the effect of nutrient addition during the growth process of V. volvacea on the microbial community and metabolic pathways of the substrate. The study found that the main bacteria in the N3P3 group were Proteus and Microsporidium, while in the CK group, Bacillus marinosus and Microsporidium globosa were more common. At all stages of V. volvacea growth, Proteobacteria and Firmicutes dominated. Metabolic function analysis showed that the N3P3 group significantly increased amino acid metabolism, nitrogen metabolism, genetic information processing, and cellular processes, while reducing the contents of pathogenic and saprophytic symbiotic fungi. Nitrogen metabolism, phosphorus metabolism, and carbon metabolism were closely related to the growth of V. volvacea, and nutrient addition significantly improved microbial community diversity and metabolic levels, which can be used as a substrate optimization formula. This is of great significance for the development of sustainable agriculture.}, }
@article {pmid41597613, year = {2026}, author = {Jarrín-V, P and Carrión-Olmedo, JC and Loján, P and Reyes-Barriga, D and Lara, M and Oña, A and Quiroz-Moreno, C and Castillejo, P and Tenea, GN and Díaz, M and Monfort-Lanzas, P and Molina, CA}, title = {Predicted Bacterial Metabolic Landscapes of the Sumaco Volcano: A Picrust2 Analysis of 16S rRNA Data from Amazonian Ecuador.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597613}, issn = {2076-2607}, support = {NA//National Institute of Biological Resources (NIBR) and the Korea International Cooperation Agency (KOICA) of the Republic of Korea/ ; }, abstract = {The Sumaco volcano in Ecuador, which has a distinct geological origin from the Andes and is located in the Amazon basin, offers an opportunity to study untouched microbiomes. We explored comparative patterns of abundance from predicted functional profiling in soil samples collected along the elevation and sulfur gradients on its slopes. Using 16S rRNA gene metabarcoding, we inferred metagenome functional profiles, contrasting sample groups by altitude or soil sulfur concentration. We inferred that high-altitude communities may have higher predicted abundance for anaerobic metabolism (crotonate fermentation), coenzyme B12 synthesis, and degradation of diverse carbon sources (sugars and octane). High-sulfur soils were associated with an inferred enrichment of pathways for degrading complex organic compounds and nitrogen metabolism, reflecting adaptation to unique geochemical conditions. In contrast, low-sulfur soils are consistent with a higher predicted abundance of glycerol degradation. Within the limitation imposed by the potential weak associations of the applied predicted functional profiling to actual gene content, we propose that the inferred metabolic changes represent different ecological strategies for resource acquisition, energy generation, and stress tolerance, and they are optimized for varying conditions in this unique volcanic ecosystem. Our findings highlight how environmental gradients shape soil microbiome functional diversity and offer insights into microbial adaptation in Sumaco's exceptional geochemistry within the Amazon. Further efforts linking functional predictions back to specific taxa will offer a complete ecological perspective of the microbiome exploration in the Sumaco volcano.}, }
@article {pmid41597664, year = {2026}, author = {Liepa, E and Ustinova, M and Gudra, D and Roga, A and Kalnina, I and Dejus, B and Dejus, S and Strods, M and Tomsone, LE and Kibilds, J and Bartkevics, V and Berzins, A and Dumpis, U and Juhna, T and Fridmanis, D}, title = {Urban Wastewater Metagenomics Reveals the Antibiotic Resistance Gene Distribution Across Latvian Municipalities.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597664}, issn = {2076-2607}, support = {VPP-COVID-2020/1-0008//Latvian Council of Science/ ; No.5.2.1.1.i.0/2/24/I/CFLA/001//CFLA/ ; }, abstract = {Antimicrobial resistance (AMR) poses a global health threat, with urban wastewater systems serving as key reservoirs for resistance dissemination. This study aimed to investigate the relationships among urban environments, bacterial communities, and AMR patterns, and evaluate the specific municipal-scale drivers of resistance gene distribution. Shotgun metagenomic analysis was conducted on 45 wastewater samples collected from 15 municipalities across Latvia to determine the composition of the resistome and its correlation with local factors. The analysis identified 417 distinct antibiotic resistance genes (ARGs) belonging to 108 families, with geographic location serving as the primary driver of ARG distribution, which explained 65.87% of community variation (p = 0.001). Local industrial factors demonstrated significant effects, with food industry wastewater significantly influencing both bacterial taxonomy and ARG profiles (p < 0.05). While the presence of a regional hospital did not shape the overall municipal resistome, hospital-associated wastewater showed 19 overlapping ARGs, including clinically critical carbapenemases. Municipal wastewater systems function as geographically structured reservoirs of AMR that are shaped by localized industrial and healthcare outputs. These findings support wastewater-based AMR surveillance as a valuable tool for tracking specific resistance sources.}, }
@article {pmid41597665, year = {2026}, author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N}, title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597665}, issn = {2076-2607}, support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; }, abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.}, }
@article {pmid41597701, year = {2026}, author = {Mollova, D and Baev, V and Borisova, T and Rusinova, M and Iliev, I}, title = {A Metagenomic Comparison of the Colostrum Microbiome in Bulgarian Mothers by Delivery Mode: A Pilot Study.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597701}, issn = {2076-2607}, support = {KP-06-M81/6//Bulgarian Science Fund/ ; }, abstract = {Colostrum harbors a highly diverse microbial community, predominantly composed of genera such as Staphylococcus, Streptococcus, Lactobacillus, Bifidobacterium, and Enterococcus. The composition and diversity of this microbiota are influenced by maternal factors-including age, body mass index, lactation activity, stress levels, and gestational diabetes-as well as external factors such as mode of delivery, antibiotic exposure, diet, and geographic location. This microbial community plays a critical role in maternal and neonatal health by contributing to early gut colonization, supporting digestion, promoting immune system development, and protecting against pathogenic microorganisms through mechanisms such as antimicrobial peptide production by lactic acid bacteria. The primary aim of this study was to evaluate the impact of mode of delivery on colostrum microbiota by comparing mothers who delivered vaginally with those who underwent cesarean section. Colostrum samples from 15 mothers were subjected to DNA extraction, high-throughput sequencing, and bioinformatic analyses to characterize microbial composition and predicted functional profiles. Although substantial inter-individual variability was observed, no statistically significant differences were detected in overall microbial diversity or community structure between the two delivery groups. However, distinct bacterial taxa and functional characteristics were identified that were specific to each mode of delivery, suggesting subtle delivery-related influences on colostrum microbiota composition.}, }
@article {pmid41597714, year = {2026}, author = {Isgandarov, I and Abilda, Z and Kanat, R and Daurov, D and Sapakhova, Z and Daurova, A and Zhambakin, K and Volkov, D and Begaly, A and Shamekova, M}, title = {Long-Read Metagenomics Profiling for Identification of Key Microorganisms Affected by Heavy Metals at Technogenic Zones.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597714}, issn = {2076-2607}, support = {BR24992837//Ministry of Agriculture of the Republic of Kazakhstan/ ; }, abstract = {Heavy metal pollution poses a serious threat to soil ecosystems worldwide, as long-term exposure can alter microbial community functioning and reduce overall ecosystem resilience. This study investigated the impact of heavy metal contamination in technogenic industrial areas of the East Kazakhstan Region on soil microbial communities. Soil samples were collected for chemical and metagenomic analyses. Concentrations of Zn, Pb, Cu, and Cd were quantified by flame atomic absorption spectrometry (FAAS). Using long-read whole-metagenome nanopore sequencing, we conducted strain-level profiling of soils with different levels of metal contamination. This approach provided high-resolution taxonomic data, enabling detailed characterization of microbial community structure. Heavy metal exposure did not significantly reduce microbial diversity or richness but influences the quality of community composition. Metal-resistant taxa dominated contaminated soils. Overall, the results highlight the value of long-read sequencing for resolving strain-level responses to environmental contamination.}, }
@article {pmid41597726, year = {2026}, author = {Lee, HJ and Park, SH and Han, SY and Lee, JH and Kim, DU and Seo, HI}, title = {Differences in the Biliary Microbiome Between Biliary Tract Cancer and Benign Biliary Disease.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597726}, issn = {2076-2607}, support = {202100350001//Biomedical Research Institute, Pusan National University Hospital/ ; }, abstract = {Bile contains many bacteria that can contribute to various diseases. Therefore, identifying bile microbiome differences between benign and malignant conditions is essential. In this study, bile samples were collected aseptically from 141 patients with biliary tract cancer (BTC) or benign biliary diseases (BBDs) who underwent endoscopic retrograde cholangiopancreatography or biliary tract surgery. Quality control PCR was performed to amplify the V3-V4 region of the bacterial 16S rRNA gene. Metagenomic sequencing of bile was successfully performed in 35 of 56 samples collected from patients with BTC and 24 of 85 samples from patients with BBD. The mean alpha diversity values comprised 2.788 ± 2.833 and 2.319 ± 1.355 in the BBD and BTC groups, respectively (p = 0.399). The bacterial species (4.7%) were shared between groups, whereas 12.3% and 83% were indicated to patients with BTC and BBD, respectively. Bacteroides coprocola, Prevotella copri, and Bacteroides plebeius were more frequently identified in the bile of patients with BTC, whereas Bacteroides vulgatus and Bacteroides uniformis were more abundant in the bile of patients with BBD. Distinct patterns of microorganism abundance between the two groups of patients suggest association of bile microbiome with disease status, so its diagnostic potential should be validated in further studies.}, }
@article {pmid41597735, year = {2026}, author = {Moser, K and Ballif, A and Pillonel, T and Concu, M and Montenegro-Borbolla, E and Nickel, B and Stampfli, C and Ruf, MT and Audry, M and Kapel, N and Gerber, S and Jacot, D and Bertelli, C and Galpérine, T}, title = {Fecal Microbiota Transplantation Donor Screening: Is Dientamoeba fragilis a Valid Criterion for Donor Exclusion? A Longitudinal Study of a Swiss Cohort.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597735}, issn = {2076-2607}, support = {//internal funding at the Lausanne University Hospital (CHUV)/ ; grant number 51NF40 180575//he salaries of K.M. and E.M.-B. were supported as a part of NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation/ ; }, abstract = {Dientamoeba fragilis is a protozoan of the human digestive tract, yet its transmission and pathogenic role remain poorly understood. This study aimed to evaluate its impact on the efficacy and safety of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI). This longitudinal cohort study analyzed stool samples from FMT donors and recipients pre-treatment and at 2 and 8 weeks post-FMT. All samples were retrospectively tested using real-time PCR. Shotgun metagenomics was also performed on selected donor-recipient pairs to explore transmission. CDI cure rates, gastrointestinal adverse events (AEs), and serious adverse events (SAEs) were assessed prospectively. A total of 53 FMT were analyzed (179 samples), with 23 (43%) derived from D. fragilis-positive donor stool (4 of 10 donors, 40%). Four of 52 recipients (18.2%), initially negative and who received treatment from positive donors, tested positive post-FMT. Shotgun metagenomics could not definitely confirm transmission due to the lack of a good reference genome. No significant differences in efficacy, AE, or SAE were observed between FMT from D. fragilis-positive versus -negative donors, even in immunocompromised patients. No SAEs were attributed to FMT. D. fragilis may be transmitted via FMT without evidence of short-term clinical impact. Consequently, RT-PCR detection should be interpreted cautiously in the context of donor exclusion decisions.}, }
@article {pmid41597738, year = {2026}, author = {Xi, D and Zhu, F and Zhang, Z and Zhou, S and Zhang, J}, title = {Forest Type Shapes Soil Microbial Carbon Metabolism: A Metagenomic Study of Subtropical Forests on Lushan Mountain.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597738}, issn = {2076-2607}, support = {20232BAB205020//Jiangxi Provincial Natural Science Foundation/ ; 22-315-6-18//the Science and Technology Program of Shenyang/ ; JJXC2023010//Jiujiang City's "Xuncheng Talent" Program/ ; 20242BCC32138//Jiangxi Provincial Key Laboratory of Carbon Neutrality and Ecosystem Carbon Sinks/ ; }, abstract = {Forest type strongly influences soil microbial community composition and associated carbon cycling, yet its influence on microbial functional traits remains poorly understood. In this study, metagenomics sequencing was used to investigate soil microbial communities and carbon metabolism genes across three forest types: deciduous broadleaf (DBF), mixed coniferous-broadleaf (CBMF), and coniferous forest (CF) at two soil depths (0-20 cm and 20-40 cm) on Lushan Mountain in subtropical China. The results showed that CF exhibited higher bacterial diversity and a distinct microbial composition, with an increase in Actinomycetota and Bacteroidota and a decrease in Acidobacteriota and Pseudomonadota. The Calvin cycle was the dominant carbon fixation pathway in all forests, while the relative abundance of secondary pathways (i.e., the 3-hydroxypropionate bi-cycle and reductive citrate cycle) varied significantly with forest type. Key carbon fixation genes (sucD, pckA) were more abundant in CF and CBMF, with higher levels of rpiA/B and ackA in DBF. Functional profiling further indicated that CF soils, especially in the surface layer, were enriched in glycoside hydrolases (GHs) and carbohydrate esterases (CEs), while CBMF showed a greater potential for starch and lignin degradation. Multivariate statistical analyses identified soil available phosphorus (AP) and pH as primary factors shaping microbial community variation, with AP emerging as being the dominant regulator of carbon-related functional gene abundance. Overall, the prevalence of these distinct genetic potentials across forest types underscores how vegetation composition may shape microbial functional traits, thereby influencing the stability and dynamics of the soil carbon pool in forest ecosystem.}, }
@article {pmid41597740, year = {2026}, author = {Lowell, JL and Brown, L}, title = {Metals and Microbes: Microbial Community Diversity and Antibiotic Resistance in the Animas River Watershed, Colorado, USA.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597740}, issn = {2076-2607}, support = {RL5GM118990//NIH Building Infrastructure Leading to Diversity (BUILD) Initiative (U54)/ ; }, abstract = {Antimicrobial resistant (AMR) infections are a persistent public health issue causing excess death and economic impacts globally. Because AMR in clinical settings is often acquired from nonpathogenic bacteria that surround us, environmental surveillance must be better characterized. It has been well established that metals can co-select for bacterial AMR. Furthermore, recent studies have shown that compromised microbial community diversity may lead to community invasion by antibiotic resistance genes (ARGs). Widespread legacy mining has led to acid mine drainage and metal contamination of waterways and sediments throughout the western United States, potentially compromising microbial community diversity while simultaneously selecting for AMR bacteria. Our study objectives were to survey metal contaminated sediments from the Bonita Peak Mining District (BPMD) in southwestern Colorado, USA, compared to sites downstream in Durango, CO for bacterial and ARG diversity. Sediment bacteria were characterized using 16S rRNA Ilumina and metagenomic sequencing. We found that overall, bacterial diversity was lower in metal-contaminated, acidic sites (p = 0.04). Metagenomic sequencing revealed 31 different ARGs, with those encoding for efflux pumps (mex and spe gene families) substantially more prevalent in the BPMD sites, elucidating a specific AMR marker fingerprint from the high metal concentration sediments. Raising awareness and providing antimicrobial tracking techniques to resource limited communities could help provide information needed for better antibiotic use recommendations and environmental monitoring.}, }
@article {pmid41597751, year = {2026}, author = {Liu, PY and Tang, HJ and Lee, SS and Liao, CH and Huang, CH and Kuo, HY and Sheng, WH and Taiwan Metagenomic Sequencing Microbiology Study Group, }, title = {Comparative Analysis of Microbial Detection in Traditional Culture Versus Metagenomic Next-Generation Sequencing in Patients with Periprosthetic Joint Infection: A Prospective Observational Study.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597751}, issn = {2076-2607}, support = {M09A7321 and MOHW113-TDU-B-211-114006//the Ministry of Health and Welfare of Taiwan/ ; NSTC 113-2321-B-002-016//the National Science and Technology Council of Taiwan/ ; }, abstract = {Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve hospitals in Taiwan. Both conventional bacterial culture (CMT) and mNGS of joint fluid and debrided tissue were performed. Demographic characteristics, laboratory results and clinical outcomes were collected. The diagnostic performance of these two methods was analyzed. A total of 42 patients with a mean age of 67.9 years were enrolled in analysis. The knee was the most common joint involved (69.1%). A high proportion of patients (78.6%) received prior antibiotics within the two weeks at sample collection. mNGS identified pathogens in 28 out of 42 patients (66.7%), whereas CMT yielded positive results in 12 out of 42 patients (28.6%) (McNemar's test, p = 0.01). Staphylococcus species was the most common genus detected (n = 11), followed by Cutibacterium (n = 4). Other detected genera included Escherichia, Mycobacterium, Enterobacter, Klebsiella (n = 2 each), Acinetobacter, and Corynebacterium (n = 1 each). Our results support the idea that mNGS could serve as a valuable diagnostic tool for PJI in addition to traditional culture methods.}, }
@article {pmid41597762, year = {2026}, author = {Xiong, Y and Dai, Z and He, F and Liu, R and Wang, J and Zhan, Z and Jia, H and Chen, S and Cai, L}, title = {Effect of Hantavirus Infection on the Rodent Lung Microbiome: Specific Regulatory Roles of Host Species and Virus Types.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597762}, issn = {2076-2607}, support = {2024JJ9472//The natural science foundation of Hunan provincial/ ; }, abstract = {The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.}, }
@article {pmid41598263, year = {2026}, author = {Liu, Y and Zhao, M and Zhong, S and Wu, G and Yang, F and Zhou, J}, title = {Review on Mining Robust Lactic Acid Bacteria for Next-Generation Silage Inoculants via Multi-Omics.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {1}, pages = {}, pmid = {41598263}, issn = {2075-1729}, support = {2023J06019//Fujian Provincial Outstanding Youth Fund Projects/ ; KFB25053A and KFB25010A//Science and Technology Innovation Specia Fund Project of Fujian Agriculture and Forestry University/ ; }, abstract = {Lactic acid bacteria (LAB), as the core microorganisms in silage fermentation, play a crucial role in improving silage quality and ensuring feed safety, making the screening, identification, and functional characterization of LAB strains a significant research focus. Researchers initially isolate and purify LAB from various samples, followed by identification through a combination of morphological, physiological, biochemical, and molecular biological methods. Systematic screening has been conducted to identify LAB strains tolerant to extreme environments (e.g., low temperature, high temperature, high salinity) and those possessing functional traits such as antimicrobial activity, antioxidant capacity, production of feruloyl esterase and bacteriocins, as well as cellulose degradation, yielding a series of notable findings. Furthermore, modern technologies, including microbiomics, metabolomics, metagenomics, and transcriptomics, have been employed to analyze the structure and functional potential of microbial communities, as well as metabolic dynamics during the ensiling process. The addition of superior LAB inoculants not only facilitates rapid acidification to reduce nutrient loss, inhibit harmful microorganisms, and improve fermentation quality and palatability but also demonstrates potential functions such as degrading mycotoxins, adsorbing heavy metals, and reducing methane emissions. However, its application efficacy is directly constrained by factors such as strain-crop specific interactions, high dependence on raw material conditions, limited functionality of bacterial strains, and relatively high application costs. In summary, the integration of multi-omics technologies with traditional methods, along with in-depth exploration of novel resources like phyllosphere endophytic LAB, will provide new directions for developing efficient and targeted LAB inoculants for silage.}, }
@article {pmid41598312, year = {2026}, author = {Thant, EP and Klaysubun, C and Suwannasin, S and Dechathai, T and Singkhamanan, K and Yaikhan, T and Chaichana, N and Pomwised, R and Wonglapsuwan, M and Chusri, S and Surachat, K}, title = {Global Comparative Genomics of Stenotrophomonas maltophilia Reveals Cryptic Species Diversity, Resistome Variation, and Population Structure.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {1}, pages = {}, pmid = {41598312}, issn = {2075-1729}, abstract = {Background:Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim-sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia.}, }
@article {pmid41598908, year = {2026}, author = {González-Peña, R and Hidalgo-Martínez, DO and Laredo-Tiscareño, SV and Huerta, H and de Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and Rubio-Tabares, E and García-Rejón, JE and Muñoz-Ramírez, ZY and Tangudu, C and Garza-Hernández, JA}, title = {Characterization of the Bacteriome of Culicoides reevesi from Chihuahua, Northern Mexico: Symbiotic and Pathogenic Associations.}, journal = {Insects}, volume = {17}, number = {1}, pages = {}, pmid = {41598908}, issn = {2075-4450}, support = {419- 395 24-23//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; SIP20250075//Secretaría de Investigación y Posgrado from Instituto Politécnico Nacional/ ; }, abstract = {Culicoides biting midges are vectors of veterinary and zoonotic pathogens, yet the bacteriome of several species remains unexplored. Culicoides reevesi, a poorly studied species in northern Mexico, represents an opportunity to investigate microbial associations that may influence vector biology. Adults of C. reevesi were analyzed using 16S rRNA amplicon sequencing, followed by functional prediction with PICRUSt2. Heatmaps and pathway summaries were generated to highlight dominant taxa and functions. The bacteriome was dominated by Pseudomonadota, followed by Actinomycetota, Bacillota, and Bacteroidota. Symbiotic taxa such as Asaia and Cardinium were identified alongside potentially pathogenic bacteria, including Escherichia coli, Mycobacterium avium, Vibrio parahaemolyticus, and Enterococcus faecalis. Functional predictions indicated metabolic versatility, with abundant pathways related to aerobic respiration, the TCA cycle, amino acid biosynthesis, and quorum sensing. Despite all samples being collected from the same site and date, apparent differences in bacterial composition were observed across pools, suggesting microhabitat or host-related variability. This study provides the first taxonomic and functional baseline of the C. reevesi bacteriome. The detection of both symbiotic and pathogenic bacteria highlights the dual ecological role of the microbiome in host fitness and pathogen transmission potential. In conclusion, we suggest that these microbial associations influence vector physiology and competence, providing a basis for future microbiome-based control strategies. These findings emphasize the importance of integrating microbiome analyses into entomological surveillance and vector control strategies in endemic regions.}, }
@article {pmid41598945, year = {2026}, author = {Hirata, K and Suzuki, T and Yura, K and Asahi, T and Kataoka, K}, title = {Gut Microbiome Differences Across Mixed-Sex and Female-Only Social Rearing Regimes in Female Field Crickets Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Insects}, volume = {17}, number = {1}, pages = {}, pmid = {41598945}, issn = {2075-4450}, support = {24KJ2101//Japan Society for the Promotion of Science/ ; JPJ009237//Cabinet Office/ ; }, abstract = {The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets.}, }
@article {pmid41599039, year = {2026}, author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z}, title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41599039}, issn = {2076-0817}, support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Female ; Cohort Studies ; }, abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.}, }
@article {pmid41599943, year = {2026}, author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC}, title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.}, journal = {Nutrients}, volume = {18}, number = {2}, pages = {}, pmid = {41599943}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; }, abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.}, }
@article {pmid41600629, year = {2026}, author = {Wang, D and Sun, J and Zhang, Y and Yuan, L and Xu, X and Xue, Y and Sun, H}, title = {Integrated 13C-DNA Stable Isotope Probing and Metagenomics Approaches to Identify Bisphenol A Assimilating Microorganisms and Metabolic Pathways in Biofilms.}, journal = {Toxics}, volume = {14}, number = {1}, pages = {}, pmid = {41600629}, issn = {2305-6304}, support = {52100082//National Natural Science Foundation of China/ ; KYCX25_3358//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; SJCX25_1722//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; BK20240983//Natural Science Foundation of Jiangsu Province/ ; ZMF23020040//Changzhou University Research Start-up Fund Project/ ; }, abstract = {Bisphenol A (BPA) is a persistent environmental contaminant requiring effective removal strategies. Biofilms offer advantages over conventional activated sludge for refractory compound degradation, yet the specific microorganisms and mechanisms driving BPA removal in biofilms remain poorly understood. This study employed an integrated approach, combining [13]C-DNA stable isotope probing (SIP) and metagenomics to identify BPA-assimilating microorganisms and elucidate their metabolic pathways in biofilms. Two moving bed biofilm reactors (MBBRs) were operated at contrasting BPA concentrations (500 μg/L and 10 mg/L) to enrich distinct microbial communities. Using DNA-SIP, we revealed differences in assimilating bacteria across diverse concentrations of BPA-enriched biofilms. Simultaneously, we reconstructed the genomes of these assimilating bacteria, dissecting the functional genes essential to the degradation process and identifying significant gene variations among different assimilating bacteria. By integrating these gene functions, we constructed the BPA metabolic pathway, which surprisingly comprised genes from various assimilating bacteria. This research significantly advances our understanding of BPA-assimilating bacteria within biofilms and provides valuable insights for refining biofilm technologies aimed at BPA removal from wastewater.}, }
@article {pmid41600842, year = {2026}, author = {Hake, N and von Holtum, C and Höper, D and Nijhof, AM and Dietze, K and Hoffmann, B}, title = {Identification and Long-Term Detection of Hepacivirus bovis Genotype 1 and 2 on a Cattle Farm in Germany.}, journal = {Viruses}, volume = {18}, number = {1}, pages = {}, pmid = {41600842}, issn = {1999-4915}, mesh = {Animals ; Cattle ; Germany/epidemiology ; *Cattle Diseases/virology/epidemiology/diagnosis ; *Genotype ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Farms ; Genome, Viral ; Female ; Real-Time Polymerase Chain Reaction ; }, abstract = {In 2020, a dairy farm in northwest Germany reported several cows with severe respiratory disease, fever, and reduced milk production. Multiple direct and indirect diagnostic methods were used to identify the cause of the disease. However, the pathogens detected could not be correlated with the severity of the clinical symptoms, so further diagnostic steps were taken. Blood and nasal swab samples were examined using next-generation sequencing (NGS) as part of a metagenomic analysis. For the first time in Germany, Hepacivirus bovis genotype 2 was detected. Real-time RT-PCR assays confirmed the presence of BovHepV genotypes 1 and 2 in the herd between 2020 and 2023. Analyses of complete and partial genome sequences demonstrated the presence of different virus variants in the herd over several years. In addition, the sequence data indicated that cattle can be reinfected with viruses belonging either to different BovHepV subtypes or to the same subtype. Although no direct link could be established between the detection of bovine hepaciviruses and the observed clinical symptoms, the PCR and sequence data obtained provide valuable insights into the epidemiology and pathogenesis of BovHepV infections.}, }
@article {pmid41600881, year = {2026}, author = {Li, J and Baumgartner, W and Wang, L}, title = {Histopathologic and Genomic Characterization of a Novel Caprine Astrovirus Identified in a Boer Goat Kid in Illinois, United States.}, journal = {Viruses}, volume = {18}, number = {1}, pages = {}, pmid = {41600881}, issn = {1999-4915}, mesh = {Animals ; Goats/virology ; *Goat Diseases/virology/pathology ; *Astroviridae Infections/veterinary/virology/pathology ; Phylogeny ; Genome, Viral ; *Astroviridae/genetics/classification/isolation & purification ; Genomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Astroviruses are non-enveloped, positive-sense single-stranded RNA viruses known to infect various mammals and birds, including humans, often causing gastrointestinal disorders. In recent years, astroviruses have also been linked to neurological and respiratory diseases across several species, including ruminants, mink, deer, and other mammals. Notably, astrovirus infections in goats have been documented in countries such as Switzerland and China, where novel genotypes have been identified in fecal samples. However, their role in the context of disease remains unclear, and reports focusing solely on goat astrovirus in the United States have not been published. A necropsy case of a Boer goat kid with a history of diarrhea was submitted for investigation following death in January 2025. Fresh tissues were received and used for histopathology and enteric pathogen testing, including parasitic, bacterial, and viral workups. Metagenomic-based next-generation sequencing (mNGS) was also applied for this case. Histological examination revealed severe necrotizing enterocolitis. The small intestine exhibited epithelial ulcerations, villus atrophy, hyperplastic and dilated crypts with necrotic debris, few intraenterocytic coccidian parasites, and increased inflammatory cells in the lamina propria. The large intestine showed similar findings with pleomorphic crypt enterocytes. Standard enteric pathogen tests were negative except for aerobic culture that identified Escherichia.coli and Enterococcus hirae. mNGS and bioinformatic analysis identified a novel astrovirus in the intestinal content that showed the highest nucleotide identity (86%) to the sheep strain Mamastrovirus 13 sheep/HA3 from China based on BLAST analysis. Phylogenetic analysis indicated that the newly identified caprine astrovirus IL90175 clustered with astrovirus strains from small ruminants in Asia and Europe. This research reports the discovery, histopathologic features, and genetic characteristics of a gastrointestinal disease-causing astrovirus in a goat kid, which had not been previously described in the United States.}, }
@article {pmid41601042, year = {2026}, author = {Sun, Y and Tu, Q and Shao, Z and Li, H}, title = {The normalization of gene abundance affects the discovery: A case of metal resistance genes in coastal sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119608}, doi = {10.1016/j.ecoenv.2025.119608}, pmid = {41601042}, issn = {1090-2414}, mesh = {*Geologic Sediments/microbiology/chemistry ; China ; Metagenomics/methods ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/toxicity/analysis ; *Metals/toxicity ; Estuaries ; }, abstract = {The advent of metagenomic technologies has given rise to a plethora of gene abundance calculation methods, which have emerged in a successive manner. Nevertheless, the extent to which these approaches are appropriate for metagenomic data and the specific research objectives remain subjects of debate. In this study, metagenomics sequencing was utilised to analyse the sediments from two coastal regions of China: the Beibu Gulf (BBG) and the Liaohe Estuary (LHE). The abundance of metal resistance genes (MRGs), which are critical genetic elements that influence ecosystem functioning and health, in the regions under study was obtained by two different calculation methods: the cell-normalized abundance (copies per prokaryotic cell) and the ppm abundance (sequences per million sequences). The application of diverse abundance calculation methodologies yielded markedly divergent outcomes. The cell-normalized and ppm abundances indicated a substantial elevation of total MRG abundance in the BBG and LHE sediments, respectively. Furthermore, disparate comparison outcomes were identified based on the varied abundance calculation methodologies employed across distinct MRG types, including genes demonstrating resistance to Fe, Al, Cr, Se, and multi-metals. These disparities can be ascribed to the variations in the prokaryotic biomass among different sediments, signifying that it is imperative to select an appropriate abundance calculation method according to whether the research objective necessitates the consideration of biomass differences. Furthermore, the results of multiple correlation analyses indicated that petroleum content was the key factor, and the ruvB gene was identified as an indicator for the MRG level based on both two abundance calculation methods. These findings establish a methodological foundation for metagenomics-based research and offer insights into the MRGs present in coastal sediments.}, }
@article {pmid41601044, year = {2026}, author = {Sun, X and Zheng, L and Qi, R and Li, H}, title = {Salinity and redox-driven niche differentiation of ammonia-oxidizing microbes in a saline-alkaline river system.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119613}, doi = {10.1016/j.ecoenv.2025.119613}, pmid = {41601044}, issn = {1090-2414}, mesh = {*Ammonia/metabolism ; Oxidation-Reduction ; *Rivers/microbiology/chemistry ; *Salinity ; *Bacteria/metabolism/genetics ; *Archaea/metabolism/genetics ; Nitrification ; Geologic Sediments/microbiology ; Wetlands ; China ; Ecosystem ; Soil Microbiology ; }, abstract = {The ammonia oxidation process constitutes a critical step in the nitrogen cycle within river ecosystems. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are the major contributors to this process; however, their relative contributions differ substantially across different environments, particularly in saline-alkaline regions. To investigate the differences in ammonia oxidation processes between soil and sediment across various riparian zones in the Yinbei Irrigation District in Ningxia, samples were collected from five representative riparian types along the Third Drainage Ditch: a gravel-reed mixed zones, a reed zones, a high-salt Kochia scoparia zones, an Iris lactea embankment zones, and a bare soil zone. The potential nitrification rate (PNR) and associated environmental factors were quantified, and the community structure of microorganisms was analyzed by metagenomic sequencing, while the abundances of AOA and AOB functional genes (amoA) were quantified by quantitative PCR (qPCR). Through a multi-dimensional investigation of the ammonia oxidation process in riparian zones and sediments of saline-alkali wetlands, this study provided critical evidence for the mechanisms underlying habitat-specific nitrogen transformations. Pronounced physical and chemical differences were observed between sediments and riparian zones. Whereas the sediments exhibited strong reducing conditions, the riparian zones were characterized by pronounced saline-alkali stress. PCoA analysis revealed a clear separation between AOA and AOB communities, with saline-alkali-tolerant AOA predominating in riparian zones and AOB predominating in sediments. The strong reducing condition impedes the activity of AOB in sediments, thereby resulting in the accumulation of NH4[+] -N. AOA contributed 67-68.9 % of the total PNR in riparian zones, thereby driving substantial NO3[-]-N production. Seasonal variations exhibited no significant influence on the partitioning of microbial functions, which were jointly regulated by the saline-alkali gradient and redox state. This study demonstrates that the ammonia oxidation process of saline-alkali wetlands exhibits a pronounced mechanism of habitat-specific functional differentiation: AOB in sediments are constrained by the anoxic conditions induced by elevated total organic carbon (TOC), whereas AOA in riparian zones overcome the inhibition of nitrification under high pH or electrical conductivity (EC) through evolved salt-tolerant adaptations This discovery provides a novel theoretical framework for elucidating the microbial mechanisms driving the nitrogen cycle in saline-alkaline environments.}, }
@article {pmid41601218, year = {2025}, author = {Li, CT}, title = {[Applications and challenges of forensic microbiomics].}, journal = {Fa yi xue za zhi}, volume = {41}, number = {5}, pages = {441-442}, doi = {10.12116/j.issn.1004-5619.2025.551105}, pmid = {41601218}, issn = {1004-5619}, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; }, }
@article {pmid41601644, year = {2025}, author = {Song, DJ and Dong, R and Liu, YM and Wang, T and Ma, J}, title = {Autoimmune cerebellar ataxia with anti-Homer3 antibodies associated with herpesvirus infection: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1709326}, pmid = {41601644}, issn = {1664-3224}, mesh = {Humans ; Female ; Adolescent ; *Cerebellar Ataxia/cerebrospinal fluid/immunology/virology ; *Herpesviridae Infections/cerebrospinal fluid/complications/immunology ; Herpesvirus 7, Human ; Homer Scaffolding Proteins ; Autoantibodies ; }, abstract = {Autoimmune cerebellar ataxia (ACA) is a cerebellar syndrome mediated by autoimmune mechanisms. ACA is particularly rare, and cases of ACA with anti-Homer-3 antibodies associated with herpesvirus infection are even rarer. In this study, we report a case of a 15-year-old girl who was admitted with a one-month history of progressive vertigo and unsteady gait. Metagenomic next-generation sequencing (mNGS) of her cerebrospinal fluid (CSF) revealed eight sequences of human herpesvirus 7 (HHV-7). Anti-Homer-3 antibodies were detected in both serum and CSF samples. Following a series of immunotherapy, the patient showed improvements in dizziness and gait stability. However, her symptoms recurred during the tapering of corticosteroids. The patient developed three episodes of generalized seizures. Concurrently, gait instability significantly worsened. Repeat first-line immunotherapies including corticosteroid and IVIG were not effective. Rituximab was initiated and symptoms were partial improved. In this study, we present the clinical symptoms of this patient with anti-Homer-3 antibody-associated ACA, conduct long-term follow-up, and review relevant literature. Our aim is to enhance the understanding of this rare disease by summarizing key clinical features, thus providing valuable insights into the diagnosis and treatment of ACA.}, }
@article {pmid41602101, year = {2025}, author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H}, title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1730098}, pmid = {41602101}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Nanopore Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Metagenomics/methods ; Microbiota ; Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.
METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.
RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.
CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.}, }
@article {pmid41602753, year = {2025}, author = {Nissan, I and Peretz, A}, title = {Editorial: Innovation in tackling the global challenge of eradicating antibiotic-resistant microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1774105}, doi = {10.3389/fmicb.2025.1774105}, pmid = {41602753}, issn = {1664-302X}, }
@article {pmid41602756, year = {2025}, author = {Chisompola, D and Luwaya, E and Nzobokela, J and Mwansa, P and Chakulya, M}, title = {AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1717859}, pmid = {41602756}, issn = {1664-302X}, abstract = {Emerging viral outbreaks continue to pose a persistent global health threat, underscoring the urgent need for a shift from reactive to proactive health security strategies. Viral metagenomic next-generation sequencing (mNGS) offers an unbiased, powerful approach to pathogen detection and discovery, yet its utility has been constrained by the computational complexity and slow turnaround time of data analysis during outbreak crises. The integration of artificial intelligence (AI) and mNGS is dismantling these barriers, enabling faster, more scalable outbreak response. This review synthesizes how AI-driven analytics are transforming mNGS applications, from genome assembly to sequence classification, using advanced architectures such as convolutional neural networks, recurrent neural networks, and transformers. Beyond accelerating workflows, AI's capacity for pattern recognition outperforms traditional homology-based methods, facilitating the discovery of novel viral families and tracing hidden transmission chains through anomaly detection. Nonetheless, critical challenges remain, including limited training data, the interpretability of AI models, and resource-intensive computational demands that risk widening an "AI divide" in global health. We evaluate these obstacles and highlight forward-looking strategies, including federated learning for privacy-preserving data sharing and explainable AI for improving trust and biological insight. Looking ahead, we envision an "AI-first" paradigm for outbreak preparedness, anchored in integrated "Digital Immune Systems" for continuous, global-scale surveillance. By framing the synergy between mNGS and AI as a transformative leap, this review underscores its potential to strengthen resilience against future pandemics.}, }
@article {pmid41602763, year = {2025}, author = {Xu, J and Li, J and Kong, X and Zhang, C and Qi, B and Zhu, X and Zhu, Y and Xu, Y}, title = {Dysbiosis and metabolic pathway shifts in the gut microbiome of children with sepsis: a comparative analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1715990}, pmid = {41602763}, issn = {1664-302X}, abstract = {BACKGROUND: The newly published Phoenix Sepsis Score in 2024 for assessing sepsis in children mainly focuses on respiratory, cardiological, coagulation and neurological indicators, whereas the gut microbiome also plays key roles in the occurrence and progression of sepsis. Additionally, emerging evidence suggests that specific biomarkers in gut microbiome are associated with disease progression. This study aimed to explore the differences in gut microbiome diversity, composition and function between septic and healthy children, and to establish correlations with clinical indicators and outcomes, providing new possibilities for the diagnosis and treatment of sepsis.
RESULTS: Analysis of gut microbiome was performed in 20 sepsis children and 9 healthy controls aged between 3 and 18 years old. The anal swab samples were analyzed by metagenomic next-generation sequencing. Significant differences were observed in α and β diversity of gut microbiome between sepsis group and healthy controls groups. Especially, Shannon diversity was significantly correlated with white blood cell count, serum lactate, length of pediatric intensive care unit stay and length of hospital stay (all R > 0, p < 0.05). Firmicutes and Bacteroidetes were both dominant in most of children in SG and HC groups, while three in SG showed extremely low combined abundances of Firmicutes and Bacteroidetes (<10%), which might be associated with chemistry therapy and death outcome. Bacteria associated with nosocomial infections, including genus taxa Acinetobacter, Prevotella, Escherichia, Klebsiella, Bacteroides, and Corynebacterium, can be dominant (relative abundance>70%) in sepsis group, which were absent in healthy control group. Enterococcus abundance not only predicted sepsis risk (AUC = 0.85) but also was correlated with 28-day mortality (R > 0, p = 0.004). Gene function prediction based on Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated significant differences profile in SG and sepsis-deaths groups. The enriched gut microbiome genes were related to cellular proliferation, energy metabolism, signal transduction, the oxidative stress response and arginine metabolism.
CONCLUSION: Significant differences in diversity, taxa composition and gene function in the gut microbiome existed between septic and healthy children. The associations between gut microbiome dysbiosis and clinical indicators were identified. Enterococcus could be a biomarker to predict sepsis risk.}, }
@article {pmid41602774, year = {2025}, author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z}, title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1766907}, doi = {10.3389/fmicb.2025.1766907}, pmid = {41602774}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].}, }
@article {pmid41602901, year = {2025}, author = {Sun, Y and Yuan, L and Hu, T and Sun, C and Yang, D and Tian, M and Dong, S and Gu, H}, title = {Isavuconazole as initial antifungal therapy combined with surgical management of pediatric pulmonary mucormycosis: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1701905}, pmid = {41602901}, issn = {2296-2360}, abstract = {Invasive mucormycosis (IM) in pediatric patients is a rare but life-threatening fungal disease with limited treatment options. Isavuconazole is a new triazole that has shown efficacy and safety in adults for both primary and salvage treatment of mucormycosis. However, data regarding the initial use of isavuconazole in children are rare. In this study, we report a case of a 6-year-old girl with diabetes mellitus. Metagenomic next-generation sequencing detected Rhizopus oryzae in her bronchoalveolar lavage fluid , and a chest computed tomography revealed a reversed halo sign. Oral isavuconazole was given as primary monotherapy with continuous control of blood glucose. After the lesion partially shrank and became confined, the patient visited the thoracic surgery department to undergo lobectomy; she recovered well after the procedure. This report highlights the importance of quick diagnosis of mucormycosis and may provide a reference for providing the initial antifungal treatment in pediatric mucormycosis. All of the aforementioned interventions helped buy time for subsequent surgical treatment, leading to the curing of the child. Isavuconazole may represent an effective and safe therapeutic option as first-line monotherapy for pediatric mucormycosis.}, }
@article {pmid41603333, year = {2026}, author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R}, title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {110}, number = {2}, pages = {562-575}, doi = {10.1177/13872877261415612}, pmid = {41603333}, issn = {1875-8908}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/psychology/microbiology/therapy ; Male ; *Yoga/psychology ; Female ; Case-Control Studies ; Aged ; *Cognition/physiology ; Middle Aged ; Depression/psychology/therapy ; Cognitive Dysfunction ; }, abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.}, }
@article {pmid41603547, year = {2026}, author = {Gschwind, R and Bonnet, M and Abramova, A and Jarquín-Díaz, VH and Wenne, M and Löber, U and Godron, N and Kampouris, ID and Tskhay, F and Nahid, F and Debroucker, C and Bui-Hai, M and El Aiba, I and Klümper, U and Berendonk, TU and Forslund-Startceva, SK and Zahra, R and Bengtsson-Palme, J and Ruppé, E}, title = {Cefiderocol resistance genes identified in environmental samples using functional metagenomics.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41603547}, issn = {1751-7370}, support = {//Establishing a Monitoring Baseline for Antibiotic Resistance in Key Environments/ ; }, mesh = {*Metagenomics ; *Cephalosporins/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Cefiderocol/pharmacology ; Wastewater/microbiology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Fresh Water/microbiology ; beta-Lactamases/genetics ; *Genes, Bacterial ; Germany ; *Environmental Microbiology ; }, abstract = {Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the "One Health" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a "Trojan Horse" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/l), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.}, }
@article {pmid41603859, year = {2026}, author = {Ahmed, N and Abdjan, MI and Aminah, NS and Helianti, I}, title = {Computational design of carbohydrate binding modules-fused PETase like enzyme for enhanced polycaprolactone (PCL) degradation: structural insights, molecular dynamics, and QM/MM simulations.}, journal = {Journal of biomolecular structure & dynamics}, volume = {}, number = {}, pages = {1-28}, doi = {10.1080/07391102.2026.2619892}, pmid = {41603859}, issn = {1538-0254}, abstract = {A novel PET hydrolase-like enzyme identified from metagenomic databases using HMMR search was computationally fused with five different carbohydrate-binding modules (CBMs). AlphaFold3 predicted the 3D structures of the fused enzyme-CBM, which were validated using ERRAT, Verify3D, and PROCHECK. Molecular docking was performed with polycaprolactone triol using AutoDock Vina, followed by 100 ns molecular dynamics (MD) simulations using AMBER. Trajectory analyses and binding free energy calculations (QM/MM-GBSA) were conducted. The putative PET hydrolase-like enzyme shared 49.62% similarity with Ideonella sakaiensis PETase (5XJH). The fused models exhibited the best stability, with an instability index of <40 and a thermostability aliphatic index between 58.83 and 68.27. Structure validation confirmed high-quality 3D models, with >90% of the residues in the allowed Ramachandran regions. All the fused models showed favourable binding to PCL-triol, exhibiting strong interactions. In MD simulations, BlCBM5 and TrCBM complexes displayed a minimal fluctuation: all-atom RMSD ∼0.35 and ∼0.45 nm, backbone RMSD ∼0.48, ∼0.41 nm, atom contacts ∼4.2-5, ∼2-6, and H-bonds ∼2-5, ∼1-2, respectively. The BlCBM5 and TrCBM complexes showed the lowest binding energies, with MM-GBSA values of -36.66 ± 0.12 and -21.48 ± 0.11 kcal/mol, and QM/MM-GBSA values of -37.36 ± 0.13 and -21.70 ± 0.11 kcal/mol, respectively. Residue-level analysis identified key contributors (M133, W157, and F62) in both models. BlCBM5 and TrCBM complexes were the top candidates for enhancing PCL plastic degradation. The findings of this study were based on predictive insights, and experimental validation is required in the future.}, }
@article {pmid41604101, year = {2026}, author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R}, title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {47}, pmid = {41604101}, issn = {1678-4405}, support = {952583//H2020 European Research Council/ ; }, abstract = {UNLABELLED: High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-025-01866-9.}, }
@article {pmid41604102, year = {2026}, author = {Rocha, LBA and Gonçalves, VN and de Oliveira, FS and Corrêa, GR and Senra, EO and Duarte, EB and Lopes, FAC and Silva, MC and Convey, P and Câmara, PEAS and Rosa, LH}, title = {Endolithic fungal diversity is present in the unique phosphatized rocks of an environmentally extreme equatorial archipelago revealed by DNA amplicon metagenomics.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {46}, pmid = {41604102}, issn = {1678-4405}, abstract = {We evaluated endolithic fungal diversity associated with rocks sampled at the polyextreme Brazilian São Pedro and São Paulo archipelago using a DNA amplicon metagenomics approach. We detected 808,547 fungal DNA reads grouped into 92 amplicon sequence variants (ASVs). The rocks sampled were geologically characterized as mylonitized peridotites, serpentinized peridotites, and carbonate-matrix sedimentary breccias. Ascomycota was the dominant phylum, followed by Basidiomycota, Mucoromycota, Mortierellomycota and Chytridiomycota. Hortaea werneckii, Cladosporium sp., Simplicillium sp., Blastobotrys serpentis, Penicillium sp., P. simplicissimum, Malassezia restricta, Ascomycota sp., Verrucariaceae sp., and Fungal sp. were the dominant assigned taxa. The endolithic assemblages displayed moderate to low diversity indices. Among the fungal community, only the dominant Fungal sp. occurred in all samples. The data obtained in our environmental DNA (eDNA) amplicon metagenomics approach suggest that the rocks of the isolated equatorial São Pedro and São Paulo archipelago host a complex fungal diversity, including taxa regarded to be cosmopolitan, extremophilic hypersaline and xerophilic, plant pathogens, and human/animal opportunistic pathogens. As eDNA studies do not confirm the presence of viable organisms or propagules, further research using culturing approaches is now required to develop strategies to recover these fungi for physiological, biogeochemical, genetic and potential biotechnological studies.}, }
@article {pmid41604220, year = {2026}, author = {Yao, ML and Lin, P and Hua, K and Zhang, W}, title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuag005}, pmid = {41604220}, issn = {1476-5535}, abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have identified hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs, and quantified their metagenomic abundance and transcriptional activity. We found that aryl polyene, ribosomally synthesized and post-translationally modified peptide (RiPP), and nonribosomal peptide (NRP) encoding BGCs were the most prominent BGCs identified across the three metagenomic datasets. We grouped the identified BGCs into homology-based gene cluster families (GCFs) and found that specific GCFs were consistently associated with either health or caries across diverse taxa, suggesting that some specialized metabolites may perform conserved ecological functions. Conversely, other BGCs showed more restricted taxonomic distributions and were linked to disease-associated taxa, such as Propionibacterium acidifaciens, suggesting niche-specific biosynthetic capacities within the oral environment. Applying elastic-net regression to the metatranscriptomic dataset further identified a subset of 51 BGCs out > 3 000 that distinguished healthy from caries samples, reinforcing the discriminatory power of BGC expression patterns. Together, these results demonstrate that BGCs provide functional resolution beyond taxonomic profiling and that BGC expression, rather than genomic presence alone, differentiates oral microbial community states. This underscores the relevance of specialized metabolism to oral health and supports the use of BGC-centric analyses to interrogate microbial interactions underlying community stability and disease-associated shifts.}, }
@article {pmid41604225, year = {2026}, author = {Bilhalva, LC and Yacoub, MN and Dos Santos, AP and Manley, SR and Guasch, PM and Krumbeck, JA and Brinker, EJ and Martinez-Romero, G and Conrado, FO and Knoll, JS and Sharkey, LC}, title = {First report of Castellaniella spp. infection in dogs and the genomic evidence of a novel species.}, journal = {Journal of applied microbiology}, volume = {137}, number = {2}, pages = {}, doi = {10.1093/jambio/lxag033}, pmid = {41604225}, issn = {1365-2672}, mesh = {Animals ; Dogs ; *Dog Diseases/microbiology/pathology/diagnosis ; *Gram-Negative Bacterial Infections/veterinary/microbiology/pathology/diagnosis ; Phylogeny ; Male ; Pleural Effusion/microbiology/veterinary ; High-Throughput Nucleotide Sequencing ; Female ; Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Alcaligenaceae/genetics/isolation & purification/classification ; Metagenomics ; }, abstract = {AIMS: This study reports the first documented cases of Castellaniella spp. infection in dogs, describing associated clinical and pathological findings and characterizing a novel species within this genus.
METHODS AND RESULTS: Pleural effusions from two dogs presenting with acute respiratory distress and systemic illness were evaluated via cytology, bacterial culture, and next-generation sequencing. Both cases exhibited neutrophilic-macrophagic inflammation with intracellular Gram-negative rods, primarily within macrophages. Bacterial culture failed to identify the organisms. Metagenomic analysis identified organisms belonging to the genus Castellaniella in both cases. In case 2, an unclassified Castellaniella species was detected, suggesting the presence of a previously undescribed species within the genus. Both dogs died shortly after presentation, and necropsy and histopathology findings were described.
CONCLUSIONS: Castellaniella spp. warrant consideration as potential emerging pathogens in domestic animals, challenging their previous classification as non-pathogenic environmental bacteria. The identification of a novel species also underscores the genus's genetic diversity and adaptive potential.}, }
@article {pmid41604303, year = {2026}, author = {Guo, Z and Cheng, H and Shi, H and Liu, D and Zhai, X and Li, X and Zhang, X and Liu, L and Zhang, XH and Zhang, Y}, title = {Potential for microbial methanethiol-dependent dimethylsulfide production in different marine sediments.}, journal = {Cell reports}, volume = {45}, number = {2}, pages = {116891}, doi = {10.1016/j.celrep.2025.116891}, pmid = {41604303}, issn = {2211-1247}, mesh = {*Geologic Sediments/microbiology ; *Sulfides/metabolism ; Hydrogen Sulfide/metabolism ; *Sulfhydryl Compounds/metabolism ; *Bacteria/metabolism/genetics ; Phylogeny ; }, abstract = {Dimethyl sulfide (DMS) plays a pivotal role in sulfur cycling and climate regulation. This study investigates microbial DMS production via the methylation of hydrogen sulfide (H2S) and methanethiol (MeSH) in nearshore, pelagic deep-sea, and cold-seep sediments using culture-dependent and -independent methods. DMS production is detected in all sediments with exogenous MeSH addition. High mdd abundance is found in pelagic deep-sea sediments (24.55%-26.73%) from the Kuroshio-Oyashio Extension region, as well as in the nearshore sediments (25.78%). Metagenomic analyses reveal previously unrecognized Mdd-encoding taxa, such as Polyangia, and eight Bacteroidota and Bacillota isolates may possess unknown Mdd enzymes. Importantly, a widespread alternative pathway that converts H2S to MeSH is identified, representing a significant source of MeSH. These findings reveal a prevalent and diverse microbial pathway for DMS production in marine sediments, underscoring the need for further investigation to discover Mdd[+] microbial contributors.}, }
@article {pmid41604988, year = {2026}, author = {Zhou, Y and Wu, Y and Shu, B and Xu, F}, title = {Resourceful utilization of Bougainvillea horticultural waste for synchronous degradation and power generation in MFCs.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {170}, number = {}, pages = {109237}, doi = {10.1016/j.bioelechem.2026.109237}, pmid = {41604988}, issn = {1878-562X}, mesh = {*Bioelectric Energy Sources/microbiology ; Biodegradation, Environmental ; Lignin/metabolism ; Polysaccharides/metabolism ; }, abstract = {The disposal of horticultural waste derived from Bougainvillea species poses substantial environmental challenges in coastal cities of southeastern China. This study innovatively employs Bougainvillea horticultural waste (BHW) as the main substrate in microbial fuel cells (MFCs) for simultaneous organic degradation and bioenergy recovery, with an acid-pretreated BHW-fed MFC (MFC-ABG) included for comparison. Results indicated that the untreated BHW-fed MFC (MFC-BG) achieved a peak voltage of 0.401 V and sustained operation for 19 days, coupled with 78.7% polysaccharide removal. Metagenomics showed that MFC-BG significantly enriched electroactive Geobacter (29.39%) and hydrolytic Proteiniphilum (2.69%), driving lignocellulose decomposition through oxidative auxiliary enzymes (AA4/AA6). Comparatively, MFC-ABG achieved an enhanced voltage of 0.706 V and a high polysaccharide reduction efficiency of 85.6%, benefits attributable to acid-induced substrate solubilization and glycoside hydrolase (GH)-dominated enzymatic shifts. Although microbial community diversity declined in both MFC systems, MFC-BG retained a higher species richness (MFC-BG: Sobs = 28,209; MFC-ABG: Sobs = 25,746), reflecting the adaptive resilience of the associated microbial community. This study confirms BHW as a viable feedstock for MFCs and clarifies the microbial mechanisms underlying the synergistic coupling of substrate degradation and electron transfer.}, }
@article {pmid41605063, year = {2026}, author = {Tang, B and Lin, L and Li, W and Li, Z and Zhao, J and Zhao, W and Zhao, C}, title = {Successful treatment with oseltamivir of an atypical influenza B-associated encephalitis identified by mNGS: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {1}, pages = {117286}, doi = {10.1016/j.diagmicrobio.2026.117286}, pmid = {41605063}, issn = {1879-0070}, mesh = {Humans ; *Oseltamivir/therapeutic use/administration & dosage ; Female ; Middle Aged ; *Influenza, Human/drug therapy/virology/diagnosis/complications ; *Antiviral Agents/therapeutic use/administration & dosage ; *Influenza B virus/genetics/isolation & purification ; *Encephalitis, Viral/drug therapy/diagnosis/virology ; High-Throughput Nucleotide Sequencing ; Treatment Outcome ; Metagenomics ; }, abstract = {This case report describes a 51-year-old female with influenza B-associated encephalitis (IBAE) presenting primarily with insomnia, headache, and dizziness, but without fever, following an initial cough. Routine microbiological tests (cultures, staining, multiplex PCR) on cerebrospinal fluid (CSF) and initial brain/chest CT scans were negative. Diagnosis was confirmed by metagenomic next-generation sequencing (mNGS) detecting influenza B virus in the CSF. Treatment involved oral oseltamivir and fluid replacement for headache/intracranial pressure. Symptoms significantly improved after eight days of oseltamivir, leading to discharge. This case highlights sleep disturbances and headache as primary IBAE symptoms without fever. Routine CSF testing often fails to detect influenza B; early mNGS enables definitive diagnosis, allowing precise, timely treatment (like oseltamivir) and avoiding ineffective empiric therapy or disease worsening.}, }
@article {pmid41605275, year = {2026}, author = {Wu, L and Li, H and Gu, Y and Zhou, Y and Shen, Z and Zuo, J}, title = {In situ ammonia recovery relieves ammonia stress in anaerobic digestion and multi-omics elucidate community-dominant and functionally dominant genera of methanogens.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134098}, doi = {10.1016/j.biortech.2026.134098}, pmid = {41605275}, issn = {1873-2976}, mesh = {*Ammonia/metabolism/isolation & purification ; Anaerobiosis ; *Methane/metabolism/biosynthesis ; Bioreactors/microbiology ; Biofuels ; Multiomics ; }, abstract = {The accumulation of endogenous ammonia nitrogen in anaerobic digestion (AD) is widely recognized as a critical factor inhibiting methanogenesis. Gas-permeable membranes (GPM), leveraging their selective permeation properties, provide a large gas-liquid mass transfer interface and demonstrate significant potential in preventing ammonia accumulation. In this study, integrating GPM into AD achieved in situ ammonia removal and recovery, fundamentally alleviating ammonia inhibition and enabling ammonia valorization. GPM reactors (with H2SO4 absorption/vacuum distillation) maintained ammonia at 1300-1500 mg/L (vs. >5000 mg/L in controls) and sustained biogas yield 0.67-0.72 L/g VS at 7 g VS/(L·d) OLR (controls inhibited at 5 g VS/(L·d)). Multi-omics revealed microbial mechanisms: community-dominant Methanobacterium contributed little to methanogenesis, while functionally dominant Methanothrix retained robust activity via dual methanogenic pathways and upregulated biosynthesis-related proteins. This study validates GPM-AD efficacy and provides theoretical support for optimization.}, }
@article {pmid41605932, year = {2026}, author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W}, title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41605932}, issn = {2055-5008}, support = {N42A660907//National Research Council of Thailand/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Thailand ; *Prebiotics/administration & dosage ; Adult ; *Diet ; Fatty Acids, Volatile/metabolism ; Male ; Female ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics ; Models, Biological ; Young Adult ; Middle Aged ; Systems Biology ; Southeast Asian People ; }, abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.}, }
@article {pmid41606121, year = {2026}, author = {Duttagupta, S and Messaoudene, M and Hunter, S and Desilets, A and Jamal, R and Mihalcioiu, C and Belkaid, W and Marcoux, N and Fidelle, M and Suissa, D and Ponce, M and Geiger, M and Malo, J and Piccinno, G and Punčochář, M and Filin, A and Heidrich, V and Rusu, D and Mbaye, B and Durand, S and Ben Aissa, I and Puller, V and de Lahondès, R and Blais, N and Tehfe, M and Owen, S and Bélanger, K and Parvathy, SN and Shieh, B and Raphael, J and Lenehan, J and Breadner, D and Rothenstein, J and Rozza, N and Maillou, J and Nili, S and Prifti, DK and Pinto, F and Armanini, F and Kim-Schulze, S and Marron, TU and Kroemer, G and Derosa, L and Zitvogel, L and Silverman, M and Segata, N and Maleki Vareki, S and Routy, B and Elkrief, A}, title = {Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41606121}, issn = {1546-170X}, abstract = {Immune checkpoint inhibitors (ICI) have improved outcomes for patients with non-small cell lung cancer (NSCLC) and melanoma, yet over half of patients exhibit primary resistance. Fecal microbiota transplantation (FMT) may overcome resistance to anti-programmed cell death protein 1 (PD-1) therapy. The clinical activity and safety of FMT plus anti-PD-1 in NSCLC or anti-PD-1 plus anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) therapy in melanoma have not been evaluated. Here we report results from FMT-LUMINate, a multicenter, open-label, phase 2 trial assessing healthy donor FMT plus anti-PD-1 in NSCLC (n = 20) or anti-PD-1 plus anti-CTLA-4 (dual ICI) in melanoma (n = 20), in the first-line setting. Eligible patients received a single FMT via oral capsules prior to ICI initiation. The primary endpoint was objective response rate (ORR) in NSCLC. Secondary endpoints included ORR in melanoma, safety and donor-host microbiome similarity. In NSCLC, the ORR was 80% (16/20), meeting the study primary endpoint. In melanoma, the ORR was 75% (15/20). FMT was deemed safe in both cohorts by an independent data and safety monitoring committee, with no grade 3 or higher adverse events (AEs) in NSCLC and 13 (65%) patients experiencing grade 3 or higher AEs in melanoma. Shotgun metagenomic sequencing revealed that responders developed a distinct post-FMT gut microbiome composition, independent of acquired donor-recipient similarity or strain-level engraftment. Responders exhibited significantly greater loss of baseline bacterial species compared to non-responders, with frequent depletion of Enterocloster citroniae, E. lavalensis and Clostridium innocuum. This finding was reproduced across three published FMT oncology trials. We recolonized antibiotic-treated, tumor-bearing mice with post-FMT stool from two responder patients, and reintroduction of the specific bacterial species that were lost after FMT abrogated the antitumor effect of ICI. Taken together, these findings confirm the clinical activity of FMT in combination with ICI and suggest that the elimination of deleterious taxa is required for FMT-mediated therapeutic benefit. ClinicalTrials.gov identifier: NCT04951583 .}, }
@article {pmid41606218, year = {2026}, author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N}, title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {2}, pages = {65}, pmid = {41606218}, issn = {1573-0972}, mesh = {Humans ; *Multigene Family ; *Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Biosynthetic Pathways/genetics ; Metagenome ; }, abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.}, }
@article {pmid41606550, year = {2026}, author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X}, title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41606550}, issn = {1471-2466}, support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; }, abstract = {AIM OF THE STUDY: Invasive aspergillosis is a life-threatening complication in mechanically ventilated patients with pneumonia, predominantly caused by Aspergillus fumigatus. However, its independent mortality risk and early-warning strategies in critically ill populations remain unclear.
METHODS: In this multicenter retrospective cohort study, we enrolled 1567 mechanically ventilated patients with severe pneumonia who underwent bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) across 12 tertiary hospitals in China (January 2019–March 2023). Propensity score matching (1:1) balanced confounders, and Cox regression quantified the independent mortality risk of A. fumigatus infection.
RESULTS: The A. fumigatus detection rate was 10.27% (161/1567). Post-matching, 28-day mortality was significantly higher in A. fumigatus-positive versus negative cohorts (66% vs 47%, p = 0.001). Multivariable analysis confirmed A. fumigatus as an independent mortality risk factor (HR = 1.79, 95%CI 1.49–2.17, p < 0.001), with significant associations to underlying renal disease (19% vs 12%, p = 0.005), connective tissue disease (7% vs 4%, p = 0.026), and multi-organ dysfunction (ep < 0.05). Microbial community analysis revealed co-colonization synergies with Enterococcus faecium, Enterococcus faecalis, Candida albicans, HSV-1, and EBV.
CONCLUSIONS: A. fumigatus infection independently increases 28-day mortality risk in mechanically ventilated patients. Early intensified screening and intervention are warranted for individuals with ≥ 3 organ dysfunctions, underlying renal/connective tissue diseases, or respiratory co-colonization by synergistic microbes.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-026-04131-3.}, }
@article {pmid41606854, year = {2025}, author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J}, title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 1}, pages = {117255}, doi = {10.1016/j.foodres.2025.117255}, pmid = {41606854}, issn = {1873-7145}, mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; }, abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.}, }
@article {pmid41606855, year = {2025}, author = {Yang, J and He, Y and Huang, J and Li, M and Wu, X and Pei, X and Yang, X}, title = {Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 1}, pages = {117259}, doi = {10.1016/j.foodres.2025.117259}, pmid = {41606855}, issn = {1873-7145}, mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *One Health ; *Drug Resistance, Bacterial/genetics ; *Pork Meat/microbiology ; Food Microbiology ; Abattoirs ; Metagenome ; Microbiota/genetics ; Metagenomics ; Bacteria/genetics ; }, abstract = {The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.}, }
@article {pmid41607747, year = {2026}, author = {Luo, L and Huang, G and Yang, H and Chi, H}, title = {Revisiting multi-region 16S sequencing in gastric cancer.}, journal = {World journal of gastrointestinal oncology}, volume = {18}, number = {1}, pages = {114708}, pmid = {41607747}, issn = {1948-5204}, abstract = {Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome, demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches. While the study represents a valuable methodological step forward, it remains limited by single-center design, lack of quantitative calibration, and insufficient control for contamination and inter-laboratory variability. This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized, consensus-driven workflows to ensure reproducibility and clinical reliability. The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration, particularly for recurrence prediction, treatment-response monitoring, and perioperative complication risk assessment. By addressing these methodological, economic, and ethical challenges, the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.}, }
@article {pmid41607902, year = {2025}, author = {Song, Z and Huang, Y and Gu, Y and Che, L and Zhang, K and Liu, Q and Guan, Q and Sui, L}, title = {Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1756127}, pmid = {41607902}, issn = {2296-2565}, mesh = {Humans ; China/epidemiology ; *Respiratory Tract Infections/virology/epidemiology ; Adult ; Phylogeny ; Child ; Female ; Male ; Child, Preschool ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Adolescent ; Infant ; Respiratory Syncytial Virus, Human/genetics ; Influenza B virus/genetics ; }, abstract = {OBJECTIVE: Respiratory viral infections impose a significant global health burden, necessitating continuous regional surveillance to understand pathogen circulation. This study aimed to characterize the spectrum of respiratory pathogens and identify potential causative agents in Jilin Province, northeast China, during 2023.
METHODS: Using metagenomic next-generation sequencing, we analyzed 250 respiratory samples and 195 blood samples, sequencing of all samples yielded 399,256 viral reads. Bioinformatic and phylogenetic analyses were conducted to identify and characterize the detected viruses.
RESULTS: Severe acute respiratory syndrome coronavirus 2 (lineage BA.2), human respiratory syncytial virus B (lineage GB5.0.5a), and influenza B virus (lineage V1A.3a.2) were identified as common respiratory pathogens across both pediatric and adult populations. Influenza A virus (lineage 3C.2a1b.2a.2a.3a.1), rhinovirus (subtype C), human respiratory syncytial virus A (lineage GA2.3.5), human respiratory syncytial virus B (lineage GB5.0.5a), and human metapneumovirus (lineage A2c) were detected in pediatric or adult respiratory samples. Human Pegivirus (genotype 3) was detected exclusively in adult blood samples. Strikingly, a novel picobirnavirus was identified in adult sputum samples, sequence and structural analyses consistently indicate that this picobirnavirus is closely related to human-associated strains, exhibiting ≥70% amino acid identity and an RdRP structure nearly identical to that of picobirnaviruses previously identified in human upper respiratory swabs from Cambodia. This finding was validated by nested RT-PCR, representing the first documented detection of picobirnavirus in respiratory specimens from China. As most identified strains were first reported in northeast China, we also conducted comprehensive phylogenetic analyses of representative viruses, revealing high sequence similarity with epidemic strains from other regions of China.
CONCLUSION: These findings delineate the respiratory viruses of northeast China, providing data for region-specific surveillance to mitigate future public health risks.}, }
@article {pmid41607944, year = {2025}, author = {Gao, YQ and Hou, QY and Hou, XW and Wei, YJ and Shang, KM and Ma, H and Geng, HL and Liu, R and Yang, LH and Elsheikha, HM and Ni, HB and Huang, YF}, title = {Metagenomics-based characterization of fecal microbiome and resistome of laying hens during the production cycle.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1740567}, pmid = {41607944}, issn = {2297-1769}, abstract = {The extensive use of antimicrobials in livestock has accelerated the emergence of antimicrobial resistance (AMR), raising serious global concerns. Poultry feces are recognized as important reservoirs of antibiotic resistance genes (ARGs) and their associated mobile genetic elements (MGEs); however, the microbial community characteristics and ARG profiles of laying hens across different laying stages remain poorly understood. In this study, 40 fecal samples were collected from laying hens at five sampling points, including the early laying stage (HE), three peak laying stages (HPI, HPII, and HPIII), and the late laying stage (HL), with eight randomly selected samples per stage. Shotgun metagenomic sequencing was conducted to characterize the taxonomic structure and functional profiles of the intestinal microbiota and to systematically analyze the diversity and distribution patterns of ARGs. The results showed that most ARGs were harbored by bacteria belonging to the phyla Pseudomonadota and Bacillota, with Escherichia coli serving as the primary carrier of antibiotic resistance genes. Moreover, significant correlations were observed between the co-abundance and co-occurrence of ARGs and MGEs, suggesting that MGEs play a key role in facilitating ARG dissemination. Overall, these findings provide novel insights into the prevalence of ARGs in laying hens across different laying stages and may inform strategies to mitigate the spread of antimicrobial resistance in poultry production systems.}, }
@article {pmid41608298, year = {2026}, author = {Aldoori, J and Mitra, S and Davie, A and Toogood, GJ and Edwards, C and Hull, MA}, title = {The effect of omega-3 polyunsaturated fatty acids on short-chain fatty acid production and the gut microbiome in an in vitro colonic fermentation model.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e1}, pmid = {41608298}, issn = {2632-2897}, abstract = {Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1-50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.}, }
@article {pmid41609167, year = {2026}, author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH}, title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.}, journal = {British journal of hospital medicine (London, England : 2005)}, volume = {87}, number = {1}, pages = {50163}, doi = {10.31083/BJHM50163}, pmid = {41609167}, issn = {1759-7390}, support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy ; *Microbiota ; Dysbiosis/microbiology ; *Lung/microbiology ; Disease Progression ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.}, }
@article {pmid41609355, year = {2026}, author = {Li, Y and Li, Q and Quan, K and Xie, Y and Yang, N and Ma, T and Zheng, L and Zhou, W and Li, Y and Jin, H and Sun, Z and Chen, Y and Kwok, L-Y and Lu, N and Zhu, W and Liu, W and Zhang, H}, title = {Adjunctive probiotic therapy sustains symptom relief in gastroesophageal reflux disease through gut microbiome-metabolome remodeling.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0156825}, pmid = {41609355}, issn = {2379-5077}, support = {No.2022LJRC0003//the Inner Mongolia Autonomous Region Science and Technology Leading Talent Team Project/ ; No. U22A20540//National Natural Science Foundation of China/ ; No. 2022YFD2100700//National Key Research and Development Program of China/ ; CARS-36//the Earmarked Fund for China Agriculture Research System/ ; BX20250337//the China National Postdoctoral Program for Innovative Talents/ ; }, mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Gastroesophageal Reflux/microbiology/drug therapy/metabolism/therapy ; Double-Blind Method ; Adult ; *Metabolome/drug effects ; Treatment Outcome ; Rabeprazole/therapeutic use ; Proton Pump Inhibitors/therapeutic use ; Aged ; }, abstract = {Proton pump inhibitors (PPIs) are standard therapy for gastroesophageal reflux disease (GERD), but long-term use causes dysbiosis, gastrointestinal side effects, and symptom relapse after discontinuation. Probiotics may offer adjunctive benefits by modulating the gut ecosystem. The study aimed to evaluate the efficacy of a multi-strain probiotic (Lihuo) with rabeprazole in GERD and its impact on gut microbiota and metabolome. A randomized, double-blind, placebo-controlled trial was conducted in 120 GERD patients assigned to receive rabeprazole with either Lihuo (n = 64) or placebo (n = 56) for 8 weeks, followed by 4 weeks of probiotic or placebo alone. The primary outcome was change in the Reflux Disease Questionnaire (RDQ) score. Secondary outcomes included Gastrointestinal Symptom Rating Scale, endoscopic healing, and multi-omics profiling (shotgun metagenomics, phageome, and untargeted/targeted metabolomics). Compared with the placebo group, the probiotic group exhibited a pronounced 36.51% reduction in RDQ scores after 12 weeks of intervention (P = 0.017), alongside a higher numerical endoscopic healing rate (36.84% vs 12.50%; P = 0.365). Metagenomics revealed enrichment of Bifidobacterium animalis, Lactiplantibacillus plantarum, and Clostridium sp900540255, with reductions in Bacteroides uniformis and Clostridium Q fessum. Metabolomics showed increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids levels, with interesting microbe-metabolite correlations such as Bifidobacterium animalis-γ-aminobutyric acid and Bacteroides fragilis-succinate (r ≥ 0.30, P < 0.01). Our findings support that adjunctive probiotic therapy sustains post-PPI symptom relief, associated with targeted modulation of gut microbiota and bioactive metabolites.IMPORTANCELong-term proton pump inhibitor use in gastroesophageal reflux disease (GERD) may disrupt gut microbiota and cause symptom relapse after discontinuation. We found that adjunctive probiotic therapy sustained reflux reduction post-proton pump inhibitor. Probiotic use enriched beneficial taxa (Bifidobacterium and Lactiplantibacillus plantarum) and increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids. Strong correlations linked microbial shifts to metabolic and clinical improvements. This study demonstrates that adjunctive probiotic therapy enhances symptom control and supports microbial-metabolic homeostasis in GERD.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2000038409.}, }
@article {pmid41609371, year = {2026}, author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S}, title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0191025}, pmid = {41609371}, issn = {2165-0497}, support = {HBC.2023.0154//Agentschap Innoveren en Ondernemen/ ; }, mesh = {Animals ; Swine ; *Virulence Factors/genetics ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; *Swine Diseases/microbiology/virology ; *Coinfection/microbiology/veterinary/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Porcine respiratory and reproductive syndrome virus/isolation & purification/genetics ; Influenza A virus/isolation & purification/genetics ; *Bacterial Infections/veterinary/microbiology ; Respiratory System/microbiology/virology ; Metagenomics ; }, abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.}, }
@article {pmid41609375, year = {2026}, author = {Yepes-García, J and Falquet, L}, title = {2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0084425}, pmid = {41609375}, issn = {2379-5077}, support = {//Federal Commission for Scholarships for Foreign Students/ ; }, mesh = {*Metagenomics/methods ; *Software ; *Metagenome/genetics ; *Whole Genome Sequencing/methods ; *Computational Biology/methods ; Workflow ; }, abstract = {Whole-genome sequencing has boosted our ability to explore microbial diversity by enabling the recovery of metagenome-assembled genomes (MAGs) directly from environmental DNA. As a result, the vast availability of sequencing data has prompted the development of numerous bioinformatics pipelines for MAG reconstruction, along with challenges to identify the most suitable pipeline to perform the analysis according to the user needs. This report briefly discusses the computational requirements of these pipelines; presents the variety of interfaces, workflow managers, and package managers they feature; and describes the typical modular structure. Also, it provides a compacted technical overview of 41 publicly available pipelines or platforms to build MAGs starting from short and/or long sequences. Moreover, recognizing the overwhelming number of factors to consider when selecting an appropriate pipeline, we introduce an interactive decision-support web application, 2Pipe, that helps users to identify a suitable workflow based on their input data characteristics, desired outcomes, and computational constraints. The tool presents a question-driven interface to customize the recommendation, a pipeline gallery to offer a summarized description, and a pipeline comparison based on key factors used for the questionnaire. Beyond this and foreseeing the release of novel pipelines in the near future, we include a quick form and detailed instructions for developers to append their workflow in the application. Altogether, this review and the application equip the researchers with a general outlook of the growing metagenomics pipeline landscape and guide the users toward deciding the workflow that best fits their expectations and infrastructure.}, }
@article {pmid41609629, year = {2026}, author = {Huang, R and Wang, Y and Liu, D and Wang, S and Lv, H and Yan, Z}, title = {Retraction for Huang et al., "Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0238124}, pmid = {41609629}, issn = {2165-0497}, }
@article {pmid41609929, year = {2026}, author = {Mo, Y and Ahlgren, N and Fuhrman, JA and Sun, F and Hou, S}, title = {A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets.}, journal = {Current protocols}, volume = {6}, number = {2}, pages = {e70310}, doi = {10.1002/cpz1.70310}, pmid = {41609929}, issn = {2691-1299}, support = {549943//Simons Foundation/ ; 42476109//National Natural Science Foundation of China/ ; 42276163//National Natural Science Foundation of China/ ; EF-2125142//National Science Foundation/ ; 3779//Gordon and Betty Moore Foundation/ ; }, mesh = {*Metagenomics/methods ; *Software ; *Viruses/genetics ; *Deep Learning ; Genome, Viral ; Metagenome ; }, abstract = {Identifying viral sequences from metagenomic datasets is critical for investigating their origins, evolutionary patterns, and ecological functions. Previously, we developed a novel deep learning software, DeepVirFinder, to predict viral sequences from shotgun metagenomic assemblies. This method employs a twin convolutional neural network model to extract features from known viral and prokaryotic host genomic sequences for binary classification of input query sequences. With the rapid accumulation of environmental metagenomic data, this approach has accelerated the discovery of novel viruses from diverse environments through an alignment-free and reference-free deep learning strategy. To facilitate the rapid adoption of this software for beginning users, here we have further improved DeepVirFinder by optimizing its runtime performance, while maintaining the essential user interface of the original version. This comprehensive guide provides basic workflows for the most common use cases of DeepVirFinder. Additionally, to assist users in downstream analyses, supplementary scripts were provided in the software for extracting viral sequences and inspecting the results, thereby helping researchers more effectively mine viral information from metagenomic datasets. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Predicting viral sequences in metagenomic assemblies Basic Protocol 2: An integrated pipeline for viral sequence analysis: Prediction, extraction, and visualization Basic Protocol 3: Retraining the DeepVirFinder model using a customized dataset.}, }
@article {pmid41610081, year = {2026}, author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM}, title = {Correction: Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0342019}, pmid = {41610081}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323382.].}, }
@article {pmid41610462, year = {2026}, author = {Nagy, EZ and Szeredi, L and Földi, D and Belecz, N and Kovács, ÁB and Sulyok, KM and Grózner, D and Wehmann, E and Bányai, K and Marton, S and Tenk, M and Kreizinger, Z and Gyuranecz, M}, title = {Development and efficacy test of a live, attenuated Mycoplasma hyorhinis vaccine candidate strain.}, journal = {Vaccine}, volume = {75}, number = {}, pages = {128278}, doi = {10.1016/j.vaccine.2026.128278}, pmid = {41610462}, issn = {1873-2518}, mesh = {Animals ; Vaccines, Attenuated/immunology/administration & dosage ; *Bacterial Vaccines/immunology/administration & dosage ; Swine ; *Mycoplasma hyorhinis/immunology ; Antibodies, Bacterial/blood ; *Mycoplasma Infections/prevention & control/veterinary/immunology ; *Swine Diseases/prevention & control/immunology ; Vaccination ; Vaccine Efficacy ; }, abstract = {BACKGROUND: Mycoplasma (M.) hyorhinis causes substantial economic losses in swine. Currently, prevention and treatment rely on minimizing risk factors and administering antibiotics, as no vaccines are commercially available in Europe. However, antibiotics often cannot fully eliminate the bacteria. The development of an effective vaccine could lead to a potentially long-term control method.
MATERIALS AND METHODS: A temperature-sensitive M. hyorhinis strain was developed using 1-methyl-3-nitro-1-nitrosoguanidine (NTG) mutagenesis. The immunogenicity and efficacy of this vaccine candidate clone were evaluated in combination with an adjuvant. Three-week-old piglets were immunized with the candidate vaccine strain, and the vaccination site was monitored daily. At six weeks of age, the pigs were challenged intravenously on two subsequent days. Daily clinical examinations were conducted, with blood and nasal swabs collected weekly throughout the study for M. hyorhinis enzyme-linked immunosorbent assay (ELISA), real-time PCR analysis, and isolation. Three weeks post-challenge, the animals were euthanized for gross and histopathological examinations. Body temperature was recorded daily, and body weight was measured upon arrival, and then at six and nine weeks of age.
RESULTS: Vaccination significantly reduced clinical signs (p = 0.03), as well as gross pathological (p = 0.01) and histopathological (p = 0.005) lesions compared with the positive control group. The vaccinated group exhibited an earlier and higher increase in M. hyorhinis-specific IgG antibody levels post-challenge than the positive control group. However, the vaccine candidate did not mitigate the impact of M. hyorhinis infection on the weight gain. After the challenge (days 21-42), both the vaccinated (p = 0.001) and the positive control (p = 0.003) groups exhibited reduced weight gain compared with the negative control group.
DISCUSSION: Overall, the attenuated M. hyorhinis strain, combined with the adjuvant, provided protection against M. hyorhinis infection. These results form a basis for the development of a novel vaccine candidate that offers effective prevention.}, }
@article {pmid41610548, year = {2026}, author = {Zafar, S and Alimohammadi, M and Hatami Moghadam, P and Hadei, M}, title = {Investigating the types of bacterial species with antimicrobial resistance genes in Iran's wastewaters: a systematic review.}, journal = {The Science of the total environment}, volume = {1016}, number = {}, pages = {181385}, doi = {10.1016/j.scitotenv.2026.181385}, pmid = {41610548}, issn = {1879-1026}, mesh = {*Wastewater/microbiology ; Iran ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; }, abstract = {Antimicrobial resistance (AMR) is a major global health threat, with wastewater systems performing as critical reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and resistance genes (ARGs). Despite rising AMR rates in Iran, a comprehensive understanding of resistance patterns in wastewater remains limited. This systematic review aimed to investigate the prevalence, bacterial diversity, and resistance gene profiles in hospital, municipal, and industrial wastewater across Iran. A systematic search was conducted in Scopus, PubMed, Web of Science, and Iranian databases for studies published between 1990 and September 2024. Data extraction followed PRISMA guidelines, and study quality was assessed using the JBI checklist. A total of 43 studies from 13 provinces met the inclusion criteria, with nearly half originating from Tehran (21/43, 48.8%), indicating uneven national coverage. Hospital wastewater (18 studies, 41.9%) harbored the highest burden of clinically significant AMR, including MRSA (22%), VRE (17%), and ESBL-producing E. coli (17%). Municipal wastewater (31 studies, 72.1%) frequently contained VRE Enterococcus faecium (32%) and Enterococcus faecalis (23%), ESBL-producing E. coli (19%), and MRSA (10%). Industrial wastewater (10 studies, 23.3%), primarily from slaughterhouses, exhibited high ESBL rates in E. coli (80%), with some studies reporting up to 93% ESBL production among isolates. Across studies, the most recurrent ARGs were blaCTX (16.3%), vanA (20.9%), mecA (9.3%), tetracycline genes, and intI1. Detection methods were predominantly culture- and PCR-based, with limited use of qPCR, molecular typing, or metagenomics. The most frequently detected resistance genes included blaCTX-M, mecA, vanA, tetA, and intI1. Most studies used culture and PCR-based detection; molecular typing and metagenomic approaches were rarely applied. The persistent detection of MDR pathogens and high-priority ARGs highlights significant gaps in AMR surveillance. Strengthening national wastewater monitoring through standardized protocols, broader geographic coverage, and integration of advanced molecular tools is essential to support effective One Health based public-health strategies.}, }
@article {pmid41610602, year = {2026}, author = {Phusathian, B and Pongmanee, K and Theapparat, Y and Saikhwan, N and Trairatapiwan, T and Chaosap, C and Seemacharoensri, A and Tactacan, GB and Wong, LY and Ruangpanit, Y}, title = {Bacterial xylanase supplementation improves nutrient utilization, gut integrity, and microbial metabolism in broilers fed energy-reduced diets.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106515}, pmid = {41610602}, issn = {1525-3171}, abstract = {This study evaluated the effects of bacterial xylanase supplementation on growth performance, nutrient digestibility, intestinal integrity, and microbial metabolic function in broilers fed energy-reduced diets. A total of 1,050 one-day-old male Ross 308 broiler chicks were randomly assigned to three dietary treatments, each comprising 14 replicates of 25 birds: a positive control (CON; standard corn-soybean meal diet), a negative control with reduced energy (NC; -85 kcal/kg), and an energy-reduced diet supplemented with bacterial xylanase (NCX; 100 g/ton Belfeed Xylanase™). During the starter phase, broilers fed the NC diet exhibited higher feed intake and FCR compared with those fed the CON and NCX diets (P < 0.05), with no significant difference between the CON and NCX diets. Apparent digestibility of dry matter, crude protein, and fat did not differ among dietary treatments (P > 0.05). However, broilers fed the NCX diet showed higher (P < 0.05) digestibility of crude fiber, NDF, and ADF than those fed the CON or NC diets. Apparent metabolizable energy was higher in broilers fed the CON and NCX diets compared with the NC diet. Furthermore, broilers receiving the CON and NCX diets exhibited significantly lower serum fluorescein isothiocyanate-dextran concentrations than those fed the NC diet, indicating improved intestinal barrier integrity. Bacterial xylanase supplementation increased microbial alpha diversity and altered beta diversity clustering, with enrichment of beneficial taxa such as Bifidobacteriaceae and Lactobacillaceae. Functional metagenomic prediction suggested greater representation of carbohydrate metabolism and energy production pathways in the NCX diet, whereas the NC diet was associated with enrichment of stress-related and xenobiotic degradation pathways. Overall, bacterial xylanase supplementation mitigated the adverse effects of dietary energy reduction by improving fiber utilization, maintaining gut integrity, and modulating the cecal microbiota toward a more favorable metabolic profile.}, }
@article {pmid41611023, year = {2026}, author = {Li, W and Li, J and Wu, Y and Chen, M and Fu, Y and Li, W and Liu, S and Wang, J and Chen, Y}, title = {Artificial regulation of aerobic and anaerobic layers interface enhanced efficient nitrogen removal by weaving insulating grid and conductive carbon fiber in membrane aerated biofilm reactor.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134074}, doi = {10.1016/j.biortech.2026.134074}, pmid = {41611023}, issn = {1873-2976}, mesh = {*Biofilms ; *Bioreactors/microbiology ; *Nitrogen/isolation & purification ; Aerobiosis ; *Carbon/chemistry ; Carbon Fiber ; Anaerobiosis ; *Membranes, Artificial ; RNA, Ribosomal, 16S/genetics ; Electrodes ; Electric Conductivity ; Water Purification/methods ; }, abstract = {Artificial regulation of aerobic and anaerobic biofilm thickness is crucial for enhancing nitrogen removal efficiency of the membrane aerated biofilm reactor (MABR). In this study, conductive aeration membrane modules were fabricated by physical weaving technology to couple MABR with microbial electrochemistry for efficient nitrogen removal. Insulating grids of different thickness and conductive carbon fibers were woven onto the aeration membrane to form aerobic and anaerobic layers. When the total biofilm thickness reached 254 μm (150 μm aerobic layer and 104 μm anaerobic layer), the TN removal efficiency (89.49 ± 2.89 %) was optimal. 16S rRNA gene sequencing and metagenomics analysis confirmed that the aerobic and anaerobic layers in the biofilm were completely separated, but there was a synergistic effect in nitrogen removal. The composite cathode structure provides a mechanism for efficient spatial coupling between the aerobic and anaerobic layers, establishing a basis for regulating biofilm stratification.}, }
@article {pmid41611051, year = {2026}, author = {Shi, J and Sun, C and Su, Y and Wu, Y and Zhan, M and Ji, C and Wang, R and Lv, B}, title = {Ecosystem-specific composition and drivers of plastisphere resistome in freshwater and marine environments.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123858}, doi = {10.1016/j.envres.2026.123858}, pmid = {41611051}, issn = {1096-0953}, mesh = {Fresh Water/microbiology ; *Seawater/microbiology ; *Microbiota ; *Ecosystem ; *Water Pollutants, Chemical ; *Microplastics ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; }, abstract = {Microplastics in aquatic environments facilitate the formation of specific plastisphere microbiomes and serve as potential hotspots for antibiotic resistance genes (ARGs) propagation. However, the systematic comparisons of ARG profiles on microplastics from different aquatic ecosystems remain limited, particularly the prevalent ARGs and their bacterial hosts. This study performed a comparative meta-analysis of existing metagenomic datasets to investigate the resistome between freshwater and seawater microplastics (FMP and SMP) and their driving factors. Our results revealed that the ARG profiles on both FMP and SMP were significantly distinct from their surrounding waterbody. Moreover, FMP exhibited a higher diversity and abundance of ARGs rather than SMP. Ten core ARGs were shared on FMP and SMP, while 23 core ARGs were exclusively detected on FMP. The bacterial community on microplastics exhibited an ecosystem-specific composition, and was identified as the primary determinant shaping the ARG profiles. Notably, more complex bacteria-ARG co-occurrence pattern was identified on FMP, involving a broader spectrum of core genera and potential pathogenic hosts (e.g., Mycobacterium, Streptomyces). Furthermore, a significant and specific correlation between mobile genetic elements and ARGs was identified on FMP but not SMP, suggesting a markedly elevated horizontal gene transfer potential, with mechanistic support from the concurrent enrichment of oxidative stress and SOS response genes on FMP. These findings provide a comprehensive characterization of ARGs on aquatic microplastics, and especially highlight the role of FMP in the ARG dissemination.}, }
@article {pmid41611053, year = {2026}, author = {Ma, WJ and Ma, ZS and An, ZJ and Zhang, HM and Tian, Y}, title = {Commercial powdered activated carbon achieves high-efficiency nitrogen removal in sulfur-driven autotrophic denitrification at low temperatures.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123882}, doi = {10.1016/j.envres.2026.123882}, pmid = {41611053}, issn = {1096-0953}, mesh = {*Denitrification ; *Nitrogen/metabolism ; Autotrophic Processes ; *Sulfur/metabolism ; *Charcoal/chemistry ; Cold Temperature ; *Waste Disposal, Fluid/methods ; }, abstract = {Sulfur-driven autotrophic denitrification (SAD), a nitrate removal process, is characterized by low carbon emissions and high sustainability. However, its efficiency is notably affected by low temperatures. This study confirmed that the addition of powdered activated carbon (PAC) could enhance denitrification capacity at low temperatures in the SAD process. At 15-10 °C, the nitrogen removal efficiency was 80.38 %, 1.38 times higher than that of the blank reactor. At low temperatures, PAC enhanced the activities of nitrate reductase and nitrite reductase. Meanwhile, PAC stimulated extracellular polymeric substances secretion and improved bio-electrochemical properties. Concurrently, both extracellular and intracellular electron transfer were enhanced by the addition of PAC. Microbial analysis indicated that the microbial network with PAC addition exhibited greater stability and robustness. Furthermore, PAC increased the relative abundances of denitrifying bacteria at low temperatures, particularly those of Ferruginibacter and Dokdonella. Metagenomic sequencing indicated that PAC enhanced pathways related to nucleotide sugar metabolism and synthesis, tRNA charging, and coenzyme A biosynthesis. At the genes level, the functional genes narIL, nirS, nasE, norCE, nosZ, soxA, soxZ, and dsrA were enriched with PAC addition. This study proposed and validated the feasibility of using PAC to enhance nitrogen removal efficiency in the wastewater treatment process at low temperatures, and further elucidated the underlying mechanisms.}, }
@article {pmid41611279, year = {2026}, author = {Ma, XJ and Wang, F and Han, XT and Fang, F and Han, LY and Liu, HX}, title = {[Clinical characteristics and prognostic factors in patients with cerebrospinal fluid torque teno virus positivity after allogeneic hematopoietic stem cell transplantation].}, journal = {Zhonghua yi xue za zhi}, volume = {106}, number = {5}, pages = {455-460}, doi = {10.3760/cma.j.cn112137-20250711-01704}, pmid = {41611279}, issn = {0376-2491}, mesh = {Humans ; *Torque teno virus/isolation & purification ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Retrospective Studies ; Prognosis ; Male ; Female ; Transplantation, Homologous ; Adult ; Adolescent ; Survival Rate ; Young Adult ; *DNA Virus Infections ; }, abstract = {Objective: To investigate the clinical characteristics and prognostic factors for patients with cerebrospinal fluid positivity for torque teno virus (TTV) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: A retrospective analysis was conducted on the patients who received allo-HSCT at Hebei Yanda Lu Daopei Hospital from 2022 to 2023 year and showed positive cerebrospinal fluid metagenomic next-generation sequencing (mNGS) results post-transplantation, with their clinical data collected accordingly. The patients were categorized into TTV-negative and TTV-positive groups based on the detection of TTV in cerebrospinal fluid. The TTV-positive group was further subdivided into low-RPM [TTV reads per million sequencing reads (TTV-RPM)<1] and high-RPM (TTV-RPM≥1) subgroups using the threshold of TTV-RPM. The patients were followed until December 9, 2025, to investigate the clinical features of cerebrospinal fluid TTV positive patients after allo-HSCT. The survival curve was drawn to compare the difference of survival rate between groups. The influencing factors of patient prognosis were analyzed using a multivariate Cox regression model. Results: A total of 134 patients were enrolled: sixty in the TTV-negative group, including 35 males and 25 females, aged [M (Q1, Q3)] 30 (14, 42) years, and 74 in the TTV-positive group, including 45 males and 29 females, aged 24 (15, 40) years. Within the TTV-positive group, 44 were classified as low-RPM subgroup and 30 as high-RPM subgroup. Baseline characteristics, including gender, age, primary disease, donor type, neutrophil engraftment time, platelet engraftment time, whether acute graft-versus-host disease (aGVHD) occurred, and other microbial infections in cerebrospinal fluid, showed no significant differences between the TTV-negative and TTV-positive groups, or between the low-RPM and high-RPM subgroups (all P>0.05). The median follow-up time was 30.0(18.0, 35.4) months, the median survival period was not reached in the low-RPM subgroup, while that in the high-RPM subgroup was 25.6 months (95%CI: 5.3-45.9), and the 3-year survival rate was lower than that in the low-RPM subgroup (41.1% vs 76.8%, P=0.014). Multivariate Cox regression analysis confirmed high TTV-RPM level (≥1) in cerebrospinal fluid as a risk factor for mortality in allo-HSCT patients (HR=2.57, 95%CI: 1.09-6.08). Conclusions: There is no difference in clinical characteristics among allo-HSCT patients with or without TTV infection or with different TTV viral loads. A high TTV-RPM value (≥1) in cerebrospinal fluid is a risk factor for mortality in allo-HSCT patients.}, }
@article {pmid41611489, year = {2026}, author = {Li, W and Zhang, N and Li, Z and Cui, L and Wang, X and DU, Y}, title = {[Research progress on nanopore sequencing data alignment analysis methods and reference databases].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {42}, number = {1}, pages = {77-92}, doi = {10.13345/j.cjb.250554}, pmid = {41611489}, issn = {1872-2075}, mesh = {*Nanopore Sequencing/methods ; *Sequence Alignment/methods ; *Nanopores ; *Sequence Analysis, DNA/methods ; *Databases, Genetic ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Nanopore sequencing, as an emerging hotspot in sequencing technology, demonstrates tremendous potential in species identification, genome assembly, variant detection, and transcriptome analysis, owing to its distinctive advantages including extended read lengths, rapid detection capabilities, and compact instrumentation. However, nanopore sequencing data are characterized by high error rates and presence of insertions and deletions, which pose novel challenges for the application of conventional sequence alignment tools and the construction of reference databases. Focusing on the characteristics of nanopore data, this paper systematically sorts out sequence alignment tools suitable for nanopore sequencing, and elaborates on their advantages and limitations in processing sequence data for five different application scenarios: long-read sequencing, real-time sequencing, error rate compatibility, metagenomics, and structural variation detection. Meanwhile, from the perspective of data sources, this paper conducts multi-dimensional classification and organization of reference genome databases, and sorts out the key technologies for constructing high-quality nanopore databases. Through the collaborative analysis of alignment tools and databases, this paper provides references for the optimization and innovation of nanopore sequencing data analysis, and promotes the in-depth transformation of metagenomic sequencing from data generation to functional analysis.}, }
@article {pmid41611691, year = {2026}, author = {Srivathsan, A and Arzika, AM and Maliki, R and Abdou, A and Lipsitch, M and Blumberg, S and O'Brien, KS and Porco, TC and Hinterwirth, A and Doan, T and Keenan, JD and Lietman, TM and Arnold, BF}, title = {Geographic spillover of antimicrobial resistance from mass distribution of azithromycin.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41611691}, issn = {2041-1723}, support = {R01 AI158884/AI/NIAID NIH HHS/United States ; R01 AI166671/AI/NIAID NIH HHS/United States ; /GATES/Gates Foundation/United States ; }, mesh = {*Azithromycin/administration & dosage/pharmacology/therapeutic use ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; *Mass Drug Administration ; *Drug Resistance, Bacterial/genetics/drug effects ; Infant ; Child, Preschool ; Niger/epidemiology ; Female ; Male ; Macrolides/pharmacology ; Metagenomics ; }, abstract = {Large-scale, placebo-controlled, cluster-randomized trials in high-mortality settings in sub-Saharan Africa demonstrated a 14-18% reduction in childhood mortality following twice-annual mass drug administration (MDA) of azithromycin among children aged 1-59 months. Azithromycin MDA also selected for antimicrobial resistance (AMR), particularly macrolide resistance. It is unknown whether the AMR from azithromycin MDA could spill over to neighboring untreated populations. If present, such geographic spillover effects could lead trials to underestimate AMR risks. We assess between-village geographic spillover effects of genotypic macrolide resistance using metagenomic deep sequencing in rectal swabs collected from 300 children in 30 monitoring villages in Niger after two years of MDA in 594 surrounding villages. Conditional permutation tests assess associations between proximal azithromycin treatment intensity and resistance gene abundance. We find no evidence of geographic spillover of macrolide resistance in untreated villages, as the genetic load of AMR remains at baseline levels in placebo-treated villages regardless of surrounding azithromycin treatment intensity (Spearman ρ = -0.05, P = 0.83). Sensitivity analyses confirm robustness across metrics, and no spillover effects are detected for other antibiotic classes. Azithromycin MDA-induced macrolide resistance appears localized to treated villages, mitigating some concerns about geographic spillover of AMR to nearby untreated villages at 24 months.}, }
@article {pmid41611767, year = {2026}, author = {Jain, AG and Agwan, D and Kumar, A and Pancha, I and Rathod, J and Mohapatra, B}, title = {Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6603}, pmid = {41611767}, issn = {2045-2322}, support = {GSBTM/JD(R&D)/661/2022-23/00173054//GSBTM/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Microbiota ; *Plant Development ; Soil/chemistry ; *Bacteria/genetics/classification ; *Nutrients/metabolism ; Nitrogen/metabolism ; }, abstract = {Jeevamrit, a microbial inoculant widely used in zero-budget natural farming (ZBNF) that relies on local farm-based resources to enhance overall biological health of soil, is reported for inconsistent crop yield enhancements. This is mainly due to variability in its preparation methods, e.g., mixing intensity, incubation regimes, and quality of ingredients used. Hence, the current study aimed to decipher the effect of mixing intensity (extent of oxygenation) on microbial community composition, nutrient transformation, and plant growth attributes of Jeevamrit, using a combined metagenomics-culturomics approach. Frequent mixing (Constant/Intermediate) enhanced nutrient solubilization (Fe, Zn, Cu, Mn) with higher total N and dissolved organic carbon, while less mixing (Anoxic/No-mix) led to accumulation of soluble Fe and NH4[+]-N with higher microbial diversity. Mixing-driven differential enrichment of taxa were noted, i.e., constant mixing (CM) dominated by Acinetobacter (~ 40%), Comamonas, Pseudomonas, and Lysinibacillus, linked to oxidative C/N cycling and metal dissolution. Whereas, anoxic (AO) favored Clostridium sensu stricto, Lactobacillales, Enterococcus, and Enterobacterales (> 60%), correlating to fermentative metabolism-driven reductive elemental cycling. Co-occurrence network analysis identified Acinetobacter, Pseudomonas, Comamonas, Trichococcus, and Stenotrophomonas as hubs, indicating keystone functions in structuring metabolic interactions. The metagenome-recovered MAGs belonged to Acinetobacter sp., Clostridium saccharobutylicum, Trichococcus flocculiformis, and Enterococcus gallinarum with potential to participate in multiple nutrient cycling. Cultivable members of Shigella, Rhodococcus, and Bacillus spp. showed high IAA production (135-145 µg mL[-][1]), NH3 release (~ 0.12 µg mL[-][1]), and K and P solubilization (~ 55.2 µg mL[-][1]). We hypothesize that oxygenation drives the Jeevamrit's microbial guild assembly, where mixing intensity modulates oxido-reductive metabolism and nutrient mobilization efficiency, indicating the requirement for standardization of formulation aligned to soil-specific conditions.}, }
@article {pmid41611865, year = {2026}, author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR}, title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6601}, pmid = {41611865}, issn = {2045-2322}, mesh = {Animals ; *Drosophila/microbiology/genetics ; *Genome, Bacterial ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Ecuador ; *Bacteria/genetics/classification ; }, abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.}, }
@article {pmid41612181, year = {2026}, author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X}, title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41612181}, issn = {1471-2180}, support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; }, abstract = {OBJECTIVE: To investigate the differences in gut microbiome composition among multi-center populations from coastal and high-altitude regions of China and their association with colorectal adenoma (CRA).
METHODS AND ANALYSIS: Metagenomic sequencing was performed on stool samples collected from 295 participants. Diversity, principal component, and linear discriminant analyses were conducted to assess microbial composition and functional differences related to geography and disease status.
RESULTS: In high-altitude populations, bacterial enterotypes were predominantly Prevotella, fungal enterotypes Saccharomyces, and archaeal enterotypes Methanobrevibacter, differing from those in coastal populations. Combining bacterial, fungal, and archaeal features improved classification accuracy between high-altitude and coastal populations (AUC = 0.84) and between high-altitude and coastal adenoma patients (AUC = 0.85). Specific enterotypes were observed to correlate significantly with metabolic pathways in high-altitude populations.
CONCLUSION: Significant differences in gut microbiome enterotypes exist across geographic populations, with specific enterotypes in high-altitude populations potentially associated with a lower prevalence of CRA. These findings provide new insights into the gut microbiome–geography relationship and support microbiome-based diagnostic and therapeutic strategies.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04578-0.}, }
@article {pmid41612194, year = {2026}, author = {Ballandras, V and McNamara, L and Carolan, JC and Pichon, A and Byrne, S}, title = {Whole genome sequencing of 18 economically important aphid pests with photographic vouchers for taxonomic validation.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {41612194}, issn = {2730-6844}, abstract = {OBJECTIVES: Accurate molecular identification in insect monitoring programs relies on validated genomic references, yet many pest species remain underrepresented or incorrectly annotated in public databases. This Data Note provides a curated genomic resource for 18 economically important aphid pests. For each species, we generated whole-genome shotgun sequences and captured high-resolution photographic vouchers of the sequenced individuals to ensure taxonomic verification. Specimens were collected from field or suction trap networks to incorporate intraspecific variation. This dataset will support the development of reliable DNA barcoding, metabarcoding, and mitochondrial metagenomic assays, and contribute to improved reference libraries for aphid pest surveillance.
DATA DESCRIPTION: This dataset includes whole-genome shotgun sequencing data for 18 agriculturally important aphid pest species selected from suction trap monitoring programs. Specimens were morphologically identified using standard aphid identification keys, and diagnostic traits were documented with high-resolution Leica Flexacam C3 images to provide taxonomic verification. For each species, pooled individuals (up to 15 per species) were used for DNA extraction using the Monarch[®] Genomic DNA Purification Kit. Illumina 150 bp paired-end sequencing (10.1–22.7 Gb per species) was performed by Novogene. These data enable extraction of Cytochrome Oxidase I (COI) barcodes, mitochondrial genomes, and associated endosymbiont sequences.}, }
@article {pmid41612232, year = {2026}, author = {Chen, Q and Yin, Q and Chen, J and Jin, L and Guo, W and Huang, M}, title = {Comparison of the diagnostic value of targeted next-generation sequencing, metagenomic next-generation sequencing, and Xpert MTB/RIF in adult pulmonary tuberculosis.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-12673-4}, pmid = {41612232}, issn = {1471-2334}, }
@article {pmid41612472, year = {2026}, author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y}, title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.}, journal = {European journal of medical research}, volume = {31}, number = {1}, pages = {}, pmid = {41612472}, issn = {2047-783X}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; Prospective Studies ; Aged ; Metagenomics ; *Pneumonia/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.
METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.
RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.
CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.}, }
@article {pmid41612514, year = {2026}, author = {Enagbonma, BJ and Pierneef, RE and Modise, DM and Babalola, OO}, title = {Effects of legume-based rotation on subsequent sorghum rhizosphere microbial communities and their drought tolerance-related genes.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00829-9}, pmid = {41612514}, issn = {2524-6372}, support = {CRP/ZAF22-03//ICGEB/ ; }, abstract = {INTRODUCTION: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.
OBJECTIVES: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.
METHODS: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.
RESULTS: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.
CONCLUSION: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.}, }
@article {pmid41612676, year = {2026}, author = {Asin, J and Carvallo, F and Gonzales-Viera, OA and Macías-Rioseco, M and Streitenberger, N and Abdelrazek, S and Crossley, B and Pesavento, PA and Uzal, FA}, title = {Interstitial pneumonias of undetermined etiology in foals in California, 1990-2020.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387251410524}, pmid = {41612676}, issn = {1943-4936}, abstract = {Interstitial and bronchointerstitial pneumonias of undetermined etiology in young foals are relatively common in autopsy services with an equine focus. Unknown viruses, toxins, hyperthermia, surfactant or alveolar macrophage function deficiency, certain antibiotics, and aberrant responses to Rhodococcus equi or other bacteria have been proposed as causes. We performed a retrospective study of autopsies on foals with a diagnosis of interstitial or bronchointerstitial pneumonia with an unidentified etiology. Forty-one foals (median age: 3-mo-old) were included. Most were received in summer (n = 28) and spring (n = 10). The most frequently reported clinical signs were dyspnea and/or tachypnea (n = 28) and fever (n = 19). Antibiotic treatment was reported in 21 cases, and the most frequently used antibiotics were penicillin (n = 9) and gentamicin (n = 8). Grossly, most of the lungs were diffusely rubbery-to-firm (n = 35) and did not collapse (n = 22). Histologically, combinations of exudative (E; hyaline membranes), proliferative (P; type II pneumocyte hyperplasia), and fibrotic (F; fibroplasia) phases were common (E + P, n = 15; E + P + F, n = 13) in the interstitial component. Necrosis of the bronchiolar epithelium was rare (n = 4), concurrent suppurative bronchopneumonia was common (n = 22), and a few foals (n = 5) had pulmonary pyogranulomas. Pneumocystis spp. organisms were observed in 8 cases using Grocott-Gomori methenamine silver stain. Bacteria were recovered from the lungs in 22 cases, with R. equi (n = 7) and E. coli (n = 6) being the most common isolates. No unequivocal viral causes were identified during the regular diagnostic work-up and after using novel diagnostic approaches such as herpesvirus consensus PCR and viral metagenomics in a subset of the cases.}, }
@article {pmid41613303, year = {2025}, author = {Huang, J and Lan, C and Liang, Y and Chen, H and Liang, H and He, H and Che, S and Chen, Y}, title = {Case Report: Metagenomic next-generation sequencing diagnosed a rare case of sternal tuberculosis mimicking a malignant tumour.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1708834}, pmid = {41613303}, issn = {2296-858X}, abstract = {This is a case report of a 17-year-old female patient who presented with a painless, palpable swelling on the anterior chest wall. Imaging studies revealed osteolytic lesions involving the manubrium and adjacent ribs, along with multiple enlarged lymph nodes, raising a high suspicion of malignant tumour with metastasis. An ultrasound-guided needle biopsy revealed the pathological finding of "granulomatous inflammation." Multidisciplinary consultation and clinical indicators, including a strongly positive purified protein derivative (PPD) test and markedly elevated erythrocyte sedimentation rate, were taken to indicate a potential diagnosis of tuberculosis. Consequently, subsequent metagenomic next-generation sequencing (mNGS) of the biopsy specimen identified nucleic acid sequences belonging to the Mycobacterium tuberculosis complex, thereby confirming the rare diagnosis of sternal tuberculosis. Following the administration of standardised anti-tuberculosis therapy, a substantial reduction in the size of the lesion was observed, thereby validating the accuracy of the diagnosis. This case underscores the importance of considering extrapulmonary tuberculosis in the differential diagnosis of bone-destructive lesions and demonstrates the critical value of mNGS technology in confirming challenging infectious diseases.}, }
@article {pmid41613591, year = {2025}, author = {Xu, Y and Ma, Y and Huang, Q and Guo, X and Guo, L and Ren, Y and Lu, W and Wu, X and Li, D and Li, S}, title = {The role of bronchoalveolar lavage fluid metagenomic next-generation sequencing in detecting pathogens and optimising antibiotic therapy in paediatric severe community-acquired pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1688473}, pmid = {41613591}, issn = {2235-2988}, mesh = {Humans ; *Community-Acquired Infections/drug therapy/microbiology/diagnosis ; Infant ; Child, Preschool ; *High-Throughput Nucleotide Sequencing/methods ; Child ; Male ; Retrospective Studies ; Female ; *Anti-Bacterial Agents/therapeutic use ; *Metagenomics/methods ; Adolescent ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; ROC Curve ; *Pneumonia/drug therapy/microbiology/diagnosis ; Severity of Illness Index ; Community-Acquired Pneumonia ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of mortality in the paediatric population, with current diagnostic and treatment approaches often proving insufficient and contributing to the growing challenge of antibiotic resistance. This study explored the potential of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid as a tool to enhance the precision of antibiotic management in children with SCAP.
METHODS: A retrospective cohort study of 202 paediatric patients with community-acquired pneumonia (aged 1 month-18 years) admitted to the First Affiliated Hospital of Xinxiang Medical University (November 2020-March 2023) was conducted. Patients were grouped by severity (intensive care unit [ICU]/non-ICU) and mNGS timing (early: ≤72 hours post-admission; late: >72 hours). The diagnostic efficacy of mNGS versus conventional microbiological techniques (CMT) was evaluated using sensitivity, specificity, positive/negative predictive values and area under the receiver operating characteristic curve (AUC) analysis. Antibiotic adjustments and clinical outcomes were analysed via survival statistics.
RESULTS: Metagenomic next-generation sequencing showed a higher positive detection rate (98.51%) than CMT (47.52%) (AUC = 0.82, 95%CI: 0.76-0.88). Of the 202 patients, 127 (62.87%) were male, with a median age of 1.88 years (interquartile range: 0.29-7 years). Early mNGS was associated with fewer extrapulmonary complications (69.63% vs 55.22% in the late group, p < 0.05), and shorter hospitalisation (median 13 vs 15 days, p <0.01). Antibiotic escalation occurred in 50 (24.75%) cases, de-escalation in 22 (10.89%) and same-level adjustment in 25 (12.38%).
CONCLUSION: Metagenomic next-generation sequencing outperforms CMT in pathogen detection. Early mNGS is associated with improved clinical outcomes, suggesting its potential utility in paediatric SCAP management.}, }
@article {pmid41614121, year = {2025}, author = {Shi, M and Guo, A and Qin, S and Kang, Y and Zhang, W and Yang, X}, title = {Metagenomic insights into short-term legume rotation: modulating potato rhizosphere microbiota to enhance tuber yield and quality.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1680056}, pmid = {41614121}, issn = {1664-302X}, abstract = {OBJECTIVE: This study aims to investigate the effects of legume crop rotation on the rhizosphere microbiota and its potential to improve potato (Solanum tuberosum L.) productivity and tuber quality. We specifically focus on the microbial functional potential revealed through metagenomic sequencing under different legume rotation systems in the intensive agricultural region of the Chinese Loess Plateau.
METHODS: A five-year field experiment (2018-2022) was conducted to establish three cropping systems: (1) continuous potato monocropping for 5 years (CK), (2) continuous potato cropping for 3 years followed by one-year pea rotation and one-year potato cropping (T1), and (3) continuous potato cropping for 3 years followed by one-year faba bean rotation and one-year potato cropping (T2). The impacts of these rotation regimes on potato yield formation, tuber quality, and rhizosphere microbial communities were systematically evaluated, with a focus on microbial diversity and functional potential, using metagenomic sequencing and network analysis.
RESULTS: Metagenomic analysis demonstrated that legume rotation, particularly the T2 system, significantly enriched the relative abundances of Actinobacteria (38.31%) and Proteobacteria (28.40%) in the potato rhizosphere while reducing Acidobacteria (10.03%). Functional annotation further revealed that T2 promoted the expression of microbial genes involved in carbon fixation (K00626, K01895, etc.), nitrogen assimilation (narB, narA, etc.), and sulfur metabolism (cysNC, cysN, etc.), enhanced potential for nutrient cycling. Co-occurrence networks revealed Actinobacteria and Acidobacteria as keystone taxa forming robust interaction modules potentially linked to soil ecological stability. Compared to CK, T2 increased the commercial tuber rate by 85.82%, overall tuber yield by 28.38%, starch content by 34.85%, and vitamin C content by 30.79%, while reducing sugar levels decreased by 9.35%.
CONCLUSION: Faba bean-potato rotation (T2) effectively mitigated the adverse impacts caused by continuous potato cropping by altering the rhizosphere microbial structure and enhancing microbial functional pathways related to nutrient cycling. This study provides a detailed metagenomic perspective on the microbial mechanisms underlying the benefits of crop rotation and offers a theoretical basis for developing microbiome-informed ecological management strategies to mitigate continuous cropping obstacles in potato production on the Loess Plateau.}, }
@article {pmid41614128, year = {2025}, author = {Wang, J and Bai, C and Tian, Y and Bao, J and Liu, J}, title = {Intercropping reshapes soil stress resistance and growth promotion capabilities through rhizosphere exudates in conjunction with the microbiome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1708938}, pmid = {41614128}, issn = {1664-302X}, abstract = {Terrestrial plants can affect the growth and health of neighboring plants through interspecific interactions. Long-term monoculture in agricultural and pastoral production can lead to the occurrence of soil-borne diseases, depletion of nutrients, and a decline in soil microbial diversity, thereby affecting the sustainable development of cultivated ecosystems. In this study, we employed three cultivation patterns: monoculture of Melilotus officinalis (L.) Pall. (M. officinalis), monoculture of Avena sativa L. (A. sativa), and intercropping of M. officinalis and A. sativa. To introduce ecologically protective plants into cultivated ecosystems and investigate the effects of plant root exudates on the recruitment of rhizosphere microbiota of neighboring plants, as well as the disease resistance and growth promotion capabilities of intercropping, we conducted non-targeted metabolomics and metagenomics analyses on root exudates and soil microbiota. The sequencing data obtained provided strong evidence for the interaction mechanisms between root exudates and microorganisms in intercropping ecosystems. We observed that in intercropping ecosystems, the abundance and variety of root exudates were more similar to those of the crop plants. The differential metabolites between intercropping and A. sativa were inclined to be chemically defensive, while those between intercropping and M. officinalis were more inclined to promote material synthesis. Compared with A. sativa, intercropping enhances the alpha and beta diversity of soil microbial communities, particularly increasing the enrichment abundance in pathways such as the bacterial secretion system, sulfur metabolism, and phenylpropanoid biosynthesis, which is closely associated with the suppression of soil-borne pathogens. Compared with M. officinalis, intercropping further enhanced the synthesis of plant-available substances in the soil, driving microorganisms to optimize the levels of carbon, nitrogen, and trace elements in the soil. In comparison, intercropping had a significant impact on the aggregation of soil-specific microorganisms, which can optimize nitrogen utilization to promote plant growth and enhance plant defense and stress tolerance. The results of this study will provide a theoretical basis for cultivated ecosystems and sustainable land management.}, }
@article {pmid41614136, year = {2025}, author = {Zhao, S and Wang, X and Zhu, H and Guo, G and Mustafa, GR and Mustafa, A and Chen, Y and Li, X and Wang, Y and Zhao, B}, title = {Metagenomic analysis revealed the distribution of antibiotic resistance genes of Awang sheep (Ovis aries) gut microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1740198}, pmid = {41614136}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) in livestock is a major contributor to the global AMR crisis, yet little is known about its dynamics in high-altitude pastoral systems. We performed deep metagenomic sequencing of 100 fecal samples from Tibetan Awang sheep reared under grazing (aw_fm) and captive (aw_qs) conditions. Microbiome profiling revealed striking community shifts: grazing sheep were enriched in Bacteroidetes and Firmicutes, whereas captive sheep showed expansion of Proteobacteria, particularly Acinetobacter, suggesting dysbiosis. The resistome comprised 302 unique ARGs, dominated by rpoB2 (43.3%), Bifidobacterium_adolescentis_rpoB (11.2%), and ugd (10.2%). Grazing sheep carried ARGs mainly against rifamycins and peptide antibiotics, reflecting natural selective pressures, while captive sheep exhibited significantly broader resistance, including tetracyclines, macrolides, and fluoroquinolones (p < 0.05). Enrichment of efflux pump genes (MexK, adeJ) in captive sheep highlighted a shift toward multidrug resistance. These findings demonstrate that rearing practices profoundly restructure the gut resistome, underscoring the need for targeted antibiotic stewardship in high-altitude livestock systems.}, }
@article {pmid41614172, year = {2026}, author = {Li, Y and Wang, J and Zhang, Z and Zhang, Y and Müller, R and Huo, L}, title = {Deep-Sea Genome Mining Reveals Cooperative ATP-Grasp Ligase-Directed Biosynthesis of Pentacyclic Myxomiditides with Potent Protease Inhibition.}, journal = {JACS Au}, volume = {6}, number = {1}, pages = {607-620}, pmid = {41614172}, issn = {2691-3704}, abstract = {Microviridins are ribosomally synthesized and post-translationally modified peptides, typically featuring a conserved tricyclic structure formed by two ATP-grasp ligases. However, the diversity and evolution of these enzymes remain incompletely understood. Here, we identify a distinct ATP-grasp ligase subclade (MyxF) that specifically modifies the conserved (KxxE)n motif, defining a new subclass of microviridins with the (KxxE)nTxKxPSDx-(D/E)-(D/E) sequence signature. Guided by SSN analysis, we discovered a deep-sea myx biosynthetic gene cluster from 10,000 m sediments and heterologously expressed two pentacyclic microviridin-like peptides, Myxomiditide A and B. Using mass spectrometry and NMR, we fully elucidated their chemical structures, revealing not only the conserved tricyclic core but also two additional N-terminal lactam rings within the KxxEKxxE motif, distinguishing them from known microviridins. Combined in vivo coexpression and in vitro reconstitution uncovered a noncanonical division of labor among four ATP-grasp ligases involved in myxomiditide biosynthesis. MyxF and MyxD1 act as functional isozymes responsible for installation of the N-terminal lactam moieties, whereas MyxD2(?)catalytically inactive on its own(?)requires the synergistic presence of both MyxF and MyxD1 to enable formation of the C-terminal lactone rings. The pathway is finalized by MyxC, which catalyzes the terminal lactam macrocyclization, collectively revealing a highly cooperative enzymatic assembly mechanism governing myxomiditide maturation. Furthermore, MyxF exhibited remarkable catalytic plasticity, catalyzing multiple lactam macrocyclizations beyond its native substrate architecture. Notably, Myxomiditide A potently inhibited elastase with nanomolar IC50 values. Collectively, this study expands the enzymatic landscape of ATP-grasp ligases and highlights the deep sea as a rich source of evolutionary innovation in RiPP biosynthesis.}, }
@article {pmid41614733, year = {2025}, author = {Kim, D and Kim, WJ and Woo, HM and Jeong, H}, title = {PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.}, journal = {Current issues in molecular biology}, volume = {47}, number = {12}, pages = {}, pmid = {41614733}, issn = {1467-3045}, support = {ncheon National University Research Grant in 2023. 284//Incheon National University/ ; }, abstract = {16S rRNA amplicon sequencing has been an effective method for profiling microbial taxonomy in microbiome research, as it offers lower per-sample costs and higher sample throughput than shotgun metagenomics. Although 16S rRNA sequencing offers clear advantages over shotgun sequencing, it depends on precise trimming of low-quality bases at the 3' ends of reads. Given the widespread use of 16S rRNA amplicon sequencing, there is an increasing demand for analysis tools that can identify errors in the 3' region of reads and remove erroneous bases. While various algorithms for predicting trim locations are widely employed, most are command-line standalone tools, which pose challenges for users with limited computational background or resources. Furthermore, in the absence of biological or experimental priors such as amplicon size, trim position predictions may be unreliable. Here, we introduce PixelCut, a fully automated trim-position prediction framework that requires no hyperparameters or prior biological information for accurate prediction. Unlike most available algorithms that operate on raw FASTQ data, PixelCut analyzes the per-base quality report generated by FastQC to infer trimming positions. Based on the recommended quality score threshold from the quality report, PixelCut inspects the quality scores across bases and automatically determines the recommended trim position using character recognition techniques based on computer vision. We have also developed a user-friendly web application to make the method accessible to those without programming expertise, while offering a command-line version for advanced users. Through comprehensive computer simulations, we show that PixelCut produces taxonomic profiling results that are consistent with those from popular trim-location prediction algorithms.}, }
@article {pmid41615027, year = {2025}, author = {Jiménez, DJ and Marasco, R and Schultz, J and Díaz Rodríguez, CA and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS}, title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41615027}, issn = {1751-7370}, support = {MCIN/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation/ ; 101081782 (deCYPher)//European Union/ ; 101036768 (PROMISEANG)//European Union/ ; PID2022-139247OB-I00 (Rob3D)//European Union/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Bacteria/genetics/classification/isolation & purification/growth & development ; Microbiota ; *Archaea/genetics/classification/isolation & purification/growth & development ; }, abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.}, }
@article {pmid41615149, year = {2026}, author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y}, title = {Gut microbiome signatures associated with depression and obesity.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0126325}, pmid = {41615149}, issn = {2379-5077}, support = {EarlyCause 848158//Horizon 2020 Framework Programme/ ; Centro de Excelencia Severo Ochoa CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; FPI PRE2018-083895//Ministerio de Ciencia e Innovación/ ; Miguel Servet CP22/00031//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology/complications ; Male ; Female ; Case-Control Studies ; *Major Depressive Disorder/microbiology ; Middle Aged ; Adult ; Body Mass Index ; Metagenomics/methods ; Metagenome ; }, abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.
IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.}, }
@article {pmid41615376, year = {2026}, author = {Eichler, H and Butta, NV and Riddell, A and Augustsson, C and Kjalke, M and Jensen, K and Paramo-Florencio, A and Astermark, J and Chowdary, P and Jiménez-Yuste, V}, title = {Investigation of the Suitability of the ROTEM Assay to Measure Coagulation Potential in Blood From Patients on Concizumab Prophylaxis.}, journal = {Haemophilia : the official journal of the World Federation of Hemophilia}, volume = {32}, number = {2}, pages = {490-498}, pmid = {41615376}, issn = {1365-2516}, support = {//Novo Nordisk A/S/ ; }, mesh = {Humans ; *Thrombelastography/methods ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Blood Coagulation/drug effects ; *Hemophilia A/drug therapy/blood ; Blood Coagulation Tests/methods ; Male ; Adult ; }, abstract = {BACKGROUND: Rotational thromboelastometry (ROTEM) aims to measure the coagulation potential in whole blood. Concizumab, an anti-tissue factor pathway inhibitor (TFPI) antibody for prophylaxis in haemophilia, enhances tissue factor (TF)-initiated coagulation by preventing inhibition of activated factor X (FXa), thus increasing thrombin generation.
OBJECTIVES: To evaluate a modified ROTEM assay for monitoring patients on concizumab prophylaxis.
METHODS: The TF reagent (r_exTEM) was diluted 50,000-fold to make the ROTEM assay sensitive to haemophilia and to concizumab. The effect of concizumab was evaluated in the modified ROTEM in haemophilia A (HA)-like blood (normal blood with added anti-FVIII antibody). ROTEM analysis was performed in blood from patients participating in the explorer7/8 trials during 24 weeks of concizumab prophylaxis. Rotrol N plasma was used as quality control.
RESULTS: In vitro experiments showed concizumab concentration-dependent reduction in clot time (CT) and increase in clot development (α-angle) in HA-like blood. At three of four clinical sites, CT and clot development were stable, variance of the control plasma was ≤12.4% and TF content of the diluted reagent (r_exTEM) was consistent. At these three sites, the correlation between CT versus concizumab exposure, free TFPI and thrombin generation assay parameters was weak (-0.508 to +0.359). Prothrombin time positively correlated with CT (0.523) and negatively correlated with α-angle (-0.659).
CONCLUSION: Due to the poor correlation between ROTEM parameters, concizumab exposure, free TFPI and thrombin generation parameters and the lack of consistent and reliable performance of the modified ROTEM assay, it cannot be recommended for general monitoring of patients on concizumab prophylaxis.}, }
@article {pmid41615602, year = {2025}, author = {Fedonenko, YP and Grinev, VS and Velichko, NS and Lipatov, NN and Selivanov, NY and Kuzina, MS and Sigida, EN and Konnova, SA}, title = {Isolation and Characterization of Halophilic Bacteria of the Halomonadaceae Family, Promising Producers of Extracellular Polysaccharides.}, journal = {Doklady. Biochemistry and biophysics}, volume = {525}, number = {2}, pages = {653-658}, pmid = {41615602}, issn = {1608-3091}, mesh = {*Polysaccharides, Bacterial/biosynthesis/chemistry ; *Halomonadaceae/metabolism/isolation & purification/genetics ; }, abstract = {Exopolysaccharide (EPS) production is one of the key mechanisms of bacterial survival in hypermineralized environments. Representatives of the Halomonadaceae family are recognized as basic organisms for next-generation industrial biotechnology; however, the range of Halomonas used and information on the structural diversity of their EPSs are rather limited. The results of metagenomic analysis of salt, peloid, and soil samples from the coastal zone of salt lakes in the Volgograd region with subsequent seeding on selective mineral media made it possible to isolate bacteria of the Halomonadaceae family. For taxonomically identified strains, cultivation conditions were optimized and EPSs were obtained, the structure of which was characterized based on chemical analysis data and NMR spectroscopy. The study of the physicochemical properties of EPSs (viscosity, hygroscopicity, emulsifying activity, and antioxidant properties) showed that these polymers are promising for biotechnological applications.}, }
@article {pmid41615921, year = {2026}, author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM}, title = {Correction: Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0342098}, pmid = {41615921}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323382.].}, }
@article {pmid41616624, year = {2026}, author = {Sun, Y and Zhang, M and Teng, Y and Yin, Y and Ran, J and Su, H and Li, H and Huang, X and Long, Z and Sun, X and Pan, H and Wang, X and Li, M}, title = {Human activities and horizontal gene transfer shape the resistome landscapes of non-human primates.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141276}, doi = {10.1016/j.jhazmat.2026.141276}, pmid = {41616624}, issn = {1873-3336}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Primates/microbiology ; Humans ; *Human Activities ; China ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.}, }
@article {pmid41616686, year = {2026}, author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ}, title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.}, journal = {Current opinion in biotechnology}, volume = {98}, number = {}, pages = {103436}, doi = {10.1016/j.copbio.2026.103436}, pmid = {41616686}, issn = {1879-0429}, mesh = {*Biosensing Techniques/methods ; *Microbiota ; Synthetic Biology ; }, abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.}, }
@article {pmid41616716, year = {2026}, author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM}, title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.}, journal = {Journal of environmental management}, volume = {400}, number = {}, pages = {128747}, doi = {10.1016/j.jenvman.2026.128747}, pmid = {41616716}, issn = {1095-8630}, mesh = {*Manure/microbiology ; Animals ; Swine ; *Microbiota ; *Soil Microbiology ; Farms ; Soil ; Fertilizers ; Bacteria ; }, abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.}, }
@article {pmid41616776, year = {2026}, author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W}, title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.}, journal = {Cell host & microbe}, volume = {34}, number = {2}, pages = {201-211.e6}, doi = {10.1016/j.chom.2026.01.006}, pmid = {41616776}, issn = {1934-6069}, mesh = {*Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Rhizosphere ; *Microbial Interactions ; *Soil/parasitology ; Microbiota ; *Eukaryota/physiology ; Metagenomics ; }, abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.}, }
@article {pmid41617120, year = {2026}, author = {Hu, S and Wang, X and Xu, H and Xiong, J and Gu, Y and Cao, X and Zhou, L and Fan, Y and Wang, S and Bai, X and Shi, H and Zhu, Q and Chen, L and Shi, Z}, title = {Vaginal microbiota in late pregnancy associates with the outcomes of planned induced labor: a multicenter prospective cohort study.}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2026.01.026}, pmid = {41617120}, issn = {1097-6868}, abstract = {BACKGROUND: Induction of labor is a commonly used obstetric method for terminating pregnancy in cases of delayed or expired pregnancy or complications, with cervical maturity being a key determinant of success. Balloon-induced labor is a safe, effective, and cost-effective induction of labor method. While clinical factors such as parity, cervical Bishop score, prepregnancy body mass index, are known to influence outcomes. Emerging evidence suggests that vaginal microbiota may also play a critical role through activation of local complement mediators and inflammatory signalling that accelerates cervical ripening. Additionally, genetic factors may influence both preterm birth risk and vaginal microbiota composition. However, the specific impact of vaginal microbiota and genetic factors on balloon-induced labor outcomes remains unclear and requires further investigation.
OBJECT: To explore the impact of the vaginal microbiota prior to delivery on the maternal and fetal outcomes of planned induced labor through metagenomic sequencing and genome-wide association studies.
STUDY DESIGN: A multicenter prospective cohort study was conducted from October 2022 to June 2024 across 5 hospitals, enrolling 635 pregnant women undergoing planned sequential induction of labor using cervical balloons combined with oxytocin. The clinical data throughout the entire pregnancy and labor period, as well as samples of vaginal and cervical secretions before the induction of labor, were collected. Firstly, the characteristics of the vaginal microbiota in all pregnant women were analyzed through metagenomic sequencing, and then the impact of vaginal microbiota differences on the maternal and fetal outcomes of planned induced labor was studied. Subsequently, a nested case-control study was performed, based on human whole genome sequencing combined with genome-wide association studies analysis on vaginal secretion samples, to investigate the role of genetic factors in planned induced labor. Finally, vaginal microbiota transplantation in pregnant rats was conducted to verify the effects of vaginal microbiota on the maternal and fetal outcomes of labor.
RESULTS: Among the participants, 167 delivered within 24 hours, 318 delivered within 24-72 hours, 50 failed induction, and 100 underwent cesarean section for miscellaneous indications. Vaginal microbiota analysis in parturients revealed that the probability of delivery within 24 hours is negatively correlated with Lactobacillus iners (L. iners) abundance, while failed induction is negatively correlated with Ralstonia mannitolilytica abundance. Cesarean section probability is positively correlated with Lactobacillus crispatus (P=0.03). Additionally, the time from balloon placement to delivery is positively correlated with L. iners (P=0.002) and negatively correlated with Lactobacillus crispatus (P=0.08, not fully significant). Genome-wide association studies analysis shows that single-nucleotide polymorphisms associated with adverse pregnancy outcomes are mainly concentrated on chromosomes 1, 4, 8, and 10. Vaginal microbiota transplantation experiments showed that pregnant rats transplanted with vaginal bacteria from women who delivered within 24 hours had the shortest delivery time, while those transplanted with vaginal bacteria from women who failed to induced labor had the longest delivery time and some experienced dystocia.
CONCLUSION: This study reveals that, in addition to genetic factors, the outcomes of planned labor induction, especially the total duration of labor and the success rate of induction, are closely related to the vaginal microbiota in women during the late stages of pregnancy. The study provides new evidence to explain the different outcomes of labor induction.}, }
@article {pmid41617130, year = {2026}, author = {Wang, J and Ma, Y and Shi, X and Han, Y and Zhang, Y and Diao, Z and Li, Z and Lai, H and Meng, S and Zhang, C and Zhao, F and Qin, X and Li, J and Zhang, R}, title = {A multicentre evaluation of metagenomic sequencing for pathogen detection in central nervous system infections.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.01.015}, pmid = {41617130}, issn = {1469-0691}, abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) is a promising tool for diagnosing central nervous system infections. However, the low-biomass nature of cerebrospinal fluid (CSF) increases susceptibility to contamination and host-background interference, potentially compromising accuracy. This study aimed to evaluate CSF mNGS performance across multiple laboratories and to identify key factors influencing detection accuracy.
METHODS: A reference panel of 15 CSF samples was designed to evaluate CSF mNGS performance across laboratories, including 3 replicate samples, 5 serial concentration-gradient samples, 3 anti-interference samples with added human serum albumin or increased host nucleic acids, and 3 simulated clinical case samples, along with 1 negative sample. A total of 127 laboratories participated, which apply mNGS in clinical diagnostics or research. Each laboratory used independently developed mNGS workflow, which varied in experimental procedures, bioinformatic pipelines, and positive detection thresholds. Accuracy, repeatability, sensitivity, and anti-interference capability were systematically evaluated, and sources of erroneous results and methodological factors influencing accuracy were analysed.
RESULTS: Overall performance across 127 laboratories was favourable (average F1-score 0.98, reflecting overall accuracy by balancing sensitivity and specificity). Most false-positive results (83.43%) were due to experimental contamination, whereas false negatives were mainly attributed to RNA viruses (57.14%). Methodological factors significantly affected detection, with impact varying by microbial type. Generally, pelleting impaired the detection of all microbes. Notably, microbial enrichment through DNase treatment and Kraken2 improved detection accuracy for DNA viruses, bacteria, fungi and atypical pathogens, but had little effect on RNA viruses.
CONCLUSIONS: This large-scale study underscores the need for improved contamination controls, optimized RNA virus detection, and enhancement of key wet-lab procedures to strengthen CSF mNGS reliability. These findings provide actionable insights to refine mNGS workflows and advance its clinical utility for diagnosing central nervous system infections.}, }
@article {pmid41617300, year = {2026}, author = {Shah, D and Balendra, S and Petrushkin, H and Patel, A}, title = {Paediatric ocular toxocariasis with relentless progression despite negative metagenomic testing.}, journal = {The Lancet. Infectious diseases}, volume = {26}, number = {2}, pages = {e130-e131}, doi = {10.1016/S1473-3099(25)00685-1}, pmid = {41617300}, issn = {1474-4457}, }
@article {pmid41617710, year = {2026}, author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F}, title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41617710}, issn = {2041-1723}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Plastids/genetics/classification ; *Metagenomics/methods ; Phylogeny ; Symbiosis/genetics ; Cyanobacteria/genetics/classification ; Biodiversity ; Genetic Variation ; Haptophyta/genetics/classification ; Cryptophyta/genetics/classification ; Genome, Plastid ; Alveolata/genetics ; Photosynthesis/genetics ; Evolution, Molecular ; }, abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.}, }
@article {pmid41617723, year = {2026}, author = {Pratama, AA and Pérez-Carrascal, O and Sullivan, MB and Küsel, K}, title = {Diversity and ecological roles of hidden viral players in groundwater microbiomes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41617723}, issn = {2041-1723}, support = {EXC 2051, Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0023307//U.S. Department of Energy (DOE)/ ; }, mesh = {*Groundwater/microbiology/virology ; *Microbiota/genetics ; Metagenomics ; Archaea/virology/genetics ; Bacteria/virology/genetics/classification ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Virome/genetics ; Phylogeny ; Ecosystem ; Water Microbiology ; }, abstract = {Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.}, }
@article {pmid41617724, year = {2026}, author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG}, title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41617724}, issn = {2052-4463}, mesh = {*Symbiosis ; *Lichens/microbiology ; *Ascomycota/genetics ; *Microbiota ; *Genome, Fungal ; Metagenome ; }, abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.}, }
@article {pmid41617733, year = {2026}, author = {Thangaraj, S and Sun, J}, title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41617733}, issn = {2052-4463}, mesh = {Pacific Ocean ; *Metagenomics ; *Metagenome ; *Chlorophyll/analysis ; *Seawater/microbiology ; *Microbiota ; }, abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.}, }
@article {pmid41618101, year = {2026}, author = {Park, SJ and Özdinç, BE and Coker, KG and Walsh, DM and Fox, DJ and Evans, S and Farahnik, J and Moffat, K and Boomgaarden, M and Mischley, LK}, title = {Metagenomics indicates an interplay of the microbiome and functional pathways in Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {12}, number = {1}, pages = {}, pmid = {41618101}, issn = {2373-8057}, abstract = {Previous studies suggest there are distinct gut microbial and functional variations in patients with Parkinson's disease (PwPD) that may reveal potential microbiome signatures or biomarkers to aid in early detection of the disease. In this case-control study, we used whole genome sequencing to compare the stool samples of 55 PwPD to 42 healthy controls (HC) from a public database (BioProject Accession PRJEB39223). For bacterial phyla, we observed a greater relative abundance in Firmicutes and Actinobacteria among PwPD, while that of Bacteroidetes was lower. For phages, PwPD had a greater relative abundance of Siphoviridae, Tectiviridae, and Podoviridae, while Microviridae was lower. Moreover, we described 10 functional pathways that most significantly differed between PwPD and HC (all P < 0.0001). In conclusion, significant differences were observed in gut bacteria, phages, and functional pathways between PwPD and HC that both support and conflict with previous case-control studies and warrant further validation.}, }
@article {pmid41618136, year = {2026}, author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX}, title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41618136}, issn = {1471-2180}, support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; }, abstract = {BACKGROUND: The Tibetan antelope (Pantholops hodgsonii), an iconic species endemic to the Qinghai-Tibet Plateau, thrives at altitudes of 4,500–5,000 m under conditions of extreme hypoxia, cold, and limited nutrition. As a critical mediator of host physiology, the gut microbiome may play a key role in supporting these adaptations.
RESULTS: This study presents the first genome-centric investigation of bile acid (BA) metabolism in the gut microbiome of the Tibetan antelope, unveiling unique microbial pathways that potentially facilitate survival in harsh environments. Comparative analysis of metagenome-assembled genomes revealed that the antelope’s BA-metabolizing microbiota is taxonomically distinct from that of other Caprinae species and humans, with only two of the top ten BA-producing genera shared across groups. Importantly, individuals infected with Blastocystis exhibited marked differences in BA-related KEGG ortholog (KO) profiles compared to uninfected counterparts. Our findings highlight that the proportion of bile salt hydrolase (K01442) genes in the gut microbiota of Tibetan antelopes is higher than that in other Caprinae species and humans. Among them, the genus Alistipes carries the highest proportion of K01442 in the Tibetan antelope’s gut microbiota. Additionally, infection-associated KO gene shifts were observed, suggesting a microbial contribution to the Tibetan antelope’s remarkable physiological resilience.
CONCLUSIONS: In Tibetan antelopes, Alistipes was the dominant genus associated with bile acid synthesis. While bile acid synthesis KO distributions were broadly similar across species, K01442 higher proportion than other in Tibetan antelope gut microbiomes. Furthermore, Blastocystis infection altered three key bile acid synthesis KOs and induced distinct shifts in gut microbiome composition.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04750-0.}, }
@article {pmid41618383, year = {2026}, author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A}, title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {25}, pmid = {41618383}, issn = {1297-9716}, support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; EDU-1868-2022//Junta de Castilla y León/ ; }, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; *Swine Diseases/microbiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; *Brachyspira hyodysenteriae/physiology ; Feces/microbiology ; Disease Susceptibility/veterinary/microbiology ; }, abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.}, }
@article {pmid41618433, year = {2026}, author = {Wang, Y and Zuo, W and Huang, J and Sun, F and Du, Y}, title = {Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {41618433}, issn = {1474-760X}, support = {EF-2125142//National Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Benchmarking ; High-Throughput Nucleotide Sequencing/methods ; *Sequence Alignment/methods ; Software ; }, abstract = {BACKGROUND: Metagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) provides a powerful approach to study microbial communities by linking genomic content with spatial interactions. Hi-C complements shotgun sequencing by revealing taxonomic composition, functional interactions, and genomic organization within a single sample. However, aligning Hi-C reads to metagenomic contigs is challenging due to variable insert sizes of Hi-C paired-end reads, multi-species complexity, and gaps in assemblies. Although several benchmark studies have evaluated general alignment tools and Hi-C data alignment, none have specifically focused on metagenomic Hi-C data.
RESULTS: We evaluated seven alignment strategies commonly used in Hi-C analyses: BWA MEM -5SP, BWA MEM default, BWA aln default, Bowtie2 default, Bowtie2 -very-sensitive-local, Minimap2 default, and Chromap Hi-C default. We benchmarked these tools on one synthetic dataset and seven real-world environments. Performance was assessed based on the number of inter-contig Hi-C read pairs and their impact on downstream tasks, such as binning quality.
CONCLUSIONS: We show that BWA MEM -5SP generally outperformed all other tools across most environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrated the highest computational efficiency.}, }
@article {pmid41618437, year = {2026}, author = {Chong-Nguyen, C and Fuentes Artiles, R and Pilgrim, T and Yilmaz, B and Döring, Y}, title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.}, journal = {Biology of sex differences}, volume = {17}, number = {1}, pages = {24}, pmid = {41618437}, issn = {2042-6410}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Coronary Artery Disease/microbiology/metabolism ; *Sex Characteristics ; Female ; Male ; }, abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.
METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.
RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.
CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.}, }
@article {pmid41618766, year = {2026}, author = {Yan, Y and Li, F and Huang, T and Cheng, Y and Liao, Y and Liu, H}, title = {Intraocular infection of Moraxella nonliquefaciens accompanied by secondary angle-closure glaucoma: A case report.}, journal = {The Journal of international medical research}, volume = {54}, number = {1}, pages = {3000605251411736}, pmid = {41618766}, issn = {1473-2300}, mesh = {Humans ; Male ; Anti-Bacterial Agents/therapeutic use ; *Endophthalmitis/microbiology/complications ; *Eye Infections, Bacterial/microbiology/complications ; *Glaucoma, Angle-Closure/microbiology/etiology/diagnosis ; *Moraxella/isolation & purification ; *Moraxellaceae Infections/microbiology/complications/drug therapy/diagnosis ; Trabeculectomy/adverse effects ; Vancomycin/therapeutic use/administration & dosage ; Vitrectomy ; Middle Aged ; }, abstract = {Infectious endophthalmitis after ocular surgery is a rare complication that can result in severe vision loss. Moraxella nonliquefaciens is an opportunistic pathogen that rarely causes ocular infections. We report a rare case of Moraxella nonliquefaciens endophthalmitis complicated by secondary angle-closure glaucoma occurring years after trabeculectomy and cataract surgery. Cycloplegia resulted in deepening of the anterior chamber and opening of the angles. Metagenomic next-generation sequencing of the aqueous humor identified Moraxella nonliquefaciens. Following multiple intravitreal vancomycin injections and vitrectomy with posterior capsulectomy, direct communication between the anterior chamber and the vitreous cavity was established, leading to resolution of the condition. The patient's visual acuity was fully restored. We hypothesize that persistent infection with Moraxella nonliquefaciens may damage the lens zonules, resulting in zonular laxity and weakness; however, this represents only one possible mechanistic explanation and may play a secondary role in the development of secondary angle-closure glaucoma. Ophthalmologists should be aware that patients with Moraxella nonliquefaciens endophthalmitis may be at risk of zonular laxity and secondary angle-closure glaucoma, particularly years after trabeculectomy and cataract surgery. Prompt recognition and intervention may be vision-saving.}, }
@article {pmid41618858, year = {2026}, author = {Yang, T and Gao, Z and Huang, H and Zhang, C and Tang, Y and Qu, Q and Li, H and Ke, J and Chen, Z and Feng, M and Zhou, H and Shu, Y and Yuan, W}, title = {Gut-Metabolome-Proteome Interactions in Age-Related Hearing Loss: Insights from Fecal Microbiota Transplantation and Multi-Omics Analyses.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {18}, pages = {e14269}, doi = {10.1002/advs.202514269}, pmid = {41618858}, issn = {2198-3844}, support = {81873702//National Natural Science Foundation of China/ ; 81470694//National Natural Science Foundation of China/ ; 82225014//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 2024NF008//National Clinical Research Center for Otolaryngologic Diseases/ ; CSTB2023TIAD-KPX0059//Chongqing Technology Innovation and Application Development Special Project/ ; 2022DBXM006//Major Programs of Chongqing Science and Health Union/ ; cstc2022ycjh-bgzxm0126//Chongqing Talent Project/ ; CSTB2022NSCQ-MSX0553//Chongqing Natural Science Foundation/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation/methods ; *Proteome/metabolism ; *Metabolome/physiology ; Proteomics/methods ; Disease Models, Animal ; *Presbycusis/metabolism/microbiology ; Male ; Metabolomics/methods ; Mice, Inbred C57BL ; Aging/metabolism ; Multiomics ; }, abstract = {Age-related hearing loss (ARHL) is a prevalent sensory disorder lacking disease-modifying interventions. The biological drivers, particularly the contribution of the gut microbiota and gut-inner ear crosstalk, remain poorly defined. Here, we utilize germ-free (GF) mice and fecal microbiota transplantation (FMT) to isolate microbiota-dependent effects on ARHL progression. Through integrated metagenomic, metabolomic, and proteomic profiling, we map molecular signatures of auditory aging and uncover functional gut-inner ear network, prioritizing 5-hydroxytryptophan (5-HTP) as a key intermediate metabolite within this network. Furthermore, in an aging-like House Ear Institute-Organ of Corti 1 (HEI-OC1) model, 5-HTP exhibits protective effects, potentially mediated through the PI3K/Akt-antioxidant signaling axis. Collectively, this study provides a valuable multi-omics resource and highlights microbiota-derived metabolic regulation as a promising avenue for biomarker discovery and therapeutic development in ARHL.}, }
@article {pmid41619209, year = {2026}, author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z}, title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.}, journal = {Cell reports}, volume = {45}, number = {2}, pages = {116930}, doi = {10.1016/j.celrep.2026.116930}, pmid = {41619209}, issn = {2211-1247}, mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; Fresh Water ; *Fishes/microbiology/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.}, }
@article {pmid41619244, year = {2025}, author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS}, title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.}, journal = {Tropical biomedicine}, volume = {42}, number = {4}, pages = {435-445}, doi = {10.47665/tb.42.4.010}, pmid = {41619244}, issn = {2521-9855}, mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.}, }
@article {pmid41619271, year = {2026}, author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB}, title = {Functional Pathways of the Gut Microbiome Associated with SCFA Profiles in Preclinical Alzheimer's Disease.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2025.1539}, pmid = {41619271}, issn = {2152-5250}, abstract = {Functional activities of the gut microbiome, particularly those contributing to short-chain fatty acid (SCFA) metabolism, play a central role in host-microbe interactions and are linked to neuroinflammatory mechanisms underlying Alzheimer's disease (AD). How microbial metabolic functions relate to SCFA concentrations and cerebral amyloid-β (Aβ) burden during the preclinical stage of AD remains poorly understood. In this study, faecal metagenomes from 87 cognitively unimpaired adults were profiled using HUMAnN3 to generate MetaCyc pathway abundance data, normalised and filtered to retain pathways present in at least 30% of participants. A keyword-based search identified 362 SCFA-related pathways spanning acetate, propionate, butyrate, isobutyrate, valerate and isovalerate metabolism. Associations between microbial functions, SCFA concentrations and Aβ status were evaluated using Spearman correlations, Kruskal-Wallis tests across SCFA quartiles, and multivariable linear regression with false discovery rate correction, supported by canonical correspondence analysis and network modelling. A total of 38 significant SCFA pathway correlations were identified. Acetate, butyrate and total SCFA levels showed positive associations with biosynthetic pathways, including L-arginine biosynthesis II, peptidoglycan biosynthesis and flavin biosynthesis, whereas fermentative pathways such as pyruvate fermentation to acetone and lysine fermentation to butanoate were negatively correlated. Butyrate quartiles demonstrated dose-dependent increases in biosynthetic functions and declines in fermentative routes. Canonical Correspondence Analysis (CCA) confirmed a significant multivariate association, and network analysis revealed enhanced fermentative and methanogenic connectivity among Aβ High participants. These findings indicate that amyloid burden is associated with a shift from anabolic to fermentative microbial metabolism and may inform future studies examining potential mechanistic links in preclinical AD.}, }
@article {pmid41619464, year = {2026}, author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A}, title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.}, journal = {The Science of the total environment}, volume = {1016}, number = {}, pages = {181482}, doi = {10.1016/j.scitotenv.2026.181482}, pmid = {41619464}, issn = {1879-1026}, mesh = {*Palm Oil ; *Hydrogen/metabolism ; *Microbial Consortia ; *Petroleum/metabolism ; Biodegradation, Environmental ; Bioreactors ; Oil and Gas Fields ; Hydrocarbons/metabolism ; Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/metabolism ; }, abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.}, }
@article {pmid41619482, year = {2026}, author = {Wang, M and Ye, X and Hsu, CY and Fugate, H and Zhang, X and Adhikari, PA and Fan, P and Elliott, K and Macklin, K and Zhang, L}, title = {Application of culturomics to explore the cultivable microbiota and enable targeted bacterial isolation from the ceca of broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106527}, pmid = {41619482}, issn = {1525-3171}, abstract = {Metagenomic analyses have significantly advanced our understanding of microbial composition in the poultry gut. However, many microbes identified through metagenomic studies remain uncultured, largely due to the lack of understanding of their cultivation conditions, which hinders efforts to explore their functional roles in gut health and metabolism. In this study, we performed culturomics, a culture-dependent approach that combines diverse culture conditions with high-throughput 16S rRNA gene sequencing, to comprehensively assess the cultivability of chicken cecal microbiota and provide guidance for isolating target species of interest. Microbial profiling was performed using both culture-dependent (CD) and culture-independent (CI) approaches. For CI, genomic DNA (gDNA) was directly extracted from six broiler chicken cecal samples and subjected to full-length 16S rRNA gene sequencing. For CD, the same samples were cultured under 28 conditions, yielding 161 colony mixtures for sequencing. Based on diversity profiles of the colony mixtures, 10 conditions were selected for single-colony isolation and analysis. Results showed that CD and CI approaches identified 350 and 502 bacterial species, respectively, with 160 species detected by both methods. The dominant species recovered by the CD approach,including Escherichia coli, Proteus mirabilis, Limosilactobacillus reuteri, Enterococcus faecalis, and Ligilactobacillus salivarius, were detected at much lower abundances in the CI analysis, highlighting the capacity of culturomics to enrich and recover minority taxa that are often poorly detected by CI apparoach. Cultivation profiling showed that MRS selectively enriched Limosilactobacillus and Ligilactobacillus as well as Lactobacillus, whereas CNAB and MSA enriched Enterococcus and Bacillus, respectively. Community diversity and structure were significantly influenced by culture conditions (P < 0.01), with medium as the primary factor and air condition as a secondary factor. Subsequent single-colony analysis from 10 selected culture conditions identified 150 single-species isolates belonging to 14 distinct bacterial species. This study provides foundational insight into the cultivability of chicken cecal microbiota, facilitating future research to isolate specific strains and characterize their roles in poultry health and nutrition.}, }
@article {pmid41619490, year = {2026}, author = {Deng, S and Zheng, X and Chu, H and Hong, L and Zhang, J and Yang, H and Gu, L and Pu, L}, title = {Antibiotic-free Wenchang chickens may promote blood levels of B vitamins by modulating the gut microbiota: An integrated analysis of cecal content metagenomics and serum metabolomics.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106506}, pmid = {41619490}, issn = {1525-3171}, abstract = {Through the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related genes, cecal microbiota, and untargeted serum metabolomics in Wenchang chickens from the NS strain (Normal strain) and the AFS strain (Antibiotic-free strain), and explored the relationships between their cecal microbiota and serum metabolites. Our results show that in the ileum, antioxidant-related indicators T-AOC (P < 0.05), T-SOD (P < 0.05), and GSH-PX (P < 0.05) were significantly higher in the AFS strain than in the NS strain, while MDA (P < 0.05) was significantly lower in the AFS strain than in the NS strain. The mRNA expression level of RORγt/FoxP3, which is related to immune regulation, was significantly lower in the AFS strain than in the NS strain (P < 0.05). The differential microorganisms in the cecum primarily included Muribaculum, Cryptobacteroides, Blautia, Enterocloster, Lachnoclostridium, Hydrogenoanaerobacterium, Ruminococcus, Subdoligranulum, Clostridioides, and Evtepia. The main differential metabolites in serum included folinic acid, biotin, lysophosphatidic acid (LPA), 3-hydroxy-3-methylbutanoic acid, 3-hydroxybutyric acid, and others. The differential metabolites are primarily enriched in the following metabolic pathways: gap junction, glycolipid metabolism, and fatty acid biosynthesis. In addition, the Pearson correlation analysis between the gut microbiota and serum metabolites showed that Blautia was positively correlated with folinic acid (P < 0.05) and biotin (P < 0.05); Lachnoclostridium was positively correlated with biotin (P < 0.01); and Ruminococcus was positively correlated with 3-hydroxybutyric acid (P < 0.05). This study mainly elucidates the metabolic characteristics of the antibiotic-free Wenchang chicken strain by analyzing gut microbiota and serum metabolites.}, }
@article {pmid41619541, year = {2026}, author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Alifrangis, M and Aarestrup, FM and Sonda, T}, title = {Genomic diversity of human adenoviruses in Tanzanian children under five: Insights into F40, F41, B, and rare A18 genotypes.}, journal = {Virology}, volume = {617}, number = {}, pages = {110813}, doi = {10.1016/j.virol.2026.110813}, pmid = {41619541}, issn = {1096-0341}, mesh = {Humans ; Tanzania/epidemiology ; *Adenoviruses, Human/genetics/classification/isolation & purification ; Infant ; *Genome, Viral ; Phylogeny ; *Genotype ; *Genetic Variation ; Child, Preschool ; *Adenovirus Infections, Human/virology/epidemiology ; Diarrhea/virology/epidemiology ; Male ; Female ; Metagenomics ; }, abstract = {Human adenoviruses (HAdVs) are important pathogens that are associated with a wide array of clinical diseases, particularly in the pediatric population. Despite numerous reports of HAdV infections in Tanzania, there are currently no whole genome sequences from this region available in global public databases. This gap presents challenges to our efforts to understand their dissemination and evolution over time. This study employed nanopore-based metagenomic sequencing to detect and sequence the whole genomes of HAdV strains in Tanzanian infants with diarrhea. We present the first whole genome of HAdV-A18 from Africa, representing only the third worldwide. Additionally, it includes the first complete genomes of HAdV-F40, HAdV-F41, and HAdV-B3 obtained from Tanzania. In addition, this study provides information on the enteric adenovirus lineages circulating in Tanzania. These findings provide crucial genomic insights into the diversity of viruses in sub-Saharan Africa and underscore the importance of genomic surveillance to deepen our understanding of adenovirus transmission and evolution.}, }
@article {pmid41619556, year = {2026}, author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y}, title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {152}, number = {}, pages = {157875}, doi = {10.1016/j.phymed.2026.157875}, pmid = {41619556}, issn = {1618-095X}, mesh = {Animals ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Signal Transduction/drug effects ; NF-kappa B/metabolism ; *Diarrhea/drug therapy ; Mice ; Receptors, G-Protein-Coupled/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; *Sesquiterpenes/pharmacology ; Fatty Acids, Volatile/metabolism ; Disease Models, Animal ; Lactobacillus/drug effects ; Mice, Inbred C57BL ; *Lactones/pharmacology ; *Saponins/pharmacology ; Spleen/drug effects ; }, abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.
PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.
METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.
RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-κB signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.
CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-κB-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-κB signaling pathway, which subsequently improves SDD in mice.}, }
@article {pmid41619830, year = {2026}, author = {Zheng, C and Zhang, Y and Wang, Y and Sun, Y and Wei, F and Zhang, Y and Ma, Y and Cai, M}, title = {Two-case cluster of rapidly progressive influenza B and Staphylococcus aureus pneumonia with one death.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108442}, doi = {10.1016/j.ijid.2026.108442}, pmid = {41619830}, issn = {1878-3511}, mesh = {Humans ; *Influenza, Human/complications/diagnosis/virology ; Male ; *Influenza B virus/isolation & purification/genetics ; *Staphylococcus aureus/genetics/isolation & purification ; *Coinfection/microbiology/virology ; *Pneumonia, Staphylococcal/microbiology/diagnosis/complications/drug therapy ; Fatal Outcome ; Exotoxins/genetics ; Middle Aged ; Leukocidins ; Bacterial Toxins/genetics ; Pneumonia, Necrotizing/microbiology ; Adult ; Retrospective Studies ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVES: To report a cluster of two epidemiologically linked construction workers with fulminant necrotizing pneumonia associated with co-infection by Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible Staphylococcus aureus (MSSA) and influenza B virus.
METHODS: Clinical characteristics, imaging findings, and microbiological results were retrospectively reviewed. Metagenomic next-generation sequencing (mNGS) was performed on sputum and bronchoalveolar lavage fluid after conventional diagnostic tests failed to identify the causative pathogens.
RESULTS: Following shared occupational exposure, both patients developed severe pneumonia. One patient experienced rapid progression and died. For the second patient, mNGS successfully identified co-infection with PVL-positive sequence type 22 MSSA and influenza B virus, prompting a timely shift to targeted antimicrobial therapy that led to survival after prolonged intensive care.
CONCLUSION: This report demonstrates the extreme virulence of PVL-positive MSSA-influenza co-infection, highlights the diagnostic value of mNGS in severe treatment-refractory pneumonia, and emphasizes the need for effective respiratory protection in high-risk occupational environments.}, }
@article {pmid41619833, year = {2026}, author = {Tran, LNB and Zhuo, R and Singha, M and Sekhon, H and Yang, S and Fishbein, GA and Tymchuk, C and Allyn, PR}, title = {First reported case of Capnocytophaga cynodegmi infective endocarditis: A diagnostic odyssey.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108446}, doi = {10.1016/j.ijid.2026.108446}, pmid = {41619833}, issn = {1878-3511}, mesh = {Humans ; *Capnocytophaga/isolation & purification/genetics ; Male ; Adult ; *Gram-Negative Bacterial Infections/diagnosis/microbiology/drug therapy ; *Endocarditis, Bacterial/diagnosis/microbiology/drug therapy ; Aortic Valve/microbiology/surgery ; Anti-Bacterial Agents/therapeutic use ; *Endocarditis/microbiology/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {Capnocytophaga cynodegmi, a commensal of canine and feline oral flora, is rarely implicated in human infections, with most cases limited to localized soft tissue infections. We present the first case of C. cynodegmi-associated infective endocarditis (IE) in a 39-year-old man with bicuspid aortic valve and alcohol use disorder. The patient presented with sepsis, aortic valve vegetations, and systemic complications, including heart failure and shock liver. Despite negative blood and valve cultures, metagenomic sequencing of plasma (Karius test) initially detected Capnocytophaga canimorsus, while targeted Next-Generation Sequencing (NGS) of explanted valve tissue confirmed C. cynodegmi (100% match). The patient underwent valve replacement and completed a 6-week course of ampicillin-sulbactam with clinical recovery. This case underscores the diagnostic challenges of fastidious pathogens and demonstrates the potential of C. cynodegmi to cause life-threatening IE. It highlights the necessity of advanced molecular diagnostics, such as NGS, in atypical cases of IE. Clinicians should consider zoonotic Capnocytophaga spp. in culture-negative IE, particularly in high-risk patients with animal exposure or valvular abnormalities.}, }
@article {pmid41619990, year = {2026}, author = {Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Qin, Y and Liu, S and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H}, title = {Antimicrobial resistance and genomic characterization of Escherichia coli isolated from mink in northern China.}, journal = {Microbial pathogenesis}, volume = {213}, number = {}, pages = {108328}, doi = {10.1016/j.micpath.2026.108328}, pmid = {41619990}, issn = {1096-1208}, mesh = {Animals ; *Mink/microbiology ; China ; *Escherichia coli/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Feces/microbiology ; Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli Infections/veterinary/microbiology ; Genome, Bacterial ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Escherichia coli (E. coli) is one of the most common commensal bacteria in the intestinal tract of humans and animals. It serves as a major reservoir of antimicrobial resistance genes and may facilitate their horizontal transfer among different hosts. In this study, 212 fecal samples were collected from mink across four northern provinces of China, a total of 110 E. coli isolates were recovered (isolation rate, 51.89 %). Preliminary antimicrobial screening was conducted using four clinically critical antibiotics, including ceftazidime (CAZ), polymyxin B (PMB), meropenem (MEM), and tigecycline (TGC), with CAZ resistance being the most prevalent, followed by PMB, MEM, and TGC. Further antimicrobial susceptibility testing against ten commonly used antibiotics in 49 representative isolates revealed universal multidrug resistance (MDR), including 100 % resistance to imipenem, tetracycline, enrofloxacin, florfenicol, and sulfamethoxazole. Genetic screening identified multiple resistance genes such as aac(3')-IIa, blaCTX-M, tet(A), and mcr-1. Conjugation assays demonstrated that CAZ resistance was the most transferable. Virulence profiling revealed a low prevalence of classical pathogenic virulence factors, with only six virulence gene types detected, consistent with the results of Galleria mellonella infection assays. Whole-genome sequencing of 41 representative isolates revealed 87 unique antibiotic resistance genes (ARGs) types spanning 14 antibiotic classes including alinically important determinants such as blaCTX-M, tet, and mcr, and 71 unique virulence genes assigned to 65 functions. Metagenomic analysis further identified diverse ARGs within the mink gut microbiota, with 21 shared between whole-genome and metagenomic sequencing. Correlation analysis suggested co-occurrence patterns among ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), particularly between ARGs and MGEs. Overall, mink-derived E. coli exhibited extensive MDR but limited classical pathogenic virulence, and the mink gut microbiota may represent an important reservoir and transmission hub for resistance genes in intensive farming ecosystems.}, }
@article {pmid41620043, year = {2026}, author = {Chang, XL and Xing, BS and Qin, Y and Xie, J and Li, ZB and Wang, XC and Chen, R and Li, YY}, title = {Sustained performance and microbial succession in novel artificial rumen system coupling dynamic membrane with methanogenic granules for acid absorption.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134119}, doi = {10.1016/j.biortech.2026.134119}, pmid = {41620043}, issn = {1873-2976}, mesh = {*Rumen/microbiology/metabolism ; Animals ; *Methane/metabolism ; Fermentation ; Fatty Acids, Volatile/metabolism ; *Membranes, Artificial ; Lignin/metabolism ; Biomass ; Bioreactors/microbiology ; *Acids/metabolism ; }, abstract = {Artificial rumen systems promise for converting lignocellulosic biomass into renewable products but face challenges in long-term operation. This study developed a novel artificial rumen system combined fermentation with acid absorption using methanogenic granules and a dynamic membrane. Over 480 days, volatile fatty acids (VFAs) were effectively separated by the dynamic membrane and immediately absorbed by granules, simulating natural ruminant acid absorption. Despite increasing the organic loading rate from 3.27 to 8.18 g-VS/L/day, stable VFA yields of 0.21-0.24 g-COD/g-VS were maintained. After 440 days, removal efficiencies for cellulose, hemicellulose, and lignin reached 62.7 %, 52.1 %, and 40.7 %, respectively. The acid absorption unit efficiently converted VFAs into biomethane (302-304 mL/g COD), showing high bioenergy potential. Metagenomic analysis confirmed key rumen microbes (Firmicutes, Bacteroidetes) were dominant, with enrichment of low-abundance species like Prevotella and Solobacterium that secreted lignocellulose-degrading enzymes. The system enables long-term biomass conversion and supports future high-load artificial rumen engineering.}, }
@article {pmid41620049, year = {2026}, author = {Xia, Q and Li, J and Li, Q and Hu, Z and Wu, H and Xie, H and Lu, J and Liu, H and Zhang, J}, title = {Immobile iron-rich particles enhance simultaneous nitrogen removal and phosphorus retention in treatment wetlands.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134129}, doi = {10.1016/j.biortech.2026.134129}, pmid = {41620049}, issn = {1873-2976}, mesh = {*Wetlands ; *Nitrogen/analysis/isolation & purification ; *Phosphorus/analysis ; *Eutrophication ; Iron/chemistry ; Bacteria/classification/genetics/metabolism ; Environmental Microbiology ; Phylogeny ; *Conservation of Natural Resources/methods ; }, abstract = {Eutrophication control requires cost-effective and sustainable technologies capable of simultaneously removing nitrogen and phosphorus from wastewater treatment plant (WWTP) effluents. Widely used post-treatment systems, treatment wetlands (TWs) typically exhibit limited nutrient removal because of imbalances in electron supply and demand, and rapid saturation of substrate adsorption capacity. In this study, immobile iron-rich particles (IIRPs) were introduced into TWs via a drainage-injection strategy to enhance nutrient removal from municipal WWTP effluent. Following the start-up phase, the IIRP-amended TWs consistently achieved effluent concentrations that met the target quasi-Class IV surface water quality standards (TN ≤ 10 mg L[-1]; TP ≤ 0.3 mg L[-1]) for 300 days of continuous operation. The enhanced NH4[+]-N and TN removal with iron-rich particles amendment could not be attributed to nitrification or anammox, as evidenced using qPCR, metagenomic binning, and removal profiles. Instead, Fe-N redox-coupling processes, including Fe(III) reduction-driven and Fe(II) oxidation-driven nitrogen-removal pathways, contributed to enhanced nitrogen removal. The IIRPs amendment increased the equilibrium phosphorus adsorption capacity of wetland substrate by threefold, and the improved phosphorus retention was attributed to Fe-P interactions. These findings reveal a coupled Fe-N-P mechanism that enables efficient and stable nutrient removal and provide a mechanistic foundation for developing low-carbon, sustainable strategies to upgrade existing TWs for advanced wastewater polishing.}, }
@article {pmid41620544, year = {2026}, author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A}, title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41620544}, issn = {2399-3642}, support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {Humans ; Ethiopia/epidemiology ; *Gastrointestinal Microbiome ; Child, Preschool ; Female ; Male ; Feces/microbiology ; *Urban Population ; *Diet, Western/adverse effects ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Life Style ; *Bacteria/classification/genetics ; }, abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.}, }
@article {pmid41620643, year = {2026}, author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R}, title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2623356}, pmid = {41620643}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Socioeconomic Factors ; Bacteria/classification/genetics/isolation & purification ; *Social Class ; }, abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.}, }
@article {pmid41620752, year = {2026}, author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M}, title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41620752}, issn = {2049-2618}, support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; }, mesh = {*Groundwater/microbiology ; *Plankton/classification/genetics ; *Microbiota/genetics ; Biofilms/growth & development ; Metagenomics/methods ; Oxidation-Reduction ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; Metagenome ; Proteobacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.
RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.
CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.}, }
@article {pmid41620987, year = {2026}, author = {Tian, H and Liu, J and Li, L and Ge, J}, title = {From Interface to Cell: The Complex Interaction and Transfer Process Coupling Mechanism between Microplastics and Antibiotic Resistance Genes.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {5039-5052}, doi = {10.1021/acs.est.5c11841}, pmid = {41620987}, issn = {1520-5851}, mesh = {*Microplastics ; *Drug Resistance, Microbial/genetics ; Polypropylenes ; }, abstract = {Microplastic-phase interfaces (MPPIs) were established as critical vectors for accelerating antibiotic resistance gene (ARG) dissemination. Through integrated anaerobic/aerobic wastewater treatment system experiments combined with physicochemical characterization, metagenomic sequencing, and molecular dynamics simulations (MD), we elucidated MP-ARG interaction mechanisms from the interfacial to the cellular scale. Polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) MPPIs underwent significant aging during 60 days of exposure, resulting in elemental enrichment (C/O/P), the formation of C═C/C-H/C-O/C-OH functional groups, and elevated oxidation. These transformations enhanced extracellular polymeric substance production (184.81 mg/g MLSS) and selectively enriched antibiotic-resistant bacteria, ARGs, and mobile genetic elements (MGEs), promoting horizontal gene transfer. XDLVO theory revealed spontaneous microbial adhesion (ΔGadh = -23.63 mJ/m[2]) driven by Lifshitz-van der Waals (LW) and acid-base interactions. MD demonstrated direct MP penetration into the membrane via dominant LW forces (-1200 kJ/mol) and increased permeability. Concurrently, compared with sewage water (SW), MPPIs induced a 2.06-fold overproduction of reactive oxygen species, which upregulated genes encoding efflux pumps (acrF, 3.2-fold), outer membrane porins (OmpF, 4.1-fold), and conjugative transfer genes (traF, 3.8-fold). Material-specific (PET > PE > PP) and oxygen-driven redox mechanisms governed ARG dissemination: aerobic conditions favored radical-driven oxidation and MGE entrapment, whereas anaerobic systems enhanced hydrophobic adhesion.}, }
@article {pmid41621269, year = {2026}, author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L}, title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.}, journal = {Water research}, volume = {293}, number = {}, pages = {125448}, doi = {10.1016/j.watres.2026.125448}, pmid = {41621269}, issn = {1879-2448}, mesh = {*Antimony/metabolism ; *Geologic Sediments/microbiology/chemistry ; Water Pollutants, Chemical ; *Amaranthaceae/growth & development/metabolism ; Microbiota ; Biodegradation, Environmental ; }, abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.}, }
@article {pmid41621514, year = {2026}, author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G}, title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.}, journal = {International journal of biological macromolecules}, volume = {346}, number = {}, pages = {150646}, doi = {10.1016/j.ijbiomac.2026.150646}, pmid = {41621514}, issn = {1879-0003}, mesh = {*Probiotics/administration & dosage/pharmacology/chemistry ; *Chitosan/chemistry ; *Mannans/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/drug effects/metabolism ; Animals ; Microspheres ; *Cellulose/chemistry ; Intestinal Mucosa/metabolism ; *Drug Delivery Systems ; Oxidation-Reduction ; Humans ; Sulfhydryl Compounds/chemistry ; }, abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.}, }
@article {pmid41621540, year = {2026}, author = {Sun, H and Han, Y and Ren, S and Zhang, X and Li, X and Bi, P and Chen, L and Zhu, L and Yang, G and Ma, J and He, Q}, title = {Convergent enrichment of core functional guilds involved in Fe-N metabolism in anammox and activated sludge: Insights into genome-resolved metagenomics.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134125}, doi = {10.1016/j.biortech.2026.134125}, pmid = {41621540}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Nitrogen/metabolism ; Oxidation-Reduction ; *Iron/metabolism ; *Bacteria/metabolism/genetics ; Anaerobiosis ; Denitrification ; }, abstract = {The coupled process of ferric ammonium oxidation (Feammox) and nitrate-dependent ferrous oxidation (NDFO) is a cost-effective nitrogen removal strategy, yet insufficient molecular evidence supports its microbial mechanisms. This study successfully established anaerobic Fe-N coupling systems using anammox sludge and activated sludge as inoculum. Batch experiments and microbial community analysis revealed that two systems achieved similar nitrogen removal, dominated by anammox and Feammox performed by anammox bacteria (AnAOB), with a minor NDFO contribution, and convergently enriched core functional guilds under identical environmental pressures. Genome-resolved metagenomics further indicated that the porin-cytochrome protein complex associated with extracellular electron transfer co-occurred with anammox genes in Brocadia sapporoensis, suggesting its potential Feammox capability. Meanwhile, the iron oxidation gene Cyc2 co-occurred with mtr pathway homologs and complete denitrification genes in IGN3 sp900696555, suggesting its role in NDFO. This genomic evidence supports their dual metabolic capabilities, providing new insights into nitrogen removal in the coupled Feammox-NDFO process.}, }
@article {pmid41622108, year = {2026}, author = {Deng, Z and Sanchis-López, C and Hernández-Plaza, A and Davín, AA and Huerta-Cepas, J}, title = {TreeProfiler: large-scale metadata profiling along gene and species trees.}, journal = {Molecular biology and evolution}, volume = {43}, number = {2}, pages = {}, pmid = {41622108}, issn = {1537-1719}, support = {SEV-2016-0672-18-2:PRE2018-084075//FPI-Severo Ochoa predoctoral fellowship/ ; CPP2021-008717//FPI-Severo Ochoa predoctoral fellowship/ ; MICIU/AEI/10.13039/501100011033//Proyecto de investigación financiado por/ ; FPU19/06635//Unión Europea NextGeneration/ ; PTA2019-017593-I/AEI/10.13039/501100011033//Research Technical Support Staff Aid/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; 51NF40_225148//NCCR Microbiomes/ ; DAF2020-218584//CZI/ ; PID2021-127210NB-I00//Silicon Valley Community Foundation/ ; //National Programme for Fostering Excellence in Scientific and Technical Research/ ; }, mesh = {*Phylogeny ; *Software ; *Metadata ; Genomics/methods ; Archaea/genetics ; }, abstract = {Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), reconstruct ancestral states, and uncover ecological associations. However, existing profiling tools are typically tailored to specific use cases, have limited scalability for large datasets, and lack robust methods to aggregate or summarize traits at internal tree nodes. Here, we present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes. TreeProfiler supports the profiling of custom continuous and discrete traits, as well as ancestral character reconstruction and phylogenetic signal tests. It also integrates commonly used genomic features, including multiple sequence alignments, protein domain architectures, and functional annotations. We demonstrate TreeProfiler's utility beyond traditional phylogenetic profiling, as well as its ability to efficiently handle massive datasets, by analyzing the functional diversification of the methyl-accepting chemotaxis protein family comprising over 400,000 genomic and metagenomic sequences and by profiling the relative abundance of 124,295 bacterial and archaeal species across 51 biomes. TreeProfiler is open-source and freely available at https://github.com/compgenomicslab/TreeProfiler.}, }
@article {pmid41622302, year = {2026}, author = {Li, S and Zhang, J and Han, L and Yu, Y and Mousa, AA and Zhu, W and Leng, J and Xie, F and Mao, S}, title = {Comparative metagenomic and metatranscriptomic analyses reveal the role of the gayal rumen and hindgut microbiome in high-efficiency lignocellulose degradation.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {18}, pmid = {41622302}, issn = {1674-9782}, support = {U2202203//Joint Funds of the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The gayal (Bos frontalis), a semi-domesticated bovine species, demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo, suggesting the presence of a specialized gastrointestinal microbiome. However, the functional mechanisms underlying this host-microbiome interaction remain poorly understood. Here, we conducted integrated metagenomic and metatranscriptomic analyses of rumen, cecum, and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.
RESULTS: The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle, evidenced by significantly higher (P < 0.05) fiber digestibility, cellulase and xylanase activities, and increased volatile fatty acids production despite identical feed intake. Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle, with notable enrichment of taxa specialized in lignocellulose degradation. Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes, particularly AA6, AA2, and AA3, primarily encoded by Prevotella, Cryptobacteroides, Limimorpha, and Ventricola. These enzymes are known to modify lignin structure to increase polysaccharide accessibility. These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade, especially effective in dismantling lignin barriers.
CONCLUSIONS: This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.}, }
@article {pmid41622335, year = {2026}, author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T}, title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.}, journal = {Journal of plant research}, volume = {139}, number = {2}, pages = {195-205}, pmid = {41622335}, issn = {1618-0860}, mesh = {*Lotus/microbiology/growth & development ; *Soil Microbiology ; Symbiosis ; *Mesorhizobium/physiology/genetics ; Root Nodules, Plant/microbiology ; *Microbiota ; Rhizobium/physiology ; Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.}, }
@article {pmid41623309, year = {2026}, author = {Luo, Y and Ding, H and Pan, J and Xu, G}, title = {Use of metagenomic next-generation sequencing to diagnose Tropheryma whipplei infection-related pneumonia: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {31}, number = {3}, pages = {75}, pmid = {41623309}, issn = {1792-1015}, abstract = {Whipple's disease is caused by Tropheryma whipplei (T. whipplei), an uncommon pathogen that is often related to gastrointestinal symptoms. Extraintestinal involvement, particularly pulmonary manifestations, is rare and poses notable diagnostic challenges. An objective technique for identifying undiscovered infections is the application of metagenomic next-generation sequencing (mNGS). The present case report described a 55-year-old female presenting with community-acquired pneumonia (CAP), who received empirical treatment with moxifloxacin, ultimately diagnosed through mNGS performed on bronchoalveolar lavage fluid. The results indicated that the patient was infected with T. whipplei and that the patient exhibited notable clinical improvement within 2 weeks following intravenous moxifloxacin during hospitalization and continuation of oral moxifloxacin following discharge. The present case report highlighted the utility of mNGS in diagnosing atypical infections and identified T. whipplei as a potential etiological agent of CAP in immunocompetent hosts.}, }
@article {pmid41623458, year = {2026}, author = {Li, QM and He, LS and Wang, Y}, title = {Small proteins from prokaryotes in the marine water column at full ocean depth.}, journal = {iScience}, volume = {29}, number = {2}, pages = {114585}, pmid = {41623458}, issn = {2589-0042}, abstract = {Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors.}, }
@article {pmid41623619, year = {2025}, author = {Wei, T and Qian, N and Wang, H and Song, Y and Wang, W and Li, Y and Zhao, Z and Xu, F and Yang, W}, title = {Wilson's disease-associated gut dysbiosis: novel insights into microbial functional alterations, virulence changes, and resistance markers.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1714276}, pmid = {41623619}, issn = {1664-302X}, abstract = {BACKGROUND: Although the gut microbiota is associated with a variety of metabolic, inflammatory, and neurological disorders through microbial dysbiosis, current studies on the gut microbiota in Wilson's disease (WD) remain limited. Critical gaps exist in understanding the roles of key functional microbial factors in WD pathogenesis, which hinders the acquisition of mechanistic insights into this disease.
OBJECTIVE: This study aims to characterize alterations in the gut microbiome associated with WD, with a particular emphasis on virulence factors (VFs) and antibiotic resistance genes (ARGs), as well as functional mobile genetic elements (MGEs), in order to elucidate their potential roles in disease progression and clinical manifestations.
METHODS: We analyzed fecal samples from 37 patients with WD and 33 healthy controls (HCs) using metagenomic sequencing, with a specific focus on examining virulence gene profiles and antibiotic resistance patterns and MGE composition in relation to liver function markers.
RESULTS: Beta diversity analysis revealed significant differences in the gut microbial community structure between patients with WD and HCs, and a distinct set of microbial taxa was identified that showed significant associations with clinical indicators. A gut microbial co-occurrence network identified key species playing central roles in the microbial community structure, including Prevotella stercorea, Firmicutes bacterium CAG 110, Bacteroides salyersiae, Lactococcus petauri, Streptococcus cristatus, Actinomyces sp. HMSC035G02, and Streptococcus viridans. Widespread functional dysbiosis was detected across multiple biological levels in patients with WD, with significant correlations identified between these microbial alterations and clinical indicators. Significant disruptions were identified in key metabolic pathways, including the Pentose Phosphate Pathway, Pyruvate Metabolism, and Starch and Sucrose Metabolism, which were associated with the dysregulation of carbohydrate-active enzymes (CAZymes). These alterations showed significant correlations with clinical markers of liver dysfunction (e.g., procollagen III N-terminal peptide PIIINP, aspartate transaminase/alanine transaminase AST/ALT). A total of 54 virulence factor (VF) genes exhibited differential abundance in WD, with 36 genes depleted and 18 enriched. Notably, these included colibactin genes (clbB, clbH) from Escherichia coli and type IV secretion system genes (aec19, pilB). These VFs were significantly associated with indicators of liver function (e.g., bilirubin levels) and coagulation abnormalities. Among the detected antibiotic resistance genes (ARGs), 21 exhibited disease-specific patterns in WD, notably tetQ (encoding tetracycline resistance), ErmB (conferring macrolide resistance), and cfxA6 (mediating cephamycin resistance). Furthermore, ARG profiles were associated with Bifidobacterium enrichment and showed significant correlations with lipid metabolism markers [e.g., triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)]. Critically, we identified significant enrichment of 60 functional mobile genetic elements (MGEs) in WD, spanning categories involved in DNA replication/repair, phage activity, and conjugative transfer, indicating heightened genomic plasticity and horizontal gene transfer potential. Strikingly, correlation network analysis revealed strong and specific co-occurrence between key ARGs (e.g., ErmX) and defined suites of MGEs, suggesting MGE-facilitated dissemination of resistance determinants.
CONCLUSION: Wilson's disease (WD) patients exhibit significant alterations in gut microbial community structure and functional dysbiosis, wherein the enrichment of virulence genes (such as colibactin genes clbB/clbH) and the specific antibiotic resistance genes (such as tetQ and ErmB), and the activation of mobile genetic elements are closely associated with clinical indicators including liver function impairment, coagulation abnormalities, and lipid metabolism disorders.}, }
@article {pmid41623622, year = {2025}, author = {Li, Y and Cheng, Y and Liu, W and Li, J and Li, S and Suriguga, and Ma, T and Kwok, LY and Cai, Z and Sun, Z}, title = {Gut microbial and functional signatures in breast cancer: an integrated metagenomic and machine learning approach to non-invasive detection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1722632}, pmid = {41623622}, issn = {1664-302X}, abstract = {INTRODUCTION: Breast cancer is associated with significant restructuring of the gut ecosystem. Gut microbial composition and function may influence cancer development and progression through immune modulation, metabolic regulation, and inflammation-related pathways.
METHODS: Using shotgun metagenomic sequencing of fecal samples from 38 stage I-III breast cancer patients and 36 age- and body mass index-matched healthy controls. Machine learning models were constructed to evaluate the diagnostic potential of integrated microbial and metabolic features.
RESULTS: Significant alterations were observed in gut microbiota composition, including depletion of beneficial taxa (Limosilactobacillus fermentum, Blautia sp.) and enrichment of Prevotella copri. Pathways involved in short-chain fatty acid and purine metabolism were reduced. The gut phageome exhibited structural changes and altered correlations with bacterial hosts. Predictive analysis revealed depletion of short-chain fatty acids (butyrate, propionate), purine intermediates (hypoxanthine, xanthine), and nicotinate in patients. A machine learning model integrating microbial and predicted metabolic features achieved an area under the curve values of 0.78 in the discovery cohort and 0.73 (recall = 0.74) in an independent validation cohort.
DISCUSSION: Coordinated gut microbiome, phageome, and metabolome alterations characterize breast cancer, offering potential non-invasive biomarkers and mechanistic insights for disease detection and intervention.}, }
@article {pmid41623634, year = {2025}, author = {Zeng, J and Gong, L and Qin, S and Fang, P and Shu, F and Zhang, W and Zhou, Y and Li, X and He, Q and Sun, P and Deng, H}, title = {Multi-omics reveals glutinous rice varieties shape Baijiu flavor via microbial and metabolic modulation.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1721127}, pmid = {41623634}, issn = {1664-302X}, abstract = {INTRODUCTION: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking.
METHODS: In this study, metagenomic, metaproteomic, and non-targeted GC-MS analyses of Zaopei, along with HS-SPME-GC-MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation.
RESULTS: The Wuliangye-specific variety Dajiugu, with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis, Enterobacter, and Klebsiella. Functional genera such as Saccharopolyspora, Pediococcus, and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu.
DISCUSSION: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.}, }
@article {pmid41623638, year = {2025}, author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Wan, Z and Zhang, T and Zhang, C}, title = {The human plasma anellome exhibits age- and sex-dependent patterns with links to cardiometabolic health in older adults.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1716110}, pmid = {41623638}, issn = {1664-302X}, abstract = {The human plasma virome is dominated by anelloviruses which are increasingly associated with several clinical conditions including among others HIV-1, COVID-19, autoimmune diseases, and cardiovascular and metabolic diseases. Due to their high genetic divergence, most studies investigated human anellome at broad family or genus level. These approaches obscure the contributions of specific anellovirus species to clinical conditions. We conducted plasma metagenomics in 218 individuals from young (0-16 years) and old (63-100 years) cohorts to resolve the anellome at the species level and examine its patterns across age, sex, and associations with cytokines and cardiometabolic outcomes. Older adults exhibited near-universal anellovirus detection and significantly higher abundance compared with youth. Species-specific analysis revealed that Alphatorquevirus_homin1 and Alphatorquevirus_homin13 were markedly enriched in diseased older adults. Predictive modeling based on machine learning algorithms distinguished disease status in the young cohort with high accuracy (AUC = 0.86), but performance was limited in the elderly (AUC = 0.58), suggesting a lack of diagnostic value in advanced age. Specific species abundances and diversity were associated with stroke and coronary heart disease, while cytokine correlations revealed module-specific immune signatures: Gammatorquevirus-dominated modules associated positively with pro-inflammatory cytokines and growth factors (e.g., IL-1β, IL-15, VEGF), whereas Beta- and some Alphatorquevirus-dominated modules showed predominantly negative correlations with several inflammatory and regulatory mediators (e.g., IL-6, TNF-α, IL-10). These findings demonstrate that the anellome is influenced by age and immune status and shows associations with cardiometabolic health, although these relationships do not guarentee diagnostic or causal significance. Additonally, we found no significant differences of Human endogenous retrovirus K Env expression between disease and healthy controls. This work underscores the importance of resolving human anollome to species level in future longitudinal studies to strengthen their clinical significance and biomarker potential.}, }
@article {pmid41623642, year = {2025}, author = {Kuang, HF and Jiang, XY and Tie, SY and Lian, K and Hao, MY and Xu, H and Huang, X and Yang, Y and Guo, Q and Li, J and Chen, LL}, title = {Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1738456}, pmid = {41623642}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.
METHODS: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.
RESULTS: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.
CONCLUSION: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.}, }
@article {pmid41623646, year = {2025}, author = {Thagulisi, F and Baatjies, L and Sharma, A and Ngom, JT and Nyambo, K and Jooste, T and Tapfuma, KI and Mavumengwana, V}, title = {Antimycobacterial activity of intertidal sediment-derived bacteria from False Bay, South Africa.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1745248}, pmid = {41623646}, issn = {1664-302X}, abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global health burden due to the pathogen's ability to develop resistance to current treatment options. Consequently, drug discovery studies are essential for identifying new antimycobacterial agents with novel mechanisms of action. This study investigated the antimycobacterial activity of crude extracts derived from mixed culturable bacteria isolated from intertidal marine sediments. The bacterial diversity of the bioactive mixed cultures was characterized using 16S rRNA gene-based metagenomic analysis. Their pathogen-targeted effects were evaluated against Mycobacterium smegmatis mc[2]155 and M. tuberculosis H37Rv, and THP-1-derived macrophages infected with M. smegmatis mc[2]155. Of the 48 mixed bacterial crude extracts derived from 17 intertidal marine sediments, five-PPB1, GCR1, BB1, PPB2, and CR1-demonstrated strong antimycobacterial activity against M. smegmatis mc[2]155 and M. tuberculosis H37Rv with minimum inhibitory concentrations ranging from 31.25 to 62.50 μg/mL and 7.8125 to 15.625 μg/mL, respectively. At 62.50 μg/mL, CR1 significantly reduced the intracellular M. smegmatis mc[2]155 burden in THP-1-derived macrophages, resulting in 28.08 ± 4.25% mean decrease in bacterial survival (p < 0.0001) and 94.4% ± 1.14 mean growth inhibition. From the CR1 mixed cultures, nine axenic bacterial isolates were cultivated, and their resulting crude extracts were evaluated for bioactivity. The identified isolates included Marinobacter maritimus, Psychrobacter celer, Pseudomonas benzenivor, Bacillus altitudinis, Bacillus aerius, Bacillus stratosphericus, and Paenibacillus glucanolyticus. Metabolite profiling of axenic crude extracts identified several compounds, including tenacibactin B, maremycin D1, and tubercidine. These findings suggest that South African intertidal marine sediments host diverse microbial communities capable of producing novel antimycobacterial agents.}, }
@article {pmid41624426, year = {2026}, author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N}, title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).}, journal = {Biodiversity data journal}, volume = {14}, number = {}, pages = {e178484}, pmid = {41624426}, issn = {1314-2828}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.}, }
@article {pmid41624871, year = {2025}, author = {Zhu, H and Hu, L and Feng, Z and Zhang, Z and Zhu, H and Li, H}, title = {Case Report: Murine typhus complicated by symmetrical peripheral gangrene: first report and diagnostic insights from metagenomic next-generation sequencing.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1746919}, pmid = {41624871}, issn = {1664-3224}, mesh = {Humans ; Female ; High-Throughput Nucleotide Sequencing ; Aged ; *Gangrene/diagnosis/etiology ; Metagenomics/methods ; *Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Rickettsia typhi/genetics ; Doxycycline/therapeutic use ; }, abstract = {BACKGROUND: Murine typhus, a flea-borne infection caused by Rickettsia typhi, often presents with nonspecific symptoms that delay diagnosis. While usually self-limiting, it can rarely progress to multiple organ dysfunction syndrome (MODS). We report the first case of murine typhus complicated by symmetrical peripheral gangrene (SPG), in which metagenomic next-generation sequencing (mNGS) enabled rapid diagnosis and guided timely doxycycline therapy.
CASE PRESENTATION: A 69-year-old female from South China was hospitalized with persistent abdominal pain and low-grade fever. She was a farmer and had suspected animal exposure. Laboratory investigations revealed hypoxia, abnormal coagulation profile, hepatorenal impairment, and thrombocytopenia. Despite empirical antibiotic therapy, her condition deteriorated progressively, manifested as hemodynamic instability, respiratory failure, and the emergence of purpuric-petechial cutaneous eruptions. Immediate interventions were initiated, including administration of vasoactive agents and mechanical ventilation. Based on mNGS, R. typhi was confirmed, she received targeted antibiotic treatment with intravenous doxycycline (100 mg twice daily). On the hospital day 16, gangrene of all four extremities became evident. The patient underwent amputation of all four extremities and survived, with systemic symptoms gradually resolving during 6-months follow-up.
CONCLUSION: This first reported case of murine typhus complicated by symmetrical peripheral gangrene (SPG) establishes its potential to cause life-threatening multiorgan failure. Metagenomic next-generation sequencing (mNGS) resolved the diagnostic challenge by rapidly identifying Rickettsia typhi, guiding life-saving doxycycline therapy and underscoring its value in severe zoonotic infections.}, }
@article {pmid41625489, year = {2026}, author = {Zhou, L and Liu, J and Li, S and Xiong, Y and Qin, F and Luo, Z and Huang, D and Chen, H and Wang, X}, title = {Association between anxiety symptoms on risky e-biking riding behavior among adolescents: based on gut-brain axis.}, journal = {Comprehensive psychoneuroendocrinology}, volume = {25}, number = {}, pages = {100337}, pmid = {41625489}, issn = {2666-4976}, abstract = {OBJECTIVE: This study aimed to investigate the association between anxiety symptoms and risky e-bike riding behavior (RERB) among adolescents and to explore whether gut microbiota mediates this relationship.
METHODS: Adolescents using e-bikes were recruited through a combined online and offline recruitment approach. Data collection involved supervised electronic questionnaire completion in face-to-face settings, with biological samples collected independently by participants. Anxiety symptoms were assessed using the Generalized Anxiety Disorder-7 scale. RERB were evaluated via a structured questionnaire, yielding separate scores for aggressive behaviors (ABS), violation behaviors (VBS), and negligent behaviors (NES), along with total behavior scores (TBS). Fecal samples were obtained for metagenomic sequencing to characterize gut microbiota composition. Multiple linear regression was employed to elucidate the associations between anxiety symptoms and RERB. Partial Least Squares Path Modeling (PLS-PM) was applied to evaluate the potential mediating role of gut microbiota in these associations.
RESULTS: A total of 71 adolescents were included in this cross-sectional study. Anxiety symptoms were significantly associated with RERB, including TBS and VBS (both P < 0.05). Among the 15 microbial genera identified from fecal samples, 17 species showed significant association with both anxiety symptoms and RERB. PLS-PM modeling revealed a significant mediating effect of specific gut microbiota in the anxiety→behavior pathway, particularly for TBS and VBS. In contrast, for ABS, a reverse pathway-microbiota→anxiety→behavior-was found significant.
CONCLUSIONS: Anxiety symptoms were significantly associated with RERB among adolescents. Specific gut microbiota may mediate these associations, suggesting a potential microbiota-brain-behavior pathway.}, }
@article {pmid41625740, year = {2025}, author = {Su, J and Liu, K and Wu, X and Lin, B and Ying, F and Zhu, Y and Li, M and Guo, P}, title = {Case Report: Confocal microscopy in the early diagnosis of microsporidial keratitis.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1745070}, pmid = {41625740}, issn = {2296-858X}, abstract = {This report describes a rare case of microsporidial stromal keratitis (MSK) complicated by corneal perforation in a 69-year-old male farmer with a 5-month history of ocular redness, pain, photophobia, and epiphora. In vivo confocal microscopy (IVCM) revealed pathognomonic findings-hyperreflective double-walled spore casings and vesicular clusters, providing the earliest diagnostic clues for microsporidia infection. Subsequent metagenomic next-generation sequencing (mNGS) and histopathology confirmed Microsporidia species. The patient underwent therapeutic penetrating keratoplasty followed by targeted anti-microsporidial therapy, achieving globe preservation and visual improvement. This case underscores IVCM's pivotal role in diagnosing MSK, particularly in atypical presentations. Because MSK remains a rare corneal disorder, its insidious progression necessitates high clinical vigilance. In summary, IVCM's ability to detect microsporidial structures in real-time significantly enhances early diagnosis, complementing molecular methods like mNGS. We conclude that IVCM, as a non-invasive and rapid diagnostic tool, provides a convenient and efficient means for the early differentiation of challenging corneal infections.}, }
@article {pmid41625836, year = {2025}, author = {Matsukawa, M and Sakai, Y and Aoki, K and Ishii, Y}, title = {Urinary Microbiome Profiling by Shotgun Metagenomic Sequencing in Women Having Acute Cystitis-Like Symptoms With Negative Urine Cultures.}, journal = {Cureus}, volume = {17}, number = {12}, pages = {e100451}, pmid = {41625836}, issn = {2168-8184}, abstract = {BACKGROUND: Women presenting with typical symptoms of acute cystitis but with negative urine cultures, termed acute cystitis-like symptoms with negative urine cultures (ACNCs) in this study, are not uncommon. Despite previous attempts to detect bacterial DNA in urine, the etiology remains unclear. Although alterations in the urinary microbiome have been linked to other urological disorders, its involvement in ACNC has not been thoroughly investigated.
METHODS: Between September 2016 and December 2017, midstream urine samples were collected from women aged ≥16 years who had at least one typical symptom of acute cystitis and a negative urine culture. Samples were obtained at the initial (V1) and follow-up (V2) visits. Shotgun metagenomic sequencing (SMG) was performed via an Illumina MiSeq system. Taxonomic analysis at the genus level included taxa with ≥10 assigned reads in samples with ≥10,000 human-subtracted reads (HSRs).
RESULTS: Of 206 eligible women, 15 (7.3%; median age, 65 years) met the ACNC criteria and were enrolled. SMG was conducted for 15 samples at V1 and nine samples at V2. At V1, the HSR varied widely, and only five samples met the criteria for reliable interpretation. Seven samples, particularly those with high-grade pyuria, contained fewer than 1,000 HSRs, indicating potentially very low microbial loads or technical limitations. ACNC microbiomes demonstrated marked interindividual variation in taxonomic composition. The predominant taxa most frequently observed were Lactobacillus spp., Gardnerella spp., and JC polyomavirus. Conventional uropathogens, such as Escherichia spp., were not identified at interpretable levels. At V2, microbial diversity remained heterogeneous, but eight samples yielded sufficient read counts for interpretation.
CONCLUSIONS: While conventional uropathogens below interpretable criteria are unlikely to be responsible for most ACNCs, it is not necessarily recommended to regard the leading taxon in each case as the cause or to exclude microbiological involvement simply due to a low HSR because no validated metagenomic signature distinguishes pathogens from commensals. However, the observed diversity in ACNC microbiome profiles may reflect a heterogenous group of microbial conditions, including potentially viral, and nonmicrobial etiologies.}, }
@article {pmid41625959, year = {2026}, author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR}, title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.}, journal = {Food chemistry. Molecular sciences}, volume = {12}, number = {}, pages = {100344}, pmid = {41625959}, issn = {2666-5662}, abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.}, }
@article {pmid41625985, year = {2026}, author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {15}, pmid = {41625985}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.}, }
@article {pmid41626090, year = {2026}, author = {Chen, L and Tang, M and Wang, Q and Jiang, H}, title = {Why a Mycobacterium Avium Infected Patient Showed a Positive Xpert MTB/RIF Result?.}, journal = {Clinical case reports}, volume = {14}, number = {2}, pages = {e71965}, pmid = {41626090}, issn = {2050-0904}, abstract = {This article discusses whether a MAC infected patient with a positive Xpert MTB/RIF test has a co-infection with Mycobacterium tuberculosis (MTB). The patient presented with chronic, indolent pulmonary patchy shadows on imaging but lacked typical symptoms. The MTB antigen-specific interferon-gamma enzyme-linked immunospot assay (T-SPOT.TB) was negative. Bronchoalveolar lavage fluid (BALF) testing yielded conflicting results: Xpert MTB/RIF assay detected trace levels of MTB DNA, whereas reverse dot blot hybridization confirmed the presence of Mycobacterium avium complex (MAC); in contrast, metagenomic next-generation sequencing (mNGS) returned a negative result for all pathogens. Mycobacterial culture ultimately returned positive; however, the MPB64 assay-employed for species identification-yielded a negative result, indicating a probable nontuberculous mycobacterial (NTM) infection. Despite contradictory lab results, the patient's symptoms and culture findings favored MAC infection. However, MTB infection could not be definitively ruled out in this patient, so a treatment regimen combining anti-tuberculosis and anti-MAC medications (isoniazid, rifampicin, ethambutol, and azithromycin) was initiated, leading to significant radiographic improvement. The discordance between the positive Xpert MTB/RIF result and other diagnostic evidence highlights important diagnostic challenges, underscoring the need for integrated clinical interpretation and providing actionable insights for clinicians.}, }
@article {pmid41626263, year = {2026}, author = {Liu, Y and Fu, H}, title = {Pulmonary Tropheryma whipplei Infection Presenting With Multiple Thick-Walled Cavities on Chest CT: A Case Report and Literature Review.}, journal = {Respirology case reports}, volume = {14}, number = {2}, pages = {e70487}, pmid = {41626263}, issn = {2051-3380}, abstract = {Whipple's disease (WD) is a rare chronic multisystem infectious disease caused by the actinomycete Tropheryma whipplei. Pulmonary involvement is uncommon, and its clinical manifestations lack specificity, with diverse imaging findings, making it prone to misdiagnosis. We report a rare case of a 50-year-old woman who presented with a 2-week history of cough. Chest CT showed multiple thick-walled cavities in both lungs, a highly unusual presentation for WD pneumonia. Routine microbiological tests, including acid-fast staining and culture of bronchoalveolar lavage fluid (BALF), were negative, which made the diagnosis challenging. Metagenomic next-generation sequencing (mNGS) of BALF detected T. whipplei, confirming the diagnosis of WD pneumonia. After oral doxycycline treatment, follow-up chest CT showed complete resolution of the pulmonary cavities. This case demonstrates that multiple thick-walled cavities may be a characteristic imaging manifestation of WD pneumonia, highlights the diagnostic value of mNGS for this rare infection, and supports oral doxycycline monotherapy as an effective treatment option for isolated pulmonary TW infection.}, }
@article {pmid41626594, year = {2026}, author = {Sapino, R and Fernández-González, Á and Castresana, J}, title = {Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.}, journal = {Evolutionary applications}, volume = {19}, number = {2}, pages = {e70199}, pmid = {41626594}, issn = {1752-4571}, abstract = {Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.}, }
@article {pmid41627236, year = {2026}, author = {Yu, M and Wang, Y and Huangfu, K and Wu, S and Huang, H and Ma, Z and Wang, Y and Qiu, Y and Liu, S}, title = {Oxygen Vacancy-Engineered High-Entropy Oxide Nanozymes for Spatiotemporal Cascading Antifouling in Marine Environments.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e13363}, doi = {10.1002/smll.202513363}, pmid = {41627236}, issn = {1613-6829}, support = {52272271//National Natural Science Foundation of China/ ; }, abstract = {The catalytic versatility and compositional tunability of oxidative attack-based nanozymes offer a promising strategy for marine antifouling, yet their performance is often constrained by insufficient active-site accessibility, transient catalytic intermediates and restricted diffusion. Inspired by haloperoxidases (HPOs) in marine organisms, this study reports oxygen vacancy (Vo)-enriched high-entropy oxides (Vo-HEO) as multifunctional nanozymes to address these challenges. The entropy-stabilized multicomponent lattice, synergistically coupled with abundant Vo sites, reconfigures electronic structures and diversifies catalytic pathways, enabling efficient HPO-mimetic generation of hypobromous acid (HOBr), which is a selective and long-lived biocide (half-life > 36 days) capable of disrupting bacterial quorum sensing (QS) signals and oxidizing key biomolecules. By further integrating persistent HOBr with highly reactive hydroxyl radicals, Vo-HEO establishes a spatiotemporally cascading protective regime at the substrate interface, combining long-range QS suppression in the bulk phase with rapid oxidative eradication at the nano-biological interface, ultimately reducing bacterial adhesion by 90%. Microbiological characterization and metagenomic sequencing analyses further verify that Vo-HEO systematically collapses the coordination of microbial communication and energy metabolism across temporal and spatial scales. Collectively, this work demonstrates intelligent regulation of marine microecology and establishes a paradigm for adaptive antifouling design.}, }
@article {pmid41627458, year = {2026}, author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T}, title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {53}, pmid = {41627458}, issn = {1432-0614}, support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; }, abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.}, }
@article {pmid41627460, year = {2026}, author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT}, title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.}, journal = {Archives of microbiology}, volume = {208}, number = {4}, pages = {167}, pmid = {41627460}, issn = {1432-072X}, support = {DTDLCN.63/22//Ministry of Science and Technology/ ; }, mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification/virology ; *Bacteriophages/genetics/isolation & purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; }, abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.}, }
@article {pmid41627733, year = {2026}, author = {Hałakuc, P and Maciszewski, K and Karnkowska, A}, title = {Euglenid Extrachromosomal DNA: Assembly and Annotation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3013}, number = {}, pages = {109-120}, pmid = {41627733}, issn = {1940-6029}, mesh = {*Computational Biology/methods ; *Molecular Sequence Annotation/methods ; DNA, Ribosomal/genetics ; Genome, Mitochondrial ; *Euglenozoa/genetics ; Genome, Plastid ; DNA, Mitochondrial/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Euglenids (Euglenozoa) contain several forms of extrachromosomal DNA (ecDNA) in their cells, including the ribosomal DNA operon (rDNA), the mitochondrial genome (mtDNA), and, in photosynthetic species, the plastid genome (ptDNA). These ecDNA elements can be easily and accurately assembled and annotated even from limited sequencing data, such as single-cell genomic or metagenomic datasets. They are an important source of information for phylogenomic analyses, metabarcoding and evolutionary studies. In this chapter, we present a robust and adaptable bioinformatics pipeline for the identification, assembly, and annotation of extrachromosomal DNA from whole-genome datasets. The pipeline was developed with euglenids in mind and takes into account their unique genomic features, but can also be adapted for other Euglenozoa (and protists). This approach enables the recovery of organellar and rDNA sequences with high confidence and supports both targeted studies and large-scale environmental analyses.}, }
@article {pmid41627741, year = {2026}, author = {Castañeda, S and Ramírez, JD and Poveda, C}, title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3013}, number = {}, pages = {265-297}, pmid = {41627741}, issn = {1940-6029}, mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.}, }
@article {pmid41628276, year = {2026}, author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E}, title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {2}, pages = {e0013576}, pmid = {41628276}, issn = {1935-2735}, mesh = {Animals ; *Virome ; *Metagenome ; *Triatominae/virology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; Species Specificity ; Texas ; Female ; Arizona ; Insect Vectors/virology ; New Mexico ; }, abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.}, }
@article {pmid41628665, year = {2026}, author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM}, title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: A proof-of-concept placebo-controlled randomized trial.}, journal = {Osteoarthritis and cartilage}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joca.2026.01.630}, pmid = {41628665}, issn = {1522-9653}, abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.
METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600 mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.
RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.
CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.
TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.}, }
@article {pmid41628768, year = {2026}, author = {Frizzera, A and Vázquez, N and Sacristán, H and Tapella, F and Lovrich, G and Khalaf, A and Bojko, J and Cremonte, F}, title = {Patagonian king crabs (Lithodes santolla and Paralomis granulosa) and their diseases: Pathogen survey and taxonomic clarification of Areospora rohanae (Microsporidia).}, journal = {Journal of invertebrate pathology}, volume = {216}, number = {}, pages = {108560}, doi = {10.1016/j.jip.2026.108560}, pmid = {41628768}, issn = {1096-0805}, mesh = {Animals ; *Microsporidia/classification/genetics/isolation & purification/physiology ; *Anomura/microbiology/parasitology ; Symbiosis ; }, abstract = {Lithodid crabs constitute a valuable natural resource with commercial interest; however, their health status in South America is scarcely studied. The presence of pathogens may have a negative impact on affected populations, endangering the fishery. This study surveys the symbionts present in populations of the king crab, Lithodes santolla, and the stone/false king crab, Paralomis granulosa, using histology, transmission electronic microscopy, and molecular analyses to characterise various symbionts. The histological and molecular data revealed a wide range of infections in L. santolla, including prokaryotic microorganisms, Areospora rohanae (Microsporidia), apicomplexan gregarines, ciliated protozoans, ectoparasitic crustaceans, and various epibiotic associations. In the case of P. granulosa, apicomplexan gregarines, ciliated protozoans, and various ectoparasites were observed. Molecular analyses confirmed the presence of the microsporidian A. rohanae, occurring at high prevalences (30%) in L. santolla, and some bacterial associations. We use metagenomic tools to extract a partial genome of this parasite to aid in its identification and taxonomic position, which leads us to erect the taxonomic orders Astathelohaniida and Areosporida and further clarify the previously assigned: "Glugeida+". The results of this study represent the first broad survey for symbionts in both king crab species and take us another step forward to a more accurate microsporidian taxonomy.}, }
@article {pmid41628857, year = {2026}, author = {Theodosiou, AA and Bogaert, D and Cleary, DW and Fady, PE and Feehily, C and Gilbert, JA and Greenhough, B and Guardabassi, L and Hall, LJ and Harman, T and Kuijper, EJ and Lebeer, S and Lorimer, J and Spector, TD and Jones, CE}, title = {Microbiome research in practice: priorities for clinical translation and impact.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.01.021}, pmid = {41628857}, issn = {1469-0691}, abstract = {BACKGROUND: Rapid advances in microbiome science have sparked clinical and commercial enthusiasm for interventions, yet translation into practice risks outpacing both mechanistic understanding and the infrastructure required for safe adoption.
OBJECTIVES: To outline a coordinated research, clinical, social, and policy agenda for advancing safe, effective, and equitable microbiome-based interventions.
SOURCES: We convened an interdisciplinary Royal Society-funded expert workshop (Leeds, UK, October 2024) with international leaders in microbiome science, clinical trials, regulation, and social science. Thematic analysis of workshop discussions and written contributions identified priority domains for translation.
CONTENT: Three intersecting priorities emerged: scientific credibility, practical viability, and stakeholder engagement. Scientific credibility demands investment in multiomic and strain-level characterization of host-microbiome interactions on a large scale, benchmarking of clinical and microbiological endpoints, and harmonization of trial conduct and reporting. Clinical adoption requires fit-for-purpose regulation, diversified investment to address funding bottlenecks, and coordinated capacity building. Meaningful stakeholder engagement with clinicians, patients, policymakers, and the public is essential to foster confidence, develop clinically relevant research questions, and ensure equitable implementation of any new technology.
IMPLICATIONS: To realize the clinical impact of microbiome interventions, sustained collaboration across disciplines is essential. This review offers a translational roadmap and actionable priorities to accelerate safe, effective, and equitable microbiome-based interventions-ensuring the field fulfils its clinical potential and delivers real-world impact.}, }
@article {pmid41628881, year = {2026}, author = {Sun, G and Guo, S and Yao, Y and Lin, Z and Gao, H and Stauber, RH and Li, BC and Ding, GB}, title = {Facile immobilization of an unstable recombinant α-L-rhamnosidase on magnetite nanoparticles for efficient naringin biotransformation.}, journal = {International journal of biological macromolecules}, volume = {347}, number = {}, pages = {150652}, doi = {10.1016/j.ijbiomac.2026.150652}, pmid = {41628881}, issn = {1879-0003}, mesh = {*Flavanones/metabolism/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Magnetite Nanoparticles/chemistry ; Biotransformation ; *Glycoside Hydrolases/chemistry/metabolism/genetics ; Recombinant Proteins/chemistry/metabolism ; Enzyme Stability ; Hydrogen-Ion Concentration ; Temperature ; Humans ; Biocatalysis ; }, abstract = {α-L-Rhamnosidase is a significant biocatalyst that specifically cleaves terminal α-L-rhamnose group from natural flavonoid diglycosides, enabling the biocatalytic production of high-value flavonoid glucosides like prunin from naringin. Compared to its precursor naringin, prunin exhibits superior solubility and bioavailability, making this enzymatic conversion commercially valuable for the food and pharmaceutical industry. However, the industrial application of free α-L-rhamnosidases faces significant challenges, including enzyme instability, difficulty in recovery, and unsatisfactory reusability. To address these issues, this study developed an innovative magnetically recoverable biocatalyst (Fe3O4-Rha) through covalent immobilization of recombinant α-L-rhamnosidase from human fecal metagenome onto Fe3O4 nanoparticles using EDC/NHS chemistry, and the immobilization parameters were systematically optimized. The successful preparation of Fe3O4-Rha was verified by TEM, FTIR, TGA, and SQUID analysis. Fe3O4-Rha retained the catalytic property of free Rha in terms of optimal pH and temperature but exhibited superior tolerance on organic solvent especially ethanol and isopropanol. Moreover, Fe3O4-Rha could effectively biotransform naringin to prunin and maintained 61.34% of initial activity after 5 cycles. In a scaled-up reaction system, Fe3O4-Rha also efficiently converted naringin into prunin and the complete conversion was achieved within 10 h. This work successfully developed a magnetically recoverable immobilized α-L-rhamnosidase system for the efficient and reusable biotransformation of naringin, offering a promising approach for the enzymatic modification of bioactive small molecules using biological macromolecular catalysts.}, }
@article {pmid41629097, year = {2026}, author = {Lyu, WT and Jia, QQ and Tong, X and Fan, H}, title = {[STAT1 gain-of-function mutation leading to disseminated Talaromyces marneffei infection combined with hemophagocytic syndrome: a case report].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {2}, pages = {184-187}, doi = {10.3760/cma.j.cn112147-20250730-00456}, pmid = {41629097}, issn = {1001-0939}, mesh = {Humans ; Male ; Talaromyces ; Adult ; *Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology ; *STAT1 Transcription Factor/genetics ; *Gain of Function Mutation ; *Mycoses/genetics/complications/microbiology ; Antifungal Agents/therapeutic use ; Mutation ; }, abstract = {This study reports a 28-year-old HIV-negative male with a STAT1 gain-of-function mutation who presented with a systemically disseminated Talaromyces marneffei (TM) infection, which was complicated by hemophagocytic lymphohistiocytosis (HLH). The patient presented with recurrent fever, weight loss, oral mucosal ulcers, as well as lymphopenia and markedly elevated inflammatory markers during the acute phase of the illness. Imaging revealed scattered ground-glass opacities and nodular shadows in both lungs, as well as localized bronchiectasis, and splenomegaly. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and bone marrow aspirate specimens revealed TM-specific sequences. Whole-exome sequencing was performed to elucidate the underlying mechanism of recurrent fungal infections. This revealed a de novo heterozygous dominant mutation in the STAT1 gene (c.1151G>A, p.Gly384Asp), localized to the DNA-binding domain at amino acid position 384. This confirmed a STAT1 gain-of-function (STAT1-GOF) variant, which is consistent with the clinical phenotype of impaired antifungal immunity. Over the clinical course, the patient developed HLH. Following a two-week course of intravenous amphotericin B liposome (5 mg/kg per day), followed by oral voriconazole maintenance therapy (200 mg, twice daily), the patient exhibited significant improvements in clinical symptoms and laboratory parameters. Notably, the marked resolution of HLH was closely linked to the successful eradication of the fungal infection. This case highlights three critical clinical implications: (1) Patients with a predisposition to primary immunodeficiency disorders (e.g., STAT1-GOF mutations) should be evaluated for disseminated TM infections, even if they are HIV-negative; (2) mNGS is instrumental in etiological diagnosis and facilitates early intervention for fungal infections; (3) early identification of genetic defects establishes a theoretical basis for precision medicine and guides targeted therapeutic strategies.}, }
@article {pmid41629364, year = {2026}, author = {Spörri, L and Studer, JM and Kreuzer, M and Rotzetter, J and Schärer, D and Largiadèr, CR and Jaggi, D and Zinkernagel, MS and Zysset-Burri, DC}, title = {Linking the microbiome to the complement system in geographic atrophy.}, journal = {NPJ genomic medicine}, volume = {11}, number = {1}, pages = {}, pmid = {41629364}, issn = {2056-7944}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, abstract = {Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.}, }
@article {pmid41629500, year = {2026}, author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y}, title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6991}, pmid = {41629500}, issn = {2045-2322}, support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; }, abstract = {UNLABELLED: Metabolites play a crucial role in the interactions between the host and its microbiome, influencing disease pathogenesis. To explore metabolic signals linked to Crohn’s Disease (CD), we analyzed paired fecal and serum metabolomics, combined with microbial characterization. Metabolites were identified using liquid chromatography-mass spectrometry, and microbial data were obtained through V4-16 S sequencing and shotgun metagenomics. 202 serum and 294 fecal samples from 80 CD patients and 43 healthy controls were included. Longitudinal analysis highlighted individual variations in metabolic signals and microbial composition. 6602 significant correlations were identified between fecal metabolites and microbes, implying their involvement in microbial-driven disease pathways. Notably, five CD-enriched fecal carbohydrates positively correlated with oral bacteria (e.g., Veillonella parvula, Veillonella dispar, Streptococcus). Additionally, arachidonic acid and three of its derivatives were associated with R. gnavus and Fusobacteria, often implicated in CD pathogenesis. Active CD, defined clinically or by elevated biomarkers (CRP, fecal-calprotectin), exhibited heterogeneous metabolic signatures, with consistent associations between fecal metabolites and established microbial-based indices (CD-related dysbiosis index and alpha diversity). This suggests that specific fecal metabolites potentially sustain microbial imbalances and that targeting metabolic and microbial shifts may offer novel strategies to promote healthier states in CD.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38558-9.}, }
@article {pmid41629563, year = {2026}, author = {Suksa, W and Li, WJ and Luo, ZH and Jiao, JY and Ponce, V and Nuñez-Montero, K and Arce-Johnson, P and Sharma, NR and Thamchaipenet, A and Narsing Rao, MP}, title = {Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6922}, pmid = {41629563}, issn = {2045-2322}, support = {PHD/0136/2561//The Royal Golden Jubilee Ph.D. Program (RGJ Ph.D.), Thailand Research Fund, National Research Council of Thailand (NRCT)/ ; }, mesh = {*Hot Springs/microbiology ; *Metagenomics/methods ; Phylogeny ; *Metagenome ; Genome, Bacterial ; Base Composition ; *Actinobacteria/genetics/classification/isolation & purification ; }, abstract = {Metagenomic analysis of the hot spring led to the recovery of a high-quality metagenome-assembled genome (MAG), MPNR_HS_01, affiliated with the phylum Actinomycetota. Taxonomy analysis assigned the MAG to "Candidatus Solincola", clustering closely with "Candidatus Solincola tengchongensis". MPNR_HS_01 was 2.82 Mb in size, assembled into 27 contigs, with a G+C content of 63.4%, 49 tRNAs, 4 rRNAs, 98.7% completeness, and no detectable contamination. Functional annotation revealed the presence of complete glycolysis and nonoxidative pentose phosphate pathways, while the tricarboxylic acid cycle was incomplete. Notably, MPNR_HS_01 encoded Wood-Ljungdahl pathway, suggesting carbon assimilation. Energy conservation was supported by hydrogenases, heterodisulfide reductase, Rnf complex, and V-type ATPase. Stress adaptation traits included genes for heat shock proteins, proline biosynthesis, and ion transporters involved in osmotic homeostasis. Although lacking flagellar machinery, MPNR_HS_01 possessed type IV pili and genes associated with twitching motility. Secondary metabolite analysis identified a betalactone biosynthetic gene cluster. Genome-relatedness analyses showed that MPNR_HS_01 was distinct from "Candidatus Solincola" species, with both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values falling below the established species threshold (95-96% ANI and 70% for dDDH), supporting its designation as a novel species, for which we propose the name "Candidatus Solincola uaceae" sp. nov.}, }
@article {pmid41629580, year = {2026}, author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N}, title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6983}, pmid = {41629580}, issn = {2045-2322}, support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; }, mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Chickens/microbiology/growth & development ; *Salmonella typhimurium ; *Salmonella Infections, Animal/microbiology/prevention & control ; *Poultry Diseases/microbiology/prevention & control ; Dietary Supplements ; Animal Feed ; Ligilactobacillus salivarius ; }, abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.}, }
@article {pmid41629813, year = {2026}, author = {Astudillo-Guerrero, C and Garrido, Á and Masferrer, D and Sepúlveda, C and Olavarría, L and Del Campo, R and Bravo-Sagua, R and Cubero, FJ and Salech, F and Thumala-Dockendorff, D and Urrutia, PJ and Quera, R and Bunout, D and Espinoza, R and Jorquera, G}, title = {Randomized, double-blind, placebo-controlled trial of fecal microbiota transplantation from young physically active donors to promote resilient aging: clinical trial protocol (ARMOR study).}, journal = {BMC geriatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41629813}, issn = {1471-2318}, abstract = {BACKGROUND: Sarcopenia, characterized by the progressive loss of skeletal muscle mass and strength in older adults, is a key determinant of frailty and functional decline. Affecting up to 15% of individuals aged 65–80 years and more than 50% of those over 80, sarcopenia not only compromises physical autonomy but also increases the risk of metabolic dysfunction and cognitive decline. Emerging evidence suggests that age-related gut microbiota dysbiosis contributes to these impairments by reducing microbial diversity and altering host metabolic signaling, leading to chronic inflammation and mitochondrial dysfunction. The present study aims to evaluate the safety, tolerability, and preliminary efficacy of oral fecal microbiota transplantation derived from young, physically active donors administered to older adults, focusing on outcomes related to functional autonomy, muscle performance, metabolism and cognition.
METHODS: This is a double-blind, randomized, placebo-controlled clinical trial involving community-dwelling adults aged 65–84 years. Participants will be randomized 1:1 to receive either FMT capsules or placebo following a short course of oral rifaximin (or placebo). Assessments will be performed at baseline and at 4, 8, and 20 weeks post-intervention. The primary outcomes are safety and tolerability, as well as changes in the Global Index of Functional Autonomy (GDLAM battery) and muscle strength. Secondary outcomes include gait speed, body composition (DXA), metabolic biomarkers, gut microbiota composition (shotgun metagenomics), cognitive performance, and psychological well-being.
EXPECTED IMPACT: By restoring microbial diversity and function, FMT from young, active donors may enhance muscle quality, cognitive resilience, and metabolic health in older adults. This study introduces a novel, non-invasive therapeutic approach based on lyophilized and encapsulated microbiota, offering a feasible and scalable strategy to promote healthy aging.
TRIAL REGISTRATION: ClinicalTrials.gov NCT06649981. Date of registration October 21, 2024.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12877-025-06920-7.}, }
@article {pmid41629849, year = {2026}, author = {Li, L and Wang, J and Li, Z and Xing, D}, title = {High fever with rash: a case report of spotted fever group rickettsial infection at a construction site.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41629849}, issn = {1471-2334}, abstract = {BACKGROUND: Spotted Fever Group Rickettsiae (SFGR) infection is one of the global public health threats. With the improvement of current hygiene conditions, the incidence of rickettsial infections has significantly decreased compared with previous years; however, in clinical practice, rickettsial infections should still be considered in the differential diagnosis of febrile cases of unknown etiology.
CASE PRESENTATION: A construction worker, residing in crowded and poor sanitary conditions, presented with high fever and diffuse cutaneous rash, without reporting other associated discomfort. Empirical treatment with cephalosporin antibiotics failed to alleviate the symptoms. Given the unknown etiology of the patient’s high fever and rash, routine etiological tests yielded negative results, with concurrent abnormalities in the white blood cell differential count of the complete blood count. A strong suspicion of infection by an unusual microorganism prompted the performance of metagenomic next-generation sequencing (mNGS) on venous blood. This test identified infection with Rickettsia rickettsii belonging to the spotted fever group, confirming a rickettsial infection. Following the establishment of the etiology, the antimicrobial treatment regimen was adjusted, and the patient was administered doxycycline for antimicrobial therapy. After treatment, the patient’s body temperature returned to normal, the rash resolved, and the patient was discharged in a state of full recovery.
SUMMARY: For patients working at construction sites with poor living conditions who present with high fever and rash but lack evidence of conventional microbial infection, clinicians should enhance their differential diagnostic capabilities and maintain vigilance for the occurrence of rickettsial infection.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12735-7.}, }
@article {pmid41629888, year = {2026}, author = {Luo, M and Xiao, X and Wu, Y}, title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41629888}, issn = {1471-2431}, support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; }, abstract = {BACKGROUND: Phototherapy serves as the primary treatment for neonatal hyperbilirubinemia (NH). This research aims to investigate the impact of phototherapy on the gut microbiota of NH, and to provide reliable theoretical evidence for the clinical application of phototherapy in such cases.
METHODS: In this self-controlled longitudinal study, 26 newborns diagnosed with NH were enrolled. Fecal samples were collected before (pre-treatment) and 48 h after (post-treatment) initiating phototherapy. The gut microbiota was profiled using high-throughput 16 S ribosomal RNA (rRNA) gene sequencing. Gut microbiota composition and diversity were analyzed using standard bioinformatics pipelines. Data were processed with standard bioinformatics tools for taxonomic annotation, diversity analysis, and functional prediction based on the COG, KEGG, and MetaCyc databases. Statistical significance was assessed using the Wilcoxon signed-rank test (P < 0.05).
RESULTS: While no significant differences were observed at the species level, analysis at the genus level revealed significant alterations in the gut microbiota. The genera Clostridium and Megamonas were identified as significantly increased post-phototherapy. Linear discriminant analysis effect size (LEfSe) analysis further confirmed distinct microbial signatures between the two groups: pre-treatment samples were enriched with families such as Porphyromonadaceae, Lachnospiraceae, Alcaligenaceae, Ruminococcaceae, Moraxellaceae, and the order Pseudomonadales. In contrast, post-treatment samples were predominantly characterized by the class Erysipelotrichi and its associated taxa (Erysipelotrichales and Erysipelotrichaceae). α-diversity indices (Sobs, Chao, Shannon, Simpson) showed no significant differences between the two groups, whereas β-diversity analysis indicated significant microbial community separation (P < 0.05). Predicted functional profiles (based on 16 S rRNA gene data using PICRUSt2) suggested predominant roles in metabolism, genetic information processing, and biosynthesis. However, no significant differences were observed between the pre- and post-treatment groups.
CONCLUSIONS: Phototherapy significantly modulated the gut microbial composition of neonates with NH, notably increasing the abundance of Clostridium and Megamonas, and shifting the community towards Erysipelotrichi, while overall microbial functional capacity remained stable. These findings highlight the dynamic yet resilient nature of the neonatal gut microbiota under phototherapy and provide a foundation for microbiome-informed management strategies in neonatal hyperbilirubinemia.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06531-0.}, }
@article {pmid41630069, year = {2026}, author = {Jia, X and Zhang, Y and Tian, B and Zhang, G and Mao, S and Qian, W and Sun, D and Liu, J}, title = {Integrative analysis of rumen microbiota and host multi-organ interactions underlying feed conversion efficiency in Hu sheep.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {19}, pmid = {41630069}, issn = {1674-9782}, support = {2021YFF1000703//National Key Research and Development Program of China/ ; KJJQ2025020//Fundamental Research Funds for the Central Universities/ ; HS202302//Research Fund of Tarim University/ ; }, abstract = {BACKGROUND: Rumen microbiota drive fermentation and contribute to variation in feed efficiency among ruminants, yet the underlying host-microbe mechanisms remain poorly understood. This study explores how rumen microbes shape feed conversion efficiency (FCR) through integrated interactions with multiple host organs.
RESULTS: We applied a multi-omics strategy-combining rumen metagenomics and host multi-organ transcriptomics-in Hu sheep with divergent FCR. From a uniform cohort of 150 weaned male Hu lambs, 13 low-FCR (LFCR) and 13 high-FCR (HFCR) individuals were selected for integrated analyses. LFCR sheep exhibited greater growth performance and higher ruminal propionate concentrations compared with HFCR animals. The ruminal microbiomes were enriched in Saccharofermentans and Succinivibrionaceae_UBA2804, and showed functional convergence on amino acid biosynthesis, central carbon metabolism, and propionate-oriented fermentation in LFCR sheep. Carbohydrate-active enzyme profiles indicated that LFCR animals favored fiber- and starch-associated modules (GH126, CBM27, EPS-GT), whereas HFCR animals were enriched in host-glycan and uronic acid-degrading families (CE14, GH89, PL15). Hydrogen metabolism highlighted a clear dichotomy: LFCR animals redirected H₂ toward propionate and sulfate reduction, while HFCR animals retained greater butyrate-producing and methanogenic capacity. Transcriptomic profiling across rumen epithelium, liver, and muscle identified tissue-specific regulatory modules. Only the liver showed strong enrichment of carbohydrate metabolism, with a complete glycogen turnover and glucose export system (GYS2, PYGL, PGM2, G6PC1) and pathways linking microbial short-chain fatty acids to gluconeogenesis. In contrast, muscle efficiency modules were dominated by contractile and cytoskeletal genes (e.g., MYL2, TNNC1, TPM3), reflecting optimized energy expenditure rather than substrate metabolism. No efficiency-associated modules were detected in the rumen epithelium, consistent with its role in propionate absorption rather than metabolism.
CONCLUSIONS: The rumen microbiota of LFCR sheep possess highly efficient capacities for volatile fatty acid and amino acid synthesis, thereby enhancing energy utilization at its source. The resulting propionate further promotes hepatic gluconeogenesis, directly supplying energy for muscle cell growth and ultimately improving FCR. Thus, co-metabolism between rumen microbiota and the liver provides energy for muscle cell growth and is a key determinant of improved feed efficiency.}, }
@article {pmid41630101, year = {2026}, author = {Zheng, A and Wang, F and Li, Y and Li, W and Wu, W and Gan, J and Jin, Y}, title = {Concurrent pulmonary candidiasis and tuberculosis in type 2 diabetes mellitus: immune pathogenesis and multidisciplinary management challenges: a case report.}, journal = {Journal of medical case reports}, volume = {20}, number = {1}, pages = {}, pmid = {41630101}, issn = {1752-1947}, mesh = {Humans ; Male ; *Diabetes Mellitus, Type 2/complications ; Aged ; *Tuberculosis, Pulmonary/drug therapy/complications/diagnosis/immunology ; Tomography, X-Ray Computed ; Antifungal Agents/therapeutic use ; Antitubercular Agents/therapeutic use ; Mycobacterium tuberculosis/isolation & purification ; Fluconazole/therapeutic use ; Insulin/therapeutic use ; }, abstract = {BACKGROUND: Type 2 diabetes mellitus predisposes to opportunistic pulmonary infections. We report sequential invasive pulmonary candidiasis followed by tuberculoma in a patient with newly diagnosed type 2 diabetes mellitus and summarize diagnostic pitfalls and management lessons.
CASE PRESENTATION: A 67-year-old Han Chinese man with no previously known diabetes presented with cough and severe hyperglycemia (random glucose 36.3 mmol/L; HbA1c 12.7%). Initial chest computed tomography showed right‑upper‑lobe consolidation. Bronchoalveolar lavage metagenomic next‑generation sequencing detected abundant Candida albicans and sputum Gram stain showed Gram‑negative bacteria predominance; sputum culture yielded no definite pathogen, blood cultures were negative, and human immunodeficiency virus test was negative. After intravenous then oral fluconazole plus intensive insulin therapy, the consolidation regressed. Suspected secondary organizing pneumonia was treated with tapering methylprednisolone. One month later, a new 1.5 cm × 1.3 cm solid nodule appeared in the prior lesion bed. computed tomography‑guided biopsy revealed necrosis, and tissue metagenomic next-generation sequencing confirmed Mycobacterium tuberculosis; standard anti‑tuberculosis therapy was initiated.
CONCLUSION: In patients with diabetes and pulmonary lesions, concomitant or sequential fungal and tuberculous infections should be actively sought with stepwise microbiology (including bronchoalveolar lavage and tissue‑based methods) and early molecular testing (metagenomic next-generation sequencing/Xpert). Steroid exposure for organizing pneumonia may worsen or unmask tuberculosis and must be weighed against infectious risk. Multidisciplinary care (endocrinology-pulmonology-infectious diseases) and rigorous glucose control are essential.}, }
@article {pmid41630175, year = {2026}, author = {Lim, SJ and Breitbart, M}, title = {Genetic Features of the Scuticociliate Pathogen Philaster sp. Isolate FWC2 That Causes Sea Urchin Mass Mortality.}, journal = {The Journal of eukaryotic microbiology}, volume = {73}, number = {2}, pages = {e70065}, pmid = {41630175}, issn = {1550-7408}, support = {//University of South Florida/ ; OCE- 2527605//National Science Foundation/ ; }, mesh = {Animals ; *Sea Urchins/parasitology/microbiology ; Phylogeny ; *Oligohymenophorea/genetics/isolation & purification/classification ; Base Composition ; Genome, Mitochondrial ; Sequence Analysis, DNA ; }, abstract = {A scuticociliate most closely related to Philaster apodigitiformis caused mass mortalities of diadematoid sea urchins and was cultured as Philaster sp. isolate FWC2. We sequenced the metagenomic content of this isolate, which was predicted to represent ≤ 56% of the complete genome. Based on k-mer counts, the haploid genome size was predicted to be 122-136 Mbp. We assembled and annotated a 4,088 bp nuclear ribosomal operon, a 41,396 bp mitochondrial genome with 19.22% G + C content, 24 protein-coding genes, 6 tRNA genes, and 2 rRNA genes, and a protein sequence homologous to β-PKA in Philaster apodigitiformis potentially involved in host infection.}, }
@article {pmid41630294, year = {2026}, author = {Li, R and Liu, X and Song, G and Zhang, CQ and Shen, LJ and Li, WX and Bai, ZP}, title = {Misdiagnosis of pulmonary paragonimiasis as tuberculosis: A case report.}, journal = {Medicine}, volume = {105}, number = {5}, pages = {e47555}, pmid = {41630294}, issn = {1536-5964}, mesh = {Humans ; *Paragonimiasis/diagnosis/drug therapy ; Female ; Adolescent ; *Tuberculosis, Pulmonary/diagnosis/drug therapy ; *Diagnostic Errors ; Praziquantel/therapeutic use ; Antitubercular Agents/therapeutic use ; Anthelmintics/therapeutic use ; *Lung Diseases, Parasitic/diagnosis/drug therapy ; Animals ; }, abstract = {RATIONALE: Pulmonary paragonimiasis and pulmonary tuberculosis exhibit overlapping clinical and imaging manifestations, resulting in frequent misdiagnosis in endemic areas. This case underscores the value of metagenomic next-generation sequencing (mNGS) in correcting such misdiagnoses and emphasizes the importance of managing drug-drug interactions between antituberculosis agents and praziquantel.
PATIENT CONCERNS: An 18-year-old female from Yunnan, a paragonimiasis-endemic region, presented with recurrent cough, expectoration, and hemoptysis for 4 years. She was initially diagnosed with pulmonary tuberculosis based on a positive tuberculin pure protein derivative test and chest computed tomography findings but failed to respond to antituberculosis therapy.
DIAGNOSES: Pulmonary paragonimiasis (initially misdiagnosed as pulmonary tuberculosis).
INTERVENTIONS: In-hospital tuberculosis-related tests (GeneXpert MTB/RIF, sputum/bronchoalveolar lavage fluid culture, bronchoscopic biopsy) were negative. Bronchoalveolar lavage fluid mNGS identified 87 Paragonimus sequences, and Paragonimus antibody enzyme-linked immunosorbent assay was positive. A history of raw crab ingestion was confirmed. Antituberculosis treatment was discontinued for 4 weeks (due to drug interaction), followed by oral praziquantel (1.2 g, 3 times daily for 3 consecutive days).
OUTCOMES: Hemoptysis resolved within 15 days of treatment initiation, and peripheral blood parameters returned to normal ranges. Chest computed tomography at 2 months posttreatment showed marked reduction in lesion size, and complete resolution of pulmonary cavities was observed at the 6-month follow-up, with no recurrence of symptoms.
LESSONS: For chronic respiratory symptoms unresponsive to antituberculosis treatment in endemic regions, proactive inquiry of raw freshwater crustacean consumption history and combined use of serology/mNGS can improve diagnostic accuracy. A 4-week washout period after rifampicin discontinuation is critical before praziquantel administration.}, }
@article {pmid41630746, year = {2025}, author = {Yang, B and Zhang, Y and Su, S and He, J and Hu, J and Wang, K}, title = {Metagenomic next-generation sequencing identifies tick-carried pathogens on Tarim Red Deer in Southern Xinjiang.}, journal = {Open veterinary journal}, volume = {15}, number = {11}, pages = {6109-6117}, pmid = {41630746}, issn = {2218-6050}, mesh = {Animals ; *Deer/parasitology ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics ; China/epidemiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Ticks/virology/microbiology ; }, abstract = {BACKGROUND: Ticks are important vectors for a wide range of pathogens, including viruses, bacteria, and protozoa, that impact both humans and animals. Recent advances in metagenomic sequencing have established it as a powerful tool for uncovering the microbial diversity within ticks, enabling the discovery of previously unrecognized pathogens.
AIM: This study aimed to enrich the pathogen database for Tarim red deer in southern Xinjiang and provide experimental data to aid in the diagnosis, prevention, control, and treatment of viral diseases in Tarim red deer.
METHODS: Metagenomic sequencing was employed to analyze the viral species carried by ticks parasitizing the red tarim deer. Additionally, enzyme-linked immunosorbent assay based antibody testing was conducted on 195 red deer samples from four farms M01, M02, M03, and M04 to detect antibodies against the Orf virus.
RESULTS: Next-generation sequencing was used to obtain partial sequences of viruses and bacteria, with further analysis focusing on viruses with higher abundance, such as mule deer pox virus and Orf virus. Serological testing for Orf virus antibodies in 195 red deer samples identified 7 positive cases, resulting in a positivity rate of 3.59% (7/195). Positivity rates were 5.26% (4/76) and 6.12% (3/49) for farms M02 and M04, respectively, whereas no seropositive individuals were identified at farms M01 and M03.
CONCLUSION: This study expands the current knowledge of tick-borne pathogens in southern Xinjiang by identifying diverse viral species associated with tick-infested Tarim red deer. The findings confirm the presence of Orf virus in red deer populations, particularly on farms M02 and M04. These results underscore the importance of ongoing surveillance efforts and offer valuable insights into the diversity and geographical distribution of tick-associated viruses within the arid and semi-arid ecosystems of southern Xinjiang.}, }
@article {pmid41630783, year = {2026}, author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS}, title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100544}, pmid = {41630783}, issn = {2666-5174}, abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.}, }
@article {pmid41630880, year = {2026}, author = {Liu, MK and Liu, CY and Tang, YM and Liu, Y and Su, Y and Tian, XH and Feng, J and Ni, XL}, title = {Innovative use of unhulled rice in Baijiu brewing: impact on flavor and microbial composition.}, journal = {Food chemistry: X}, volume = {34}, number = {}, pages = {103569}, pmid = {41630880}, issn = {2590-1575}, abstract = {The quality of light-flavor Baijiu (LFB), a traditional Chinese liquor, is strongly influenced by fermentation raw materials. Traditional Baijiu brewing uses rice husk as an excipient, requiring energy-intensive steaming to remove off-flavors-a process that increases production time and costs. This study introduces an innovative co-fermentation technique using unhulled rice (Jingkangyou/Pinxiangyou varieties) with sorghum, improving LFB quality while reducing expenses. Metagenomic and flavoromic analyses compared three groups: a rice husk control and two experimental groups with varying proportions of unhulled rice. Results showed significant flavor differences, with D-lactic acid, leucinic acid, and putrescine levels correlating significantly positively to unhulled rice content. Experimental groups exhibited altered microbial diversity, flavor profiles, and physicochemical properties compared to the control. Key metabolic pathways, including galactose, phenylalanine, and lysine metabolism, were significantly modified, indicating unhulled rice reshaped biochemical reactions. These findings advance understanding of LFB fermentation dynamics and offer strategies for raw material optimization.}, }
@article {pmid41631112, year = {2026}, author = {Ji, X and Wang, M and Jin, P and Kong, L and Xu, Y and Chen, W and Liu, B and Wang, Q}, title = {Intracranial hepatitis B virus (HBV) infection following intracerebral hemorrhage in a patient with seronegative occult HBV infection.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02502}, pmid = {41631112}, issn = {2214-2509}, abstract = {Hepatitis B virus (HBV) infection is primarily associated with liver diseases but can also manifest with various extrahepatic complications. While numerous extrahepatic manifestations have been reported in acute or chronic hepatitis B patients, intracranial HBV infection remains clinically rare. A 43-year-old male had a pre-existing diagnosis of serologically negative occult HBV infection (OBI), which was initially diagnosed by detecting HBV DNA in serum while HBsAg, anti-HBs, anti-HBe, and anti-HBc were all negative. Following intracerebral hemorrhage, the patient's consciousness gradually restored through a course of rehabilitation therapy. Subsequently, the patient developed persistent fever and his level of consciousness progressively deteriorated. Serological testing confirmed the presence of HBsAg and HBeAg, the HBV loads in the serum was high, subsequent metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid (CSF) revealed positivity for HBV. After 8 weeks of treatment with entecavir, the HBV loads in the serum and CSF decreased significantly, the patient's consciousness improved, and the patient's temperature returned to normal. This study first reported a seronegative OBI patient developing intracranial HBV infection following intracerebral hemorrhage and clarified the diagnostic value of mNGS in rare intracranial infections.}, }
@article {pmid41632094, year = {2026}, author = {Gómez-Martínez, D and Ngou, JS and Ugolini, V and Lai, FY and Nilsson, RH and Kristiansson, E and Corcoll, N}, title = {Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {3}, pages = {}, pmid = {41632094}, issn = {1574-6941}, support = {AF2022-0079//Adlerbertska forkningsstifelsen/ ; 2019-01161//Formas/ ; }, mesh = {*Rivers/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology/analysis ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Geologic Sediments/microbiology ; Sweden ; Genes, Bacterial ; Water Purification ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Sewage/microbiology ; }, abstract = {Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in the river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from that of the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.}, }
@article {pmid41632347, year = {2026}, author = {Yang, H and Hensley, MK and Nguyen, VD and Al-Yousif, NS and Britton, N and Haidar, G and Yang, L and Shah, F and Bain, W and Wang, X and Qin, S and Ahmed, AA and Blauwkamp, T and Bercovici, S and Kaufman, BA and Redding, KM and Fitch, A and Methé, B and Benos, PV and McVerry, BJ and Morris, A and Kitsios, GD}, title = {Microbial lung-to-blood translocation associates with systemic inflammation in severe pneumonia: evidence from paired plasma and lower respiratory tract metagenomics.}, journal = {Intensive care medicine experimental}, volume = {14}, number = {1}, pages = {10}, pmid = {41632347}, issn = {2197-425X}, support = {P01 HL114453/HL/NHLBI NIH HHS/United States ; R01 HL176668/HL/NHLBI NIH HHS/United States ; R01HL176668/HL/NHLBI NIH HHS/United States ; P01 HL 114453/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Biological heterogeneity in host inflammatory responses to severe pneumonia predicts clinical outcomes and may influence the effectiveness of immunomodulatory therapy. The upstream drivers of this heterogeneity remain poorly defined. We hypothesized that microbial translocation from the lungs to the bloodstream, detectable via multi-compartment metagenomic analysis, contributes to divergent host responses in pneumonia.
METHODS: In this nested case-control study of mechanically ventilated patients with severe pneumonia, we collected paired plasma and endotracheal aspirate samples at baseline. Plasma samples underwent microbial cell-free DNA (mcfDNA) sequencing, and endotracheal aspirates were analyzed by Nanopore metagenomic sequencing. Host-response biomarkers were measured in both plasma and endotracheal aspirate samples. Microbial translocation of pulmonary origin was defined by the genus-level concordance of detectable taxa between matched endotracheal aspirate and plasma samples.
RESULTS: Among 98 patients (76 pneumonia, 22 controls), plasma mcfDNA was markedly higher in microbiologically confirmed pneumonia compared with culture-negative pneumonia (median 4015 vs. 210 molecules/μL, p = 0.0006). Pulmonary microbial translocation was identified in 31 (41%) pneumonia patients and correlated significantly with plasma soluble ST2 levels, independent of clinical severity. Patients classified into the prognostically adverse hyperinflammatory subphenotype exhibited greater translocating microbial DNA levels compared to hypoinflammatory patients (p = 0.04), further linking translocation to host-response heterogeneity.
CONCLUSIONS: Microbial lung-to-blood translocation is a measurable biological process associated with systemic inflammatory heterogeneity in severe pneumonia. This pathway may represent a novel mechanistic target for precision therapeutic strategies aimed at mitigating immune dysregulation.}, }
@article {pmid41633028, year = {2026}, author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y}, title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.}, journal = {Research in veterinary science}, volume = {203}, number = {}, pages = {106092}, doi = {10.1016/j.rvsc.2026.106092}, pmid = {41633028}, issn = {1532-2661}, mesh = {Animals ; Cattle/growth & development/microbiology/metabolism ; *Rumen/microbiology/metabolism ; Male ; Metabolomics ; *Gastrointestinal Microbiome ; Metagenomics ; *Metabolome ; *Microbiota ; Multiomics ; }, abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.}, }
@article {pmid41633112, year = {2026}, author = {Tang, X and Bao, Y and Li, J and Liu, B and Huang, Y and Hou, L and Lee, PKH and Han, P}, title = {Microplastics promote N2O emissions by enhancing nitrification via ammonia-oxidizing bacteria in estuarine and coastal sediments.}, journal = {Water research}, volume = {293}, number = {}, pages = {125458}, doi = {10.1016/j.watres.2026.125458}, pmid = {41633112}, issn = {1879-2448}, mesh = {*Nitrification ; *Microplastics ; Ammonia/metabolism ; *Geologic Sediments/microbiology ; Bacteria/metabolism ; *Nitrous Oxide ; Archaea/metabolism ; Oxidation-Reduction ; Estuaries ; }, abstract = {Estuarine and coastal ecosystems are critical interfaces between land and ocean, serving as sinks for anthropogenic pollutants such as ammonium and microplastics. However, the impact of microplastic pollution on nitrification processes in these environments remains largely unexplored. This study investigates the coastal region of the Yangtze River to examine how different microplastic types (polyethylene terephthalate, polypropylene, and polyethylene) affect nitrous oxide (N2O) emissions and the dynamics of nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) Nitrospira, and nitrite-oxidizing Nitrospira. Results from incubation experiments show that all microplastic types significantly increase N2O emissions across sediment samples. The reconstructed representative metagenome-assembled genomes revealed that AOA belong to group I.1a, while AOB are classified within the Nitrosomonas genus. Microplastics were found to have a stronger stimulatory effect on AOB, which are linked to higher N2O production, than on AOA, which are associated with low N2O production, thereby enhancing N2O emissions during nitrification. Furthermore, AOB genomes encode a range of putative plastic-degrading enzymes, which may partially explain their enrichment in microplastic-contaminated environments, although other factors such as differential tolerance to ammonium or oxidative stress cannot be ruled out.}, }
@article {pmid41633137, year = {2026}, author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R}, title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.}, journal = {Forensic science international. Genetics}, volume = {83}, number = {}, pages = {103435}, doi = {10.1016/j.fsigen.2026.103435}, pmid = {41633137}, issn = {1878-0326}, mesh = {*Lung/microbiology ; Animals ; *Drowning/diagnosis/microbiology ; Humans ; *Microbiota ; Metagenomics ; Mice ; Biomarkers ; Postmortem Changes ; Immersion ; Real-Time Polymerase Chain Reaction ; Male ; Bacteria/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.}, }
@article {pmid41633147, year = {2026}, author = {Klaes, S and Gerundt, K and Deobald, D and Henneberger, L and Escher, B and Adrian, L and Cooper, M}, title = {Sequential exposure to anoxic/oxic conditions leads to biotransformation and reduced sitagliptin toxicity in urban hyporheic zones.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141299}, doi = {10.1016/j.jhazmat.2026.141299}, pmid = {41633147}, issn = {1873-3336}, mesh = {*Sitagliptin Phosphate/toxicity/metabolism/chemistry ; *Water Pollutants, Chemical/toxicity/metabolism/chemistry ; Biotransformation ; Geologic Sediments/chemistry/microbiology ; Pseudomonas/metabolism/genetics ; Oxidation-Reduction ; *Hypoglycemic Agents/toxicity/metabolism ; Groundwater ; Animals ; Anaerobiosis ; }, abstract = {Pharmaceuticals are increasingly recognized as contaminants of concern in aquatic environments. Sitagliptin, an antidiabetic drug that carries a C-CF3 group, which is a precursor of the persistent trifluoroacetic acid, is excreted largely unmetabolized and inefficiently removed in wastewater treatment plants, leading to its widespread detection in surface waters. The hyporheic zone, a region between surface water and groundwater, serves as a natural bioreactor with high microbial activity and diverse redox conditions, offering the potential for sitagliptin attenuation. This study explored the biotransformation of sitagliptin in hyporheic sediments under varying redox conditions through batch experiments and field observations. We showed that batch experiments can complement field observations to capture both mechanistic insights and their environmental relevance. Batch experiments revealed amide hydrolysis and N-acetylation of sitagliptin under anoxic conditions, with subsequent deamination and oxidation of transformation products under oxic conditions. Metagenome-resolved metaproteomics suggested Pseudomonas asiatica as a key player in the oxic transformation. Field analysis of pore water samples identified up to 6.47 µg L[-1] sitagliptin and ten transformation products with concentrations of up to 4.82 µg L[-1] . Amide hydrolysis products were the most abundant transformation products and preferentially formed under anoxic conditions. All investigated transformation products exhibited lower cytotoxicity and oxidative stress responses than sitagliptin in in vitro bioassays, highlighting the toxicity reducing potential of the hyporheic zone. By identifying conditions that promote sitagliptin transformation and characterizing its transformation products toxicologically, our work provides parameters for enhanced sitagliptin removal in aquatic environments and improved risk assessment of fluorinated trace organic contaminants.}, }
@article {pmid41633490, year = {2026}, author = {Kelly, MS and Huang, CY and Kim, M and Haghnazari, D and Baig, A and Sun, Y and Lenneman, BR and Tisza, MJ and Cunningham, A and Gold, D and Phipatanakul, W and Lai, PS}, title = {Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, pmid = {41633490}, issn = {1097-6825}, support = {R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R21 AI178155/AI/NIAID NIH HHS/United States ; U01 AI110397/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.
OBJECTIVE: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.
METHODS: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated multikingdom changes to the nasal microbiome during infection. A sparse partial least-squares discriminant analysis model identified microbial signatures associated with prospective viral infection risk.
RESULTS: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus being the most prevalent. Cold and asthma symptoms within the previous 14 days had a sensitivity of 79% and 59%, respectively, for quantitative RT-PCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted odds ratio, 0.41 [95% CI, 0.25-0.67]; P < .001), whereas phageome profiles increased risk (adjusted odds ratio, 3.74 [95% CI, 1.85-7.55]; P < .001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.
CONCLUSIONS: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.}, }
@article {pmid41634308, year = {2026}, author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A}, title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {7016}, pmid = {41634308}, issn = {2045-2322}, support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Africa ; Feces/microbiology ; Nanopores ; Switzerland ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Bacteria/genetics/classification/drug effects ; Nanopore Sequencing ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.}, }
@article {pmid41634410, year = {2026}, author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY}, title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.}, journal = {Inflammation}, volume = {49}, number = {1}, pages = {78}, pmid = {41634410}, issn = {1573-2576}, support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; }, abstract = {UNLABELLED: A decreased abundance of fecal Akkermansia muciniphila (Akk) has been observed in patients with psoriasis and psoriatic arthritis. The potential beneficial effects of Akk in managing psoriasis have been proposed, yet results remain inconsistent and mechanisms unclear. Using imiquimod (IMQ)-treated C57BL/6 mice, we conducted a metagenomic association study of pasteurized Akk (pAkk) in the IMQ mice through whole-genome shotgun sequencing. We also performed a dextran sodium sulfate (DSS)-induced colitis experiment and an intestinal permeability test. The association among pAkk supplements, skin thickness, inflammatory profiles, fecal microbiota alterations, functional genetic predictions, intestinal epithelium inflammation, and barrier integrity was investigated. The study demonstrated that pAkk supplementation ameliorated IMQ-induced skin thickening, weight loss, spleen weight gain, serum IL-17A, TNF-α levels, and DSS-induced colitis. pAkk supplementation was linked to greater fecal microbial diversity and alterations in fecal microbiota composition, with increased prevalence of Muribaculaceae, Bifidobacterium pseudolongum, Desulfovirionaceae, Erysipelotrichaceae, and Alistipes ihumi, which have been implicated in the Gamma-Aminobutyric Acid (GABA) shunt, cholinergic synapse, cell cycle, and Mitogen-Activated Protein Kinase (MAPK) pathways. In conclusion, pAkk may mitigate IMQ-induced skin thickening and DSS-induced colitis, associated with reduced levels of TNF-α and IL-17A. pAkk supplementation alters fecal microbiota and metabolic pathways in IMQ-treated mice.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10753-025-02436-9.}, }
@article {pmid41634542, year = {2026}, author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y}, title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41634542}, issn = {1471-2180}, support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; }, abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear.
METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10⁸ CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process.
RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties.
CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04776-4.}, }
@article {pmid41634815, year = {2026}, author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X}, title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41634815}, issn = {2049-2618}, mesh = {*Triticum/growth & development/microbiology/physiology ; *Droughts ; *Caragana/microbiology ; *Plant Roots/microbiology ; Biofilms/growth & development ; *Microbiota ; Desert Climate ; Quorum Sensing ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; Drought Resistance ; }, abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.
RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.
CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.}, }
@article {pmid41634818, year = {2026}, author = {Schuster, L and Greening, C and Malerba, ME and Trevathan-Tackett, S and Athukorala, N and Ricci, F}, title = {Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {59}, pmid = {41634818}, issn = {2049-2618}, support = {APP1178715//National Health and Medical Research Council/ ; FT240100502//Australian Research Council/ ; DE220100752//Australian Research Council/ ; DE210101029//Australian Research Council/ ; ECPF24-4273843556//Faculty of Medicine, Nursing and Health Sciences, Monash University/ ; }, mesh = {*Methane/metabolism/analysis ; *Nitrous Oxide/metabolism/analysis ; Animals ; *Manure/microbiology ; *Denitrification ; Cattle ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Farms ; Greenhouse Gases/metabolism ; Australia ; Agriculture ; }, abstract = {BACKGROUND: Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia.
RESULTS: We found that in situ methane (CH4) and nitrous oxide (N2O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N2O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH4 and N2O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions.
CONCLUSIONS: Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions. Video Abstract.}, }
@article {pmid41634852, year = {2026}, author = {Yan, A and Li, X and Cheng, J and Cheng, Y and Gebeyew, K and Tan, Z and Kang, J and He, Z}, title = {The developmental trajectory and maturation of the Hulunbuir sheep (Ovis aries) microbiome.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {10}, pmid = {41634852}, issn = {2524-4671}, support = {32350410422//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; 32350410422//the National Natural Science Foundation of China/ ; 32302783//Natural Science Foundation of China/ ; }, abstract = {The rumen microbiota plays a pivotal role in the growth performance of host animals, primarily due to its ability to ferment ingested feed. Hulunbuir sheep exhibited a slow growth rate compared to other local breeds. A deeper comprehension of the development of the rumen bacteria community in Hulunbuir sheep can offer insights into the factors contributing to their slow growth rate. This study utilized metagenomic analysis of rumen content samples from Hulunbuir sheep to investigate the patterns of microbial growth and their relationship with the ADG. The results of the PCoA and enterotype analyses demonstrated that the ruminal bacterial community developed distinct characteristics following weaning. The dominant bacterial phyla in the rumen of Hulunbuir sheep, Bacteroidetes and Firmicutes, exhibited a significant age-related change. At the genus level, while the abundance of dominant bacterial genera changed with the growth of Hulunbuir sheep, Prevotella consistently maintained a high abundance across all age time points. We then examined the effects of age on microbial function by analyzing carbohydrate-metabolizing enzymes and protein-metabolizing peptidases. The abundance of carbohydrate-metabolizing enzymes decreased with growth, while peptidases showed opposite dynamics. Under the current feeding conditions correlation analysis showed that the abundances of Firm-04, CAG-83, and GCA-900,199,385 were negatively correlated with ADG (R<-0.4, p < 0.05), while the abundance of Ga6A1 was positively correlated with ADG (R > 0.5, p < 0.05). In addition, we found 67 MAGs related to ADG, which are capable of secreting carbohydrates-metabolizing enzymes and peptidase. This study uncovers the temporal dynamics of rumen microbiota development during the early to late fattening phase and identifies microbes associated with ADG, which could inform strategies to improve growth and production efficiency.}, }
@article {pmid41635301, year = {2025}, author = {Jin, X and Ren, L and Ren, X and Wang, J}, title = {Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract.}, journal = {Biosafety and health}, volume = {7}, number = {1}, pages = {5-16}, pmid = {41635301}, issn = {2590-0536}, abstract = {It is crucial to understand how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sheds in human respiratory tract, but this question remains elusive due to technical limitations. In this study, we integrated published human metagenomic data of SARS-CoV-2 and developed a novel algorithm named RedeCoronaVS to systematically dissect SARS-CoV-2 shedding modes with single-cell data as reference. Our study demonstrated that SARS-CoV-2 particles were the dominant mode of viral shedding in the very early infection phase (≤24 h after hospitalization). Within the first week after hospitalization, SARS-CoV-2 replicas within host cells dominated viral shedding alongside viral particles. One week later, viral fragments became the dominant mode in patients with mild or moderate symptoms, while viral replicas still dominated in some patients with severe symptoms. In addition to epithelial cells, SARS-CoV-2 replicas in neutrophils, macrophages, and plasma cells also played significant roles and were associated with sampling time and disease severity.}, }
@article {pmid41635321, year = {2026}, author = {Ozturk, SZ and Aydin, B and Cifcibasi, E}, title = {Antibiotic Resistance Genes in the Subgingival Microbiome in Periodontitis: A Scoping Review of Prevalence, Mobility, and Future Directions.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e100685}, pmid = {41635321}, issn = {2168-8184}, abstract = {The objective of the study is to evaluate the prevalence, diversity, and mobility of antibiotic-resistant species and resistance genes within the subgingival microbiome of patients with periodontitis. A systematic scoping review was conducted in accordance with PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines. Five electronic databases were searched for studies published between January 2020 and December 2025 that used molecular techniques (shotgun metagenomics, PCR/qPCR, 16S + PCR) to detect antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the subgingival plaque of patients with clinically diagnosed periodontitis. Only peer-reviewed articles presenting original data were included; reviews, animal studies, and investigations lacking clear methodological details were excluded. Data extraction included study design, sample size, identified ARGs, associated MGEs, and clinical context. Nine eligible studies involving over 900 subgingival samples were identified. A core resistome was consistently identified across all cohorts, predominantly comprising tetracycline genes (tetM, tetQ, tet32) and macrolide-lincosamide determinants (ermB, ermF, msrD), as well as β-lactamase genes such as cfxA. Sites affected by periodontitis showed higher abundance of these ARGs than healthy controls. Mobile elements, especially Tn916-family conjugative transposons, were often associated with macrolide resistance genes, suggesting potential for horizontal transfer. Methodological differences prevented meta-analysis, and no study compared results based on the 2017 stage/grade classification of periodontitis. The subgingival resistome in periodontitis features a consistent set of tetracycline, macrolide, and β-lactam resistance genes that are increased in disease and frequently associated with mobile transposons. Currently, the evidence remains primarily descriptive; future research should include standardized antibiotic washout periods, longitudinal follow-up, stage/grade stratification, and integrated multi-omics approaches to evaluate functional activity and guide personalized antimicrobial therapies.}, }
@article {pmid41635749, year = {2025}, author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É}, title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.}, journal = {Current research in parasitology & vector-borne diseases}, volume = {8}, number = {}, pages = {100333}, pmid = {41635749}, issn = {2667-114X}, abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.}, }
@article {pmid41636304, year = {2026}, author = {Brown, LP and Marizzi, A and Borrego, CM and Gionchetta, G and Zhengzheng, Z and Carneiro, RB and Gago-Ferrero, P and Matamoros, V and Subirats, J}, title = {Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {4632-4647}, pmid = {41636304}, issn = {1520-5851}, mesh = {*Wastewater ; Sewage ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Water Purification ; Waste Disposal, Fluid ; }, abstract = {The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse-oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel antibiotic resistance families for monitoring. Reclaimed effluents exhibited lower AMR exposure levels than those typically reported for secondary effluents (<0.5 ARGs/cell), while mobile genetic element (MGE) abundances were comparable to secondary effluents (1-2 MGEs/cell). Effluent communities differed by WWTP configuration: membrane bioreactor combined with ultrafiltration favored nutrient-removal/oxidative-stress taxa and reduced transferable MGEs, whereas plants relying on physical separation (sand filtration or reverse osmosis) retained fecal-associated taxa and MGEs. Specific clinically relevant ARGs persisted after treatments, including aadA and aph(3'')-Ibs (resistance to aminoglycosides), ermB and mphA (resistance to macrolides), and blaOXA-129 (resistance to beta-lactams), which we identify as sentinel markers for monitoring reclaimed water and sludge. We advance a generalizable two-step framework, metagenomic discovery to identify sentinel markers, followed by targeted assays for streamlined surveillance, that provides the first operational blueprint for integrating AMR into water reuse management under the EU regulation.}, }
@article {pmid41636495, year = {2026}, author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC}, title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0226425}, pmid = {41636495}, issn = {2165-0497}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, mesh = {Humans ; Female ; *Tears/chemistry/metabolism ; Male ; *Dry Eye Syndromes/microbiology/etiology ; *Proteome/analysis ; *Microbiota ; Adult ; *Contact Lenses/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Middle Aged ; Eye Proteins ; }, abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.}, }
@article {pmid41636510, year = {2026}, author = {Anne Hallowell, H and Malogan, J and Suez, J}, title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0100225}, pmid = {41636510}, issn = {2379-5077}, mesh = {Humans ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Computational Biology/methods ; *Viruses/genetics ; Feces/virology ; Bacteriophages/genetics ; Genome, Viral ; Bacteria/virology/genetics ; }, abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.}, }
@article {pmid41636536, year = {2026}, author = {Della-Negra, O and Servien, R and Milferstedt, K and Hamelin, J and Klopp, C and Hoede, C}, title = {Metagenome-assembled genomes from oxygenic photogranules obtained from photobioreactors treating synthetic wastewater.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0131025}, pmid = {41636536}, issn = {2576-098X}, support = {ANR-21-CE45-0036-0//Agence Nationale de la Recherche/ ; }, abstract = {Twenty-five high-quality metagenome-assembled genomes (MAGs) were recovered from photogranules to treat synthetic wastewater. They were dominated by Leptolyngbya boryana. Cyanobacterial MAGs encoded photosynthesis and nitrogen fixation pathways, supporting internal oxygen and nitrogen cycling. Most heterotrophic MAGs contributed to nitrogen removal, highlighting the metabolic complementarity within photogranules studied for wastewater treatment.}, }
@article {pmid41637142, year = {2026}, author = {Dos Santos, SJ and Gloor, GB}, title = {Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.}, journal = {Current protocols}, volume = {6}, number = {2}, pages = {e70307}, pmid = {41637142}, issn = {2691-1299}, mesh = {Uncertainty ; *Gene Expression Profiling/methods ; *Software ; *Transcriptome ; Humans ; Principal Component Analysis ; *Metagenomics/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods ; }, abstract = {Differential abundance or expression analyses are routinely performed on metagenomic, metatranscriptomic, and amplicon sequencing data. In such datasets, analysts usually have no information regarding the true scale (i.e., size) of the microbial community or sample under study, with inter-sample differences in sequencing depth instead being driven by technical variation rather than biological factors. Recent work has demonstrated that normalizations used in all analysis tools make incorrect assumptions about the biological scale of the system in question, leading to unacceptably high false-discovery rates in the output. To mitigate this, analysts can acknowledge and account for the uncertainty of the overall system scale during normalization by building scale models of the data-a feature that has been integrated into the ALDEx2 R package. Here, we provide reproducible examples that demonstrate how to incorporate scale models into differential expression analyses of RNA-seq data using bulk transcriptome and metatranscriptomic datasets, as well as the consequences of not doing so. We also show how to use the output of ALDEx2 to create high-level exploratory visualizations of their data through principal component analysis. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using a simple scale model for differential expression analysis to avoid dual-cutoff P value/significance thresholds Basic Protocol 2: Implementing a full informed scale model to correct scale-related data asymmetry in differential expression analyses Basic Protocol 3: Visualizing ALDEx2 outputs using a compositional approach: Principal component analysis.}, }
@article {pmid41637508, year = {2026}, author = {Kaur, G and Crawford, SE and Javornik Cregeen, S and Surathu, A and Ayyar, BV and Apostol, CV and Phuc, HN and Ettayebi, K and Boussattach, A and Zeng, XL and Blutt, SE and Doddapaneni, H and Muzny, DM and Coarfa, C and Anish, R and Prasad, BVV and Atmar, RL and Ramani, S and Estes, MK}, title = {Overcoming host restrictions to enable continuous passaging of GII.3 human norovirus in human intestinal enteroids.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eaeb0455}, pmid = {41637508}, issn = {2375-2548}, support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; S10 OD030414/OD/NIH HHS/United States ; P01 AI057788/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Norovirus/physiology/genetics ; Virus Replication/drug effects ; *Caliciviridae Infections/virology ; *Intestines/virology ; *Host-Pathogen Interactions ; *Organoids/virology ; Chemokines/metabolism/genetics ; Gastroenteritis/virology ; }, abstract = {The establishment of human intestinal enteroids (HIEs) as a model for human norovirus (HuNoV) replication has been transformative for studying this leading cause of gastroenteritis. However, indefinite passaging of HuNoVs in HIEs remained a challenge, necessitating the use of patient stool samples as viral inocula. Using RNA-seq, we identified CXCL10, CXCL11, and CCL5 as up-regulated chemokines, suggesting their potential as host restriction factors. TAK-779, a CXCR3/CCR5/CCR2 antagonist, enhanced GII.3 HuNoV replication and viral spread in a dose- and time-dependent manner, enabling successful passaging of GII.3 HuNoV in two different HIE lines and generation of viral stocks. Sequencing passaged virus revealed one consensus change in the major capsid protein and several dynamic adaptations, suggesting emergence of variants. TAK-779 also enhanced replication of GI.1 and GII.17 strains, but not GII.4, suggesting strain-specific host interactions. This breakthrough in passaging provides insight into HuNoV-host interactions, establishes a scalable in vitro system for virus propagation, and opens avenues for structural, biochemical, and therapeutic studies.}, }
@article {pmid41637515, year = {2026}, author = {Liu, X and Cheng, X and Zhang, Y and Zhao, R and Wang, W and Li, Y and Chen, ZQ and Qiu, X and Tuovinen, OH and Bull, ID and Evershed, RP and Wang, H}, title = {High-efficiency methane consumption by atmospheric methanotrophs in subsurface karst caves: The irrefutable methane sink.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eady5942}, pmid = {41637515}, issn = {2375-2548}, mesh = {*Methane/metabolism ; *Caves/microbiology ; Oxidation-Reduction ; *Atmosphere/chemistry ; Soil Microbiology ; Phylogeny ; }, abstract = {Subsurface karst systems represent substantial but underexplored methane sinks, yet the identities and activities of cave-dwelling methanotrophs remain poorly characterized. We detected increased methane oxidation rates from 2.9 ± 0.1 to 90.7 ± 4.5 ng·g[-1]·hour[-1] while supplied with 2 to 500 parts per million (ppm) CH4 to cave sediments. Atmospheric methanotroph Upland Soil Clusters γ (USCγ), responsible for this oxidation, was further assigned to three genera within the family Candidatus (Ca.) Methyloligotrophaceae, including two previously unrecognized genera. Nano-scale secondary ion mass spectrometry (NanoSIMS) imaging and the produced [13]C-PLFAs (phospholipid fatty acids) and [13]CO2 in [13]CH4-fed microcosm confirmed methane as both carbon and energy sources. These methanotrophs exhibited low half-saturation constant (Km; 138.8 ± 15.8 ppm), high carbon assimilation efficiency (>50%), and metabolic versatility, as revealed by metagenomics and metatranscriptomics analyses. By extrapolating global distribution of Ca. Methyloligotrophaceae and comparing methane oxidation rates between caves and soil ecosystems, we conservatively estimate that subsurface karst in southwest China sequester ~0.56 Tg CH4 annually. These findings highlight the ecological importance of karst ecosystems as a previously overlooked methane sink.}, }
@article {pmid41638014, year = {2026}, author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L}, title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {292}, number = {}, pages = {107742}, doi = {10.1016/j.aquatox.2026.107742}, pmid = {41638014}, issn = {1879-1514}, mesh = {Animals ; Larva/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; Metagenomics ; *Norfloxacin/toxicity ; *Bile Acids and Salts/metabolism ; *Anti-Bacterial Agents/toxicity ; Metabolomics ; *Dysbiosis/chemically induced/veterinary ; *Bufonidae/microbiology ; }, abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.}, }
@article {pmid41638332, year = {2026}, author = {Wu, B and Zhang, N and Yang, G and Yu, N and Xie, Z and Xia, J and Luo, W and Liu, X and Wang, D and Zhang, Y and Tang, L}, title = {Unraveling the microbial and functional mechanisms driving rapid algal-bacterial granular sludge formation in mariculture wastewater.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123941}, doi = {10.1016/j.envres.2026.123941}, pmid = {41638332}, issn = {1096-0953}, mesh = {*Sewage/microbiology ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; Aquaculture ; *Bacteria/metabolism ; Salinity ; Nitrogen ; }, abstract = {Algal-bacterial granular sludge (ABGS) has unique advantages and broad application prospects in the treatment of mariculture wastewater. However, the rapid granulation process and performance evolution of ABGS under high salt stress have not been clearly defined. Compared with AGS, the influence of algal intervention on the structural integrity and metabolic activity of particles under the same salinity gradient is also unknown. Therefore, in this study, a parallel ABGS and AGS system was established. The results showed that intertwined algal filaments provided a structural skeleton for particle formation and led to complete granulation of ABGS within 20 days. Compared with conventional AGS, ABGS formed under high-salinity conditions exhibited a larger average particle size (1.07 mm), higher biomass (7.59 g/L) and higher extracellular polymeric substance (EPS) secretion (258.56 mg/g VSS). Additionally, chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal efficiencies exceeded 99% and 66%, respectively. Metagenomic analysis revealed that Thauera, Fragilaria and Nitzschia were dominant taxa associated with granule formation and stabilization. ABGS also showed an elevated abundance of functional genes associated with nitrogen metabolism (nxrA, nasA, and nasD) and polysaccharide metabolism (glmM, glmU, and pmm-pgm), which were in accordance with the enhanced nitrogen removal and granulation capability. Increased abundance of tricarboxylic acid cycle genes further indicated the superior granulation performance of ABGS. Overall, this study clarifies the morphological evolution and microbial functional mechanisms underlying rapid ABGS formation in mariculture wastewater, offering valuable insights for engineering optimisation and application of this technology in saline wastewater treatment.}, }
@article {pmid41638346, year = {2026}, author = {Behrens, LMP and Fernandes, GDS and Gonçalves, GF and Nunes, FVM and Weimer, RD and Moreira, JCF and Dorn, M}, title = {Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review.}, journal = {Neuroscience}, volume = {599}, number = {}, pages = {76-93}, doi = {10.1016/j.neuroscience.2026.01.019}, pmid = {41638346}, issn = {1873-7544}, mesh = {Humans ; *Mental Disorders/genetics/metabolism ; *Neurodegenerative Diseases/genetics/metabolism ; *Genomics/methods ; *Neurodevelopmental Disorders/genetics/metabolism ; *Metabolomics/methods ; Proteomics/methods ; Epigenomics ; Computational Biology/methods ; Animals ; Multiomics ; }, abstract = {Recent advances in high-throughput technologies have led to an increased generation of biological data across genomics, transcriptomics, proteomics, epigenomics, and metabolomics. However, a major challenge remains: effectively integrating these multi-omics datasets to allow a more holistic understanding of the complex, interconnected mechanisms underlying human diseases. Neurodevelopmental, neurodegenerative, and psychiatric disorders are particularly multifactorial and heterogeneous, making them candidates for multi-omics approaches. In this context, this systematic review assesses the current state of multi-omics integration in neurological research. Records retrieved from five major databases were processed, and 156 studies were included for further analysis. The most frequently studied conditions were Alzheimer's Disease, Depressive Disorder and Parkinson's Disease, with epigenomics-transcriptomics and metagenomics-metabolomics emerging as the most common omics pairings. The field remains dominated by studies integrating pairs of omics layers. Only a limited number of computational tools are currently being applied to the integration of more than two omics layers, highlighting a gap in comprehensive multi-omics modeling. Despite progress, key challenges persist, including data accessibility and the need for standardized frameworks to allow cross-study comparisons. Moreover, most computational findings lack experimental validation in wet-laboratory settings. Future research should address these challenges, develop scalable algorithms for integrating multi-omics data, and leverage large, open-access datasets. Integrating computational predictions with experimental validation could help researchers prioritize high-confidence biomarkers relevant to clinical applications. Collaborative efforts among bioinformaticians, clinicians, and experimentalists will be essential to translating these advances into clinically actionable solutions.}, }
@article {pmid41638592, year = {2026}, author = {Xiao, Y and Cheng, Z and Cai, J and Guo, Z and Chen, J and Su, Y and Cao, F and Chen, D}, title = {Metagenomic and metatranscriptomic analysis of sulfur-driven autotrophic denitrification coupled with carbon assimilation: roles of sulfur-to-nitrogen ratio and hydraulic retention time.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134153}, doi = {10.1016/j.biortech.2026.134153}, pmid = {41638592}, issn = {1873-2976}, mesh = {*Sulfur/metabolism ; *Denitrification/genetics ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Autotrophic Processes/genetics ; Bioreactors/microbiology ; *Metagenomics/methods ; Gene Expression Profiling ; *Transcriptome ; Nitrates/metabolism ; }, abstract = {The sulfur autotrophic denitrification (SAD) process is a promising technology for nitrogen-containing wastewater treatment, with research predominantly focused on nitrate and sulfide transformations, while the potential for inorganic carbon assimilation remains underexplored. In this study, a long-term stable SAD system was maintained in an airlift bioreactor by adding an inorganic carbon source to evaluate the effects of sulfur-to-nitrogen (S/N) ratio and hydraulic retention time (HRT) on operational performance. Under optimal operating conditions (S/N = 3:2; HRT = 8 h), the system sustained high performance, achieving 99.56 ± 1.47% nitrate removal, 60.28 ± 4.19% elemental sulfur yield, and 46.48 ± 4.07% inorganic carbon assimilation efficiency. Biomass sulfur acted as a sink for extracellular free organic carbon (EFOC), thereby alleviating its accumulation-induced negative feedback on carbon assimilation. Microbial community analysis revealed a substantial enrichment of the autotrophic sulfur-oxidizing bacterium Sulfurovum, showing a marked 9.46-fold increase in relative abundance compared with the original sludge. At S/N = 3:2, metagenomic and metatranscriptomic analyses detected a 6.39-fold increase in the transcription of CBB cycle genes (rbcL/rbcS), driving a clear shift in metabolic flux toward carbon assimilation. Shortening the HRT (4 h) preferentially activated the denitrification pathway, which was evidenced by an 84.65% rise in nosZ expression (from 2,623.29 to 4,844.01 TPM), thereby bolstering N2O reduction. Our findings offered critical insights for designing engineering solutions that enable concurrent efficient denitrification, sulfur recovery, and reduced carbon emissions.}, }
@article {pmid41639055, year = {2026}, author = {Lai, D and Mosier, D and Palmer, M and Mayali, X and Johnston, J and Saldivar, W and Covington, JK and Jiao, JY and Murali, R and Seymour, CO and Liu, L and Hua, ZS and Li, WJ and Weber, PK and Pett-Ridge, J and Colman, DR and Boyd, ES and Nunoura, T and Dodsworth, JA and Hedlund, BP}, title = {Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41639055}, issn = {2041-1723}, support = {1557042//National Science Foundation (NSF)/ ; 2038420//National Science Foundation (NSF)/ ; 80NNSC17KO548//National Aeronautics and Space Administration (NASA)/ ; 80NSSC25M0046//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370011//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Amino Acids, Branched-Chain/metabolism ; Phylogeny ; *Archaea/metabolism/genetics/classification/growth & development ; Metagenome ; Proteomics ; Archaeal Proteins/metabolism/genetics ; Genome, Archaeal ; }, abstract = {Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10[6] cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.}, }
@article {pmid41639269, year = {2026}, author = {Piera Líndez, P and Danielsen, LS and Kovačić, I and Pielies Avellí, M and Nesme, J and Jensen, LJ and Andersen, JN and Sørensen, SJ and Rasmussen, S}, title = {Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41639269}, issn = {1546-1696}, support = {NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, abstract = {Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistance. Despite their importance, plasmids are underrepresented in genomic databases because of challenges in assembling them, caused by mosaicism and microdiversity. Current plasmid assemblers rely on detecting circular paths in single-sample assembly graphs but face limitations because of graph fragmentation, entanglement and low coverage. We introduce PlasMAAG (plasmid and organism metagenomic binning using assembly-alignment graphs), a method to recover plasmids and cellular genomes from metagenomic samples. PlasMAAG complements assembly graph signals across samples by generating an 'assembly-alignment graph', which is used alongside common binning features for improved plasmid reconstruction. On synthetic benchmark datasets, PlasMAAG reconstructed 50-121% more near-complete plasmids than competing methods and improved the Matthews correlation coefficient of geNomad contig classification by 28-106%. On hospital sewage samples, PlasMAAG outperformed competing methods, reconstructing 33% more plasmid sequences. PlasMAAG enables the study of organism-plasmid associations and intraplasmid diversity across samples.}, }
@article {pmid41639568, year = {2026}, author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X}, title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41639568}, issn = {2045-2322}, support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity & Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Asthma/drug therapy/metabolism/pathology/microbiology ; Mice ; *Glutamine/metabolism ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Metabolomics ; Disease Models, Animal ; Mice, Inbred BALB C ; Th17 Cells/immunology/drug effects ; Powders ; Cytokines/metabolism ; Female ; Lung/pathology/drug effects ; Ovalbumin ; Th2 Cells/immunology/drug effects ; Multiomics ; }, abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.}, }
@article {pmid41639832, year = {2026}, author = {Ma, R and Sun, J and Zhu, J and Wu, Y and Shi, Y and Yang, Y and Wang, S and Han, X and Li, S and Gao, L and Zhao, X and Hua, R and Wang, Y}, title = {Metagenomic next-generation sequencing for efficient detection of human parvovirus B19 in amniotic fluid: a case study of diagnosis and prenatal management of fetal infection.}, journal = {BMC pregnancy and childbirth}, volume = {26}, number = {1}, pages = {}, pmid = {41639832}, issn = {1471-2393}, support = {HHJH2412//Medical Science and Technology Talent Promotion Project of The International Peace Maternity and Child Health Hospital/ ; 2023YFC2705901//National Science and Technology Major Project/ ; 22Y11902300//Science and Technology Commission of Shanghai Municipality/ ; 202440131//Shanghai Municipal Health Commission/ ; YG2023ZD26//Shanghai Jiao Tong University/ ; }, abstract = {OBJECTIVE: Human parvovirus B19 (B19V) infection during pregnancy can lead to a range of adverse outcomes such as miscarriage, premature delivery, fetal hydrops, severe anemia, myocarditis, heart failure, and even fetal demise, posing significant risks to maternal and fetal health. The aim of this study was to establish a more efficient method for detecting B19V in amniotic fluid and to explore and optimize early diagnosis and treatment strategies for fetal B19V infection.
METHODS: Intrauterine transfusion (IUT) was performed due to the occurrence of severe fetal anemia and hydrops. Amniotic fluid was obtained for genetic detection. Metagenomic next-generation sequencing (mNGS) and bioinformatic analysis were performed on the amniotic cells to identify the viral genome.
RESULTS: In this study, the B19V genome was identified in the amniotic cells of the suspected case, with three viral coding sequences mapped. The coverage density reached 99.9% of the viral sequences. No other pathogen sequences, including bacteria, fungi, parasites, chlamydia, mycoplasma, rickettsia and other viruses, were identified.
CONCLUSION: Our study confirmed the diagnosis of fetal B19V infection in a suspected case via amniotic fluid virus genome detection. It is the first time to exhibit the clinical application of mNGS to systematically detect the B19V genome in amniotic fluid in prenatal practice, and to achieve good results in combination with clinical management. The study highlighted the importance of comprehensive management of B19V fetal infection and demonstrated the advantages and wide application prospects of mNGS in intrauterine infection diagnosis.}, }
@article {pmid41640388, year = {2026}, author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J}, title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.}, journal = {Ecology and evolution}, volume = {16}, number = {2}, pages = {e72952}, pmid = {41640388}, issn = {2045-7758}, abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.}, }
@article {pmid41640402, year = {2025}, author = {Williams, AD and Hooton, SPT and King, E and Avery, LM and Hough, RL and Hobman, JL and Stekel, DJ and Neal, AL and West, HM}, title = {Temporal signals in dairy cattle slurry and fertilized field soil resistomes and bacterial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1666851}, pmid = {41640402}, issn = {1664-302X}, abstract = {INTRODUCTION: Dairy cattle waste is a globally significant source of organic fertilizer which contains a cocktail of microbes and antibiotic resistance genes (ARGs). These ARGs may present a risk to human and animal health, yet there is still limited farm-system-level understanding of how long-term and multiple slurry applications alter field soil resistomes and total microbial communities.
METHODS: Using metagenomics, we assessed both immediate and longer-term changes in grassland field soil resistomes and bacterial communities over a year of routine cattle slurry application.
RESULTS: Our findings suggest that soil microbial communities are resilient to bacteria and ARGs introduced via slurry, even after repeated applications. Most slurry-borne ARGs were not enriched in field soil, however, those common in soil, such as rifamycin resistance genes, were consistently elevated relative to field soil with no history of slurry application. We observed transient increases in slurry-associated macrolide-lincosamide-streptogramin ARGs, however, their persistence appeared to be influenced by timing of slurry application. Similar transient effects were shown by the recovery of a high quality, slurry-associated Proteiniphilum spp. metagenome assembled genome (MAG).
DISCUSSION: We show that MAGs represent a powerful tool for examining the transfer of slurry-borne microorganisms, as they can be more characteristic of these environments than typical sentinel organisms which are easily cultivated. Our findings indicate that while the soil bacterial community shows considerable resilience to slurry-borne bacteria and ARGs, this may be diminished by temporal factors that remain largely unexplored and poorly understood. This is important because resilience inferred from short-term observations may not fully capture delayed or transient responses, potentially leading to underestimation of the persistence of slurry-borne bacteria and ARGs.}, }
@article {pmid41640408, year = {2025}, author = {Sun, G and Zou, Q and Wang, B}, title = {The interplay of carbon and nitrogen cycling driven by watershed microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1696238}, pmid = {41640408}, issn = {1664-302X}, abstract = {Microorganisms play central roles in regulating carbon and nitrogen cycling across watersheds, driving processes such as organic matter decomposition, primary production, nitrification, and denitrification. Rapid advances in high-throughput sequencing and environmental monitoring have enabled unprecedented insights into the taxonomic diversity and functional capacities of microbial communities under global change. In this review, we synthesize findings from studies published in recent years to evaluate how hydrological connectivity, redox gradients, temperature shifts, and nutrient loading shape microbial metabolism across rivers, lakes, wetlands, and coastal interfaces. We further summarize emerging evidence on how antibiotic resistance genes (ARGs) propagate through these ecosystems and influence microbial functions. The integration of multi-omics technologies including metagenomics, metatranscriptomics, combined with ecological and biogeochemical modeling provides new opportunities to quantify microbe-mediated carbon sequestration and nitrogen transformation. Finally, we discuss current knowledge gaps, including the limited understanding of ARG-driven community restructuring and the insufficient mechanistic resolution of microbe-environment interactions under future climate scenarios. This review highlights the need for cross-scale, data-integrated frameworks to better predict how microbial processes regulate watershed-level biogeochemical cycles in a rapidly changing world.}, }
@article {pmid41640705, year = {2026}, author = {Wang, HJ and Zhang, YN and An, L}, title = {Clinical and radiographic feature of pulmonary nocardiosis: A study of 102 cases.}, journal = {World journal of radiology}, volume = {18}, number = {1}, pages = {114552}, pmid = {41640705}, issn = {1949-8470}, abstract = {BACKGROUND: Nocardia pneumonia is an infection that occurs in patients with underlying diseases. Previously, due to limited detection methods, its detection rate and typing posed significant challenges. However, with advancements in detection techniques, the detection rate has significantly increased, and different Nocardia species exhibit distinct imaging characteristics.
AIM: To retrospectively analyze the etiological and imaging features of pulmonary Nocardia pneumonia and to examine the differences in chest imaging manifestations among different Nocardia species.
METHODS: The medical records of 102 patients with pulmonary nocardiosis who were admitted to Beijing Chaoyang Hospital from January 2017 to December 2024 were collected. Data including name, gender, underlying comorbidities, etiological characteristics, diagnostic methods, chest computed tomography features, and therapeutic agents were recorded.
RESULTS: Among the 102 patients, 55 were male and 47 were female, with a median age of 61 years. Bronchiectasis was the most common comorbidity, observed in 54 patients (52.9%). Sixty percent were diagnosed using metagenomic next-generation sequencing. Nocardia gelsenkin was the most prevalent Nocardia specie, while Aspergillus and Pseudomonas aeruginosa were identified as the predominant co-pathogens in these pulmonary nocardiosis cases. Pneumonia caused by Nocardia wallacei primarily presented with bronchopneumonia as the main imaging feature, while other Nocardia species more commonly manifested as consolidation, often accompanied by nodules, cavities, and pleural effusion. The imaging features in immunosuppressed patients were more diverse, with frequent coexistence of multiple patterns.
CONCLUSION: Nocardia pneumonia commonly coexists with bronchiectasis. While metagenomic next-generation sequencing has greatly enhanced its detection rate, Nocardia wallacei pneumonia is distinguished on chest computed tomography by its primary presentation of bronchopneumonia, unlike other types.}, }
@article {pmid41640872, year = {2026}, author = {Chen, YX and Sun, NQ and Mo, SJ}, title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.}, journal = {World journal of gastroenterology}, volume = {32}, number = {4}, pages = {114468}, pmid = {41640872}, issn = {2219-2840}, mesh = {*NF-E2-Related Factor 2/metabolism ; Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Parkinson Disease/complications ; *Gastrointestinal Diseases/etiology/therapy/microbiology ; Mice ; Disease Models, Animal ; Kelch-Like ECH-Associated Protein 1/metabolism ; Signal Transduction/drug effects ; Fecal Microbiota Transplantation ; Brain-Gut Axis/drug effects ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; }, abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.}, }
@article {pmid41640977, year = {2026}, author = {Xia, L and Xu, J and Chen, Z and Shen, Y and Zou, Y}, title = {Disseminated tuberculosis secondary to polymicrobial co-infection following long-term immunotherapy for sarcomatoid mesothelioma: A case report.}, journal = {Respiratory medicine case reports}, volume = {59}, number = {}, pages = {102367}, pmid = {41640977}, issn = {2213-0071}, abstract = {Malignant pleural mesothelioma (MPM), particularly its sarcomatoid subtype, is a highly aggressive sarcoma of the pleural lining with a dismal prognosis. Prolonged use of immune checkpoint inhibitors (ICIs), while improving survival in selected patients, can induce profound immunosuppression, increasing susceptibility to life-threatening opportunistic infections. This report describes a 77-year-old male with sarcomatoid MPM who developed fatal disseminated tuberculosis (TB), accompanied by concurrent Aspergillus and herpesvirus infections during extended immunotherapy. The case underscores the critical role of metagenomic next-generation sequencing (mNGS) in enabling rapid diagnosis of atypical TB reactivation in an immunocompromised host, even when conventional cultures are negative. mNGS identified co-infections with Aspergillus flavus and herpesviruses (HHV-5, HHV-4, HHV-1), demonstrating its superiority in polymicrobial infection detection.}, }
@article {pmid41641055, year = {2025}, author = {Lai, SY and Chang, L and Duan, JX and Che, GL and Yang, QX and Teng, J and Jian, H and Liu, XJ and Liu, F}, title = {Clinical and epidemiological characteristics of cat scratch disease in children from southwestern China: a retrospective analysis of mNGS-confirmed cases.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1743423}, pmid = {41641055}, issn = {2296-2565}, mesh = {Humans ; *Cat-Scratch Disease/epidemiology/diagnosis/drug therapy ; Child ; Male ; Retrospective Studies ; Female ; China/epidemiology ; Adolescent ; *Bartonella henselae/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; Cats ; Animals ; }, abstract = {BACKGROUND AND AIM: Cat scratch disease (CSD) is a zoonotic infection predominantly caused by Bartonella henselae, typically featured by regional lymphadenopathy and febrile illness. Although these classic features characterize most cases, the clinical spectrum extends to severe systemic manifestations including meningitis and neuroretinitis, leading to poor prognosis. Given this potential for diverse clinical presentations, prompt microbiological confirmation becomes essential for accurate diagnosis and appropriate management of CSD. The present study aimed to provide a comprehensive analysis of epidemiological patterns, clinical characteristics, diagnostic findings, and therapeutic outcomes in pediatric CSD cases, with the ultimate goal of optimizing early detection and enhancing the clinical understanding of this disease.
METHODS: This single-center retrospective study analyzed 20 pediatric cases diagnosed with CSD at West China Second University Hospital in southwestern China between September 2021 and July 2025. All diagnoses were established based on comprehensive clinical evaluation including medical history, characteristic symptoms, and imaging findings. Definitive B. henselae identification was achieved through metagenomic next-generation sequencing (mNGS). These diagnostic characteristics were systematically evaluated and discussed in detail.
RESULTS: Among the 20 patients with CSD included in the study, 18 (90.00%) reported a history of cat contact. Ten patients were male (50.00%). School-aged children (6-14 years) accounted for the majority of patients. Eleven cases (55.00%) occurred in autumn. Fever and lymphadenopathy were the primary reasons for hospitalization. B. henselae was detected in all cases using mNGS. Nine patients were diagnosed with atypical CSD, seven of whom were female. Atypical CSD was associated with higher body temperature and longer hospitalization stay. Antimicrobial agents, including azithromycin, doxycycline, and rifampin, achieved satisfactory therapeutic outcomes.
CONCLUSION: This study elucidates the epidemiological, clinical, and laboratory characteristics of CSD in children. mNGS may serve as a powerful tool to facilitate the diagnosis of CSD, including its atypical manifestations.}, }
@article {pmid41641352, year = {2025}, author = {Cao, XG and Zhu, XF and Ni, JX and Meng, HD and Huang, CJ}, title = {Optimizing metagenomic next-generation sequencing in CNS infections: a diagnostic model based on CSF parameters.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1681643}, pmid = {41641352}, issn = {2235-2988}, mesh = {Humans ; Female ; Male ; Retrospective Studies ; Middle Aged ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Aged ; ROC Curve ; *Cerebrospinal Fluid/cytology/chemistry ; Logistic Models ; Young Adult ; }, abstract = {OBJECTIVE: This study aimed to assess the association between routine cerebrospinal fluid (CSF) biochemical parameters and metagenomic next-generation sequencing (mNGS) results, and to develop a predictive model to optimize mNGS testing strategies in patients with suspected central nervous system (CNS) infections.
METHODS: We retrospectively enrolled 110 patients with suspected CNS infections between December 2019 and January 2024. All underwent both CSF analysis and mNGS testing. Patients were divided into mNGS-positive (n = 62) and negative (n = 48) groups. Logistic regression identified independent predictors, and a nomogram was constructed based on CSF cell count and protein concentration. Model performance was assessed via receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA). Internal validation included 10-fold cross-validation and 1000-sample bootstrap. An external validation was performed using a cohort of 40 patients enrolled from another hospital campus (May-October 2024). The derivation cohort was retrospectively collected, whereas the external validation cohort was prospectively enrolled.
RESULTS: mNGS positivity rate was 56.36%, significantly higher than CSF culture (6.36%), with an overall diagnostic concordance of 79.09%. Compared to the mNGS-negative group, positive patients had significantly higher CSF cell counts, protein levels, turbidity, ICU admission (ICUA), antimicrobial regimen adjustment (AAR), and mortality, while glucose was significantly lower (P < 0.05). Logistic regression confirmed CSF cell count binary variables (BV) and protein-BV as independent predictors (P < 0.05). The areas under curve (AUCs) for the cell-count, protein-only, and combined models were 0.827, 0.813, and 0.782, respectively. Internal validation showed stable results: 10-fold CV AUC = 0.773 ± 0.184 (95% CI: 0.641-0.904), bootstrap AUC = 0.770 ± 0.064 (95% CI: 0.766-0.774). External validation yielded an AUC of 0.763 (95% CI: 0.554-0.918), with sensitivity and specificity of 77.8% and 67.7%. Calibration and DCA demonstrated good agreement and clinical utility.
CONCLUSION: CSF cell count and protein are reliable predictors of mNGS positivity. The model for practice showed consistent diagnostic performance and may aid in guiding precision mNGS testing, particularly in resource-constrained settings.}, }
@article {pmid41642002, year = {2026}, author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB}, title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.}, journal = {mBio}, volume = {17}, number = {3}, pages = {e0364525}, pmid = {41642002}, issn = {2150-7511}, support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; K01AI163413//National Institute of Allergy and Infectious Diseases/ ; T32 AI162579/AI/NIAID NIH HHS/United States ; R01NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Female ; *Vagina/microbiology/immunology ; Humans ; *Microbiota/immunology/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Gardnerella/genetics/classification/immunology/isolation & purification ; Algorithms ; Metagenome ; Dysbiosis/microbiology ; Host Microbial Interactions/immunology ; }, abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.}, }
@article {pmid41642221, year = {2026}, author = {Pavan, RR and Sullivan, MB and Tisza, MJ}, title = {CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation.}, journal = {Microbial genomics}, volume = {12}, number = {2}, pages = {}, pmid = {41642221}, issn = {2057-5858}, mesh = {*Computational Biology/methods ; Genome, Viral ; *DNA Viruses/genetics/classification ; *DNA, Single-Stranded/genetics ; Phylogeny ; Metagenomics/methods ; *Molecular Sequence Annotation/methods ; *Software ; }, abstract = {ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.}, }
@article {pmid41644119, year = {2026}, author = {Hung, JY and Cooke, I and Sato, Y and Miller, DJ and Bourne, DG}, title = {Microbial Metabolism and Disease Virulence Changes Across Day and Night in Coral Black Band Disease Lesions.}, journal = {Environmental microbiology}, volume = {28}, number = {2}, pages = {e70219}, pmid = {41644119}, issn = {1462-2920}, support = {//Earthwatch Institute/ ; //James Cook University/ ; //Mitsubishi Corporation/ ; //JCU CTBMB grant/ ; //JCU OIRS Morris Family Trust grant/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; Virulence ; *Bacteria/metabolism/genetics/pathogenicity ; *Cyanobacteria/metabolism/genetics ; Photosynthesis ; Metagenome ; Microbiota ; Light ; }, abstract = {Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.}, }
@article {pmid41644290, year = {2026}, author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y}, title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.}, journal = {Journal of cosmetic dermatology}, volume = {25}, number = {2}, pages = {e70714}, pmid = {41644290}, issn = {1473-2165}, support = {//Proya Cosmetics Co. Ltd/ ; }, mesh = {Humans ; Female ; *Sebum/metabolism ; *Lipidomics/methods ; *Scalp/microbiology/metabolism ; Young Adult ; Adult ; *Dermatitis, Seborrheic/microbiology ; Metagenomics ; Microbiota ; *Scalp Dermatoses/microbiology ; China ; Dandruff/microbiology ; Lipids/analysis ; Paper ; East Asian People ; }, abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.
AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.
METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.
RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).
CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.}, }
@article {pmid41644450, year = {2026}, author = {Yan, D and Huang, W and Li, KS}, title = {[Advances in clinical diagnosis and treatment of pythium keratitis].}, journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology}, volume = {62}, number = {2}, pages = {156-160}, doi = {10.3760/cma.j.cn112142-20250820-00351}, pmid = {41644450}, issn = {0412-4081}, support = {2025JJ90271//Enterprise Joint Fund Project/ ; }, mesh = {Humans ; *Pythium ; *Keratitis/diagnosis/therapy/microbiology ; *Pythiosis/diagnosis/therapy ; }, abstract = {Pythium insidiosum is an aquatic algal oomycete that can induce Pythium insidiosum keratitis (PIK). PIK typically presents as acute, highly invasive corneal ulcers, rapidly progressing to corneal dissolution and perforation, and in severe cases, may lead to blindness. Due to its clinical presentation resembling fungal infections, it is often misdiagnosed as fungal keratitis. Epidemiological studies indicate that PIK is predominantly found in tropical and subtropical regions, with a higher incidence during the monsoon season. It is often associated with exposure to contaminated water sources or minor trauma caused by plants. Diagnostic methods include staining of corneal scrapings, PCR, metagenomic next-generation sequencing, and confocal microscopy. Since PIK shows a poor response to conventional antifungal treatments, antibiotics are the preferred treatments, with a combination of linezolid and azithromycin often used as the first-line therapy. Severe cases may require penetrating keratoplasty. In China, reports of PIK cases are relatively rare. This review summarizes the epidemiology, etiology, clinical manifestations, diagnosis, and treatment of PIK, aiming to provide a reference for its clinical management.}, }
@article {pmid41644553, year = {2026}, author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J}, title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41644553}, issn = {2055-5008}, support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Echinococcus multilocularis/physiology ; Mice ; *Depression/microbiology/etiology ; *Echinococcosis/microbiology/psychology/parasitology ; Mice, Inbred BALB C ; Disease Models, Animal ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Behavior, Animal ; Metabolomics ; Metagenomics ; }, abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.}, }
@article {pmid41644585, year = {2026}, author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E}, title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41644585}, issn = {2045-2322}, mesh = {*Manure/microbiology ; *Composting/methods ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Dairying ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Cattle ; Genes, Bacterial ; }, abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.}, }
@article {pmid41644796, year = {2026}, author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J}, title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.}, journal = {Nature microbiology}, volume = {11}, number = {3}, pages = {664-677}, pmid = {41644796}, issn = {2058-5276}, support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, mesh = {*Renal Insufficiency, Chronic/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Humans ; Glomerular Filtration Rate ; Male ; Female ; Feces/microbiology ; Middle Aged ; Dysbiosis/microbiology ; *Kidney/physiopathology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Aged ; Cresols/metabolism ; Biomarkers ; Disease Progression ; Adult ; }, abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.}, }
@article {pmid41645054, year = {2026}, author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H}, title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41645054}, issn = {1471-2164}, support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Enterocytozoon/physiology ; *Vitamin K 2 ; *Rodentia/microbiology ; *Microsporidiosis/microbiology/veterinary/metabolism ; Biosynthetic Pathways ; }, abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.}, }
@article {pmid41645073, year = {2026}, author = {Xu, C and Zhang, L and Liu, T and Zhu, G and Wei, H and Zheng, Y and Shi, J and Qiu, L and Xiao, Z and Zhu, X and Wang, J and Guo, J and Fan, Y and Song, Y and Jiang, E and Feng, S}, title = {Respiratory and blood samples metagenomic sequencing in diagnosing pulmonary infections in hematologic patients.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41645073}, issn = {1471-2334}, support = {2021-I2M-1-039//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2021-I2M-1-017//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2023ZD0510400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 3332024210//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; 82470208//National Natural Sciences Foundation of China/ ; }, abstract = {BACKGROUND: Bacterial and fungal pulmonary infections (BFPI) are common in hematological patients and pose significant diagnostic challenges. Metagenomic next-generation sequencing (mNGS) is valuable for diagnosing BFPI. However, for hematological patients with limited access to lower respiratory tract samples (LRTS), the clinical value of blood-mNGS compared to LRTS-mNGS requires further investigation.
METHODS: A retrospective analysis was conducted on 160 cases with suspected pneumonia who underwent both blood-mNGS and LRTS-mNGS within one week. Diagnostic performance and impacts on antimicrobial adjustments were evaluated using clinical composite diagnosis (CCD) as the reference.
RESULTS: Compared to CCD, LRTS-mNGS showed significantly higher positive percent agreement (PPA) than blood-mNGS [93.7% (119/127) vs. 34.6% (44/127), P < 0.001], with negative percent agreements (NPA) of 87.5% (21/24) and 91.7% (22/24), respectively. Blood-mNGS showed higher PPA in neutropenic than non-neutropenic patients [56.8% (21/37) vs. 25.6% (23/90), P = 0.001], with unique fungal detection advantages, identifying additional fungi in 7 cases: Mucorales (3), Aspergillus spp. (2), both Mucorales and Aspergillus spp. (1), and Pneumocystis spp. (1). Resistance genes were detected only by LRTS-mNGS. mNGS positively influenced antimicrobial adjustments in 54.3% (69/127) of cases, particularly for pathogens with low empirical coverage, such as Legionella spp. (0.0%, 0/7), Pneumocystis spp. (52.4%, 11/21), and Mucorales (55.6%, 5/9). Blood-mNGS detected these pathogens at rates of 71.4% (5/7), 23.8% (5/21), and 77.8% (7/9), respectively.
CONCLUSION: LRTS-mNGS outperformed blood-mNGS in diagnostic performance and resistance detection. Blood-mNGS identified pathogens in one-third of BFPI cases, with value for certain fungal infections, especially in hematologic patients with limited LRTS access.
TRIAL REGISTRATION: Not applicable. This study is a retrospective analysis and does not require clinical trial registration.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12734-8.}, }
@article {pmid41645099, year = {2026}, author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z}, title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41645099}, issn = {1471-2180}, support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Forests ; *Ecosystem ; *Bacteria/classification/genetics/isolation & purification ; Calcium Carbonate ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Feces/microbiology ; Metagenomics ; Metagenome ; }, abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.
RESULTS: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.
CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.}, }
@article {pmid41645132, year = {2026}, author = {Ma, D and Xu, S and Yu, D and Peng, A and Yang, L and Yang, H and Yuan, Q and Li, Y}, title = {Cytomegalovirus-induced severe enterocolitis associated with ANCA-associated vasculitis and diffuse alveolar haemorrhage in a child: a diagnostic and therapeutic dilemma.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41645132}, issn = {1471-2431}, abstract = {BACKGROUND: ANCA-associated vasculitis (AAV) is rare in children and may be triggered by infections. Cytomegalovirus (CMV), a common pathogen, can rarely cause severe gastrointestinal complications like stricture, obstruction, and perforation. While adult cases suggest a potential association between CMV and AAV, reports of severe intestinal complications leading to AAV in immunocompetent children are scarce.
CASE PRESENTATION: A previously healthy 12-year-old boy presented with fever, abdominal pain, and vomiting. Abdominal CT revealed intestinal obstruction and perforation. Emergency surgery confirmed acute hemorrhagic necrotizing enterocolitis, and metagenomic next-generation sequencing (mNGS) diagnosed CMV viremia. His condition deteriorated rapidly, culminating in acute respiratory failure and acute kidney injury requiring continuous renal replacement therapy. Serological testing using indirect immunofluorescence was positive for cytoplasmic-ANCA (C-ANCA). Confirmatory ELISA testing confirmed positivity for anti-proteinase 3 (PR3) antibodies at a titer of 1:51; anti-myeloperoxidase (MPO) antibodies were negative. Chest CT and bronchoscopy confirmed diffuse alveolar haemorrhage. AAV was diagnosed per the 2022 ACR/EULAR criteria. The central management challenge was the co-occurrence of active CMV infection and fulminant vasculitis. Immunosuppressive therapy was withheld until sepsis parameters normalized. A life-threatening bleeding event on day 13 prompted initiation of high-dose methylprednisolone and cyclophosphamide, leading to rapid clinical improvement. A subsequent renal biopsy showed subacute tubulointerstitial injury without crescents.
CONCLUSION: Severe CMV enterocolitis may be temporally associated with fulminant AAV in children. In pediatric cases of severe CMV infection with multi-organ dysfunction, a high index of suspicion for AAV and ANCA serology testing is warranted. Furthermore, multidisciplinary team input is crucial for guiding optimal timing of immunosuppression in the context of concurrent active infection, which is pivotal for improving patient outcomes.}, }
@article {pmid41645540, year = {2026}, author = {Cuong, TM and Dan, NH and Hang, TTT and Le Luu, T and Scheynen, J and Dries, J}, title = {Enhanced the Treatment of Seafood Processing Wastewater Using the Anaerobic-Anoxic-Oxic (AAO) Process With Granular Sludge.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {98}, number = {2}, pages = {e70293}, doi = {10.1002/wer.70293}, pmid = {41645540}, issn = {1554-7531}, support = {FWO.105-2022.03//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; }, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Wastewater ; Bioreactors/microbiology ; *Seafood ; Phosphorus ; Bacteria/classification/genetics ; Nitrogen ; Aerobiosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Seafood processing wastewater contains high concentrations of organics and nutrients that need to have an effective solution. This study aims to explore the use of granular sludge in seafood wastewater treatment using anaerobic-anoxic-aerobic (AAO) process. The results showed that the granular sludges were successfully cultivated from the traditional activated sludge sources. The bioreactor demonstrated robust treatment performance, achieving a high chemical oxygen demand (COD) removal efficiency exceeding 93%, total nitrogen (TN) removal ranging from 56.6% to 68.6%, and ammonium removal (NH4 [+]-N) of 80% to 88.57%. However, total phosphorus (TP) removal efficiency was relatively moderate at 47.36% ± 10.33%. Metagenomic analysis (16S rRNA) revealed a diverse and evenly distributed microbial community within the granular sludge. In anaerobic granular sludge, the dominant phylum was Bacillota (45.3%), followed by Thermodesulfobacteriota (18.2%) and Synergistota (11.24%), with minor contributions from Campylobacterota (7.58%), Chloroflexota (3.98%), and Bacteroidota (3.6%), alongside other less abundant phyla (10.1%). Anoxic granular sludge exhibited a shift, with Pseudomonadota (32.87%) and Thermodesulfobacteriota (25.08%) dominating, while Bacillota (11.95%), Bacteroidota (7.9%), and Chloroflexota (4.1%) contributed less, and other phyla comprised 18.21%. For aerobic granular sludge, Pseudomonadota represented the most prevalent phylum (42.21%), followed by Thermodesulfobacteriota (14.94%) and Bacillota (14.87%), with lower abundances of Bacteroidota (7.74%) and Chloroflexota (4.91%), while other phyla accounted for 15.42%.}, }
@article {pmid41646408, year = {2026}, author = {Bosquet, JG and Osazuwa-Peters, O and Wagner, VM and Polio, A and Hoyd, R and Tarhini, AA and Cosgrove, CM and Huang, MS and Corr, BR and Leiser, AL and Salhia, B and Darcy, K and Dood, RL and Dockery, LE and Cavnar, MJ and Landrum, L and Chambers, L and Tan, AC and Jin, N and Rounbehler, RJ and Churchman, ML and Spakowicz, D}, title = {Intrinsic tumor factors and extrinsic environmental and social exposures contribute to endometrial cancer recurrence patterns.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41646408}, issn = {2693-5015}, support = {P30 CA086862/CA/NCI NIH HHS/United States ; R01 CA099908/CA/NCI NIH HHS/United States ; }, abstract = {PURPOSE: In a previous study, we trained, validated and tested models of endometrial cancer (EC) recurrence integrating clinical, genomic and pathological data from the Oncology Research Information Exchange Network (ORIEN). Preliminary studies also have demonstrated that bacterial communities may influence the risk of EC recurrence by altering the local environment within the upper female genital tract. The objective of this study was to evaluate whether extrinsic and environmental factors, including tumor-associated bacterial communities, tumor immune contexture and air pollution alongside clinical, pathologic and genomic features are associated with EC recurrence across clinically relevant risk groups.
PATIENTS AND METHODS: We performed a retrospective, multi-institution, case-control study with data from the ORIEN network EC dataset. Data was stratified into low-risk, FIGO grade 1 and 2, stage I (N = 329), high-risk, or FIGO grade 3 or stages II-IV (N = 324), and non-endometrioid histology (N = 239) groups. RNA and DNA were extracted from tumor specimens and processed to obtain the necessary genomic/metagenomic data. Genus level microbiome data were extracted and curated) from RNA sequencing using Kraken2, Bracken and exotic software packages. Risk of EC recurrence was evaluated by integrating microbiome and environmental data alongside existing clinical, pathological and genomic data using topic modelling with latent dirichlet allocation (LDA). Prediction models of EC recurrence were created using machine and deep learning analytics (ML and DL) with MATLAB apps and TensorFlow. Finally, performance of both topic and prediction models were externally validated in an independent EC dataset from TCGA.
RESULTS: The resulting models, analyzed with topic modelling, demonstrated the complexity of factors involved in recurrence of disease for EC. The components of the resulting topic models, and specifically the microbiome, changed when environmental factors, like air pollutants, were introduced in the model. In the low-risk EC group, microbes that were quite abundant in models before introducing environmental factors, were scarcely seen afterwards, like genera Thermothielavioides, Theileria, Rhizoctonia. Bacillus was the genus with higher per-topic probability within all risk groups, especially for low-risk EC (28%). Ozone (O3) was a resulting component of all risk groups' models. BMI was the sole informative clinical variable after data integration, and only present in the low-risk group. Resulting models from the high-risk and non-endometrioid groups included differential gene expressions: MMP13, S100A7, SMOC1, ACACA and ADD2, DLX5, SLCO2B1, NWD1 respectively. CNVs also were present in both low-risk and non-endometrioid groups, but their per-topic probabilities were low. The same was true for the immune contexture data. The components of the resulting topic models were used to train, validate and test prediction models of EC recurrence by risk groups. Performances of these models were excellent (@ 0.9). Despite some missing microbiome data in TCGA from resulting topic models, prediction models trained in the ORIEN set, had similar performances in TCGA testing set, with overlapping AUC 95% CIs.
CONCLUSION: Both extrinsic factors (tumor-associated bacterial communities, tumor immune contexture and air pollution) and intrinsic factors predict EC recurrence. The complexity of tumor and host factors influencing cancer relapses underscore the need for more individualized prediction models of disease outcomes.}, }
@article {pmid41647522, year = {2026}, author = {Liu, J and Chen, Y and Sheng, X and Gao, Y}, title = {Case Report: Nocardia farcinica infectious arthritis and myositis in an immunocompromised host: diagnostic and management challenges.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1762442}, pmid = {41647522}, issn = {2296-858X}, abstract = {BACKGROUND: Nocardia farcinica is a rare opportunistic pathogen predominantly affecting immunocompromised hosts. Infectious arthritis, cutaneous and deep soft tissue infections caused by this organism often present with nonspecific clinical manifestations. Additionally, due to its slow-growing and oligotrophic nature, both cultivation and identification pose considerable challenges, thereby complicating clinical diagnosis and management.
CASE PRESENTATION: This case report described an elderly female patient presenting with right shoulder redness, swelling, and pain. Her history included diabetes, local corticosteroid injections, and newly identified humoral immunodeficiency (hypogammaglobulinemia with low B-cell count). Imaging revealed infectious arthritis of the right shoulder, accompanied by infectious myositis and an intermuscular abscess in the right upper arm. Nocardia farcinica was confirmed by metagenomic next-generation sequencing (mNGS) and culture of aspirated fluid. Initial therapy with trimethoprim-sulfamethoxazole (TMP-SMX) and ceftriaxone was limited by renal impairment and gastrointestinal intolerance, and susceptibility testing indicated TMP-SMX resistance. Treatment was switched to linezolid. Due to inadequate clinical response, multiple surgical debridements were performed. Subsequently, therapy was changed to oral minocycline because of linezolid-induced bone marrow suppression and intolerance. At discharge, the maintenance regimen consisted of moxifloxacin combined with minocycline.
CONCLUSION: This case highlights the importance of considering low-virulence pathogens such as Nocardia in immunocompromised patients with atypical infections that respond poorly to initial empiric therapy. Pathogen identification, aided by tools like mNGS for rapid detection, is essential. When classic regimens are limited by adverse effects, susceptibility-guided alternative therapies can be effective. For localized infections refractory to medical management, multidisciplinary surgical intervention remains a critical component of care.}, }
@article {pmid41647993, year = {2025}, author = {Jayakrishnan, T and Sangwan, N and Nair, KG and Kamath, SD and Patel, MH and Joyce, D and Walsh, M and Simon, R and Vadehra, D and Iyer, RV and Fountzilas, C and Khorana, AA}, title = {Tumor microbiome differences in early-onset versus average-onset pancreatic adenocarcinoma.}, journal = {ESMO gastrointestinal oncology}, volume = {9}, number = {}, pages = {100194}, pmid = {41647993}, issn = {2949-8198}, abstract = {BACKGROUND: Compelling evidence supports the biomarker potential of microbiome in pancreatic adenocarcinoma. Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age <50 years), we aimed to evaluate microbiome profiles in resected specimens from individuals with eoPDAC and average-onset PDAC (aoPDAC, age >50 years).
MATERIALS AND METHODS: We carried out shotgun metagenomic sequencing in resected specimens from individuals with eoPDAC (n = 24) and aoPDAC (n = 20). Statistical tests included Wilcoxon test, permutational analysis of variance, multiomic classifier modeling, differential abundance analysis, and linear regression. All P values were adjusted for multiple testing and P < 0.05 was considered statistically significant.
RESULTS: We successfully sequenced several bacteria and fungi in the tumor specimens from 44 individuals with resected PDAC (24 eoPDAC and 20 aoPDAC). The alpha diversity of the bacterial microbiome was higher in eoPDAC tumor tissue compared with aoPDAC (P = 0.04). In contrast, the fungal mycobiome's alpha diversity was higher for aoPDAC tumor tissue (P = 0.02). Key organisms with differential abundance between tumor tissue from individuals with eoPDAC and aoPDAC included Bacillus, Candida, Collimonas, Cupriavidus, Enterobacter, Escherichia, Klebsiella, Malasseiza, Mucilaginibacter, Neisseria, and Sphingomonas. Higher bacterial diversity in tumor tissue was associated with better overall survival for individuals with eoPDAC (R = 0.26, P = 0.02).
CONCLUSIONS: Shotgun metagenomic sequencing identified bacterial microbiome and fungal mycobiome in tumors from individuals with eoPDAC and aoPDAC. We observed significant differences in alpha and beta diversity and relative abundances of organisms suggesting distinct microbiome signatures. Microbiome associations with survival were observed in eoPDAC indicating unique potential as prognostic biomarker.}, }
@article {pmid41648002, year = {2025}, author = {Zhang, H and Chen, K and Chen, R and Jia, E}, title = {Feeding patterns reprogram a gut microbial virulence-iron-quorum sensing functional axis linked to atherosclerotic risk.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1751844}, pmid = {41648002}, issn = {1664-302X}, abstract = {The feeding rhythm is a major temporal regulator of metabolic physiology, yet its impact on microbiome-derived functional traits relevant to cardiometabolic disease remains insufficiently understood. Our previous work demonstrated that ad libitum, daytime-restricted, and nighttime-restricted feeding produce markedly different atherosclerotic outcomes in Apoe[-]/[-] mice, indicating that the feeding rhythm acts as a modifiable determinant of atherogenic susceptibility. Here, we used shotgun metagenomics to profile risk-associated microbial functional modules-including Type III and Type VI secretion systems (T3SS/T6SS), siderophore-based iron acquisition pathways, quorum-sensing (QS) regulators, and antimicrobial resistance determinants-across feeding regimens. The feeding rhythm induced pronounced functional segregation independent of α-diversity, which was consistent with selective functional reprogramming rather than taxonomic restructuring. Daytime feeding, which is misaligned with the murine active phase, is associated with coordinated enrichment of the T3SS/T6SS, iron uptake, and QS pathways, forming a tightly interconnected "virulence-iron-QS-ARG" functional consortium. In contrast, circadian-aligned nighttime feeding resulted in attenuated virulence orientation and enhanced metabolic-cooperative signatures. Network inference further revealed strong coactivation of virulence secretion, iron mobilization, and QS modules under circadian misalignment. These findings show that the feeding rhythm modulates atherogenic susceptibility not only through host metabolism but also by remodeling gut microbial functional capacities, highlighting microbial functional ecology as an integral component of diet-host interactions.}, }
@article {pmid41648004, year = {2025}, author = {Goncalves, AR and Ranganathan, H and Valdes, C and Zhu, H and Zhang, B and Kok, CR and Martí, JM and Mulakken, NJ and Thissen, JB and Jaing, C and Be, NA}, title = {Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1695501}, pmid = {41648004}, issn = {1664-302X}, abstract = {Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.}, }
@article {pmid41648005, year = {2025}, author = {Liu, JJ and Yang, H and Xiao, ZY and Xie, JH and Su, L and Li, YT and Zheng, XY and Hu, WH and Fu, SJ and Li, CL and Huang, L and Yu, SY and Yu, Z and Yang, S and Yang, J}, title = {Gut microbiota and metabolic dysregulation in polycystic ovary syndrome: effects of acupuncture as an adjunct to in vitro fertilization on gut dysbiosis, metabolism, and oocyte quality.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1730714}, pmid = {41648005}, issn = {1664-302X}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is marked by disruptions in metabolic and reproductive endocrine functions. This study synthesizes systemic metabolic profiles, alterations in gut microbiota, and follicular fluid metabolism to elucidate the reproductive and endocrine metabolic changes associated with PCOS. Furthermore, it aims to elucidate the potential mechanisms through which acupuncture may exert therapeutic effects.
METHODS: In this open-label randomized controlled trial conducted in China (November 2021-January 2023), 60 women with PCOS scheduled for In Vitro Fertilization (IVF) were randomized to receive acupuncture combined with IVF treatment or IVF treatment alone, with 30 healthy women serving as controls. Gut microbiota was sequenced and analyzed by 16S rRNA and metagenomics; follicular fluid metabolites were determined by untargeted metabolomics.
RESULTS: Compared with healthy controls, PCOS exhibited gut microbiota dysbiosis and metabolic disorders. The specific gut microbiota in PCOS dominated by s_Lachnospiraceae, s_Blautia_sp. and g_Escherichia-Shigella, which correlated with body mass index (BMI), waist circumference, waist-to-hip ratio, and hormone levels. Acupuncture combined with IVF significantly regulated glucose and lipid metabolism, reduced g_Escherichia-Shigell abundance, and showed potential advantages in enhancing oocyte quality and embryonic developmental potential (p = 0.011). Analysis of the correlation between differential metabolites and oocyte and embryo quality demonstrated that methionine sulfoxide and boldione may be key metabolites to affect follicle quality.
CONCLUSION: PCOS is associated with systemic multi-pathway metabolic dysregulation and gut microbiota dysbiosis. It described the potential therapeutic benefits of acupuncture combined with IVF for PCOS, laying a foundation for further understanding the disease and the mechanisms of acupuncture for PCOS metabolic disorders, and providing directions for future research.}, }
@article {pmid41648007, year = {2025}, author = {Schnabel, E and Vuillemin, A and Esser, S and Griesdorn, L and Soares, AR and Mørkved, PT and Jørgensen, SL and Probst, AJ and Kallmeyer, J and , }, title = {Geochemical variability and microbial metabolic functions in oligotrophic sediments exposed to minor seepage.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1720187}, pmid = {41648007}, issn = {1664-302X}, abstract = {Low primary productivity in Barents Sea surface waters and limited nutrient flux to the seafloor favor nitrification and nitrogen fixation in deep waters, resulting in a dearth of organic substrates in local sediments. The addition of labile hydrocarbons naturally occurring through seepage from subsurface reservoirs could promote microbial activity in organic-lean sediments, notably by denitrifying and sulfate-reducing microbes. Using gravity cores from an area with numerous hydrocarbon reservoirs, we document pore water geochemistry, dissolved gas concentrations, and total cell counts supplemented with taxonomic and functional marker gene analyses from metagenomes and metagenome-assembled genomes. We assess the contribution of the subsurface biosphere in producing geochemical gradients in oligotrophic sediments facing different exposure to minor seepage. In pristine seabed, i.e., not affected by hydrocarbon seepage, nitrate and ammonium profiles were consistent with denitrification down to 1 m below seafloor. By contrast, minor hydrocarbon seepage caused very different pore water profiles, which were indicative of more reducing geochemical conditions in the sediment and more advanced consumption of electron acceptors in pore water. Delivery of favorable organic substrates to anaerobic microbes through seepage was reflected in slightly higher cell densities, CH4 and CO2 concentrations, but appeared to have little impact on community diversity. This could be explained by metabolic versatility across functional guilds, with limited differentiation of sedimentary niches, favoring polyvalent fermenters at the expense of canonical denitrifiers and sulfate reducers. These versatile fermenters exhibited diverse predicted capabilities for nitrate and sulfate reduction combined with hydrocarbon degradation, (homo)acetogenesis, and nitrogen fixation. Our results further indicate that specific clades of homoacetogens (Lokiarchaeia, Bathyarchaeia, and Dehalococcoidia) could support cross-feeding interactions when fueled by simple hydrocarbons through seepage, particularly those associated with dissimilatory sulfur metabolism and fermentation of intermediate metabolites. In the absence of hydrocarbon-derived electron donors, the same clades appear capable of energy-conserving (homo)acetogenic fermentation on organic residues. Thus, we conclude that slow-growing (homo)acetogens that are ubiquitous in the marine subseafloor actively contribute to balancing biogeochemical cycles in oligotrophic sediments impacted by minor hydrocarbon seepage.}, }
@article {pmid41648008, year = {2025}, author = {Pasquali, F and Crippa, C and Lucchi, A and Manfreda, G}, title = {Artisanal food of animal origin as reservoir of putative pathogenic Escherichia coli: a combined genomic and in vivo approach.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1718380}, pmid = {41648008}, issn = {1664-302X}, abstract = {The lack of a full automation and control of environmental parameters might result in potential risk of microbial contamination in small-scale production plants such as artisanal cheese and salami Italian productions. In a previous study, genomes of 33 E. coli isolates were sequenced. In the present study, the pathogenicity potential of E. coli strains was investigated by: (1) phylogenomic comparison with 202 public genomes of human, animal and environmental Italian origin; (2) pathogenicity assessment of strains with virulence patterns predicting specific E. coli pathotypes by using larvae of Galleria mellonella as in vivo infection model. Phylogenetic reconstruction revealed raw material and not the processing environment as source of salami contamination. Moreover, close proximity of some strains isolated from salami production with wild boar and extraintestinal human public strains was observed suggesting pigs and wild boar as potential reservoirs of pathogenic E. coli. The virulome of salami strains revealed the presence of genes already described as gene markers of atypical enteropathogenic E. coli (aEPEC; bfp-, eae+). Interestingly the analysis of virulence genes pointed toward additional genomes which showed genetic markers previously described as strongly associated to and/or extraintestinal pathogenic E. coli (ExPEC). In vivo experiments, confirmed the higher pathogenicity of strain 5STM5 with genetic pattern corresponding to hybrid aEPEC/ExPEC and two strains 3CP1522 and 6MB5 of cheese and salami production, respectively, with virulence genes previously associated to ExPEC pathotype. The combined approach pointed toward two genes espC for aEPEC, as well as malX for ExPEC which were significantly enriched in clinical genomes in comparison to genomes of other origins. These genes are worth of future investigations which could help to assess the risk for consumers after the consumption of contaminated artisanal food.}, }
@article {pmid41648108, year = {2026}, author = {Martinez, NAP and Arnaldi, MR and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA}, title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in a Drosophila Autism-like Model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648108}, issn = {2692-8205}, support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; }, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that has no cure and is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B or KDM5C are found in patients with intellectual disability and ASD. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5 [LOF]) ASD-like model revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.
METHODS: Here, we evaluated multiple microbiota-based interventions, including probiotic supplementation with Lactiplantibacillus plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in Kdm5 [LOF] flies. Gut bacterial abundance was quantified using colony-forming unit (CFU) assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.
RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5 [LOF] and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5 [LOF] flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5 [LOF] mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5 [LOF] recipient flies.
CONCLUSIONS: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships relevant to ASD and for evaluating targeted probiotic and microbiota-transfer strategies.}, }
@article {pmid41648142, year = {2026}, author = {Mastrorilli, E and Herd, P and Rey, FE and Goodman, AL and Zimmermann, M}, title = {Linking interpersonal differences in gut microbiota composition and drug biotransformation activity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648142}, issn = {2692-8205}, support = {P30 AG017266/AG/NIA NIH HHS/United States ; R01 AG060737/AG/NIA NIH HHS/United States ; R01 AT010014/AT/NCCIH NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; }, abstract = {Individuals vary widely in their responses to drugs, and growing evidence implicates the gut microbiome as a contributor to this variability. While prior studies show that gut bacteria can metabolize drugs, how differences in microbial community composition influence drug metabolism remains poorly understood. Here, we characterize the biotransformation of 271 drugs by 89 gut microbial communities derived from human donors and preclinical animal models. Over 90% of tested drugs were metabolized by at least one microbiome. We identified 66 drugs exhibiting highly variable metabolism across human-derived microbiomes and several drugs whose biotransformation differed markedly between human and animal microbiomes. To enable prediction of microbiota-mediated drug metabolism, we developed and compared multiple modeling approaches based on metagenomic data. These results, together with the provided data and analytical resources contribute to a better understanding of microbiome-drug interactions and support their future integration into drug discovery, personalized prescription, and therapeutic drug monitoring.}, }
@article {pmid41648310, year = {2026}, author = {Szenei, J and Burke, A and Liong, A and Korenskaia, A and Lukowski, AL and Ziemert, N and Nikel, PI and Leão, PN and Moore, BS and Weber, T and Blin, K}, title = {Computational pipeline reveals nature's untapped reservoir of halogenating enzymes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648310}, issn = {2692-8205}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; R35 GM159745/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbial halogenated natural products (hNPs) hold ecological, agricultural, and biomedical relevance. The hNP-producing potential of the organism can be assessed by the precise prediction of biosynthetic enzymes, yet the detailed annotations of halogenases are often missing from genomic and metagenomic data. We created a manually curated database (https://halogenases.secondarymetabolites.org/) containing information on the halide-specificity, role, and position of verified catalytic residues and results of the mutagenesis studies of more than 120 experimentally validated or in silico inferred halogenases. The collection of experimental data supports a computational pipeline that allows the family-, substrate-, and halide-scope-level annotation of halogenating enzymes by relying on catalytic residues, conserved motifs, and profile Hidden Markov Models (pHMMs). Our analysis with sequence similarity networks (SSNs) highlighted several underexplored clusters in the UniRef50 database. Such finding was a halogenase from Rhodopirellula baltica (RhobaVHPO) previously labelled as a hypothetical chloroperoxidase, which clustered apart from the known chloroperoxidases and bromoperoxidases, but accepted chloride and preferred bromide. Our database and workflow provide extensive and scalable solutions for the systematic and precise annotation of halogenating enzymes in genomic and metagenomic data. The in-depth categorization of halogenases will improve the chemical structure prediction of microbial hNPs, supporting ecological assessments and natural product discovery.}, }
@article {pmid41648334, year = {2026}, author = {Romo Bechara, N and Bardeskar, N and Hopkins, HA and Raymann, K}, title = {Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.13.699197}, pmid = {41648334}, issn = {2692-8205}, abstract = {UNLABELLED: Opportunistic bacterial pathogens often encounter strong selective pressures outside their hosts, yet the evolutionary consequences of long-term predator exposure remain poorly understood. Here, we used experimental evolution to examine how sustained interaction with a eukaryotic predator shapes genomic adaptation, phenotypic diversification, and virulence-associated traits in Pseudomonas aeruginosa . Replicate populations of P. aeruginosa were evolved for 60 days in the presence or absence of the ciliate predator Tetrahymena thermophila , followed by whole-population metagenomic sequencing, isolate-level genome sequencing, and quantitative phenotypic assays. We observed extensive genetic diversification across all populations, with strong signatures of both positive and purifying selection and pervasive parallel evolution at gene and nucleotide levels. Predator-exposed populations accumulated mutations enriched in regulatory, metabolic, and virulence-associated pathways, revealing predictable genomic targets of selection. However, many parallel mutations were shared between predator-exposed and predator-free populations, indicating that adaptation to the abiotic environment represented a dominant selective force. Genotype-phenotype analyses revealed pleiotropic effects and trade-offs linking motility, growth, and virulence-associated traits. Despite pronounced genomic adaptation and coordinated phenotypic shifts, changes in virulence in an in vivo host model were modest and context dependent. Taken together, our results indicate that predator exposure can influence evolutionary trajectories in P. aeruginosa and highlight the value of extending such approaches across multiple ecological and host contexts.
SIGNIFICANCE: Many bacterial pathogens spend much of their evolutionary history outside hosts, where they face intense ecological pressures such as predation. How these pressures shape pathogen evolution and disease potential remains unclear. Using experimental evolution, genomics, and phenotypic analyses, we show that prolonged exposure to a eukaryotic predator drives predictable genetic and phenotypic changes in the opportunistic pathogen Pseudomonas aeruginosa . Predator exposure altered regulatory, metabolic, and virulence-associated pathways, yet much adaptation was shared with predator-free populations, highlighting the dominant role of abiotic environments. Although predator-driven evolution reshaped traits linked to motility and growth, its effects on virulence were modest and context dependent. These findings clarify how environmental interactions influence pathogen evolution and underscore the importance of studying pathogens across diverse ecological settings.}, }
@article {pmid41648417, year = {2026}, author = {Arasti, S and Şapcı, AOB and Rachtman, E and El-Kebir, M and Mirarab, S}, title = {Deconvolving Phylogenetic Distance Mixtures.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648417}, issn = {2692-8205}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; }, abstract = {Mixtures of multiple constituent organisms are sequenced in several widely used applications, including metagenomics and metabarcoding. Characterizing the elements of the sequence mixture and their abundance with respect to a reference set of known organisms has been the subject of intense research across several domains, including microbiome analyses, and methods must overcome two key challenges. First, the mixture constituents are related to each other through an evolutionary history, and hence, should not be considered independent entities. Second, sequence data is noisy, with each short read providing a limited signal. While existing approaches attempt to address these challenges, addressing both challenges simultaneously has proved challenging. For evolutionary dependencies, methods either define hierarchical clusters (e.g., taxonomies or operational taxonomic/genomic units) or use phylogenetic trees. For the second challenge, they either assemble reads into contigs, use statistical priors to summarize read placements, or attempt to analyze all reads jointly using k-mers. Despite this rich literature, a natural approach to simultaneously address both challenges has been underexplored: compute a distance from the mixture to all references, deconvolve those distances, and place the sample on multiple branches of a reference phylogeny with associated abundances. This multi-placement approach is a natural extension of the single-read phylogenetic placement used in practice. We argue that by placing the entire sample on multiple branches instead of placing reads individually, we can obtain a less noisy profile of the mixture. We formalize this approach as the phylogenetic distance deconvolution (PDD) problem, show some limits on the identifiability of PDDs, propose a slow exact algorithm, and an efficient heuristic greedy algorithm with local refinements. Benchmarking shows that these heuristics are effective and that our implementation of the PDD approach (called DecoDiPhy) can accurately deconvolve phylogenetic mixture distances while scaling quadratically. Applied to metagenomics, DecoDiPhy consolidates reads mapped to a large number of branches on a reference tree to a much smaller number of placements. The consolidated placements improve the accuracy of downstream tasks, such as sample differentiation and detection of differentially abundant taxa.}, }
@article {pmid41648756, year = {2025}, author = {Grønbæk, IMB and Halkjær, SI and Hansen, EH and Mollerup, S and Paulsen, SJ and Konrad, CV and Engel, S and Bulinska-Balas, M and Wellejus, A and Haaber, AB and Christensen, AH and Engsbro, AL and Petersen, AM}, title = {Eight weeks of treatment with probiotic Bifidobacterium breve, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome: results from a randomised, clinical trial.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1701341}, pmid = {41648756}, issn = {2296-861X}, abstract = {UNLABELLED: Patients with irritable bowel syndrome experience abdominal pain and stool habit disturbances, and often also extraintestinal symptoms, such as fatigue. The disorder is linked to gut dysbiosis, and manipulation of the microbiota is considered a possible treatment strategy. This randomised, double-blinded, placebo-controlled study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (DSM 33360) (Bif195), on symptoms and gut microbiome composition in patients with diarrhoea-predominant irritable bowel syndrome. Sixty-one patients with moderate-severe disease activity were allocated to 8 weeks of treatment with either Bif195 or placebo (1:1), followed by 8 weeks of follow-up. The primary outcome was a change in symptom scores measured by the validated questionnaire, IBS-symptom severity scale. Secondary and explorative outcomes were the effects of Bif195 on intestinal symptoms, quality of life, fatigue, and the gut microbiota. Modulation of the transepithelial electrical resistance (TEER) of Caco-2 cells by Bif195 was investigated in vitro as a model of barrier integrity. The results showed no effect of Bif195 on primary or secondary outcomes; however, Bif195 lowered fatigue scores compared to placebo. Significantly increased TEER readings in vitro indicated enhanced barrier integrity, suggesting GI permeability as a mechanism for further clinical exploration.
CLINICAL TRIAL REGISTRATION: clinicaltrials.gov, identifier NCT04808271.}, }
@article {pmid41649276, year = {2026}, author = {Castillo-Ramírez, S and López-Sánchez, R and Peralta, H}, title = {Acinetobacter-the bad, the ugly, but also the good!.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0001026}, doi = {10.1128/msphere.00010-26}, pmid = {41649276}, issn = {2379-5042}, abstract = {The genus Acinetobacter is vast and diverse regarding its hosts. However, it is best known as an opportunistic pathogen that causes hard-to-treat nosocomial infections. Yet, some species of the genus can be beneficial for some hosts. Such is the case of Acinetobacter calcoaceticus, which can have a significant impact on tomato plants, as was recently shown in a paper by Robertson et al. (S. Robertson, A. Mosca, S. Ashraf, A. Corral, et al., mSphere 11:e00842-25, 2026, https://doi.org/10.1128/msphere.00842-25). Importantly, that study also exemplifies how metagenomics in general, but metagenome-assembled genomes in particular, can be employed to understand the functional specialization and identity of the bacterial species dwelling in particular environments.}, }
@article {pmid41649278, year = {2026}, author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA}, title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0117325}, pmid = {41649278}, issn = {2379-5077}, support = {PRIN 2022 Project Code 20229LEB99//European Union NextGeneration EU/ ; 12/RC/2273-P1, 12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; Phylogeny ; *Bifidobacterium adolescentis/genetics/classification ; *Evolution, Molecular ; Metagenome ; *Adaptation, Physiological/genetics ; Gene Transfer, Horizontal ; Metagenomics ; }, abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.
IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.}, }
@article {pmid41649661, year = {2025}, author = {Romão, IR and do Carmo Gomes, J and Silva, D and Vilchez, JI}, title = {The seed microbiota from an application perspective: an underexplored frontier in plant-microbe interactions.}, journal = {Crop health}, volume = {3}, number = {1}, pages = {12}, pmid = {41649661}, issn = {2948-1945}, support = {UIDB/04551/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04551/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0087/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Seed-associated microbiota represent a critical yet underexplored frontier in plant-microbe interactions, offering unique insights into plant health, resilience, and development. Unlike the soil or rhizosphere microbiome, the seed microbiota is closely tied to plant reproduction, facilitating both vertical and horizontal transmission of microbes. These microbial communities influence key plant processes, including germination, stress tolerance, nutrient acquisition, and pathogen resistance, providing plants with a pre-assembled microbial consortium tailored to their needs. Despite recent advances, significant gaps remain in understanding how seed-associated microbes are acquired, their ecological dynamics, and their functional roles. High-throughput sequencing, metagenomics, and spatial imaging techniques have revealed the diversity and complexity of the seed microbiota, emphasizing their potential for agricultural innovation. This research highlights the importance of these communities in shaping plant resilience and productivity, yet questions about their ecological and evolutionary significance persist. The present review synthesizes current knowledge on the composition, inheritance mechanisms, and functional roles of the seed microbiota. It also explores strategies to harness these microbes for sustainable agriculture, including microbiome engineering and breeding for microbial compatibility. By addressing these gaps, seed microbiota research could revolutionize sustainable agriculture, enhancing crop resilience and reducing reliance on chemical inputs.}, }
@article {pmid41650192, year = {2026}, author = {Wang, H and Shan, X and Xing, D and Wang, Y and Jin, C and Zhao, Y and Guo, L}, title = {Rhamnolipid Modulates Microbial Interspecies Electron Transfer for Synchronous Sulfidogenesis and Acidogenesis from Mariculture Solid Wastes.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {4900-4913}, doi = {10.1021/acs.est.5c16493}, pmid = {41650192}, issn = {1520-5851}, mesh = {Electron Transport ; *Glycolipids ; *Solid Waste ; Sulfides/metabolism ; }, abstract = {Synchronous sulfidogenesis and acidogenesis (SSA) are critical for pollutant removal and resource recovery. However, inefficient electron transfer and metabolic imbalance between acidogenic bacteria and sulfidogens limit SSA performance, especially from mariculture solid wastes (MSW) containing high-strength sulfate. This work unveiled the neglected role and mechanism of rhamnolipid (RL) in modulating microbial interspecies electron transfer for SSA during MSW anaerobic fermentation. RL, at environmentally relevant levels of 20-200 mg/g suspended solids, simultaneously improved sulfide (40.1-87.9%) and short-chain fatty acids (8.0-19.3-fold) yield. Extracellular polymeric substances (EPSs) exhibited higher capacitance and electroactivity to store or transfer electrons in the presence of RL. Proper RL facilitated pili-like filament formation and redox mediator secretion. The flavins and cytochrome c combination was promoted by RL to mediate one-electron transfer with a higher transfer rate via the flavin semiquinone intermediate. RL increased the dipole moment of the α-helix peptide and spontaneously interacted with the C═O of amide groups, enabling efficient electron hopping in EPSs. RL also activated key components in the intracellular electron transfer system, delivering more electron flow to sulfate reductase. Metagenomic and metatranscriptomic analyses verified the differential enrichment of microorganisms and key gene upregulation related to SSA, EPS secretion, quorum sensing, ATP, type IV pili, and electron shuttle synthesis. These findings provide new insight into the roles and interactive mechanisms of biosurfactants in modulating microbial electron transfer.}, }
@article {pmid41650276, year = {2026}, author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H}, title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eaeb6265}, pmid = {41650276}, issn = {2375-2548}, mesh = {*Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology ; Animals ; Humans ; Metagenome ; Phylogeny ; Genome, Viral ; Bacteroides/virology ; }, abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.}, }
@article {pmid41650846, year = {2026}, author = {Hosen, ME and Dunsdon, S and Sarker, S}, title = {Mosquito-borne viruses in Australia: An emerging trend of increasing prevalence in Northern Queensland.}, journal = {Virology}, volume = {617}, number = {}, pages = {110825}, doi = {10.1016/j.virol.2026.110825}, pmid = {41650846}, issn = {1096-0341}, mesh = {Queensland/epidemiology ; Animals ; *Mosquito Vectors/virology/microbiology ; Humans ; Aedes/virology/microbiology ; Wolbachia ; Prevalence ; Mosquito Control/methods ; *Arbovirus Infections/epidemiology/virology/transmission ; *Arboviruses/genetics/isolation & purification/classification ; }, abstract = {Mosquito-borne viruses (MBVs) remain a significant public health concern in Northern Queensland, Australia, with dengue virus (DENV), Ross River virus (RRV), and Barmah Forest virus (BFV) representing the most common pathogens. Wolbachia-based biological control programs have made notable contributions to reducing dengue transmission by suppressing Aedes aegypti vector competence. Recent surveillance data indicates increased MBV activity, with national case numbers nearly doubling between 2023 and 2024 and early 2025 data suggesting sustained transmission during seasonal peak. Traditional surveillance approaches, while highly valuable for disease monitoring, have limitations in detecting novel or divergent viral strains in real time. Over the past decades, more than 919 unclassified flaviviruses have been reported nationwide, including 117 in Queensland. The advent of metagenomic and metatranscriptomic approaches now enable enhanced, field-based detection of both known and emerging arboviruses. Strengthening mosquito control programs through continued Wolbachia releases, alongside integrated genomic surveillance, predictive modelling, and community engagement will enhance early detection, guide targeted interventions, and reduce the MBV burden in Northern Queensland. This integrated framework provides a strategic pathway to sustains and expand vector control effectiveness while safeguarding public health in high-risk regions.}, }
@article {pmid41650859, year = {2026}, author = {Wei, W and Zhang, Z and Li, J and Du, H and Wu, Q and Cui, R and Wang, X and Ren, L and Zhang, M and Wang, Y}, title = {Effects of microbial inoculation on mitigating odor release, curtailing nitrogen and sulfur losses, and accelerating the maturation during food-waste composting.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128800}, doi = {10.1016/j.jenvman.2026.128800}, pmid = {41650859}, issn = {1095-8630}, mesh = {*Composting ; *Odorants/prevention & control ; Nitrogen/metabolism ; Sulfur/metabolism ; Volatile Organic Compounds ; Soil ; }, abstract = {A thermotolerant, odor-suppressing microbial agent was inoculated into food-waste (FW) composting to systematically evaluate its influence on odorants, volatile organic compounds (VOCs), microbial community structure, extracellular enzyme activities, and the transcriptional profile of nitrogen- and sulfur-cycle genes. Compared with the uninoculated control, cumulative emissions of NH3, H2S, ethanol, and acetaldehyde declined by 73.45%, 65.30%, 40.22%, and 37.20%, respectively, in the bio-augmented reactor. NH3 High-throughput 16S rRNA sequencing revealed that the inoculation enhanced the microbial richness and diversity, while increasing the abundance of thermophilic strains that promote compost maturation and reduce nitrogen loss. Concomitantly, the relative abundances of acid-producing and skatole-generating populations were suppressed. Quantitative PCR showed that the expression of narG, norB, nif, nrfA, nirB, aprA, and sat genes was down-regulated. This consequently reduced the production of NH4[+]-N and inhibited the sulfate reduction process, thereby coordinating nitrogen and sulfur metabolic transformations and significantly lowering NH3 and H2S emissions. Overall, this study demonstrates the feasibility of microbial inoculation for mitigating odor emissions, retaining nutrients, and accelerating compost maturation, while providing mechanistic insights into how microbial formulations regulate enzyme activities and the expression of functional genes during composting.}, }
@article {pmid41650863, year = {2026}, author = {Wang, X and Zhao, HP and Lai, CY}, title = {Anaerobic biodegradation of ceftriaxone: Transformation pathways, toxicity assessment, and microbial mechanisms.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128859}, doi = {10.1016/j.jenvman.2026.128859}, pmid = {41650863}, issn = {1095-8630}, mesh = {*Ceftriaxone/metabolism/toxicity ; Anaerobiosis ; Biodegradation, Environmental ; Bioreactors ; Water Pollutants, Chemical/metabolism ; Wastewater ; Anti-Bacterial Agents/metabolism ; }, abstract = {The overuse of ceftriaxone has resulted in its widespread occurrence in aquatic environments, posing ecological and health risks. An anaerobic membrane bioreactor (AnMBR) was operated for 128 days to systematically investigate the anaerobic microbial transformation of CTX. The AnMBR exhibited stable and efficient performance, maintaining chemical oxygen demand removal above 90% and achieving an average CTX removal efficiency of 65.0 ± 15.2%. Several potential degradation pathways are proposed, involving β-lactam ring hydrolysis, C-S bond cleavage, and decarboxylation reactions. Toxicity assessments using ADMETlab 3.0 platform reveal that although most TPs showed reduced ecotoxicity and dermal toxicity compared to the parent compound, several intermediates exhibited elevated risks of nephrotoxicity and genotoxicity. Metagenomic analysis indicates that long-term CTX exposure reshaped the microbial community, enriching methanogens such as Methanothrix soehngenii and Methanosarcina mazei, though these taxa might not directly participate in CTX degradation. Several archaeal and bacterial MAGs carrying functional genes, including lactam hydrolase, thioesterase, and decarboxylase, were identified, suggesting a collaborative and functionally diverse microbial network involved in CTX transformation. This study offers mechanistic insights and technical foundations for advancing anaerobic biotechnologies in the treatment of antibiotic-contaminated wastewater, while highlighting the need for ongoing monitoring of potential long-term risks associated with TPs.}, }
@article {pmid41651079, year = {2026}, author = {Xin, Y and Ma, H and Li, X and Sun, R and Fang, L and Pan, L}, title = {Multi-omics reveal the key role of gut microbiota metabolism in adenine-induced chronic kidney disease.}, journal = {Toxicology and applied pharmacology}, volume = {509}, number = {}, pages = {117754}, doi = {10.1016/j.taap.2026.117754}, pmid = {41651079}, issn = {1096-0333}, mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Animals ; *Adenine/toxicity ; *Renal Insufficiency, Chronic/chemically induced/metabolism/microbiology ; *Metabolomics/methods ; Male ; Mice ; Mice, Inbred C57BL ; Disease Models, Animal ; Kidney/metabolism ; Metagenomics ; Bile Acids and Salts/metabolism ; Multiomics ; }, abstract = {The gut microbiota plays a crucial role in the progression of chronic kidney disease (CKD). The adenine-induced CKD mouse model is widely employed in preclinical research, yet the effects of adenine on the composition and metabolic function of the gut microbiota remain to be elucidated. This study aimed to test the hypothesis that adenine-induced alterations in the structure and function of the gut microbiota are significantly associated with the onset and progression of CKD. To this end, a mouse CKD model was established by alternating feeding with 0.15% and 0.20% adenine for 7 weeks. Multi-omics analysis (untargeted metabolomics, metagenomics, and spatial metabolomics) was performed to compare the adenine-induced CKD group with a standard diet-fed normal control group. Integrated analysis of plasma metabolomics and intestinal content metabolomics identified 94 differentially co-regulated metabolites: among these, indolelactic acid was significantly upregulated, while indole-3-propionic acid was significantly downregulated. The bile acid metabolic pathway also underwent marked perturbations: taurochenodeoxycholic acid and tauro-β-muricholic acid (two taurine-conjugated bile acids) were significantly elevated, whereas nordeoxycholic acid and norcholic acid were notably reduced. Integrated metabolomics-metagenomics analysis further demonstrated that Lactobacillus exhibited a significant positive correlation with a subset of upregulated metabolites (including indolelactic acid), while Taurinivorans muris showed a strong negative correlation with the taurine-conjugated bile acids. Additionally, renal spatial metabolomics revealed that phospholipid metabolic disorders in the adenine-induced CKD group directly contributed to the aggravation of renal inflammatory responses. Collectively, these findings reveal a gut microbiota-metabolite-kidney axis perturbed by adenine, providing novel insights into the pathogenesis of CKD and potential targets for metabolic intervention.}, }
@article {pmid41651131, year = {2026}, author = {Hantsoo, L and Ford, E and Friedman, ES and Hao, F and Patterson, AD and Bittinger, K and Wu, GD and Zemel, BS and Tanes, C}, title = {The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression.}, journal = {Brain, behavior, and immunity}, volume = {134}, number = {}, pages = {106479}, pmid = {41651131}, issn = {1090-2139}, support = {R03 HD101336/HD/NICHD NIH HHS/United States ; }, abstract = {BACKGROUND: Adverse childhood experiences (ACEs) are associated with poor health outcomes in adulthood including obesity, psychiatric symptoms, and elevated levels of inflammatory markers. Our previous work found ACEs are associated with altered gut microbiota composition. In the present work, we examined ACE associations with gut microbiota and peripheral measures of inflammation in pregnant women with or without obesity, and explored potential modifying factors including diet and depressive symptoms.
METHODS: Female participants were recruited in the third trimester of pregnancy as part of a larger growth study of African-American infants. Participants were categorized as healthy weight (BMI < 25) or obese (BMI ≥ 30) based on their early pregnancy BMI. They completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and Center for Epidemiologic Studies Depression Scale (CES-D). Stool samples, blood, and dietary data were collected in the third trimester. Shotgun metagenomic sequencing was performed on DNA isolated from stool. Statistical models assessed relationships between gut microbiota and ACE. A false discovery rate (fdr) adjusted p-value q < 0.1 was considered statistically significant.
RESULTS: 107 women completed questionnaires and provided stool in the third trimester. ACEs were positively associated with BMI and depressive symptom severity but not with gut microbiota composition. Depressive symptoms were significantly negatively associated with abundance of gut Bifidobacterium longum (q = 0.02) and positively associated with Bacteroides thetaiotaomicron (q = 0.02). Path analysis revealed that ACEs predicted pre-pregnancy BMI which predicted elevated inflammatory markers. ACEs also predicted more severe depressive symptoms in pregnancy, which was associated with gut microbiome composition. Finally, ACEs interacted with dietary intake of sugar and whole grains to impact markers of inflammation, the gut microbiome, and enzymes produced by gut microbiota.
DISCUSSION: ACEs led to two risk pathways in pregnancy: one in which high pre-pregnancy BMI was linked with high levels of serum inflammatory markers during pregnancy, and the other in which greater depressive symptom severity was associated with alterations to the gut microbiome. Further, data suggested ACEs may influence the metabolic potential of the gut microbiome.}, }
@article {pmid41651145, year = {2026}, author = {Wang, Y and Sun, T and Li, L and Wang, M and Hu, B and Chen, Z and Hu, S}, title = {Synergistic effects of carbon dots and arbuscular mycorrhizal fungi on mitigating PFAS stress and reinforcing the purification performance of constructed wetlands.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123952}, doi = {10.1016/j.envres.2026.123952}, pmid = {41651145}, issn = {1096-0953}, mesh = {*Mycorrhizae/physiology ; *Wetlands ; *Carbon ; *Water Pollutants, Chemical/metabolism ; *Fluorocarbons/toxicity/metabolism ; Biodegradation, Environmental ; Rhizosphere ; }, abstract = {Per- and polyfluoroalkyl substances (PFASs) are highly persistent pollutants that disrupt plant-microbe interactions and compromise the performance of constructed wetlands (CWs). Here, we demonstrate a synergistic strategy combining carbon dots (CDs) and arbuscular mycorrhizal fungi (AMF) to alleviate PFAS-induced stress and enhance CW remediation efficiency. CD amendment markedly improved plant physiological performance under PFAS exposure, increasing photosynthetic efficiency and antioxidant enzyme activities, while simultaneously facilitating AMF colonization. Under high PFAS concentrations, the AMF-CDs treatment increased AMF colonization density by 33.3-100% relative to AMF alone, indicating substantial protection of symbiotic functionality. Metagenomic and community analyses revealed that the AMF- CDs combination reshaped the rhizosphere microbiome, enriching taxa such as Chloroflexi, Planctomycetes, and Campylobacterota that are functionally linked to nitrogen cycling, PFAS transformation, and metabolic resilience. These microbial shifts enhanced nutrient turnover and strengthened redox coupling processes critical for pollutant degradation. Consequently, the AMF-CDs system achieved pronounced improvements in water quality, with total phosphorus (TP), chemical oxygen demand (COD), total nitrogen (TN), and NH4[+]-N removal efficiencies elevated by 34.3-158.3% compared with untreated controls. This study provides the first evidence that CDs function as nano-bridging agents that stabilize the root-microbe interface, reinforce AMF-plant symbiosis, and drive microbial community specialization toward pollutant degradation. The AMF-CDs synergistic mechanism offers a sustainable and scalable nano-bio strategy for restoring PFAS-contaminated ecosystems and advancing next generation constructed wetland technologies.}, }
@article {pmid41651377, year = {2026}, author = {Scholand, KK and Schaefer, L and Shao, J and Yu, Z and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {Investigating conjunctival immune pathways in Sjögren and non-Sjögren disease associated dry eye.}, journal = {The ocular surface}, volume = {40}, number = {}, pages = {52-62}, doi = {10.1016/j.jtos.2026.02.001}, pmid = {41651377}, issn = {1937-5913}, support = {U24 EY035067/EY/NEI NIH HHS/United States ; }, abstract = {PURPOSE: Dry eye disease (DED) is classified based on its predominant etiology into aqueous tear-deficient (ATD), evaporative, or mixed. Sjӧgren disease keratoconjunctivitis sicca (SjD-KCS) is a very severe autoimmune form of ATD DED. The purpose of this work was to compare transcriptomic changes in the conjunctiva sampled from patients with ATD, SjD-KCS, and healthy controls (HC) to evaluate distinctions in the immune response on the ocular surface based on diagnosis.
METHODS: Impression cytology of the temporal bulbar conjunctiva was collected using the EyePrim device. RNA was extracted and submitted with the Nanostring nCounter Human Immunology V2 panel for gene expression analysis. Results were uploaded to ROSALIND and Metascape to identify DEGs by comparison (all DED vs HC; SjD vs HC; ATD vs HC) and associated predicted pathways. A subset of samples (n = 4 per group) were used for immunofluorescent staining of LAMP3 and HLA-DR.
RESULTS: 49 patients were enrolled in the study (25 HC; 12 SjD; 12 ATD). 100 DEGs were found in the comparison of all DED vs HC. 69 DEGs were found in the SjD vs HC. 11 DEGs were found in the ATD vs HC. There were no DEGs identified in the SjD vs ATD comparison. DEGs were involved in immune pathways related to viral response, adaptive immunity, and cell to cell communication. DED conjunctiva had increased expression of LAMP3 and HLA-DR compared to HC.
CONCLUSIONS: Our findings demonstrate that DED, regardless of the diagnosis, have similar immune-related DEGs and associated pathways on the ocular surface.}, }
@article {pmid41651389, year = {2026}, author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M}, title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.}, journal = {Developmental and comparative immunology}, volume = {176}, number = {}, pages = {105565}, doi = {10.1016/j.dci.2026.105565}, pmid = {41651389}, issn = {1879-0089}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Vibrio parahaemolyticus/physiology ; *Penaeidae/microbiology/immunology ; *Vibrio Infections/immunology/microbiology ; Virulence ; Host-Pathogen Interactions ; }, abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.}, }
@article {pmid41651877, year = {2026}, author = {Zhang, E and Claesson, MJ and Cotter, PD}, title = {Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {}, pmid = {41651877}, issn = {2396-8370}, support = {23/FFP-A/11857//Research Ireland/ ; 101060218//European Commission/ ; }, abstract = {The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.}, }
@article {pmid41651883, year = {2026}, author = {Pantiukh, K and Org, E}, title = {Human gut archaea collection from Estonian population.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41651883}, issn = {2052-4463}, support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Estonia ; *Archaea/genetics ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Genome, Archaeal ; Metagenomics ; Feces/microbiology ; }, abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.}, }
@article {pmid41651909, year = {2026}, author = {Kanyerezi, S and Ayitewala, A and Kabahita, JM and Oundo, HR and Sseruyange, J and Tenywa, W and Tusabe, G and Were, S and Murungi, M and Nabukyu, M and Nakintu, V and Makoha, C and Sserwadda, I and Onywera, H and Tanui, C and Mugerwa, I and Kagirita, A and Lubwama, B and Michael, ER and Kateete, DP and Otita, M and Giduddu, S and Jjingo, D and Nsawotebba, A and Mboowa, G and Ssemaganda, A and Nabadda, S and Tessema, SK and Ssewanyana, I}, title = {Targeted metagenomics reveals hidden chickenpox epidemic amid Mpox surveillance in Uganda.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41651909}, issn = {2045-2322}, abstract = {In regions where both monkeypox virus (MPXV) and varicella zoster virus (VZV) are co-circulating, overlapping clinical manifestations can complicate clinical diagnosis. During the MPXV outbreak declared in Uganda in July, 2024, symptomatic suspected cases tested PCR negative for Mpox. To determine the cause of symptoms, we employed metagenomic sequencing with a targeted Viral Surveillance panel in 284 MPXV negative samples. VZV was identified as the predominant pathogen in 86% of MPXV-negative cases, suggesting a concurrent chickenpox surge. Using the VaricellaGen pipeline for variant calling, clade typing, and phylogeny, 118 (49%) samples that achieved ≥ 70% genome coverage were of clade 5 based on the single-nucleotide polymorphism (SNP) dataset. This data confirms co-circulation of VZV during the MPXV outbreak in Uganda. Our results underscore the need for laboratory confirmation of MPXV and the inclusion of VZV in the testing algorithm during the Mpox outbreak.}, }
@article {pmid41652580, year = {2026}, author = {He, L and Cheng, Y and Huang, L and Zhang, Z and Zhang, Q and Gong, L and Li, T and Lu, X and Cai, X and Yan, G}, title = {Metagenomic next-generation sequencing to detect Pneumocystis jirovecii pneumonia in critically ill, HIV-negative children: a retrospective multicenter study.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41652580}, issn = {1471-2466}, support = {2021YFC2701800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; Retrospective Studies ; Child ; *Pneumocystis carinii/genetics/isolation & purification ; Female ; Male ; Child, Preschool ; Infant ; Adolescent ; Critical Illness ; *High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology ; *Metagenomics/methods ; ROC Curve ; C-Reactive Protein/analysis ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) plays a critical role in the rapid detection of infectious pathogens. We aimed to analyze the clinical characteristics of Pneumocystis jirovecii infection in children without HIV infection and to evaluate the performance of mNGS in distinguishing P. jirovecii colonization from true infection.
METHODS: A multicenter, retrospective analysis was conducted on critically ill, non-HIV-infected pediatric patients who tested positive for P. jirovecii via mNGS analysis of bronchoalveolar lavage fluid (BALF). Group differences were assessed using Mann-Whitney U-tests (for continuous data) and chi-square tests (for categorical data). Discriminatory performance was evaluated by calculating the area under the receiver operating characteristic curve.
RESULTS: A total of 59 HIV-negative children (age range: 2 months to 14 years) from four children's hospitals were included and classified into two groups based on P. jirovecii status: P. jirovecii pneumonia (PCP; n = 51) and P. jirovecii colonization (PCC; n = 8). Compared with the PCC group, the PCP group had significantly higher serum C-reactive protein levels and median P. jirovecii read counts in mNGS (both P < 0.05). The optimal threshold value for discriminating P. jirovecii infection from colonization appeared to be 556 reads (sensitivity, 77.6%; specificity, 100.0%). Eighteen patients (35.3%) in the PCP group died. Compared with survivors, these patients were significantly younger, had lower T-cell subset counts (CD3[+], CD4[+], and CD8[+]), and a higher prevalence of primary immunodeficiency (all P < 0.05).
CONCLUSIONS: BALF mNGS analysis may have utility for differentiating between colonization and infection by P. jirovecii, warranting further investigation.}, }
@article {pmid41652998, year = {2026}, author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I}, title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004261423546}, doi = {10.1177/10998004261423546}, pmid = {41652998}, issn = {1552-4175}, abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.}, }
@article {pmid41653012, year = {2026}, author = {Asis, A and Rodríguez, A and Reyes, LF and Díaz, E and Nseir, S and Martín-Loeches, I}, title = {The double threat: bacterial and fungal co-/superinfection in viral pneumonia.}, journal = {Expert review of respiratory medicine}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/17476348.2026.2629003}, pmid = {41653012}, issn = {1747-6356}, abstract = {INTRODUCTION: Respiratory viral pneumonias are a leading cause of severe respiratory failure and intensive care unit (ICU) admission worldwide. Although viral infection itself drives significant morbidity and mortality, secondary bacterial and fungal superinfections represent a critical 'double threat' in critically ill adults, exacerbating lung injury, prolonging organ dysfunction, and complicating antimicrobial management. Experience from the Influenza A (H1N1) pdm09 and SARS-CoV-2 pandemics highlights a persistent mismatch between low documented bacterial co-infection rates and widespread empiric antibiotic exposure, underscoring diagnostic uncertainty and antimicrobial stewardship challenges in the ICU.
AREAS COVERED: This review examines the epidemiology, immunopathogenesis, and diagnostic approaches to bacterial and fungal superinfection in adult ICU patients with severe viral pneumonia. Evidence is synthesized from large ICU cohorts, pandemic data, and established consensus definitions for influenza- and COVID-19-associated pulmonary aspergillosis (IAPA, CAPA). The review discusses advances in molecular diagnostics, lower respiratory tract sampling, bronchoalveolar lavage - based mycology, and biomarker-guided strategies, with a focused literature search of ICU-specific studies.
EXPERT OPINION: Bacterial and fungal superinfections, while infrequent, carry substantial clinical impact in severe viral pneumonia. A multimodal, ICU-adapted diagnostic strategy integrating pathogen detection with host-response assessment is essential to support timely therapy, enable antimicrobial de-escalation, and align superinfection management with stewardship principles.}, }
@article {pmid41653157, year = {2026}, author = {Qian, J and Fang, J}, title = {Letter to the editor regarding: 'Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios - a retrospective study from a single center'.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2624190}, pmid = {41653157}, issn = {1365-2060}, }
@article {pmid41653605, year = {2026}, author = {Cho, DY and Haque, MA and Lee, HY and Jang, MY and Jeong, JB and Lee, GY and Son, KH and Lee, JH and Cho, KM}, title = {Amending metagenomic bacterial community in soybean-cultivated soils to enhance phytoestrogen in soybean roots by communicating with mixture of culturable rhizospheric bacteria.}, journal = {Plant physiology and biochemistry : PPB}, volume = {232}, number = {}, pages = {111093}, doi = {10.1016/j.plaphy.2026.111093}, pmid = {41653605}, issn = {1873-2690}, mesh = {*Glycine max/microbiology/metabolism ; *Plant Roots/metabolism/microbiology ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/genetics/metabolism ; *Metagenomics ; Soil/chemistry ; }, abstract = {The amendment of metagenomic bacterial community in soybean-cultivated soils to enhance phytoestrogen levels in soybean roots through communicating with mixture of culturable rhizospheric bacteria (RB) were rarely studied. RB from soybean roots and soybean-cultivated soils were isolated and applied to soybean plants. Treated soybean plants were divided into three groups: control (CTL), soybean root RB (SRR), and soybean-cultivated soil RB (SSR). Each group had a distinct influence on the metagenomic bacterial community of the soybean rhizosphere. The α-proteobacteria were the dominant class in all three groups, although SRR was enriched with Actinomycetes, Fimbriimonadia, and γ-proteobacteria, while SSR was enriched with Bacilli, Chitinophagia, and Gemmatimonadia classes. Additionally, at the significantly species level, SRR was enriched with Arthrobacter sp. and Azospirillum lipoferum, while SSR was enriched with Bradyrhizobium sp. and Rhizobium sp. Moreover, the RB treatment significantly affected the root metabolite composition. In the SSR-treated group, phenylalanine (18.80-47.81 mg/100 g) and tyrosine (8.03-21.98 mg/100 g) tended to be significantly enhanced. Additionally, secondary metabolites, such as isoflavones, total phenolics, and total flavonoids, were also significantly affected by the RB treatment; secondary metabolites were the highest in the SSR-treated group. These changes in metabolites also affected radical scavenging activities, with the SSR-treated group displaying significantly increased activities compared to the other groups. As a result, DPPH increased from 32.44 % to 47.21 % and ABTS from 53.41 % to 74.23 %. Therefore, RB treatment can influence the bacteria and root metabolite compositions within the soybean rhizosphere, revealing its potential applications in soybean productivity.}, }
@article {pmid41653958, year = {2026}, author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ}, title = {Household environmental characteristics influence the house dust metagenome.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123889}, pmid = {41653958}, issn = {1096-0953}, support = {Z01 CP010119/ImNIH/Intramural NIH HHS/United States ; ZIA ES049030/ImNIH/Intramural NIH HHS/United States ; ZIA ES102385/ImNIH/Intramural NIH HHS/United States ; ZIA ES103390/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Dust/analysis ; *Metagenome ; Humans ; *Microbiota ; *Family Characteristics ; Housing ; *Air Pollution, Indoor/analysis ; *Environmental Exposure ; }, abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.}, }
@article {pmid41654251, year = {2026}, author = {Sun, L and Wang, Y and Fang, J and Li, Z and Yin, Y and Guo, Y and Wang, Q and Chen, H and Cao, B and Wang, H}, title = {Clinical experience with metagenomic next-generation sequencing (mNGS) for the detection of Tropheryma whipplei in respiratory specimens: A multicenter retrospective observational study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108457}, doi = {10.1016/j.ijid.2026.108457}, pmid = {41654251}, issn = {1878-3511}, mesh = {Humans ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; *Tropheryma/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Aged, 80 and over ; *Whipple Disease/diagnosis/microbiology ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {OBJECTIVES: Tropheryma whipplei (T. whipplei) is the causative bacterium of Whipple's disease (WD), a chronic and systemic infectious condition that predominantly affects the gastrointestinal tract. Sporadic cases of T. whipplei pneumonia have been documented recently.
METHODS: This multicenter retrospective observational study was conducted on patients with T. whipplei positive respiratory specimens admitted to Peking University People's Hospital and China-Japan Friendship Hospital, from Apr 2021 to Jul 2024. Metagenomic next-Generation sequencing (mNGS) was performed using the patient's bronchoalveolar lavage fluid (BALF), and the quantitative polymerase chain reaction (qPCR) of T. whipplei was also adopted. The clinical data of patients were systematically evaluated.
RESULTS: Among 91 patients (aged 25-82, mean 57; 48% male), common symptoms included cough (60%), expectoration (48%), dyspnea (42%), and fever (30%). Notably, 22% were asymptomatic. Besides, 20 patients (22%) had a pre-existing condition of interstitial lung disease. Among all 91 patients, 14 were diagnosed with pneumonia, while the remaining 77 had bacterial colonization. Pneumonia cases showed higher T. whipplei mNGS reads than colonization (P = 0.0298). Samples testing positive for T. whipplei by qPCR exhibited significantly higher mNGS sequence reads compared to qPCR-negative samples (P < 0.0001). All pneumonia patients received antibiotics therapy tailored to their condition. One died from respiratory failure, while the remaining 13 recovered.
CONCLUSION: The application of mNGS on respiratory specimens stands as an exceptional diagnostic modality, proficient in identifying rare microbial infections, exemplified by those induced by T. whipplei. Future research should launch prospective trials to optimize regimens, assess outcomes, and track long-term survival precisely.}, }
@article {pmid41654659, year = {2026}, author = {Damgaard, F and Jespersen, MG and Møller, JK and Coia, JE and Dessau, RB and Sydenham, TV and Strube, ML and Møller-Jensen, J and Justesen, US}, title = {Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {41654659}, issn = {2730-664X}, abstract = {BACKGROUND: Colorectal cancer (CRC) patients exhibit distinct gut microbiota disruption, known as dysbiosis, which is believed to play a causative role in CRC. One of the key bacterial species implicated in CRC dysbiosis is Bacteroides fragilis, which presents a paradox as it is also present in most healthy individuals. This discrepancy underscores the need for analysis beyond species-level associations and to investigate intraspecies variation within B. fragilis.
METHODS: From a highly specific collection of B. fragilis isolates from CRC patients and controls, a pangenome-wide association study was conducted, identifying intraspecies genetic variations associated with CRC. The CRC association of these genetic variations were then validated in a metagenome sequencing cohort of faecal samples from 877 individuals, with and without CRC. To test group differences a mixed effects logistic regression with cohort as a random effect was performed for each genetic variation.
RESULTS: Here we show that CRC-associated B. fragilis isolates are infected with specific Caudoviricetes prophages, significantly more often than negative controls. The initial discovery was made in our highly specific isolate collection and then validated in an independent metagenome sequencing cohort, finding that CRC patients were twice as likely to have detectable levels of these phages (OR = 2.05, p = 2.522E-7, SE = 0.139).
CONCLUSIONS: To our knowledge, these findings mark the first link between one of the most implicated driver bacteria and phages in CRC and suggest a more complex role of phages in CRC dysbiosis than current models suggest and highlights the potential of phages as CRC biomarkers.}, }
@article {pmid41654729, year = {2026}, author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J}, title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41654729}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; Feces/microbiology ; *Essential Hypertension/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Sex Factors ; Cohort Studies ; Metagenomics ; Aged ; Adult ; Fatty Acids, Volatile/metabolism ; China ; Hypertension/microbiology ; Sex Characteristics ; }, abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.
METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.
RESULTS: Our study confirmed a statistically significant difference in the β-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.
CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.}, }
@article {pmid41654875, year = {2026}, author = {Chen, Y and Ding, C and Ren, M and Li, Z and Liu, S and Sun, H and Yu, S and Niu, Q and Li, X and Li, B and Li, L and Yang, X and Sun, Q}, title = {Liver-muscle metabolic crosstalk: xanthosine as a key effector of broiler myogenesis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {24}, pmid = {41654875}, issn = {1674-9782}, support = {No.2022YFF1001000//National Key Research and Development Program of China/ ; NSFC, No.82370639//the National Natural Science Foundation of China/ ; 2023-YBSF-138//Shaanxi Provincial Key R&D Program General Project-Social Development Field/ ; No. 2022JC-11//Science Fund for Distinguished Young Scholars of Shaanxi Province/ ; }, abstract = {BACKGROUND: Nutritional strategies aimed at augmenting growth performance remain a central focus in poultry science. The liver, as a pivotal metabolic organ, exerts profound influence on skeletal muscle development. Nevertheless, the mechanistic interplay between hepatic metabolism and myogenesis has not been fully delineated. Here, by integrating multi-omics analyses with functional validation, we identified xanthosine, a metabolic derivative of hepatic caffeine catabolism, as a previously unrecognized regulator of broiler muscle growth. We further elucidated its mechanistic role in promoting myoblast proliferation.
RESULTS: Comparative phenotypic assessment of high- and low-body-weight broilers revealed substantial differences in breast muscle mass. Metagenomic profiling of cecal microbiota demonstrated only a limited association between microbial composition and body weight. In contrast, untargeted plasma metabolomics uncovered a systemic upregulation of amino acid metabolism in high-body-weight broilers, concomitant with a pronounced activation of caffeine metabolism. Consistently, hepatic transcriptomic profiling revealed marked induction of cytochrome P450 family 1 subfamily A member 2 (CYP1A2), encoding a key enzyme catalyzing caffeine catabolism. Integrated KEGG pathway enrichment across metabolomic and transcriptomic datasets highlighted caffeine metabolism as a significantly perturbed pathway. Among its downstream metabolites, plasma xanthosine was robustly elevated in high-body-weight broilers. Functional validation via in ovo injection demonstrated that xanthosine administration significantly augmented post-hatch growth performance by increasing skeletal muscle mass. Mechanistic investigations further established that xanthosine drives myoblast proliferation through activation of the ERK/GSK3β/β-catenin signaling cascade.
CONCLUSIONS: Together, these findings delineate a liver-muscle metabolic axis in which hepatic CYP1A2-driven caffeine metabolism elevates circulating xanthosine, which in turn acts as a pivotal molecular effector of myogenic growth. This study uncovers a previously unappreciated metabolic mechanism by which hepatic activity orchestrates skeletal muscle development. It also highlights targeted modulation of xanthosine metabolism as a promising strategy to enhance broiler growth performance and production efficiency.}, }
@article {pmid41655211, year = {2026}, author = {Su, XJ and Ma, L and Xiong, X and Meng, JH and Wu, Q and Zhang, Y and Dong, SG and Wang, YF and Wu, JH and Zeng, QY and Zhang, HF and Li, LL and Meng, L and Peng, M and Huang, XD and Wu, LQ and Wang, X}, title = {DRD2 Deficiency Underlies Pituitary Adenoma Dependent on Escherichia coli Translocation from the Gut.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e04247}, doi = {10.1002/advs.202504247}, pmid = {41655211}, issn = {2198-3844}, support = {2020]74//Hubei Provincial Engineering Research Center for Inflammation Repair/ ; 2020ZYYD026//Special Funds for Local Science and Technology Development guided by the Central Government/ ; 2023AFA079//Hubei Science Foundation for Distinguished Young Scholars/ ; WX23Z27//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ22A01//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ24B86//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; }, abstract = {Pituitary adenoma (PA) are common intracranial tumor types that have harmful effects on human health. However, the pathogenesis of PA remains unclear yet. The intratumoral microbiome has been reported playing an important impact on the occurrence, metastasis, immune monitoring, and drug resistance of various tumors. While normal dopamine receptor D2 (DRD2) expression is enriched in the apical junction of pituitary epithelium and colonic enterocytes, various factors-induced drd2 loss dampened its expression at both sites. DRD2 deficiencies are characterized by chronic hyperprolactinemia, pituitary lactotroph hyperplasia, and prolactinomas in mice, but the role of intratumoral microbiome in prolactinomas is not known. We employed specific pathogen-free (SPF) and germ-free (GF) mice models and patient samples of pituitary adenoma. In the mice pituitary tumor model, we used mice that developed prolactinomas following estradiol treatment or DRD2 deficiencies. Pituitary tumor samples from patients with nonfunctional pituitary adenoma or prolactinomas were obtained after surgical excision. Various molecular, cellular, and sequencing techniques were used to determine the role of intratumoral microbiome in pituitary adenoma. We demonstrate that human patients or murine bearing estradiol-induction or DRD2 loss are all characterized by the presence of live intratumor bacteria in the pituitary adenoma. Using metagenomic next-generation sequencing and mass spectrometry techniques, we confirm that the bacterial species of pituitary tumor tissues is Escherichia coli. In vitro tracing and immunofluorescence assay results showed that the pathobiont Escherichia coli translocates from the gut into the pituitary gland along with DRD2 loss while the blood pituitary barrier were both destroyed in mice. The Escherichia coli are phagocytosed by the microglial cells in the pituitary gland, then activate GSDMD protein releasing HMGB1, and promote the tumorigenesis of pituitary adenoma by activating the MAPK pathway. The depletion of bacteria systemically, microglial depletion or HMGB1 inhibitor ethyl pyruvate rescued prolactinomas. Our findings suggest that DRD2 deficiency underlies pituitary adenoma dependent on Escherichia coli translocation from the gut and activating microglia GSDMD/ HMGB1/MAPK pathway, and provide a novel preclinical rationale for antimicrobial agents, microglial depletion, or HMGB1 inhibitor ethyl pyruvate for the treatment of pituitary adenoma.}, }
@article {pmid41655253, year = {2026}, author = {Shi, Y and He, S and Li, C and Chan, H and Liu, Z and Yang, B and Li, Q}, title = {Bifidobacterium Breve Yang08 Alleviates Atopic Dermatitis By Enriching Akkermansia Muciniphila and Inhibiting Neutrophil Extracellular Traps Formation In Mice.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e18588}, doi = {10.1002/advs.202518588}, pmid = {41655253}, issn = {2198-3844}, support = {32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 82574001//National Natural Science Foundation of China/ ; 2025A04J4030//Guangdong Provincial Science and Technology Plan Project/ ; }, abstract = {Atopic dermatitis (AD) is linked to gut microbiota dysbiosis, yet the mechanisms connecting specific commensals to cutaneous immunoregulation remain elusive. We observed reduced Bifidobacterium breve (B. breve) abundance in AD patients. A new B. breve strain was isolated from human stools and nomenclated as Yang08. In MC903-induced AD-like mouse models, Yang08 outperformed a standard strain, ameliorating disease severity, including reduced ear thickening, epidermal hyperplasia, and mast cell infiltration in a manner dependent on viable bacteria and an intact gut microbiota. Antibiotic-mediated microbiota depletion abrogated its efficacy, while fecal microbiota transfer from Yang08-treated mice conferred protection, confirming microbial remodeling as essential. Metagenomics revealed Yang08 specifically enriched Akkermansia muciniphila, which was required for therapeutic effects in germ-free mice. Mechanistically, Yang08 abolished both neutrophil influx and NET deposition in lesions, with ex vivo experiments showing blunted NETosis capacity. Its therapeutic benefits were reversed by neutrophil depletion, NET degradation, or PAD4 inhibition. Overall, Yang08 alleviates AD by enriching A. muciniphila and inhibiting skin NETosis, emerging as a promising prophylactic candidate prevention for AD prevention.}, }
@article {pmid41655310, year = {2026}, author = {Cheng, L and Li, H and Luo, C and Zhang, Y and Cheng, K and Wang, S and Hu, Z}, title = {In situ reactivation of aerobic granular sludge after extended idle conditions: Effect of different N-acyl-homoserine lactones (AHLs).}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128866}, doi = {10.1016/j.jenvman.2026.128866}, pmid = {41655310}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Acyl-Butyrolactones ; Bioreactors ; Quorum Sensing ; Aerobiosis ; Waste Disposal, Fluid ; Phosphorus ; 4-Butyrolactone/analogs & derivatives ; }, abstract = {Prolonged idle conditions pose a major challenge to aerobic granular sludge (AGS) systems by compromising granule integrity and pollutant removal performance. This study investigates the in situ reactivation of AGS after three months of static storage using two quorum sensing molecules, N-hexanoyl-L-homoserine lactone (C6-HSL) and N-octanoyl-homoserine lactone (C8-HSL). All reactors rapidly restored COD and NH4[+]-N removal efficiencies to >92% and >98%, respectively. C6-HSL significantly accelerated phosphorus recovery, reaching removal efficiencies above 90% by day 26, compared to day 34 in the control and C8-HSL groups. C8-HSL enhanced EPS secretion and granule growth, yielding the largest granule size (1210 μm), which was 1.26-fold and 1.71-fold larger than those in the control and C6-HSL groups, respectively. Metagenomic analysis revealed comparable microbial structures at the phylum level, but distinct functional responses. C6-HSL increased the abundances of phosphorus metabolism genes (ppk, ppx, ppa), while C8-HSL notably upregulated genes related to the biosynthesis of tyrosine, tryptophan, and structural polysaccharides (e.g., alginate and Psl), supporting enhanced EPS production and granule stability. These results demonstrate molecule-specific regulatory roles of individual N-acyl-homoserine lactones during AGS reactivation, linking functional recovery and structural regeneration to distinct quorum sensing pathways. This study provides mechanistic and engineering insights into an energy-efficient strategy for restoring AGS performance after prolonged ambient idle conditions, with direct relevance to the stable operation and management of full-scale wastewater treatment systems.}, }
@article {pmid41655382, year = {2026}, author = {Gupta, N and Biswas, R and Koley, A and Mukherjee, R and Das, N and Balachandran, S and Hoque, RR}, title = {Degradation of chrysene by Rhodococcus pyridinivorans C7 isolated from earthworm gut - Deciphering microbial community dynamics of the earthworm gut.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141328}, doi = {10.1016/j.jhazmat.2026.141328}, pmid = {41655382}, issn = {1873-3336}, mesh = {Animals ; *Rhodococcus/metabolism/genetics/isolation & purification ; *Oligochaeta/microbiology ; *Soil Pollutants/metabolism/toxicity ; Biodegradation, Environmental ; *Chrysenes/metabolism/toxicity ; }, abstract = {This study investigates the degradation of chrysene (a priority polycyclic aromatic hydrocarbon) by Rhodococcus pyridinivorans C7, isolated from the gut of Perionyx excavatus after 60 days acclimatization in petroleum-contaminated soil. After six days of incubation, strain C7 exhibited notable enzymatic activities, with catechol 1,2-dioxygenase (1.72 ± 0.14 U/mL) and catechol 2,3-dioxygenase (2.26 ± 0.19 U/mL). The strain achieved up to 75 % degradation of chrysene (40 mg/L) within this period. Gas chromatography-mass spectrometry analysis identified dibutyl phthalate as an intermediate product on day 2 and phenol 2,6-di-tert-butyl on days 4 and 6. Cytotoxicity assays revealed that the initial byproduct was highly toxic (IC50 = 0.19 µg/mL), whereas the final metabolite exhibited markedly reduced toxicity (IC50 = 19 µg/mL), indicating detoxification. Comparative genomics using Mauve software revealed strong genomic synteny between strain C7 and other PAH-degrading Rhodococcus species. Metagenomic analysis of earthworm gut microbiomes under different treatment - control (EG-C), petroleum contaminated (EG-P) and fly ash (EG-F) identified Proteobacteria as the predominant phylum with relative abundance of 21.17 %, 33.3 %, and 34.53 % respectively. Notably, the Rhodococcus genus exhibited a 1.46-fold and 1.42-fold increase in EG-P and EG-F, respectively compared to EG-C. R. pyridinivorans was detected in both EG-P and EG-F gut samples confirming its isolation through the earthworm gut. These results demonstrate that environmental perturbations can drive distinct shifts in gut microbial composition, enriching for hydrocarbon-degrading taxa. Understanding such adaptive microbial communities provides valuable insights for developing sustainable bioremediation strategies and identifying novel microbes for environmental cleanup.}, }
@article {pmid41655417, year = {2026}, author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P}, title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.}, journal = {Water research}, volume = {294}, number = {}, pages = {125493}, doi = {10.1016/j.watres.2026.125493}, pmid = {41655417}, issn = {1879-2448}, mesh = {*Groundwater/microbiology/chemistry ; Metagenomics ; Humans ; Human Activities ; Microbiota ; China ; Nitrogen ; Bacteria/genetics ; }, abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.}, }
@article {pmid41655422, year = {2026}, author = {Wang, L and Liang, Z and Lu, D and Lv, S and Li, Z and Tan, R and Guo, Z and Wu, H and Wang, Y and Xu, X and Yu, J and Li, Z and Zhang, W and Zheng, W and Jiang, F and Yao, M and Zhou, P and Jiang, Z}, title = {Artificial reefs promote coastal carbon stabilization potential through hydrological condition and microbial pathways.}, journal = {Water research}, volume = {294}, number = {}, pages = {125502}, doi = {10.1016/j.watres.2026.125502}, pmid = {41655422}, issn = {1879-2448}, mesh = {Hydrodynamics ; *Coral Reefs ; *Carbon ; Geologic Sediments/chemistry ; Hydrology ; Seawater ; }, abstract = {Artificial reefs (ARs) reshape near-bed hydrodynamics and benthic microbial functions, yet links to coastal carbon stabilization remain insufficiently resolved. Here, we combined hydrodynamic modeling with sediment geochemistry, fluorescence spectroscopy, and metagenomics across contrasting AR habitats in the northern Yellow Sea. Structurally complex ARs enhanced upwelling and wake turbulence and were associated with finer sediments and higher sediment total organic carbon (TOC). Path modeling showed that hydrodynamic indices, hydrographic state variables, and microbial functional gene profiles jointly explained spatial variations in sediment TOC and humic-like fluorescent. During a 42-day dark incubation, protein-like fluorescent dissolved organic matter (FDOM) fractions declined while the humic-like component (C2) increased, indicating net enrichment of humic-like byproducts during microbial reworking of labile DOC. Microbial succession included increased relative abundance of ammonia oxidizing archaea (e.g., Crenarchaeota, Nitrososphaeria), and the SAR202 clade, accompanied by higher functional potentials related to aromatic-compound transformation and nitrogen redox pathways. Collectively, these results support a framework in which AR-induced hydrodynamic modulation couples with nitrogen-redox linked microbial functions, promoting carbon stabilization potential reflected by humic-like DOM enrichment and benthic carbon storage proxies.}, }
@article {pmid41655600, year = {2026}, author = {Susiyanti, M and Febrina, F and Putera, I and Jelita, A and Rokim, FS and Edwar, L and Aziza, Y and Sitompul, R and Nora, RD}, title = {Metagenomic sequencing in various ocular infections: A systematic review of diagnostic utility.}, journal = {Survey of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.survophthal.2026.01.006}, pmid = {41655600}, issn = {1879-3304}, abstract = {Ocular infections are a common cause of visual morbidity worldwide and continue to pose significant diagnostic and therapeutic challenges. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of wide range of pathogens; however, its diagnostic utility in ocular infections warrant further evaluation. We evaluate the diagnostic performance of mNGS, highlighting its advantages, limitations, and future directions for clinical application. Twenty-one studies involving 1219 eyes were included. mNGS positivity rates ranged from 10 % to 94 %. Sensitivity ranged from 15 % to 100 % and specificity from 12 % to 100 %. Viral pathogens were the most frequently detected (15 out of 21 studies), followed by bacteria (14 out of 21), fungi (10 out of 21), and parasites (6 out of 21). A broad spectrum of pathogens at both the genus and species levels was identified. mNGS also helps in assessing AMR-associated genes and mutations linked to therapy susceptibility. mNGS appears to be a valuable tool for pathogen indentification in ocular infections, particularly for organisms undetectable by conventional diagnostic methods, although careful interpretation is required. Overall, mNGS demonstrated promising diagnostic performance across different types of ocular infections. Larger, well-designed studies employing standardized protocols are needed to address current limitations and to enhance the clinical applicability of mNGS in routine clinical practice.}, }
@article {pmid41655688, year = {2026}, author = {Jin, M and Xu, F and Liu, Y and Jiang, Z}, title = {Limosilactobacillus fermentum LF61: A multidimensional study on safety and functionality from genomics to clinical application.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {211}, number = {}, pages = {116002}, doi = {10.1016/j.fct.2026.116002}, pmid = {41655688}, issn = {1873-6351}, mesh = {Humans ; Animals ; *Limosilactobacillus fermentum/genetics/physiology ; Mice, Inbred ICR ; Caco-2 Cells ; Mice ; *Probiotics/adverse effects ; Female ; Genomics ; Double-Blind Method ; Male ; Adult ; Milk, Human/microbiology ; }, abstract = {This study presents a comprehensive multidimensional assessment of the safety and functional efficacy of Limosilactobacillus fermentum LF61, a strain isolated from human milk. Genomic analysis revealed no virulence factors (VFDB), drug resistance genes (CARD), or toxin synthesis gene cluster (antiSMASH) within its chromosome (2.04 Mb) and plasmid (15.5 kb), meeting EFSA's QPS safety criteria. In vitro studies demonstrated that LF61 exhibited a 2-h survival rate of >98% in gastric acid (pH 2.0) and a survival rate of 99.66% in intestinal fluid (pH 8.0). LF61 was also nontoxic to Caco-2 cells (metabolic activity at 20% concentration: 100.3 ± 2.1%). An acute oral toxicity test (in ICR mice) demonstrated an LD50 > 2 × 10[10] CFU/kg. In a randomized, double-blind clinical trial (n = 49), daily intake of 3 × 10[10] CFU of LF61 for 8 weeks increased serum levels of the antimicrobial peptide LL-37 by 12.3% (p < 0.05), and IgA, IgG, and IgM by 18.7%, 15.2%, and 9.8%, respectively (p < 0.05). Metagenomic analysis revealed that LF61 promoted colonization by short-chain fatty acid-producing bacteria, such as Mitsuokella and Turicibacter (LDA >3), activated the carbohydrate metabolism pathway (p = 0.002), and maintained stable α-diversity in the microbiome (Shannon index p > 0.05). Collectively, our findings indicate that LF61 exerts beneficial effects via a gut-immune axis bidirectional regulatory mechanism, offering a theoretical basis and clinical evidence for the development of novel immunomodulatory probiotics targeting the gut-immune axis.}, }
@article {pmid41655773, year = {2026}, author = {Lala Bouali, M and Kezai, AM and Beaulieu, MJ and Roy, J and Badiane, PY and Lévesque, V and Filion, L and Vallières, L and Blanchet, MR and Hébert, SS}, title = {Indoor rewilding of laboratory mice recalibrates pulmonary mucosal immunity and mechanics.}, journal = {Mucosal immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mucimm.2026.02.003}, pmid = {41655773}, issn = {1935-3456}, abstract = {Laboratory mice raised under specific-pathogen-free (SPF) conditions experience restricted microbial and antigenic exposure, which favours an immature immune system and limits their translational value for respiratory research. While microbial enrichment in "dirty" mouse models restores immune maturation, its impact on integrated respiratory function and model transferability to human disease remains understudied. Here, we tested whether ecological exposure through indoor rewilding of SPF-reared mice could reshape immune complexity and recalibrate pulmonary physiology. Two-month-old female C57BL/6J mice were housed for three months under SPF or indoor-rewilding conditions and assessed for immune, mechanical, and systemic parameters. Rewilded mice exhibited expanded pulmonary immune subsets, increased dendritic-cell immune checkpoint, with TNF/IFN-γ activation coupled to regulatory IL-10 signaling. Despite sustained exposure, the alveolar-capillary barrier integrity was preserved. Functionally, respiratory oscillometry revealed improved pulmonary mechanics, including lower airway resistance, higher compliance, and reduced airway responsiveness to methacholine. Systemic cytokine analyses indicated compartmentalized pulmonary immune activation, maintaining an overall anti-inflammatory balance. Importantly, PRIA screening detected no reportable pathogens introduced during rewilding, while cecal shotgun metagenomics confirmed microbial enrichment. Together, these findings demonstrate that indoor rewilding reestablishes coordinated lung immune and mechanical homeostasis in SPF-reared mice, providing a safe and scalable model for studying human-like mucosal immunity and respiratory physiology with broad implications for preclinical respiratory research and therapeutic testing.}, }
@article {pmid41655932, year = {2026}, author = {Kannan, EP and Venkatachalam, P and Gopal, J and Sarkaraisamy, P and Muthu, M}, title = {Antimicrobial resistance status of small marine fishes off the coastal cities of east and west coast of India: an adaptive nanopore sequencing based metagenomics raises concerns.}, journal = {International journal of biological macromolecules}, volume = {347}, number = {}, pages = {150754}, doi = {10.1016/j.ijbiomac.2026.150754}, pmid = {41655932}, issn = {1879-0003}, mesh = {Animals ; *Fishes/microbiology/genetics ; India ; *Metagenomics/methods ; *Nanopore Sequencing ; Cities ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Humans ; Bacteria/genetics/drug effects ; }, abstract = {Transmission of Antimicrobial resistance (AMR) through edible fishes has recently upsurged as a global health hazard owing to its potential impact on human and one health. India, as the second largest consumer of edible fish faces a high risk of AMR transmission, given the nutritional value, accessibility and affordability of fishes to people from all economic classes. The present study investigated the presence of Antimicrobial resistance genes (ARGs) in edible muscle, gills and intestines of five commercially important fishes, Nemipterus japonicus, Sardinella longiceps, Selaroides leptolepis, Stolephorus indicus, and Sardinella gibbosa sourced from two major densely populated cities of the East coast (Chennai) and the West coast (Mangalore) using adaptive nanopore sequencing technique. A total of 54 distinct ARGs associated with 12 classes of AMR were detected across both coasts with enhanced resistance observed towards aminoglycosides, macrolides, beta lactam, tetracycline and chloramphenicol. Cumulatively, the most abundant ARGs across both coasts includes cxpE, aac(3')-IIa, aac(6)-IB-cr, oqxA and oqxB. However, significant variation in the distribution of ARGs among the two coasts were studied with varying abundance patterns. Furthermore, this study predicted human pathogens such as Klebsiella sp., Escherichia sp., Staphylococcus sp. and Pseudomonas sp. as putative reservoirs of ARGs indicating potential zoonotic and foodborne transmission to humans. This study offers a novel, and in-depth characterization of edible fish associated AMR contamination in east and West coast of India, providing essential data for assessing the public health hazards posed by ARGs and the pathogenic taxa.}, }
@article {pmid41656299, year = {2026}, author = {Fang, T and Bogensperger, L and Feer, L and Allam, A and Bezshapkin, V and Balázs, Z and von Mering, C and Sunagawa, S and Krauthammer, M and Schwank, G}, title = {Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41656299}, issn = {2041-1723}, support = {//SNSF/ ; //Swiss National Science Foundation (SNSF)/ ; /ERC_/European Research Council/International ; }, mesh = {*Machine Learning ; *CRISPR-Cas Systems/genetics ; *Metagenomics/methods ; *CRISPR-Associated Protein 9/genetics/metabolism ; Genome, Archaeal ; Gene Editing/methods ; Genome, Bacterial ; Bacteriophages/genetics ; Data Mining ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Recognition of protospacer adjacent motifs (PAMs) is crucial for target site recognition by CRISPR-Cas systems. In genome editing applications, the requirement for specific PAM sequences at the target locus imposes substantial constraints, driving efforts to search for novel Cas9 orthologs with extended or alternative PAM compatibilities. Here, we present CRISPR-PAMdb, a comprehensive and publicly accessible database compiling Cas9 protein sequences from 3.8 million bacterial and archaeal genomes and PAM profiles from 7.4 million phage and plasmid sequences. Through spacer-protospacer alignment, we infer consensus PAM preferences for 8003 unique Cas9 clusters. To extend PAM discovery beyond traditional alignment-based approaches, we develop CICERO, a machine learning model predicting PAM preferences directly from Cas9 protein sequences. Built on the ESM2 protein language model and trained on the CRISPR-PAMdb database, CICERO achieves an average cosine similarity of 0.69 on test data and 0.75 on experimentally validated Cas9 orthologs. For Cas9 clusters where alignment-based predictions are infeasible, CICERO generates PAM profiles for an additional 50,308 Cas9 proteins, including 17,453 high-confidence predictions with CICERO confidence scores above 0.8. Together, CRISPR-PAMdb and CICERO enable large-scale exploration of PAM diversity across Cas9 proteins, accelerating design of next-generation CRISPR-Cas9 tools for precise genome engineering.}, }
@article {pmid41656341, year = {2026}, author = {Cai, J and Wu, W and Wang, L and Meng, D and Yang, H and Liu, S and Hou, S and Cao, Y}, title = {Dietary β-hydroxy-β-methyl butyrate supplementation improves intestinal health and growth performance in Tibetan sheep lambs via modulating small intestinal microbiota.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {25}, pmid = {41656341}, issn = {1674-9782}, support = {2022-NK-169//Construction of Standardized Production System for Improving quality and efficiency of Tibetan sheep industry/ ; 2025-YYKF-03//Key Laboratory of Qinghai-Tibet Plateau Grazing Yak and Tibetan Sheep Animal Nutrition and Feed-Forage, Ministry of Agriculture and Rural Affairs, P. R. China/ ; }, abstract = {BACKGROUND: Tibetan sheep grazing on the Qinghai-Tibet Plateau require dietary protein supplementation; however, they face economic constraints due to the high cost of feed transportation in this region. Given that the leucine metabolite β-hydroxy-β-methyl butyrate (HMB) enhances both protein synthesis and intestinal nutrient absorption, this study employed metagenomics and untargeted metabolomics to systematically evaluate HMB's effects on antioxidant capacity, immune response, microbiota, metabolites, and the health of the small intestine in Tibetan sheep. A total of 120 healthy weaned 60-day-old male Tibetan lambs were assigned to diets containing 0 mg/kg (control group, CON), 430 mg/kg (low HMB, L-HMB), 715 mg/kg (medium HMB, M-HMB), or 1,000 mg/kg (high HMB, H-HMB) for 90 d. At the end of the experiment, 6 lambs from each group were slaughtered for intestinal tissue and content sampling.
RESULTS: The M-HMB treatment significantly increased average daily gain of the lambs without affecting feed intake, thereby improving feed utilization efficiency. M-HMB promoted the development of small intestinal morphological and elevated villus height, while also enhancing the activities of digestive enzyme and disaccharidase activities. Furthermore, M-HMB enhanced the antioxidant capacity, immune response, and barrier function of the small intestine. Metagenomic analysis revealed that M-HMB supplementation improved the composition of the small intestinal microbiota in Tibetan sheep, specifically increasing the relative abundance of Ruminococcus bacterium P7 and R. bromii, and enhanced microbial carbohydrate degradation capacity. Metabolomic analysis demonstrated that M-HMB supplementation significantly altered the small intestinal metabolite profile, enhancing carbohydrate metabolic pathways and increased the production of short-chain fatty acids (SCFAs). M-HMB upregulated PLCβ1 and ERK1/2 protein expression levels in small intestinal tissue and elevated the proportion of Ki67-positive cells at the basal crypt region of small intestinal crypts, suggesting enhanced proliferative activity of intestinal epithelial cells.
CONCLUSIONS: In summary, dietary supplementation with M-HMB (715 mg/kg) promoted small intestinal growth and development, enhanced digestive and absorptive functions, optimized the microbial composition, improved carbohydrate degradation, and increased the production of SCFAs, ultimately improving the growth performance of Tibetan sheep lambs.}, }
@article {pmid41656480, year = {2026}, author = {da Silva, EC and Beserra, MMN and Leitão, MGS and Vieira Camelo Maia, IF and de Souza Alves, BE and Gonçalves, PG and de Assis Leite, DC and Neves, BG and Pereira, KMA and Rodrigues, LKA and Gondim, DV}, title = {Fermentation time Determines Anti-inflammatory and Osteoprotective Activity of Green Tea Kombucha in a Rat Model of Experimental Periodontitis.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41656480}, issn = {1867-1314}, abstract = {This study aimed to characterize the microbial composition of green tea-fermented kombucha at different fermentation times and to evaluate its effects on inflammation and alveolar bone loss in rats with periodontitis. Microbial diversity was first assessed by metagenomic sequencing targeting bacterial 16 S rRNA and fungal 18 S rRNA regions. Sixty male rats were divided into six groups: control, periodontitis without treatment, green tea treatment, and kombucha fermented for 4, 8, or 12 days. Kombucha or green tea was administered daily by oral gavage for 39 days. Periodontitis was induced by ligation of the maxillary second molar on day 28. After euthanasia, hemimaxillae, liver, kidney, and blood samples were collected for analysis. Kombucha fermented for 4 days showed the highest abundance of bacteria from the Acetobacteraceae family and yeasts from the Saccharomycetaceae family. This fermentation time also produced the most pronounced reduction in periodontal inflammation and alveolar bone loss, with lower expression of tumor necrosis factor-alpha (42,9%) and receptor activator of nuclear factor kappa-B (43,6%), as well as higher expression of osteoprotegerin (approximately 55,4%) in periodontal tissues compared to animals with periodontitis without treatment. Notably, kombucha did not induce renal or hepatic toxicity regardless of fermentation time. These findings suggest that kombucha, particularly after 4 days of fermentation, reduces inflammation and alveolar bone loss without systemic toxicity, supporting its potential as an adjunctive therapy for periodontitis.}, }
@article {pmid41656820, year = {2025}, author = {Zhang, W and Han, K and Zhao, K and Yang, C and Jin, M and Wang, Y and Jiang, Z}, title = {[Application of flavonoid in disease treatment based on multi-omics technologies].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {50}, number = {10}, pages = {1915-1929}, pmid = {41656820}, issn = {1672-7347}, support = {XZ202201ZR0061G//the Natural Science Foundation of Xizang Autonomous Region/ ; 24MDQ05//Nationalities Youth Fund Project of Xizang Minzu University/ ; }, mesh = {*Flavonoids/therapeutic use/pharmacology ; Humans ; Metabolomics/methods ; Proteomics/methods ; Genomics/methods ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Multiomics ; }, abstract = {Flavonoids are naturally occurring polyphenolic compounds widely distributed in nature, exhibiting pharmacological activities including anti-inflammatory effects and inhibition of cell proliferation. Their broader application has been constrained by unclear therapeutic targets. Recent advances in high-throughput sequencing and high-resolution mass spectrometry have elevated the importance of multi-omics analysis for elucidating flavonoid pharmacological effects, therapeutic targets, and regulatory networks. Integration of genomics, transcriptomics, proteomics, metabolomics, and metagenomics enables systematic characterization of flavonoid targets and modulation networks. Clarifying the application of multi-omics technologies in this field may support the clinical translation of flavonoids and provide new strategies for precision research in traditional Chinese medicine.}, }
@article {pmid41657444, year = {2026}, author = {Zhong, S and Shan, W and Xiang, L and Wang, Y and Zhang, L}, title = {Human bocavirus 1 viremia-associated pediatric sepsis with a triphasic urinary course: a case report.}, journal = {Translational pediatrics}, volume = {15}, number = {1}, pages = {22}, pmid = {41657444}, issn = {2224-4344}, abstract = {BACKGROUND: Human bocavirus 1 (HBoV1) is a common pediatric respiratory virus, yet, its potential to cause severe systemic illness as a sole pathogen and its specific effects on the urinary system are not fully recognized. This report describes the first case of pediatric sepsis, meeting the 2024 Phoenix sepsis criteria, caused by high-load HBoV1 viremia, which was characterized by a novel triphasic urinary course.
CASE DESCRIPTION: A previously healthy 4-year-old girl presented with fever and cough and developed asymptomatic sterile pyuria on illness day 4. On day 7, her condition deteriorated to sepsis (Phoenix Sepsis Score of 2), with acute respiratory distress and a depressed level of consciousness. Blood metagenomic next-generation sequencing (mNGS) identified high-load HBoV1 viremia (7,513 reads) as the sole pathogen, with negative blood and urine cultures. During the septic peak, urinary tract ultrasonography was normal; however, follow-up imaging on day 13 revealed delayed-onset, non-obstructive pyelectasis and increased post-void residual (PVR) volume. These functional abnormalities were resolved completely within 2.5 months.
CONCLUSIONS: HBoV1 can act as a sole pathogen to cause pediatric sepsis. The observed triphasic urinary course-early sterile pyuria, imaging quiescence at the sepsis peak, and delayed functional impairment-supports an inflammation-mediated pathogenesis rather than direct viral invasion. This case highlights the critical role of advanced molecular diagnostics in identifying viral etiologies in culture-negative sepsis and underscores the necessity of longitudinal functional surveillance, as clinically significant organ dysfunction may manifest after the acute inflammatory phase has resolved.}, }
@article {pmid41657896, year = {2026}, author = {Wicaksono, WA and Thorsen, J and Stokholm, J and Berg, G}, title = {Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729707}, pmid = {41657896}, issn = {1664-302X}, abstract = {INTRODUCTION: The nasopharyngeal microbiome presents an important environmental human interface and a window in the fight against chronic diseases like asthma, respiratory infections, and antimicrobial resistance. To identify the microbial structure and function, we designed a pilot study with individuals with asthma, COVID-19 infection, and healthy controls.
METHODS: We compare the microbial and resistome profiles of healthy individuals, patients with asthma, and patients with PCR-confirmed COVID-19 using shotgun metagenome sequencing. Additionally, metagenome-assembled genomes were generated to assess the virulence potential of the bacteria identified in the nasopharynx.
RESULTS: We found different patterns in microbial diversity, richness, and structure between individuals with asthma and those who are healthy, but not for those with COVID-19. Our results revealed unexpected insights into the quite diverse nasopharynx resistome encompassing 23 distinct drug classes, mainly based on antibiotic efflux (63.9%) and antibiotic inactivation (24.6%), regardless of the disease state. The majority of the antimicrobial resistance genes (ARGs) confer resistance to multidrug (45%), followed by those genes that confer resistance to aminoglycosides, tetracyclines, polymyxin, beta-lactam, and macrolide-lincosamide-streptogramin. A high proportion of ARGs was associated with various Pseudomonas species, which was confirmed by analysing metagenome-assembled genomes. Pseudomonas brenneri exhibited the highest number of ARGs and virulence factors, indicating notable pathogenic potential.
CONCLUSION: The study reveals distinct bacterial community compositions in healthy individuals and individuals with asthma. Pseudomonadales, particularly Pseudomonas species, contribute to the nasopharyngeal resistome. No association was found between nasopharyngeal resistome profiles and asthma development. Future research may explore airway microbial functions' influence on asthma development.}, }
@article {pmid41657901, year = {2026}, author = {Farinas, LMF and Dela Peña, LBRO and Rivera, WL}, title = {Shotgun metagenomics reveals the prevalence and mobility of antibiotic resistance genes in the West Bay of the human-impacted Laguna Lake.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1742578}, pmid = {41657901}, issn = {1664-302X}, abstract = {Laguna Lake, the largest freshwater lake in the Philippines, has been reported to harbor antibiotic-resistant bacteria, posing health risks to the millions who depend on it. However, limited knowledge of antibiotic resistance genes (ARGs) in the lake highlights the need for a comprehensive assessment of its resistome. In line with this, we characterized ARGs in the West Bay of Laguna Lake using shotgun metagenomic sequencing based on six metagenomes collected from three stations across two sampling months at a single depth. ARGs were quantified from short reads, and assembled contigs containing these genes-antibiotic-resistant contigs (ARCs)-were analyzed to assess mobility through associations with plasmids and mobile genetic elements (MGEs). β-lactam resistance genes (0.023-0.048 copies per cell) were the most prevalent, corroborating previous reports. Meanwhile, the detection of bacitracin (0.013-0.028 cpc) and polymyxin (0.009-0.011 cpc) resistance genes raises new concerns, as resistance to these antibiotic classes has not been previously reported in the lake. Furthermore, 44.8 and 30.4% of ARCs were associated with plasmids and MGEs, respectively. ARCs carrying genes for resistance to β-lactams, chloramphenicol, and tetracyclines were frequently identified as mobile, indicating a high potential for horizontal gene transfer and suggesting possible antibiotic contamination in the lake. Overall, this study provides the first metagenomic insight into the resistome of Laguna Lake using short-read sequencing and highlights its role as an environmental reservoir of mobile ARGs. The findings underscore the need for expanded ARG surveillance to improve antimicrobial resistance risk prediction.}, }
@article {pmid41657906, year = {2026}, author = {Wu, H and Qin, J and Li, B and Huang, Z and Liao, G and Tang, X and Li, Z and Xiong, J and Gao, Z and Jiang, J and Zhong, R and Han, Z and He, L and Tang, R}, title = {The combined application of chemical and microbial fertilizers enhanced microbial diversity and improved soil fertility in the peanut rhizosphere within a sugarcane-peanut intercropping system.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751211}, pmid = {41657906}, issn = {1664-302X}, abstract = {The decline in soil microecological balance and fertility caused by continuous cropping obstacles and excessive application of chemical fertilizers has become a critical bottleneck restricting the sustainable development of the peanut industry. However, intercropping can enhance resource utilization efficiency, and microbial fertilizers can improve soil properties and increase nutrient usability. Therefore, we evaluated the effects of six fertilization treatments [no fertilization (CK), 100% chemical fertilizer (T1), microbial fertilizer (T2), 100%chemical fertilizer+microbial fertilizer (T3), 80% chemical fertilizer+microbial fertilizer (T4) and 60% chemical fertilizer+microbial fertilizer (T5)] on chemical properties and microbial communities of the rhizosphere soil of intercropped peanuts. The results showed that compared with T1, the combined application of chemical and microbial fertilizers significantly increased soil organic matter content and alleviated soil acidification. Microbial analysis indicated that the T4 treatment had the highest Shannon diversity, which was significantly higher than T1, demonstrating its effectiveness in reversing the suppressive effect of chemical fertilizer alone on microbial diversity. Principal coordinate analysis and redundancy analysis further confirmed that fertilization significantly altered microbial community structure, with a clear separation between the combined application and chemical-fertilizer-alone treatments, forming a distinct microbial community. Specifically, the T4 treatment significantly increased the abundance of rhizobia. Under T4 treatment, the abundance of assimilatory nitrate reductase genes (such as nasB and NR) decreased, while that of narB, and nirA increased; simultaneously, the abundance of dissimilatory nitrate reductase and denitrification-specific genes significantly increased. Mantel test analysis revealed significant positive correlations between soil total nitrogen, available nitrogen content, microbial communities, and crop yield. In summary, the combined application of chemical and microbial fertilizers optimizes the soil microenvironment by synergistically enhancing soil fertility (increasing organic matter, regulating pH) and reshaping microbial community structure (increasing diversity, enriching beneficial bacteria). These findings can provide theoretical basis for the optimization of fertilization strategy in peanut intercropping system.}, }
@article {pmid41657910, year = {2026}, author = {Pilgrim, J and Widlake, E and Wilson, R and Vaux, AGC and Medlock, JM and Darby, AC and Baylis, M and Blagrove, MSC}, title = {Mosquito viromes across England and Wales reveal hidden arbovirus signals and limited ecological structuring.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1749228}, pmid = {41657910}, issn = {1664-302X}, abstract = {Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of Culex mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (Peribunyaviridae), Umatilla virus (Sedoreoviridae), and Atherstone virus (Peribunyaviridae), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of Culex mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.}, }
@article {pmid41657984, year = {2025}, author = {Li, JL and Hu, W and Chen, XQ and Li, LH and Phurbu, D and Zheng, YY and Zhang, YW and Sun, J and Yang, ZF and Xie, KQ and Yang, LQ and Yin, YR}, title = {Characterization of thermophilic xylanases from Tengchong Qiaoquan hot spring for lignocellulose bioprocessing and prebiotic production.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1731615}, pmid = {41657984}, issn = {1664-302X}, abstract = {INTRODUCTION: Xylanases are key catalysts for valorizing lignocellulosic biomass, yet many available enzymes lack sufficient thermal stability and exhibit suboptimal activity on complex substrates. To address these limitations, we combined enrichment culturing with metagenomic analysis to discover and characterize two novel GH10 family xylanases, Tc15-Xyn6 and Tc15-Xyn10, from the Qiaoquan geothermal area in Tengchong, Yunnan Province.
METHODS: Following molecular cloning, heterologous expression, and purification by Ni[2+]-chelating affinity chromatography, both enzymes were comprehensively profiled.
RESULTS: Tc15-Xyn6 displayed optimal activity at 65 °C and pH 6.6 with a half-life of 2 h at 65 °C, while Tc15-Xyn10 exhibited optimal activity at 60 °C and pH 6.0 with a half-life of 1 h at 60 °C. Both enzymes showed broad pH stability at low temperature: after incubation at 4 °C for 12-24 h across pH 4.0-10.0, Tc15-Xyn6 and Tc15-Xyn10 retained more than 60 and 40% of their initial activity, respectively. Both efficiently hydrolyzed xylan in alkali-treated wheat straw, rice straw, and corn stover, as well as xylan from hot water-treated wheat bran, but yielded distinct product profiles: Tc15-Xyn6 primarily produced xylobiose and xylotetraose, whereas Tc15-Xyn10 generated xylotriose as the main product. The resulting xylooligosaccharides significantly promoted the growth of Lactococcus lactis. Kinetic analyses showed K m and V max values of 4.675 mg/mL and 125 μmol/min/mg for Tc15-Xyn6, and 9.36 mg/mL and 59.52 μmol/min/mg for Tc15-Xyn10.
DISCUSSION: Collectively, Tc15-Xyn6 and Tc15-Xyn10 combine thermophilicity, thermostability, near-neutral pH preference, and strong performance on complex lignocellulosic substrates, supporting their application in feed processing and targeted production of prebiotic xylooligosaccharides from biomass.}, }
@article {pmid41657996, year = {2025}, author = {Kong, M and Pan, Z and Wang, X and Huang, J and Tulafu, H and Xu, Y and Sulaiman, Y and Wu, W}, title = {Integrated multi-omics analysis reveals rumen and rectal microbiota-metabolite interaction features in polytocous fine-wool sheep with divergent residual feed intake.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1712307}, pmid = {41657996}, issn = {1664-302X}, abstract = {Residual feed intake (RFI) is a key indicator of feed efficiency in ruminants. To elucidate the potential regulatory roles of microorganisms and metabolites under different RFI levels, we investigated 24 polytocous fine-wool sheep (12 high-RFI and 12 low-RFI) using metagenomic sequencing and non-targeted metabolomics of rumen and rectal contents. Significant differences in average daily feed intake, residual feed intake, and feed conversion ratio were observed between groups (p < 0.001). LEfSe analysis identified four and seventeen RFI-associated microbial biomarkers in the rumen and rectum, respectively, with s_Ruminococcus_albus and s_Ruminococcus_bicirculans as common core taxa. Functional annotation revealed that high-RFI sheep were enriched in amino acid metabolism and xenobiotic degradation pathways in the rumen, whereas low-RFI sheep were enriched in pathways related to development and regeneration. In the rectum, high-RFI sheep showed enrichment in protein folding and degradation, carbohydrate metabolism, and energy metabolism, while low-RFI sheep were enriched in transcriptional regulation and signal transduction pathways. Metabolomic analysis detected 297 and 1,130 differential metabolites in the rumen and rectum, respectively, mainly lipids, organic acids, and derivatives. KEGG enrichment indicated that rumen metabolites were primarily involved in bile acid biosynthesis and riboflavin metabolism, while rectal metabolites were enriched in energy metabolism and multiple amino acid pathways, including arachidonic acid, tryptophan, tyrosine, lysine, and methionine metabolism. Integrated analysis revealed significant associations between key bacterial taxa and metabolites, and network construction identified core nodes potentially engaged in synergistic regulation, providing insights into their roles in RFI phenotype formation. Collectively, these findings highlight the distinct contributions of the rumen and rectum to feed efficiency in sheep and offer theoretical support for nutritional regulation strategies to improve ruminant production performance.}, }
@article {pmid41658006, year = {2025}, author = {Tada, Y and Nakajima, R and Kitamura, M and Marumoto, K}, title = {Distribution and function of prokaryotes involved in mercury methylation, demethylation, and reduction in the western North Pacific Subtropical Gyre.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1642479}, pmid = {41658006}, issn = {1664-302X}, abstract = {Methylmercury (MeHg), a bioaccumulative neurotoxic heavy metal, substantially threatens environmental and human health. In natural environments, MeHg formation and degradation are primarily mediated by microorganisms containing hgcAB, merA, or merB genes. However, these genes have not been simultaneously analyzed in open-ocean samples. This study aimed to investigate the distribution and phylogeny of functional genes associated with mercury (Hg) methylation (hgcA and hgcB), demethylation (merB), and reduction (merA), as well as dissolved total Hg (THg) and MeHg concentrations in the western North Pacific Subtropical Gyre (WNPSG) using metagenomic analysis. Although THg levels varied across sampling sites, MeHg concentrations consistently increased with depth. A strong correlation between dissolved MeHg and apparent oxygen utilization indicated a link between Hg methylation and microbial respiration. hgcA, merB, and merA were predominantly detected at depths of 500-1,500 m, where MeHg concentrations peaked, indicating active microbial Hg speciation within mesopelagic layers. A higher abundance of hgcA than merB suggests that microbial Hg methylation may surpass demethylation in this region. Phylogenetic analyses of hgcAB identified the Nitrospina lineage as dominant Hg methylators. Metabolic pathway analyses of metagenome-assembled genomes (MAGs) showed that Nitrospina harboring hgcAB possesses the nitrite reductase pathway, suggesting a linkage between Hg methylation and nitrogen cycling. MAGs with hgcA affiliated with Myxococcota (Deltaproteobacteria) exhibited a strong association with sulfur cycling. Diverse lineages harboring merB and merA genes were identified, suggesting that MeHg demethylation and Hg(II) reduction likely co-occur. Methanogenesis pathways in some Alphaproteobacteria with merB or merA suggest a potential connection between methane production and MeHg degradation and Hg(II) reduction. These findings provide novel insights into the intricate interactions between microbial communities, functional gene distributions, and Hg biogeochemical cycling in the WNPSG.}, }
@article {pmid41658007, year = {2025}, author = {Alfonsi, S and Racciatti, F and Guzman, F and Fabbretti, A and Milon, P and Vitali, LA and Spurio, R and Petrelli, D}, title = {The plastisphere and river systems as reservoirs for antibiotic resistant bacteria.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1721325}, pmid = {41658007}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a critical global health threat. This phenomenon involves the diffusion of bacteria and genes among humans, animals and the environment. In particular, the presence of third generation cephalosporin (3GC)-resistant Enterobacteriaceae in natural environments is of high concern as they are classified as critical-priority pathogens of public health importance. In this work we studied the relation among plastic pollution in freshwater ecosystems, the spread of multidrug-resistant (MDR) bacteria and diffusion of antibiotic resistance genes (ARGs). Caged plastic fragments were deliberately introduced in a river of central Italy. Plastic samples were collected and analyzed in parallel with river water samples. Out of 267 cefotaxime (CTX) resistant isolates obtained, 65 CTX-resistant Enterobacteriaceae were selected for further analysis. Most of the isolates (75% of plastic-derived and 84% of water-derived isolates) were MDR with seven being carbapenem-resistant enterobacteria (CRE). Five of them synthesize KPC (Klebsiella pneumoniae carbapenemases) enzymes, and two strains were positive for metallo-β-lactamases (NDM). Among the KPC producers, three isolates were identified as K. pneumoniae sequence type ST1519. Their isolation in a natural ecosystem is alarming because they can potentially re-enter human populations through environmental pathways. Shotgun metagenomic analysis provided a comprehensive snapshot of the microbial communities associated to the plastisphere, revealing dominance of families such as Comamonadaceae, Sphaerotilaceae, and Flavobacteriaceae, which play key roles in environmental biofilm formation and stability. The resistome analysis highlighted the presence of ARGs conferring resistance to clinically important antibiotics, such as beta-lactams, vancomycin, and tetracyclines, alongside mobile genetic elements (MGEs) such as integrons, which facilitate the horizontal transfer of resistance genes. This study provides crucial experimental evidence that riverine plastic debris acts as a genetic reservoir and could act as an efficient vehicle for the accumulation and transfer of clinically relevant resistance determinants.}, }
@article {pmid41658353, year = {2026}, author = {Liu, X and Li, Y and Xiao, J and Zhang, X and Liu, Y and Li, Z and Wang, L and Zhang, L and Liu, Y and Liang, P and Xu, Z and Liu, Y and Song, C}, title = {Emergence of a Novel CRESS-DNA Virus Associated with Swine Reproductive Failure in China.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {}, pages = {4053892}, pmid = {41658353}, issn = {1865-1682}, mesh = {Animals ; Swine ; China/epidemiology ; *Swine Diseases/virology/epidemiology ; *Circoviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; *DNA Viruses/genetics/isolation & purification/classification ; *Circovirus/isolation & purification/genetics ; Genome, Viral ; }, abstract = {The continuous emergence of circular Rep-encoding single-stranded (CRESS) DNA viruses across diverse hosts has been closely associated with the occurrence of severe diseases. Four circoviruses within the genus Circovirus have been identified in pigs, including porcine circovirus Type 1 (PCV1), PCV2, PCV3, PCV4, and PCV5. In late 2021, a large pig farm experienced an outbreak of reproductive disorders that were undiagnosed by standard tests. Subsequent viral metagenomic analysis of stillborn piglets identified a novel single-stranded circular DNA virus, designated porcine megalocircovirus (PMCV). PMCV has a large genome of 9426 nt and encodes nine open reading frames. Biochemical analyses of Rep confirm PMCV as a CRESS DNA virus. However, PMCV Rep showed low amino acid sequence identities to the four PCV species and several human CRESS DNA viruses, with the highest identity of 23.6% to PCV4 Rep. The genetic evolutionary tree indicates that PMCV belongs to an unknown family of the CRESS DNA viruses. The positive detection rate for PMCV in tested samples was 24% (30/125), while the positive rate regarding pig farms was 41.18% (14/34) in China. The emergence of PMCV warrants further investigation.}, }
@article {pmid41658610, year = {2026}, author = {Bautista, J and Bedón-Galarza, R and Martínez-Hidalgo, F and Masache-Cruz, M and Benítez-Núñez, M and Valencia-Arroyo, C and López-Cortés, A}, title = {Decoding the microbial blueprint of pancreatic cancer.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1737582}, pmid = {41658610}, issn = {2296-858X}, abstract = {Pancreatic cancer (PC) represents one of the most formidable challenges in oncology, characterized by its asymptomatic onset, delayed clinical detection, and dismal prognosis. Among pancreatic neoplasms, pancreatic ductal adenocarcinoma (PDAC) accounts for over 90% of cases and remains the most aggressive form, driven by late diagnosis, intrinsic chemoresistance, and a profoundly immunosuppressive tumor microenvironment. Recent advances have reframed the human microbiome not as a passive bystander but as an active architect of pancreatic tumor biology. This review delineates the mechanistic axes through which microbial ecosystems orchestrate PDAC progression across four key anatomical niches-gastrointestinal, oral, urogenital, and intrapancreatic. We elucidate how microbial dysbiosis fosters oncogenesis through immune evasion, metabolic reprogramming, and chronic inflammation, implicating specific taxa such as Fusobacterium nucleatum, Malassezia spp., and Porphyromonas gingivalis in immune suppression and chemoresistance. Microbial enzymatic inactivation of gemcitabine and modulation of cytokine networks further underscore the microbiome's pivotal role in therapeutic failure. Conversely, commensal and probiotic species may potentiate immunosurveillance and enhance treatment efficacy. This review also explores microbiota-derived biomarkers for early detection and the translational promise of microbiome-targeted interventions, including fecal microbiota transplantation, probiotics, and selective antibiotics. By decoding the microbial blueprint of PC, we propose a paradigm in which the microbiome emerges as both a biomarker and a therapeutic axis, offering novel avenues for precision oncology. Furthermore, this integrative synthesis emphasizes the multi-omic, immunometabolic, and therapeutic dimensions of the pancreatic cancer-microbiome interface, where metagenomic, transcriptomic, metabolomic, and immunomic layers converge to shape tumor evolution and therapeutic response, advancing the vision of microbiome-informed precision oncology.}, }
@article {pmid41658619, year = {2026}, author = {Pan, T and Zhuang, X and Xiang, L}, title = {Case Report: From trivial trauma to fulminant septic shock: multidisciplinary rescue of Vibrio vulnificus necrotizing fasciitis via a seven-stage surgical protocol with limb salvage.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1714153}, pmid = {41658619}, issn = {2296-858X}, abstract = {OBJECTIVE: To report a successful case of an inland seafood vendor who developed Vibrio vulnificus necrotizing fasciitis complicated by septic shock following a minor calf abrasion, and to explore its special epidemiological implications and key points for standardized management.
CASE SUMMARY: A 46-year-old male seafood vendor (hospitalized from July 3 to 10 August 2025) presented on post-injury day 7 with fulminant necrotizing fasciitis, septic shock, and multiple organ dysfunction syndrome. Vibrio vulnificus was identified by wound culture and metagenomic sequencing. Management included early combination antibiotics, ICU organ support, and seven sequential surgical interventions. The patient was successfully weaned from mechanical ventilation and extubated after 25 days of ICU care, and discharged on hospital day 30 with satisfactory wound healing.
CONCLUSION: This case alerts that high inoculum exposure due to cold-chain disruption can prolong the incubation period of V. vulnificus infection to 7 days, transcending traditional epidemiological boundaries. Successful management depended on early fasciotomy and strict adherence to standardized treatment protocols. Mandatory wound monitoring for high-risk occupational populations should become a new priority in public health prevention and control.}, }
@article {pmid41658717, year = {2026}, author = {Al-Najjar, AS and Shata, FN and Ba Mhel, O and Gutob, Y and Alhazmi, M and Alharbi, Z and Choghari, RA and Qashar, AA and Basudan, B and Aljohani, N and Al-Juhani, A}, title = {Diatom Analysis in Drowning: A Critical Review of Reliability, Contamination, and Medico-Legal Interpretation.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e100870}, pmid = {41658717}, issn = {2168-8184}, abstract = {The diagnosis of fatal drowning remains one of the most challenging tasks in forensic pathology, as no single autopsy finding is pathognomonic, and interpretation relies on the integration of scene information, circumstances, and ancillary investigations. Among supportive tests, diatom analysis has been used for decades, yet its medico-legal value continues to be debated due to methodological heterogeneity, contamination risks, and inconsistent interpretive frameworks. This review critically examines diatom evidence in drowning from a comparative and fit-for-purpose perspective, focusing on mechanistic plausibility, alternative non-drowning explanations, and methodological blind spots that undermine evidentiary reliability. Conventional microscopy-based diatom testing and emerging DNA-based and metagenomic approaches are compared with respect to what they detect, how contamination may arise, and how results are currently interpreted in forensic casework. Particular emphasis is placed on low-count diatom findings in closed organs, where recent evidence demonstrates substantial vulnerability to laboratory, consumable, and postmortem contamination. Drawing on recent systematic syntheses, controlled postmortem studies, and newly identified contamination sources, this review argues that mechanistic plausibility does not equate to forensic reliability. Diatom findings are best interpreted as supportive evidence whose weight depends on explicit contamination control, transparent reporting, and alignment with a clearly defined medico-legal proposition. To address persistent comparability and interpretation gaps, a minimum reporting dataset, minimum contamination-control principles, and a decision-oriented interpretive framework are proposed. In conclusion, diatom testing should neither be regarded as definitive proof nor dismissed outright. When applied selectively and interpreted within a contamination-aware, proposition-driven framework, diatom evidence may contribute meaningfully to drowning diagnosis and drowning-site inference, while avoiding overstatement of its probative value.}, }
@article {pmid41659075, year = {2026}, author = {Duggar, M and Sun, Y and Leardini, D and Jia, Q and Muratore, E and Dallas, RH and Ferrolino, J and Cherian, A and Cesaro, S and Faraci, M and Fraczkiewicz, J and Ussowicz, M and Englund, JA and Hakim, H and Hayden, RT and Klein, EJ and Wolf, J and Maron, G and Tang, L and Masetti, R and Margolis, EB}, title = {Pre-HCT Resistome Disruption Predicts ESBL Gene Expansion in Pediatric Transplant Recipients: A Prospective Multi-Center Study.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.20.26344466}, pmid = {41659075}, abstract = {BACKGROUND: Infections are the leading cause of non-relapse mortality in pediatric hematopoietic cell transplant (HCT) recipients. Up to 90% of bacteremias in these patients originate from gut microbiome organisms. However, selection for resistance genes, such as Extended-spectrum β-lactamase (ESBL), in these patient's gut microbiomes remains poorly understood.
METHODS: Stools were prospectively collected from pediatric HCT recipients at multiple centers (n=133 patients, five centers) on the day of HCT, the day of neutrophil engraftment, and 30 days post-HCT. Bacterial DNA was isolated and sent for shotgun metagenomic sequencing. Antibiotic resistance genes were identified using the MEGARes database. Associations between ESBL gene abundance changes and antibiotic exposure were examined using univariate and Inverse Probability of Treatment Weighting linear regression models with covariate balancing propensity scores.
RESULTS: Pre-existing gut resistome disruption at the time of HCT showed a stronger correlation with ESBL gene expansion than post-transplant antibiotic exposure. Specifically, patients with greater baseline resistome distance from healthy children showed increased ESBL genes during the neutropenic period. Post-transplant β-lactam exposure (total or ESBL-cleavable) did not correlate with increases in ESBL genes in already-colonized patients. However, aminoglycosides and anaerobic active antibiotics were associated with acquisition of new ESBL organisms during the neutropenic period, while pre-existing microbiome disruption primarily drove selection of resistant bacteria already present.
CONCLUSIONS: These findings indicate that antibiotic stewardship before HCT, in addition to reducing the use of anaerobic active antibiotics during early transplant, may be necessary to prevent ESBL-related infections in pediatric transplant recipients.
LAY SUMMARY: Infections are the leading cause of death after HCT, and recently the role of the gut microbiome in harboring dangerous bacteria has been highlighted. This study aims to understand multidrug resistant bacteria changes in the gut microbiome early after HCT.}, }
@article {pmid41659429, year = {2026}, author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT}, title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41659429}, issn = {2692-8205}, support = {UM1 TR004409/TR/NCATS NIH HHS/United States ; UL1 TR002538/TR/NCATS NIH HHS/United States ; S10 OD034321/OD/NIH HHS/United States ; T32 HG008962/HG/NHGRI NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; T32 HL105321/HL/NHLBI NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; }, abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae. At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella, and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae. By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.}, }
@article {pmid41659626, year = {2026}, author = {Priyadarshini, M and Jorgensen, J and Stauffer, SRC and Issa, L and Pandya, N and Nnyamah, C and Xu, K and Boyett, JE and Kular, P and Mhatre, A and Brahambhatt, VH and Gilbert, JA and Khan, MW and Wicksteed, B and Dai, Y and Layden, BT}, title = {A high fermentable fiber Western diet reduces indole levels.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.27.702025}, pmid = {41659626}, issn = {2692-8205}, abstract = {Changes in gut microbiota composition due to diet impact health. Fiber-rich diets promote beneficial microbiota and reduce the risk of metabolic diseases, while low-fiber, calorie-dense diets are linked to dysbiosis and increased disease risk. This study examines the effects of a Western diet (WD) and explores dietary fiber supplements as potential modifiers of those effects. 10-week-old C57Bl/6J male mice were fed control (low-fat) or WD (high-fat, high-sucrose) containing 0% fermentable fiber (FF) or WD supplemented with 20% FF (fructooligosaccharides, FOS; guar gum, GG, or pectin, Pec). After 19 weeks, analysis of the cecal metagenome using whole-genome shotgun sequencing, metabolome by untargeted and targeted LC-MS/MS, and tissue RNA and protein expression by RT-PCR and immunoblotting was undertaken. WD-FF reduced metabolic derangements from WD while also improving GM diversity and altering cecal metabolites, particularly tryptophan metabolism. A profound increase in cecal indole levels (targeted metabolomics) was noted in WD vs WD-FF groups. As the primary indole-oxidizing enzyme, CYP2E1 generates indoxyl sulfate, which contributes to oxidative stress and a leaky gut. Mice on WD displayed higher expression of Cyp2e1 mRNA in the gut. In the liver, the levels of both CYP2E1 protein and mRNA were higher in the WD group compared to the WD-FOS group, with protein levels also higher than in the WD-Pec group and mRNA levels higher than in the WD-GG group. mRNA expression of markers of oxidative stress, inflammation, and leaky barrier was significantly higher in the liver and intestine of the WD vs the WD-FF groups. FFs reduced high plasma indoxyl sulfate levels (except in WD-GG), and boosted short-chain fatty acids and indole acetic acid. Our data suggest that WD disrupts GM tryptophan metabolism, possibly by altering the balance between indole-producing and utilizing gut bacteria. Dietary fiber supplementation exerts protective effects, in part, by mitigating this imbalance.}, }
@article {pmid41659795, year = {2026}, author = {Yang, F and Yang, C and Li, H and Zhang, X and Ding, X and Zhang, S}, title = {Metagenomic next-generation sequencing in diagnosing rhino-orbital-cerebral mucormycosis presenting as cerebral Infarction: a case series and diagnostic analysis of seven patients.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1751546}, pmid = {41659795}, issn = {2673-6128}, abstract = {INTRODUCTION: Rhino-orbital-cerebral mucormycosis (ROCM) is a rare, rapidly progressive, and fatal invasive fungal infection. This case series is the first to systematically characterize ROCM presenting primarily as cerebral infarction on imaging and highlights the value of metagenomic next-generation sequencing (mNGS) in the early diagnosis of such critical and atypical cases.
All seven patients had diabetes mellitus, with six concurrently presenting with ketoacidosis. Universal clinical features included fever and a fixed, dilated pupil. Most patients exhibited facial swelling (6/7, 85.7%) and visual impairment (5/7, 71.4%). Cerebral infarction was confirmed by head magnetic resonance imaging (MRI) in all individuals.
The diagnosis was confirmed in all cases by the detection of Rhizopus species sequences via mNGS of cerebrospinal fluid (CSF). Six patients received treatment with amphotericin B cholesteryl sulfate complex, and two of these also underwent surgical debridement. Ultimately, only one patient survived, yielding a mortality rate of 85.7% (6/7).
CONCLUSION: ROCM should be highly suspected in diabetic patients presenting with acute cerebral infarction accompanied by fever and facial or ocular symptoms. mNGS enables rapid and early etiological diagnosis of ROCM, which is crucial for improving outcomes. Earlier diagnosis, combined antifungal therapy, and surgical intervention may be associated with better prognosis.}, }
@article {pmid41659841, year = {2026}, author = {Tao, Y and Liu, X and Liu, Y and Ma, Y and Liu, Y and Ding, M}, title = {The diagnostic efficacy of bronchoscopy guided by hand-drawn mapping in the diagnosis of initial treatment for sputum-smear negative peripheral pulmonary tuberculosis.}, journal = {Journal of clinical tuberculosis and other mycobacterial diseases}, volume = {43}, number = {}, pages = {100578}, pmid = {41659841}, issn = {2405-5794}, abstract = {BACKGROUND: This study aims to evaluate the clinical value and safety of hand-drawn mapping for bronchoscopic navigation combined with radial probe endobronchial ultrasound (RP-EBUS) in the diagnosis of primary peripheral sputum smear-negative pulmonary tuberculosis (SNPTB).
METHODS: Patients suspected of having peripheral-type primary SNPTB, who were admitted to Southeast University Zhongda Hospital from 2021 to 2024, were retrospectively analyzed. Patients were divided into two groups. The sensitivity, specificity, diagnostic accuracy rate, and area under the receiver-operating characteristic (ROC) curve were evaluated with different diagnostic methods.
RESULTS: A total of 212 patients were enrolled, including 149 in the SNPTB group and 63 in the non-SNPTB group. The success rate of ultrasound bronchoscopy exploration is 90.6 %. The sensitivity, specificity, diagnostic accuracy, and AUC value of bronchoscopy guided by hand-drawn mapping were 92.6 %, 95.2 %, 93.4 %, and 0.939, respectively, which were superior to those of T-SPOT detection (P < 0.05). Among the various sampling methods, EBUS-guided bronchoalveolar lavage fluid metagenomic next-generation sequencing (EBUS-BALF mNGS) demonstrated the highest sensitivity (86.6 %), positive predictive value (89.6 %), and AUC (0.917).
CONCLUSIONS: For peripheral SNPTB, the combination of hand-drawn navigation and RP-EBUS is both safe and effective. EBUS-BALF mNGS demonstrated the highest diagnostic efficiency. When radial ultrasound detects hypoechoic areas of the lesion, it is recommended to perform BALF mNGS. Conversely, in solid lesions, the negative rate of BALF mNGS is relatively high, and combining mNGS with biopsy is recommended to further improve diagnostic efficiency.}, }
@article {pmid41659959, year = {2025}, author = {Abdelmegeid, M and Zeineldin, M and Seboussi, R and Mohamadin, M and Alharthi, AS and Mansour, N and Okasha, LA and Elolimy, AA and Saliu, EM}, title = {Metagenomic analysis of the camel rumen archaeome and its functional potential.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1738018}, pmid = {41659959}, issn = {2297-1769}, abstract = {The camel rumen harbors a unique and underexplored archaeal community that plays a critical role in methanogenesis and ruminal fermentation. This study aimed to characterize the taxonomic composition and functional potential of the camel rumen archaeome using whole-genome shotgun metagenomic sequencing. Across the seven healthy racing camel rumen samples, the archaeal community was dominated by Euryarchaeota (50.1 ± 0.02%) and the Methanomada group (49.7 ± 0.03%), with Methanobacteriaceae and Methanobrevibacter representing the predominant family and genus, respectively. Species-level analysis revealed Methanobrevibacter sp. YE315 and Methanobrevibacter millerae as the most abundant archaeal species across all samples. Alpha-diversity analyses indicated a diverse and evenly distributed archaeal population in the camel rumen. Beta-diversity based on Bray-Curtis and Jaccard dissimilarities demonstrated strong similarity among samples, highlighting a conserved archaeal community structure across individuals. Core microbiome assessment (≥ 80% occurrence) identified seven dominant Methanobrevibacter species as the stable core archaeome. Functional profiling revealed a consistent metabolic repertoire dominated by methanogenesis (PWY-5209), amino acid biosynthesis, and nucleotide metabolism pathways. Functional alpha-diversity metrics and beta-diversity clustering highlighted low inter-sample variability and a stable functional architecture. Overall, the camel rumen archaeome exhibited a stable and conserved community composition and functional architecture, underscoring its central role in hydrogen utilization and methane production within the rumen ecosystem. Although based on a small number of animals from a single location and therefore descriptive in nature, this study provides a comprehensive metagenomic overview of the taxonomic and functional profiles of the camel rumen archaeal community.}, }
@article {pmid41660005, year = {2026}, author = {Wicaksono, WA and Zukancic, E and Zlatnar, M and Suwanto, A and Berg, G}, title = {Traditional fermented foods of Indonesia harbour functionally redundant but phylogenetically diverse taxa.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag005}, pmid = {41660005}, issn = {2633-6685}, abstract = {Fermented foods represent complex microbial ecosystems that contribute to food quality, functionality, and potential health benefits, yet many traditional fermented foods remain poorly characterized. The aim of this study was to study microbial diversity, and functional potential of underexplored traditional Indonesian fermented food. The fermented products displayed substantial variation in bacterial richness, ranging from 65 to 614 bacterial amplicon sequence variants across samples. The microbial communities were dominated by bacterial taxa affiliated with the orders Bacillales and Lactobacillales, alongside fungal taxa from the order Mucorales. The plant-based products i.e. tape ketan and tape singkong had a higher bacterial abundance but lower diversity than animal-based terasi. We found significant correlations between bacterial and fungal communities dominated by positive cooccurrence patterns and highly complex networks especially in terasi. Each food product was characterized by a unique functional profile of genes linked to beneficial metabolic functions (biosynthesis of bacteriocins, short-chain fatty acids, and vitamins) but tape ketan samples demonstrated the highest diversity and abundance of them. Metagenome assembled genomes reflect a high diversity of health beneficial properties as well as substrate-specific degradation capabilities. Traditional Indonesian fermented foods harbour functionally redundant but phylogenetically diverse taxa offering a potential source for probiotic traits and functional food development.}, }
@article {pmid41660022, year = {2026}, author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R}, title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.}, journal = {Journal of conservative dentistry and endodontics}, volume = {29}, number = {1}, pages = {60-64}, pmid = {41660022}, issn = {2950-4708}, abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.
AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.
MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.
STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).
RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.
CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.}, }
@article {pmid41660100, year = {2026}, author = {Jaito, N and Kaewsawat, N and Sangawthong, K and Uengwetwanit, T}, title = {Identification of novel metagenomic lipases through integrated structural and sequence-based analysis.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20462}, pmid = {41660100}, issn = {2167-8359}, mesh = {*Lipase/genetics/chemistry/metabolism ; *Metagenomics/methods ; Enzyme Stability ; Hydrogen-Ion Concentration ; *Metagenome ; Databases, Protein ; }, abstract = {Enzymes, as key biocatalysts, are essential for advancing sustainable green technologies across diverse industrial sectors. The discovery of novel enzymes is essential for expanding their applications. In this study, we identified new lipases using an integrated screening strategy. This approach combines both structural and sequence-based methods on a large-scale metagenomic database. This strategy enabled the identification of new lipases with low sequence identity to known reference proteins. Our approach, therefore, circumvents the limitations of traditional sequence-only methods, which often fail to identify functionally similar enzymes with low sequence similarity. We first used Foldseek, a state-of-the-art structural homology search tool, to rapidly screen the database for proteins with structures similar to widely used lipases. This was followed by a rigorous sequence similarity filtering against public protein databases, yielding 711 putative novel lipases. We selected and experimentally validated three candidates, confirming their lipase activity. Further biochemical characterization revealed their notable properties including thermostability with optimal activity at 50-55 °C, and distinct alkaline activity profiles, maximal at pH of 8.0-9.0. Their unique properties, including high activity at elevated temperatures and alkaline pH, suggest potential for applications in detergent formulations, bioremediation, and industrial biocatalysis. Beyond identifying these promising enzymes, this study demonstrates the power of a combined structural and sequence-based approach for finding novel biocatalysts. This methodological innovation has broad implications for future enzyme discovery from metagenomic resources.}, }
@article {pmid41660425, year = {2026}, author = {Ni, H and Zhu, J and Chen, Y and Zheng, Y and Chen, B and Dong, C and Zhang, S and Xu, Y and Jiang, Y}, title = {Clinical characteristics and prognostic impact of streptococcal colonization in critically ill patients with severe pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1647511}, pmid = {41660425}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Critical Illness ; Retrospective Studies ; Prognosis ; Middle Aged ; Aged ; *Streptococcal Infections/microbiology/mortality ; Intensive Care Units ; *Streptococcus/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; *Pneumonia, Bacterial/microbiology/mortality ; }, abstract = {BACKGROUND: Streptococcus species are predominant commensal residents of the respiratory tract in healthy individuals and contribute to immune and metabolic regulation. However, the association between streptococcal colonization and clinical outcomes in patients with severe pneumonia remains undercharacterized. This study aimed to explore the clinical characteristics and the impact of streptococcal colonization on the prognosis of critically ill patients with pneumonia.
METHOD: We conducted a multicenter, retrospective, observational cohort study of critically ill pneumonia patients admitted to 12 intensive care units (ICUs) between January 2019 and December 2023 who underwent metagenomic next-generation sequencing (mNGS). Patients were stratified into Streptococcus-colonized and non-colonized groups based on bronchoalveolar lavage fluid (BALF) mNGS results, conventional microbiological testing (CMT), and clinical assessments. Propensity score matching (PSM) was utilized to minimize baseline confounding variables. Using nearest-neighbor matching at a 1:2 ratio, baseline characteristics were balanced between groups post-matching. The primary endpoint was 28-day all-cause mortality.
RESULTS: A total of 1,897 patients were enrolled in this study. Among them, 21 patients under 18 years of age, 139 patients lost to follow-up within 28 days, and 4 patients with confirmed streptococcal infection were excluded. Finally, 1,733 patients met the inclusion criteria. The cohort had a mean age of 65 years, with the majority being males (1,213/1,733, 70%). Among these, 148 (8.5%) were classified as Streptococcus-colonized, and 1,585 (91.5%) were Streptococcus-colonization-negative. No significant difference in 28-day all-cause mortality was observed between the colonized and non-colonized groups (35.81% vs. 38.51%, p=0.578). Patients with Streptococcus colonization had a significantly shorter median length of stay (LOS) (17 days, interquartile range [IQR] 11-30) than those without colonization (22 days, IQR 12-33; P = 0.044). Similarly, their median intensive care unit (ICU) LOS (11 days, IQR 7-16) was also significantly shorter than that of non-colonized patients (14 days, IQR 8-25; P = 0.003). Multivariable Cox regression analysis further demonstrated that Streptococcus colonization was not an independent risk factor for 28-day mortality (HR = 1.10, 95% CI: 0.79-1.51, p=0.579).
CONCLUSION: Our findings suggest a potential role for Streptococcus colonization in improving clinical outcomes in severe pneumonia. The presence or absence of Streptococcus colonization may influence short-term prognostic benefits in critically ill pneumonia patients. Further research is needed to clarify the clinical significance and potential mechanisms of Streptococcus colonization.}, }
@article {pmid41660426, year = {2026}, author = {Wang, S and Yang, Y and Lei, L and Wan, R and Su, Z and Liu, Y and Tang, H and Hu, G and Li, C and Li, C and Meng, J and Yang, K}, title = {SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1754671}, pmid = {41660426}, issn = {2235-2988}, mesh = {*Androgens/biosynthesis/metabolism ; *Databases, Genetic ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Transketolase/genetics/metabolism ; *Clostridium/genetics/enzymology/metabolism ; *Microbiota ; Prostatic Neoplasms ; }, abstract = {Androgens are critical for the growth of prostate cells, as well as prostate tumor cells. For prostate cancer patients under Androgen Deprivation Therapy (ADT) such as castration treatment, investigating the potential for androgen production by gut microbes is crucial. In microbe species, the side chain cleavage activity of steroid-17, 20-desmolase (SSTD) is responsible for 11-oxy-androgens production by biotransformation from cortisol, as well as from other endogenous steroids and pharmaceutical glucocorticoids. The side-chain cleavage product of prednisone could significantly promote the proliferation of prostate cancer cells. The SSTD is a complex formed by N-terminal and C-terminal transketolases encoded by desA and desB genes, whose activity has been well-characterized in Clostridium scindens ATCC 35704. While a void still existed in evaluating the androgen producing potential by gut microbiota owing to relatively low abundance of SSTD-carrying species and the lack of professional gene database. Meanwhile, mining SSTD encoding genes in explosion sequencing data has become computationally expensive and time-consuming using comprehensive database. Here, a professional database consisted of SSTD-coding genes, named SSTDhunter, was constructed using a large-scale genomic analysis along with homologous genes as background. These SSTD-coding genes were reconstruction through comprehensive characteristics consisted of operon structures, sequence identities, phylogenetic topologies and comparative analysis. To reduce false positives, protein sequences of homologous genes tktA, which encode component of sugar transketolase, were also included in SSTDhunter database as background noise. SSTDhunter is for rapid investigation of SSTD-coding genes in massive metagenomic data, which is freely available at http://www.orgene.net/SSTDhunter/.}, }
@article {pmid41660499, year = {2025}, author = {Hensley, MK and Sayed, K and Haidar, G and Wang, X and Benos, PV and Ito, S and Im, A and Geramita, E and Shlomchik, W and Methé, B and Cruz, CD and Morris, A and Kitsios, GD}, title = {Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications.}, journal = {CHEST pulmonary}, volume = {3}, number = {4}, pages = {}, pmid = {41660499}, issn = {2949-7892}, support = {K23 AI154546/AI/NIAID NIH HHS/United States ; R01 HL159805/HL/NHLBI NIH HHS/United States ; R01 HL176668/HL/NHLBI NIH HHS/United States ; R03 HL162655/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Diagnosing pulmonary complications (PCs) in hematologic malignancies remains challenging due to insensitive conventional microbiologic testing (CMT) and overlapping clinical manifestations of infectious and noninfectious pulmonary complications. For these reasons, empirical antimicrobials and immunosuppression (eg, corticosteroids) are used for prolonged periods.
RESEARCH QUESTION: How does metagenomic sequencing of the lower respiratory tract compare with conventional microbiologic testing among patients with hematologic malignancy?
STUDY DESIGN AND METHODS: Prospective proof-of-concept cohort study of 30 adult in-patients with hematologic malignancies and PCs who underwent bronchoscopy for suspected lower respiratory tract infection.
RESULTS: CMT identified a pathogen via culture- or polymerase chain reaction-based testing in 53% of patients. 16S sequencing demonstrated 66.7% positive and 42.9% negative concordance with CMT, while also identifying additional plausible respiratory pathogens in 59.3% of patients. Nanopore demonstrated 6.7% positive and 87.5% negative concordance with CMT and identified additional plausible respiratory pathogens in 42.3% of patients.
INTERPRETATION: Culture-independent sequencing approaches had modest agreement with CMT when considering bacterial PCs and showed poor detection of fungal pathogens. Sequencing frequently identified additional plausible respiratory pathogens, and further validation is needed to determine if such detection represents clinically missed infections or nonpathogenic colonization.}, }
@article {pmid41660616, year = {2025}, author = {Liu, H and Liang, L and Wang, C and Luo, R and Luo, Q and Huang, C}, title = {Gut mycobiota dysbiosis and an emergent state of "co-dysbiosis" are associated with IgE sensitization in children with comorbid allergic rhinitis and constipation.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1745580}, pmid = {41660616}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; Child ; *Rhinitis, Allergic/immunology/microbiology/epidemiology ; *Immunoglobulin E/immunology/blood ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; Child, Preschool ; *Constipation/immunology/microbiology/epidemiology ; Case-Control Studies ; *Fungi/immunology ; Comorbidity ; Pilot Projects ; *Mycobiome/immunology ; Metagenomics ; }, abstract = {BACKGROUND: The comorbidity of allergic rhinitis (AR) and functional constipation (FC), termed ARFC, implies shared gut-immune pathways. Although bacterial dysbiosis has been implicated, the role of the gut mycobiota (fungal community) in this specific comorbidity remains unexplored.
METHODS: This pilot case-control study characterized the gut mycobiota in 19 ARFC and 17 healthy control (HC) children aged 3-6 years using metagenomic sequencing. Fungal community structure, taxonomic composition, and correlations with IgE levels were analyzed. Cross-kingdom bacterial-fungal interaction networks were constructed, and functional potential was predicted.
RESULTS: Alpha diversity was comparable, whereas beta diversity revealed significant structural shifts in the ARFC gut mycobiota. Key immunomodulatory fungi, including Cenococcum, Dentiscutata, Ambispora, and Saccharomyces, were markedly depleted in ARFC. These taxa served as top discriminators in random forest models and exhibited significant inverse correlations with total and allergen-specific IgE levels. Cross-kingdom network analysis identified dramatic ecological restructuring: the HC network was characterized by prevalent competitive interactions, whereas the ARFC network shifted exclusively to positive correlations, a state termed "co-dysbiosis." No significant differences were observed in predicted KEGG functional pathways.
CONCLUSION: This study provides the first evidence that gut mycobiota dysbiosis-marked by depletion of immunoregulatory fungi and an ecological shift toward cooperative interkingdom interactions ("co-dysbiosis")-is associated with IgE sensitization in ARFC children. These findings position the gut mycobiota as a novel element of the gut-nose axis in allergic disease, warranting further investigation.}, }
@article {pmid41660808, year = {2026}, author = {Gangloff, V and Aldeguer-Riquelme, B and Yañez, MA and Potocki-Veronese, G and Severac, E and Antón, J and Soria, E and Santos, F}, title = {Microbial Biofilms Dynamics and Functionality in an Urban Mycobacterium-Dominated Drinking Water Distribution System.}, journal = {Environmental science & technology}, volume = {60}, number = {7}, pages = {5242-5258}, pmid = {41660808}, issn = {1520-5851}, mesh = {*Drinking Water/microbiology ; *Biofilms ; *Mycobacterium ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Supply ; }, abstract = {Microbial communities in drinking water distribution systems (DWDS) develop primarily as biofilms on pipe surfaces. Despite their impact on water quality, infrastructure maintenance, and biosafety, biofilms are not routinely controlled. In this study, we investigated the bacterial community dynamics and functionality in an urban chlorinated DWDS, dominated by Mycobacterium, through a multiphasic approach which included 16S rRNA gene metabarcoding, metagenomics and microscopy. Our results showed that biofilm communities were more functionally diverse compared to those from water and that the biofilm maturity was positively correlated with the prevalence of potential Mycobacterium emerging pathogens and a broader distribution of antibiotic resistance genes (ARGs) within the microbial community. The reconstruction of metagenome-assembled genomes (MAGs) and the corresponding genomospecies allowed the identification of key microbial taxa involved in the biofilm matrix remodeling, with 22% of them strongly responsible for biofilm formation. A diverse and novel viral community was detected across the system, including new putative Mycobacterium phages that might act against mycolic acids and thus contribute to biofilm destabilization. Our findings enhance our understanding of DWDS microbial composition and biofilm formation dynamics, focusing on "who does what" and then providing a foundation for developing effective biofilm control strategies in water distribution systems.}, }
@article {pmid41660847, year = {2026}, author = {Lu, X and Kong, N and Wang, C and Lu, J and Li, W and Yang, H and Lu, X and Zhang, Z and Chen, Y and Huang, S and Zhou, C and Zhang, Y and Zhang, W and Shan, T}, title = {A novel parvovirus circulating in canine populations and sporadically detected in human oropharyngeal samples.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0332725}, pmid = {41660847}, issn = {2165-0497}, mesh = {Animals ; Dogs ; *Parvoviridae Infections/virology/veterinary ; Phylogeny ; Humans ; *Oropharynx/virology ; Genome, Viral ; *Parvovirus, Canine/genetics/isolation & purification/classification ; *Dog Diseases/virology ; Capsid Proteins/genetics ; *Parvovirus/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Most human pathogens, while originating from animals, have crossed species barriers to infect humans, often leading to outbreaks of new infectious diseases. Despite significant efforts, the mechanisms, timing, and locations of these emerging diseases remain largely uncertain. Here, using a viral metagenomic approach, we discovered a novel canine-associated parvovirus in human oropharyngeal secretions. Molecular screening revealed the presence of this parvovirus in different canine tissues, including 24 of 108 pharyngeal lymph node samples. Further molecular investigation showed that the virus was detected in the oropharyngeal secretions of pet dogs and in human samples that were not linked to these animals. This parvovirus was therefore named human-canine associated parvovirus 1 (HCAPV-1). Nine complete genomes of HCAPV-1 were acquired through next-generation sequencing, combining Sanger sequencing. Genomic and phylogenetic analyses indicate that these nine strains of HCAPV-1 belong to the genus Protoparvovirus and form a distinct clade, with their closest relatives being newlaviruses from foxes. Amino acid substitutions have been characterized in the capsid proteins of the variants of HCAPV-1, which potentially alter their infection patterns. Potential genomic recombination was also observed in HCAPV-1. Taken together, our findings reveal the presence of a novel parvovirus in both canine and human samples, highlighting the need to investigate its host range and transmission dynamics.IMPORTANCEThis study identified a novel parvovirus, human-canine associated parvovirus 1 (HCAPV-1), which was detected in human oropharyngeal secretions and various canine tissues, suggesting that its host range may extend beyond a single species. Phylogenetic analysis revealed that HCAPV-1 forms a distinct clade within the genus Protoparvovirus, closely related to newlaviruses from foxes. Amino acid substitutions observed in the capsid proteins of HCAPV-1 variants indicate genetic divergence, warranting further investigation into their potential implications for host interactions. Recombination events may have contributed to its emergence. This finding highlights the importance of continued surveillance in settings where humans and companion animals coexist and underscores the need for further research to clarify the ecological and host-range characteristics of such viruses.}, }
@article {pmid41661278, year = {2026}, author = {Zhang, H and Zhai, C and Hu, H and Qian, G and Mao, M}, title = {A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.}, journal = {Acta diabetologica}, volume = {}, number = {}, pages = {}, pmid = {41661278}, issn = {1432-5233}, support = {XFCX-DMYH//Jiaxing Institute of Arteriosclerotic Disease/ ; }, abstract = {OBJECTIVE: This study aimed to investigate gut microbiota composition and metabolic functions in patients with type 2 diabetes mellitus (DM) complicated by myocardial infarction (MI) and to explore potential mechanisms linking the gut microbiome to MI development.
METHODS: Sixty patients with DM complicated by MI and 52 patients with DM alone were initially recruited. After quality control, 29 DM + MI patients and 33 DM patients were included in the final analysis. Gut microbial profiles were characterized using shotgun metagenomic sequencing and bioinformatics analyses. Microbial diversity, composition, and gene functions were compared between groups based on KEGG, COG, and CAZy annotations.
RESULTS: Overall microbial diversity and metabolic profiles were comparable between the two groups; however, significant differences were observed in specific taxa and functional genes. Taxa enriched in the DM + MI group included Bacteroidales, Prevotellaceae, and Lachnospiraceae. In total, 510 KEGG orthology (KO) units and 21 pathways-including ABC transporters, quorum sensing, and general metabolic pathways-differed significantly between groups. Carbohydrate transport and metabolism, as well as glycoside hydrolase activity, represented the most enriched functional categories. Random forest models based on selected microbial species, KO units, and KEGG pathways achieved areas under the curve (AUCs) of 0.868, 0.885, and 0.820, respectively.
CONCLUSION: Patients with DM complicated by MI exhibit distinct gut microbial compositions and functional gene signatures compared with patients with DM alone. These microbiome-based markers may contribute to early risk stratification and provide potential targets for microbiota-focused interventions to mitigate MI risk in patients with diabetes.}, }
@article {pmid41661439, year = {2026}, author = {Moon, SH and Lee, TG and Ko, YS and Yoo, DS and Oh, Y and Cho, HS}, title = {First detection and genomic characterization of ungulate tetraparvovirus 1 in water buffalo (Bubalus bubalis) from vietnam.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, pmid = {41661439}, issn = {1572-994X}, support = {RS-2024-00400152//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)/ ; }, abstract = {Ungulate tetraparvovirus 1 (UTPV1), or bovine hokovirus, has been described in cattle but remains poorly characterized in Southeast Asia. In this study, we report the first detection and genomic characterization of UTPV1 in water buffalo (Bubalus bubalis) from Vietnam. Skin swab samples were collected from a buffalo with nodular lesions in northern Vietnam in 2024, and total nucleic acids were subjected to metagenomic sequencing. Analysis of Illumina MiSeq reads revealed the presence of both lumpy skin disease virus (LSDV) and UTPV1. The near-complete UTPV1 genome (NIVR-B12-2024) shared 90.7-93.3% nucleotide identity with reference strains but did not cluster with genotypes I or II, instead forming a distinct lineage. Phylogenetic analyses supported its independent position, and recombination detection indicated potential genetic exchange between Asian and South American strains. Several amino acid substitutions were identified in the NS1 protein, suggesting ongoing viral diversification. This study provides the first molecular evidence of UTPV1 in water buffalo and in Vietnam, expanding the recognized host range and geographic distribution of this virus. The findings highlight the value of non-invasive sampling and metagenomic sequencing for livestock surveillance and underscore the need for continued monitoring to evaluate the epidemiological significance and potential health risks of UTPV1 in Southeast Asia.}, }
@article {pmid41662353, year = {2026}, author = {Wang, Y and Liang, V and Yin, N and Liu, S and Segal, E}, title = {SGAC: a graph neural network framework for imbalanced and structure-aware AMP classification.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41662353}, issn = {1477-4054}, mesh = {*Neural Networks, Computer ; *Antimicrobial Peptides/chemistry/classification ; Algorithms ; *Computational Biology/methods ; Graph Neural Networks ; }, abstract = {Classifying antimicrobial peptides (AMPs) from the vast collection of peptides derived from metagenomic sequencing offers a promising avenue for combating antibiotic resistance. However, most existing AMP classification methods rely primarily on sequence-based representations and fail to capture the spatial structural information critical for accurate identification. Although recent graph-based approaches attempt to incorporate structural information, they typically construct residue- or atom-level graphs that introduce redundant atomic details and increase structural complexity. Furthermore, the class imbalance between the small number of known AMPs and the abundant non-AMPs significantly hinders predictive performance. To address these challenges, we employ lightweight OmegaFold to predict the 3D structures of peptides and construct peptide graphs using C$_\alpha $ atoms to capture their backbone geometry and spatial topology. Building on this representation, we propose the spatial graph neural network (GNN)-based AMP classifier (SGAC), a novel framework that leverages GNNs to extract structural features and generate discriminative graph representations. To handle class imbalance, SGAC incorporates weight-enhanced contrastive learning to cluster structurally similar peptides and separate dissimilar ones through adaptive weighting, and applies weight-enhanced pseudo-label distillation to generate high-confidence pseudo labels for unlabeled samples, achieving balanced and consistent representation learning. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly achieves state-of-the-art performance compared to baselines. The complete code and dataset are available at: https://github.com/wyxwyx46941930/SGAC.}, }
@article {pmid41662415, year = {2026}, author = {Zhang, J and Fan, J and Li, D and Yang, C and Cheng, Z and Cheng, Z and Qu, H and Li, G and Yuan, N and Song, T and Zhou, K and Zhao, Y and Wang, X}, title = {Antibiotic resistance in East Asia: current status, risks, and response strategies.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {1}, pages = {43-51}, doi = {10.3855/jidc.21637}, pmid = {41662415}, issn = {1972-2680}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; China/epidemiology ; Japan/epidemiology ; Metagenomics ; Asia, Eastern/epidemiology ; *Bacteria/drug effects/genetics ; }, abstract = {INTRODUCTION: This study investigates the current status and regional disparities of resistance to novel antibiotics in East Asia, exploring links to socioeconomic factors and identifying high-risk resistance determinants.
METHODOLOGY: Metagenomic sequencing was performed on 1024 human fecal samples (25 local, 999 public) from 12 regions across China and Japan. Antibiotic resistance genes (ARGs) were identified by aligning sequences against a comprehensive antibiotic resistance database, focusing on 8 novel antibiotic classes. The relationship between regional per capita GDP and resistance rates for clinically relevant novel antibiotics was statistically analyzed.
RESULTS: Significant regional variation in resistance rates was observed for clinically used novel antibiotics (aminocoumarins, glycylcyclines, oxacephems, oxazolidinones, pleuromutilins). A significant inverse correlation was found between per capita GDP and resistance rates for aminocoumarins, glycylcyclines, and oxacephems, particularly pronounced within inland regions. Oxacephem resistance was alarmingly high (> 55% in all regions, > 90% in some). Oxazolidinone resistance remained low (< 28%). Pleuromutilin resistance showed a strong negative GDP correlation only inland. Analysis revealed 24 high-frequency ARGs (5 exceeding 45% coverage: CfxA, IsaB, MexB, abeS, IsaE). Minimal shared resistance determinants existed among novel antibiotic classes, except between oxazolidinones and pleuromutilins.
CONCLUSIONS: Resistance to novel antibiotics in East Asia exhibits significant regional heterogeneity, strongly influenced by local economic development levels. Resistance rates for specific agents (e.g., oxacephems) critically limit their clinical utility, necessitating mandatory susceptibility testing. High-frequency ARGs linked to traditional antibiotic misuse pose cross-resistance risks. Surveillance and stewardship strategies must be regionally tailored, prioritizing vulnerable areas and tracking critical resistance loci for novel agents.}, }
@article {pmid41663920, year = {2026}, author = {Qian, Y and Shi, C and Wang, Y and Han, Q and Yu, Q and Li, M and Li, H}, title = {Metagenomic sequencing and binning reveal carbon cycling microorganisms and gene functions in park environments.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663920}, issn = {1471-2180}, support = {32471575//National Natural Science Foundation of China/ ; 24JRRA458//Gansu Province Science and Technology Plan for Youth Science Fund/ ; lzuyxcx-2022-172//Medical Innovation and Development Project of Lanzhou University/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Carbon Cycle/genetics ; *Parks, Recreational ; Carbon/metabolism ; Metagenome ; Water Microbiology ; Soil/chemistry ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {In the midst of increasing global warming and accelerated urbanization, urban parks, serving as significant carbon sinks, are increasingly recognized for their role in mitigating the urban heat island effect. However, limited research investigating the urban park carbon cycle hinders our full understanding and effective use of their carbon sink potential. This study employed metagenomics sequencing and 16S rRNA gene sequencing to characterize the carbon cycle and its influencing factors within soil and water from collected from nine city parks. Notably, the abundance and alpha diversity of carbon cycle microbes and genes were higher in soil compared to water. Specifically, soil samples exhibited enrichment of carbon cycling genes involved primarily in polysaccharide metabolism, particularly those associated with starch and cellulose metabolism. Conversely, water samples, revealed a greater prevalence of genes associated with chitin metabolism. The most important factor affecting soil carbon cycling genes was bacterial community, followed by non-nutritional factors and nutrient factors, while heavy metals demonstrated no effect on soil carbon cycling genes. The most important factor affecting water carbon cycling genes was only bacterial community. The analysis yielded 381 high-quality metagenomic assembled genomes (MAGs) containing carbon cycling genes, with significant covariation observed between the pta and carbon cycling genes ackA and acyP, which encode cellulose degradation functions. These findings contribute to a better understanding of microbial carbon metabolism within urban parks and offer a foundation for effective carbon emission management strategies.}, }
@article {pmid41663943, year = {2026}, author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W}, title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663943}, issn = {1471-2180}, support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; }, abstract = {BACKGROUND: Drought critically compromises agricultural productivity and threatens sustainable wheat production. Streptomyces pactum Act12 confers benefits to plant growth under drought stress, but its possible effects on root-associated microbiomes remain understudied. Here, shotgun metagenome sequencing and culture-dependent approaches were integrated to investigate the responses of rhizosphere and rhizoplane microbiomes in dryland winter wheat to exogenous S. pactum Act12 and their potential linkage to plant drought resistance.
RESULTS: Seed biopriming with S. pactum Act12 increased plant aboveground dry weight at flowering (by 63.2%) and maturation (by 41.9%) stages, leading to improved grain yield (by 8.7%). Microbial inoculation reduced malondialdehyde contents in wheat leaves and roots at the flowering stage alongside compartment-specific alterations in soil microbiomes. Metagenomic analysis revealed inoculation-induced enrichment of distinct taxa in rhizosphere soils (flowering: Fibrobacterota, Altererythrobacter; maturation: Mucoromycota, Rhodospirillum) and rhizoplane soils (flowering: Pseudomonadota, Serratia; maturation: Candidatus_Pacebacteria, Variovorax). Functional profiling showed up-regulation of key pathways related to oxidative phosphorylation in inoculated rhizosphere soils at the flowering stage. In rhizoplane soils, ABC transporters and pyrimidine metabolism were up-regulated across stages upon inoculation. Two key strains isolated from rhizoplane soils, designated Glycomyces lechevalierae A4 and Microbacterium algeriense B3, demonstrated the ability to enhance drought resistance in wheat seedlings.
CONCLUSIONS: Inoculation of S. pactum Act12 heightens drought resistance in dryland winter wheat through compartment-specific phylogenetic restructuring and functional reprogramming of root-associated microbiomes.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04812-3.}, }
@article {pmid41664657, year = {2026}, author = {Chuckran, PF and Blazewicz, SJ and Ceja-Navarro, JA and Pett-Ridge, J and Schwartz, E and Dijkstra, P}, title = {The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20641}, pmid = {41664657}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Transcription, Genetic ; *Microbiota/genetics ; Glucose/metabolism ; Codon Usage ; Carbon/metabolism ; }, abstract = {Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa-highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress-such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.}, }
@article {pmid41664846, year = {2026}, author = {Stolf, CS and Paz, HES and Paraluppi, MC and Miguel, MMV and Santamaria, MP and Monteiro, MF and Amgarten, DE and Franco, RRA and Branco-de-Almeida, LS and Shaddox, LM and Casarin, RCV}, title = {Molar-Incisor and Generalized Grade C Periodontitis: Distinct Microbiome-Immune Interactions Suggest Divergent Pathogenesis.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70077}, pmid = {41664846}, issn = {1600-0765}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2021/14430-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; R01DE019456/DE/NIDCR NIH HHS/United States ; }, abstract = {AIM: Molar-Incisor (PerioC-MIP) and Generalized (PerioC-G) Grade C Periodontitis could have distinctive etiopathogenesis behind their unique clinical patterns. Thus, this study aimed to distinguish these two phenotypes by analyzing the subgingival metagenomic profile and the inflammatory markers levels.
METHODS: In this cross-sectional comparative study, Gingival Crevicular Fluid (GCF) and Subgingival Biofilm (SB) were collected from 18 PerioC-MIP North Americans and 14 periodontally healthy controls (HC) from the same location (HC-MIP) and 20 PerioC-G Brazilians and 20 controls (HC-G). From GCF, immunoenzymatic analysis was performed. SB functional and taxonomic bacterial content was determined using shotgun metagenomics sequencing.
RESULTS: Taxonomic results showed significantly different alpha- and beta-diversity profiles between disease groups (p < 0.05). Aggregatibacter actinomycetemcomitans and Streptococcus sanguinis were associated with PerioC-MIP; levels of Tannerella forsythia, Filifactor alocis, Porphyromonas gingivalis, Fretibacterium fastidiosum, and Treponema denticola were significantly enriched at PerioC-G (p < 0.05). PerioC-G had the function for flagellar assembly enriched, while PerioC-MIP SB was associated with biofilm formation of Escherichia coli. Different GCF inflammatory marker levels for each pattern resulted in PerioC-G presenting higher levels of IL-1β, IL-6, and IL-10 than PerioC-MIP (p < 0.05).
CONCLUSION: PerioC-G and PerioC-MIP presented different taxonomical profiles and GCF cytokine levels, raising the hypothesis that they may represent two different stages/susceptibility patterns of Periodontitis Grade C.}, }
@article {pmid41664936, year = {2026}, author = {Shaikh-Ibrahim, A and De Lise, F and Curci, N and Gargano, M and Sacco, O and Di Fenza, M and Moracci, M and Cobucci-Ponzano, B}, title = {A Hyperthermostable Archaeal GH78 Rhamnosidase Efficiently Hydrolyzes Flavonoid Glycosides for Juice Debittering.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {6}, pages = {5562-5574}, pmid = {41664936}, issn = {1520-5118}, mesh = {*Glycoside Hydrolases/chemistry/genetics/metabolism ; *Flavonoids/chemistry/metabolism ; *Glycosides/chemistry/metabolism ; Enzyme Stability ; *Fruit and Vegetable Juices/analysis ; Hydrolysis ; *Archaeal Proteins/chemistry/genetics/metabolism ; *Archaea/enzymology/genetics/chemistry ; Hot Temperature ; Hydrogen-Ion Concentration ; Substrate Specificity ; Hot Springs/microbiology ; }, abstract = {α-L-Rhamnosidases are a class of glycosyl hydrolases (GHs) that catalyze the hydrolysis of terminal α-L-rhamnose residues from diverse glycoconjugates. While extensively characterized in bacterial and fungal sources, no archaeal α-L-rhamnosidases have been characterized to date. Herein, we report the identification and characterization of the first thermostable archaeal α-L-rhamnosidase (ArRha), derived from the metagenomic data set of Pisciarelli solfatara hot spring. ArRha, classified in glycoside hydrolase family GH78, efficiently hydrolyzes α-1,2 and α-1,6 rhamnosyl linkages in flavonoid glycosides with notable biological activities. The novel enzyme showed remarkable temperature stability, wide-range pH activity, organic solvent tolerance, and no metal dependence. Combined with a thermostable β-glucosidase, ArRha converts naringin to prunin and naringenin in sweet and blood orange juices, achieving >95% conversion within 2 h at 65 °C. This represents the first report of a hyperthermostable archaeal GH78 α-L-rhamnosidase with promising applications in industrial enzymatic juice debittering and sustainable flavonoid biotransformation.}, }
@article {pmid41665259, year = {2025}, author = {Gaisin, VA and Hadjicharalambous, C and Mujakić, I and Villena-Alemany, C and Li, J and Koblížek, M and Pilhofer, M}, title = {Thermophilic bacteria employ a contractile injection system in hot spring microbial mats.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41665259}, issn = {1751-7370}, support = {CZ.02.01.01/00/22_008/0004624//OP JAK project Photomachines/ ; CoG 101000232/ERC_/European Research Council/International ; }, mesh = {*Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; *Chloroflexi/genetics/physiology/classification/metabolism ; Cryoelectron Microscopy ; Phylogeny ; Metagenomics ; *Bacteria/genetics ; Computational Biology ; Proteomics ; }, abstract = {Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S rRNA gene amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural hot spring microbial mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.}, }
@article {pmid41665263, year = {2025}, author = {Hutchinson, TF and Holland, SR and Clarke, DA and Ricci, F and Jirapanjawat, T and Leung, PM and Lappan, R and Liu, WPA and Bay, SK and Bliss, A and McGeoch, MA and Chown, SL and Greening, C}, title = {Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41665263}, issn = {1751-7370}, support = {DE230100542//Australian Research Council Discovery Early Career Awards/ ; DE250101210//Australian Research Council Discovery Early Career Awards/ ; FT240100502//Australian Research Council Future Fellowship/ ; SR200100005//ARC SRIEAS Grant Securing Antarctica's Environmental Future/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Hydrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; Temperature ; *Carbon Monoxide/metabolism ; Oxidation-Reduction ; Methane/metabolism ; Soil/chemistry ; Metagenomics ; }, abstract = {Polar desert soils host diverse microbial communities despite limited nutrients and frequent temperature and light fluctuations. Adapting to these extremes, most bacteria possess high-affinity hydrogenases and carbon monoxide dehydrogenases, enabling them to use atmospheric trace gases such as hydrogen (H2) and carbon monoxide (CO) to generate energy and fix carbon (aerotrophy). Despite the foundational importance of this process in polar desert ecosystems, little is known about the thermal sensitivity of trace gas oxidation or how this process will respond to climate warming. Here, we show through in situ and ex situ incubations that H2 consumption is an exceptionally thermally resilient process that can occur from -20 to 75°C, at rates comparable to temperate ecosystems (peaking at 8.56 nmol H2 h-1 g dry soil-1 at 25°C). Temperature ranges of CO (-20 to 42°C) and methane (CH4; -20 to 30°C) oxidation are also wider than expected, though thermal sensitivity patterns conform with general theory. Metagenomic analyses, including generation of 554 medium- to high-quality metagenome-assembled genomes, support these data, revealing that aerotrophs are widespread, diverse, and abundant, and suggesting most Antarctic bacteria function below their temperature optima for these processes. Modelling of seasonal temperatures across ice-free Antarctica under current and future emissions scenarios indicates that H2 and CO oxidation can occur year-round, increasing by up to 35% or 44%, respectively, by 2100. Our results indicate constitutive aerotrophic activity contributing to Antarctic ecosystem functioning and biodiversity across spatial and temporal scales, with further studies required to understand how it interacts with photosynthesis in a changing climate.}, }
@article {pmid41665524, year = {2026}, author = {Gao, W and Li, X and Wang, G and Ning, Z and Wang, W and Wang, Y and Wang, H and Lu, D and Zhang, Q}, title = {A Broad-Spectrum Polysaccharide Lyase CHa2 from Marine Metagenome Exhibits Dual Activities toward Glycosaminoglycans and Alginate.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {7}, pages = {6386-6397}, doi = {10.1021/acs.jafc.5c15335}, pmid = {41665524}, issn = {1520-5118}, mesh = {*Polysaccharide-Lyases/chemistry/genetics/metabolism ; *Glycosaminoglycans/metabolism/chemistry ; *Alginates/metabolism/chemistry ; *Bacterial Proteins/chemistry/genetics/metabolism ; Substrate Specificity ; Metagenome ; *Aquatic Organisms/enzymology/genetics ; Kinetics ; Enzyme Stability ; }, abstract = {Polysaccharide lyase family 8 (PL8), which comprises glycosaminoglycans (GAGs) lyases, xanthan lyases, and alginate lyases, is an important family of Carbohydrate-Active Enzymes database. In this study, a PL8 family enzyme, CHa2, which can degrade GAGs and alginate, was identified. CHa2 exhibits the highest activity at 40/50 °C and pH 8.0, and the enzyme activities toward HA, CSA, CSC, CSD, CSE, alginate, polyM, and polyG are 54.6, 161.1, 204.0, 163.6, 66.1, 4.0, 4.1, and 0.3 U/mg, respectively. CHa2 degrades CS and HA to generate disaccharides and tetrasaccharides as the final products in the endolytic mode. And when degrading alginate, CHa2 prefers to catalyze the M-rich regions. Though they showed higher activity toward CS, the tetrasaccharides like ΔC-A, ΔA-A, and ΔD-A would resist the degradation of CHa2. The study of CHa2 provides a tool enzyme capable of selectively preparing specific structural functional oligosaccharides, which has potential application value in functional food, biomedical, and other fields.}, }
@article {pmid41666027, year = {2026}, author = {Lim, FS and González-Cabrera, J and Jehle, JA and Lefebvre, T and Wennmann, JT}, title = {No longer uncertain: the validation of tenebrionid insects as hosts of Blattambidensovirus incertum1 isolates by phylogeny and infection studies.}, journal = {The Journal of general virology}, volume = {107}, number = {2}, pages = {}, pmid = {41666027}, issn = {1465-2099}, mesh = {Animals ; *Tenebrio/virology/growth & development ; Phylogeny ; Larva/virology ; *Densovirus/genetics/isolation & purification/classification ; Genome, Viral ; Pupa/virology ; }, abstract = {The mealworm (Tenebrio molitor) is one of the most commonly mass-reared insects for food and feed. Monitoring the health status of commercially reared mealworm populations is of great importance for the early detection of entomopathogens and for preventing pathogen outbreaks. Metagenomic screening is a suitable and commonly used method for detecting entomopathogens. The approach used here previously enabled the discovery of the Tenebrio molitor densovirus (TmDV) (family Parvoviridae, subfamily Densovirinae) in symptomatic larvae. In the present study, the search for TmDV was extended to larvae, pupae and adults of T. molitor, including 19 symptomatic and asymptomatic samples obtained from a commercial mealworm mass-rearing facility. The presence of TmDV in all life stages of T. molitor was demonstrated, and its relative abundance was quantified using Nanopore sequencing. The infectivity of TmDV to T. molitor was demonstrated by isolating viral particles from sample LD2 and feeding them to mealworms. The experiment confirmed T. molitor as a susceptible host but showed a rather asymptomatic course of the infection with little effect on larval growth during 56 days of observation. It is hypothesized that this largely covert infection may explain the lack of reports of TmDV in mealworms or other insects, despite its detection in metagenomics surveillance studies of various insectivorous vertebrates. The complete genomes of 15 different TmDV genotypes present in various ratios in the different life stages of T. molitor could be reconstructed. Including these genotype sequences in phylogenetic analyses allowed us to re-evaluate the relationship and diversity of previously reported TmDV and related isolates, all belonging to the species Blattambidensovirus incertum1. Our findings suggest that T. molitor and possibly other insects are susceptible hosts of viruses of Blattambidensovirus incertum1, while its occasional detection in metagenomic datasets of insectivorous vertebrates may not represent true densovirus host associations.}, }
@article {pmid41666549, year = {2026}, author = {Kang, X and Zhao, Z and Zhu, X and Ju, F}, title = {Uncovering plasticizer-degrading potential in landfill microbiomes with curated PzDE-HMM database and multi-scale validation from isolates to synthetic consortia.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141398}, doi = {10.1016/j.jhazmat.2026.141398}, pmid = {41666549}, issn = {1873-3336}, mesh = {*Plasticizers/metabolism ; *Microbiota ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/genetics/metabolism ; Phthalic Acids/metabolism ; }, abstract = {Plasticizers are widely used additives that leach from plastic products and accumulate in landfills, yet the microbial functions supporting their degradation remain poorly resolved. Here, we combined curated functional annotation, substrate-driven enrichment, and isolate-level validation to dissect plasticizer degradation in landfill microbiomes. A plasticizer-degrading enzyme (PzDE) hidden Markov model database (PzDE-HMM) was assembled from 49 experimentally validated enzyme families. It was applied to metagenomes from five landfill niches, identifying 2219 candidate plasticizer-degrading genes, which is 3.6- and 19-fold more than those identified by KofamScan- and BLASTp-based annotation methods, respectively. Enrichment with three legacy phthalates (DEHP, DIDP, DBP) and three non-phthalate plasticizers (DOTP, DOA, ATBC) drove pronounced shifts in landfill microbial communities and functional gene repertoires, revealing coexisting broad-spectrum and substrate-specific degraders. Culture-based isolation from enriched media yielded 51 strains, and three representative isolates showed concordance between PzDE-HMM-predicted gene repertoires, substrate breadth, and degradation ability. Synthetic consortia assembled from these strains exhibited complementary degradation capacities and achieved higher removal of several plasticizers than the best single strains, illustrating how complementary gene sets can be combined to enhance multi-substrate degradation. Together, PzDE-HMM annotation workflow and this multilevel prediction-enrichment-isolate-consortium framework uncover the plasticizer-degrading and bioremediation potential of landfill microbiomes and provide a reusable resource and workflow for future plasticizer-focused microbiome studies.}, }
@article {pmid41666551, year = {2026}, author = {Cai, Y and Zhai, JY and Zhang, GH and Lin, MQ and Luo, YH}, title = {Biodegradation of three xanthates with different carbon chains in flotation wastewater.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141392}, doi = {10.1016/j.jhazmat.2026.141392}, pmid = {41666551}, issn = {1873-3336}, mesh = {*Wastewater/chemistry/microbiology ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/chemistry ; Bioreactors ; Bacteria/metabolism/genetics ; Carbon/chemistry ; Waste Disposal, Fluid/methods ; }, abstract = {Xanthates are widely used collectors in sulfide ore flotation, but pose ecological risks due to their toxicity and the releasing of carbon disulfide (CS2). This study systematically investigated the biodegradation of three representative xanthates-potassium amyl xanthate (PAX), potassium butyl xanthate (PBX), and potassium isopropyl xanthate (PIX)-in an oxygen-based membrane biofilm reactor (O2-MBfR). The O2-MBfR achieved over 98 % removal of all xanthates across surface loadings up to 6000 mg-COD/m[2]·d, with corresponding COD removals of 62-90 %. While PIX exhibited slightly lower COD removal due to the slower oxidation of its branched isopropyl group, functional gene analyses revealed the co-enrichment of alcohol and sulfur oxidation genes (adh, ALDH, soxABC/XYZ, fccAB) and C-S bond cleavage genes (cynT, ssuD). Metagenomic and metatranscriptomic results showed that Pseudomonas and Rhodanobacter predominated in PIX degradation, whereas Thiobacillus, Zoogloea, and Ottowia were mainly involved in PAX and PBX oxidation. Monod kinetics indicated that PIX had the highest maximum specific degradation rate (33.85 mg/gVSS/h) and lowest sCOD decay rate constant (0.29 h[-1]), reflecting strong microbial affinity but limited mineralization. Continuous-flow treatment of real flotation wastewater achieved > 98 % xanthate and ∼85 % COD removal, confirming system robustness. These findings provide mechanistic insight into the structure-dependent biodegradability of xanthates and demonstrate the feasibility of O2-MBfR technology for sustainable treatment of flotation wastewater.}, }
@article {pmid41666717, year = {2026}, author = {Zhang, B and Qian, G and Xie, C and Qiao, S}, title = {Microbial quorum quenching mitigates biofouling from polyvinyl chloride pipes in industrial circulating water systems.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128870}, doi = {10.1016/j.jenvman.2026.128870}, pmid = {41666717}, issn = {1095-8630}, mesh = {*Quorum Sensing/drug effects ; *Biofouling/prevention & control ; Biofilms ; }, abstract = {To destabilize biofouling resulting from extracellular polymeric substances (EPS) in industrial circulating water systems, this study introduces a quorum sensing (QS)-based inhibition strategy using methyl anthranilate (MA) to disrupt biofouling structure. Strategical application of a low dose of MA at 1 mM reduced EPS content by 48.0 ± 5.2% and decreased biofouling thickness by 25.7 ± 5.0% (from 68.6 ± 2.8 to 51.0 ± 4.0 μm) compared to the control group. Further analysis indicated that MA altered secondary structure of EPS proteins, resulting in hydrogen bonds breakage and structural unfolding, thereby compromising biofouling stability and integrity. Metagenomic profiling revealed a significant downregulation of EPS-biosynthesis pathways (amino acid and carbohydrate metabolism) and QS-and EPS-related genes (trpE and nagB) following MA exposure. Microbial diversity analysis showed a substantial reduction in the abundance of key genera (e.g., Candidatus Kuenenia, Mycobacterium, Ideonella) harboring EPS- and QS-associated genes in response to MA treatment. Moreover, co-occurrence network analysis demonstrated that MA exposure triggered the loss of keystone taxa, leading to systematic destabilization of the biofouling layer. These findings underscore the potential and utility of MA-based QS inhibition as an effective and targeted approach for biofouling control in circulating water pipelines, which could inform important clues for anti-biofouling development in engineered water systems.}, }
@article {pmid41666722, year = {2026}, author = {Mo, J and Guo, Z and Shao, M and Hu, Z and Liu, F and Guan, X}, title = {Nitrogen pollution alters bacterial carbonate mineralization potential in karst river.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128942}, doi = {10.1016/j.jenvman.2026.128942}, pmid = {41666722}, issn = {1095-8630}, mesh = {*Nitrogen ; *Rivers/chemistry/microbiology ; *Carbonates/metabolism ; Bacteria/metabolism ; }, abstract = {Karst systems represent critical carbon sinks where microbial-mediated carbonate precipitation is influenced by anthropogenic nitrogen pollution. This study investigated nitrogen pollution impacts on microbial mineralization in karst rivers using physicochemical and metagenomic analyses. Proteobacteria and Actinobacteria dominated carbonic anhydrase-producing bacterial communities, with β-carbonic anhydrases being most abundant (84.51%). Nitrogen pollution significantly reduced the diversity and relative abundance of these bacteria and drove variations in their community structure. This further triggered a cascade of changes in carbonic anhydrase activity, bicarbonate concentration, and total alkalinity. Co-occurrence network analysis showed that increased nitrogen pollution weakened interactions between carbonic anhydrase-producing and other non-producing bacteria. Functional analysis revealed that nitrogen pollution significantly impaired the potentials of alkalinity engine metabolism (particularly the Calvin-Benson-Bassham cycle and fatty acid catabolism), extracellular polysaccharides biosynthesis, and Mycobacterium cell wall formation. Furthermore, carbonate mineralization degenerates markedly beyond a critical threshold of ∼22 mg/L total inorganic nitrogen. These findings provide guidance for water resource management and establish a foundation for future carbon budget assessments in karst systems under anthropogenic influence.}, }
@article {pmid41666743, year = {2026}, author = {Tong, J and Zhang, W and Yu, F and Liu, R and Yan, Y and Li, Y}, title = {Flow regime specific regulation shapes microbial-mediated nitrogen cycling of plain tidal river network.}, journal = {Water research}, volume = {294}, number = {}, pages = {125510}, doi = {10.1016/j.watres.2026.125510}, pmid = {41666743}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Nitrogen Cycle ; Ecosystem ; Hydrodynamics ; }, abstract = {Inter-basin water diversion projects are critical for mitigating regional water scarcity yet impose complex ecological pressures on recipient river networks. Understanding their microbial impacts is essential to optimize sluice operations and minimize ecosystem disruption. As pivotal regulators of biogeochemical cycles and ecological health, microbial communities in plain tidal networks remain poorly characterized under diversion-induced hydrodynamic shifts. This study integrated intensive field sampling across water and sediment sites in the lower tidal plain river network with a calibrated one-dimensional MIKE 11 hydrodynamic model, stratifying sampling points into low, medium, and high flow-velocity regimes. Results indicate a positive correlation between hydrological regime stability and microbial community stability. While community composition reorganizes along the flow gradient, microbial diversity and core taxa abundance remain resilient. Co-occurrence network analysis reveals that intermediate flow variability maximizes network connectivity and modular cohesion, whereas extreme hydrological conditions fragment network structures. Landscape modeling further identifies high-discharge variability zones as distinct "hotspots" for denitrification and organic matter processing, while hydrologically stable reaches act as "functional shadows" (coldspots). Structural equation modeling confirms that hydrological regulation operates not merely through direct physical forcing but via a "resource-diversity-function" cascade, indirectly driving biogeochemical cycles by modulating nutrient fluxes and reshaping microbial diversity. Consequently, this study recommends shifting management strategies toward maintaining intermediate flow variability to reinforce the robustness and self-purification capacity of riverine ecological networks.}, }
@article {pmid41666744, year = {2026}, author = {Kelly, LT and Beach, DG and Blaszczak, JR and Bouma-Gregson, K and Brown, SM and Cheng, H and Davidson, JL and Fastner, J and Francis, M and Jimenez, AG and Genzoli, L and Goel, R and Gonzalez, D and Handley, KM and Hilt, S and Humbert, JF and Jamieson, R and Johnston, L and Junier, P and Lawrence, J and McCarron, P and Meissner, S and Mormando, J and Puddick, J and Quiblier, C and Rajpirathap, N and Schampera, C and Selwood, A and Shearer, K and Sohrab, A and Stancheva, R and Valadez-Cano, C and Zabrecky, JM and Wood, SA}, title = {The global proliferation of aquatic, benthic Microcoleus: Taxonomy, distribution, toxin production, ecology, and future directions.}, journal = {Water research}, volume = {294}, number = {}, pages = {125441}, doi = {10.1016/j.watres.2026.125441}, pmid = {41666744}, issn = {1879-2448}, mesh = {Ecosystem ; *Cyanobacteria/classification/metabolism ; Fresh Water/microbiology ; Rivers/microbiology ; }, abstract = {There have been sporadic reports of aquatic, benthic Microcoleus proliferations in freshwater rivers, lakes, and reservoirs for four decades, with reports increasing in frequency over the last twenty years, suggesting a possible rise in their global distribution, frequency, and intensity. Microcoleus can produce anatoxins which are neurotoxic, and ingestion of toxic mats has caused hundreds of dog fatalities and raised serious human and ecological health concerns. This review synthesizes and evaluates current knowledge on Microcoleus distribution, taxonomy, toxin production, toxicity, ecology, environmental drivers, and biotic interactions. Toxin-producing Microcoleus have been reported in at least 18 countries, though many regions have not conducted toxin testing, suggesting a broader but under-reported distribution. Proliferations occur across diverse habitats, including cobble-bedded streams, large sandy rivers, reservoirs, and lakes. Microcoleus proliferations also occur on macrophytes, both in lakes and rivers. Genomic analyses currently classify anatoxin-producing Microcoleus into distinct species, with all known anatoxin-producers isolated from freshwater ecosystems. Anatoxin concentrations vary widely over space and time, within and among waterbodies. While studies on environmental drivers remain limited, research in cobble-bedded rivers suggests that moderate enrichment of dissolved inorganic nitrogen and low dissolved reactive phosphorus concentrations in the water column promote proliferation. Metagenomic approaches have revealed unique nutrient acquisition and storage strategies used by Microcoleus. Key knowledge gaps remain around the environmental and ecological triggers of proliferation, toxin production, genomic diversity and microbial interactions. Addressing these gaps through coordinated, global studies using robust datasets and consistent methods is critical to improve prediction, monitoring, and mitigation of this increasingly widespread public and ecological health threat.}, }
@article {pmid41666834, year = {2026}, author = {S, H and A, P}, title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.}, journal = {Marine environmental research}, volume = {216}, number = {}, pages = {107903}, doi = {10.1016/j.marenvres.2026.107903}, pmid = {41666834}, issn = {1879-0291}, mesh = {*Carbon Sequestration ; *Seawater/microbiology ; Seasons ; Metagenomics ; *Microbiota ; Bacteria ; *Environmental Monitoring ; Cyanobacteria ; *Water Microbiology ; }, abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.}, }
@article {pmid41666847, year = {2026}, author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110114}, doi = {10.1016/j.envint.2026.110114}, pmid = {41666847}, issn = {1873-6750}, mesh = {Serbia ; *Microbiota ; Seasons ; *Air Microbiology ; Environmental Monitoring ; Air Pollution/statistics & numerical data ; *Drug Resistance, Microbial/genetics ; *Air Pollutants/analysis ; }, abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.}, }
@article {pmid41666920, year = {2026}, author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A}, title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.}, journal = {Cell host & microbe}, volume = {34}, number = {3}, pages = {379-392.e5}, doi = {10.1016/j.chom.2026.01.013}, pmid = {41666920}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Bacteria/classification/genetics/isolation & purification ; Vitamin B 12/biosynthesis ; Metagenomics ; }, abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.}, }
@article {pmid41666926, year = {2026}, author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P}, title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.12.051}, pmid = {41666926}, issn = {1097-4172}, abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.}, }
@article {pmid41667020, year = {2026}, author = {Lawal, MS and Hayashida, K and Sugi, T and Omoare, AA and Bile, N and Maikudi, HI and James, POI and Villeng, F and Babatunde, O and Idris, J and Yamagishi, J}, title = {Detection of novel Pegivirus C genome in an unexplained febrile outbreak, Gombe State, Nigeria, 2024 by enhanced mNGS approach.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108470}, doi = {10.1016/j.ijid.2026.108470}, pmid = {41667020}, issn = {1878-3511}, mesh = {Humans ; Nigeria/epidemiology ; *Disease Outbreaks ; *Genome, Viral ; Phylogeny ; Male ; High-Throughput Nucleotide Sequencing ; Child ; Female ; Child, Preschool ; *Flaviviridae Infections/epidemiology/virology/diagnosis ; Infant ; Metagenomics/methods ; Adolescent ; Adult ; *Fever of Unknown Origin/virology/epidemiology ; }, abstract = {OBJECTIVES: In July 2024, an outbreak of acute febrile illness occurred in Chassi village, Gombe State, Nigeria, affecting over 30 individuals, primarily children, with symptoms including fever, jaundice, abdominal pain, and mucosal bleeding. The cause remained unidentified after conventional diagnostics excluded known viral hemorrhagic fevers, malaria, and bacterial infections. This study aimed to investigate the potential etiologic agent behind the outbreak using unbiased genomic techniques.
METHODS: We employed a metagenomic next-generation sequencing (mNGS) strategy with viral enrichment to analyze serum samples from 22 symptomatic patients. A novel complete 9.3 kb genome of Pegivirus C (GOMBE-017-2025) was reconstructed and phylogenetically compared to global sequences. Detection was validated using targeted PCR and Sanger sequencing. Environmental and microbial testing were conducted on local water sources.
RESULTS: Pegivirus C was consistently detected in all 22 samples. The reconstructed genome showed 92.7% identity to a 2018 Nigerian strain and clustered with West African isolates. PCR and sequencing confirmed its presence. Environmental and bacterial sources were ruled out as causative agents.
CONCLUSION: The uniform detection of Pegivirus C in this localized outbreak raises concern over its potential pathogenic or co-pathogenic role. These findings support the need for further investigation into its transmission dynamics, tropism, and clinical relevance.}, }
@article {pmid41667040, year = {2026}, author = {Liu, J and Guan, H and Hu, S and Lu, H and Tang, X and Tang, CJ}, title = {Dialysis-controlled sulfur substrate delivery enhances Sulfur-Autotrophic denitrification under oxygen stress.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134158}, doi = {10.1016/j.biortech.2026.134158}, pmid = {41667040}, issn = {1873-2976}, mesh = {*Denitrification ; *Sulfur/metabolism ; *Oxygen/metabolism/pharmacology ; Bioreactors/microbiology ; *Autotrophic Processes ; *Dialysis/methods ; Wastewater/chemistry ; Nitrates/metabolism ; Nitrogen/isolation & purification ; Water Purification/methods ; Oxidation-Reduction ; }, abstract = {Sulfur autotrophic denitrification (SAD) is a low-carbon nitrogen removal process using reduced sulfur compounds as electron donors. However, dissolved oxygen (DO) disrupts SAD by promoting unproductive sulfur oxidation and electron loss. Here, dialysis membranes (1000 and 100 Da) were applied to regulate thiosulfate release and establish controlled substrate gradients under engineering-relevant inhibitory DO conditions (0.5-3.5 mg L[-1]). Compared with direct dosing (Rck), the 100 Da reactor (R100) achieved 19% higher nitrate removal efficiency and greater fraction of electrons allocated to denitrification (EDUden ≈ 76%), accompanied by pronounced zero-valent sulfur accumulation, indicating pathway-level reallocation. Microbial analyzes revealed enrichment of Thiobacillus-like sulfur-oxidizing denitrifiers and increased prevalence of oxygen tolerant nitrate reductase (napA), confirmed by metagenomic and qPCR. These results demonstrate that controlled sulfur release creates an electron-buffered microenvironment that enhances SAD resilience to DO, offering a donor-efficient strategy for nitrogen removal in oxygen-fluctuating wastewater systems.}, }
@article {pmid41667136, year = {2026}, author = {Tarrant, E and Cormack, IG and Hunter, CE and Werbowy, O and Dorawa, S and Wang, L and Steen, IH and Sandaa, RA and Guðmundsdóttir, EE and Ketelsen-Striberny, B and Kaczorowska, AK and Kaczorowski, T and Pohl, E and Freitag-Pohl, S}, title = {Structure, function, and applications of two novel phage recombinases from extreme environments.}, journal = {Nucleic acids research}, volume = {54}, number = {4}, pages = {}, pmid = {41667136}, issn = {1362-4962}, support = {//European Union's Horizon 2020 Research/ ; 685778//Innovation Programme Virus-X project: Viral Metagenomics for Innovation Value/ ; EP/S022791/1//Engineering and Physical Sciences Research Council/ ; UMO-2019/34/H/NZ2/00584//Norway Financial Mechanism through the National Science Center/ ; A/SP/453344/202//Ministry of Education and Science/ ; }, mesh = {Rec A Recombinases/chemistry/genetics/metabolism ; *Bacteriophages/enzymology/genetics ; *Viral Proteins/chemistry/metabolism/genetics ; Models, Molecular ; DNA, Single-Stranded/metabolism ; Escherichia coli/genetics ; Crystallography, X-Ray ; *Recombinases/chemistry/metabolism/genetics ; Escherichia coli Proteins/chemistry/genetics ; DNA-Binding Proteins ; }, abstract = {This study describes the identification and characterization of two new extremophilic phage recombinases, UvsXt and UvsXp, discovered through metagenomic analysis within the Virus-X project, and explores their potential applications in biotechnology. DNA recombinases are essential for maintaining genome integrity across all kingdoms of life by facilitating homologous recombination and repairing double-stranded DNA breaks. Their capacity to bind and stabilize single-stranded DNA (ssDNA) has led to wide-ranging applications in molecular biology. UvsXt and UvsXp show homology with known bacterial RecA and viral UvsX recombinases, including conservation of key catalytic residues and DNA-binding motifs. Biochemical assays reveal that both enzymes exhibit superior DNA strand-exchange activity compared to Escherichia coli RecA. High-resolution crystal structures of UvsXt (2.0 Å) and UvsXp (2.6 Å) confirm a conserved RecA-like core fold, with distinct structural variation at the N-terminus responsible for oligomerization. However, in spite of their similarities, we show that neither enzyme is capable to functionally replace RecA in E. coli. Their remarkable thermostability and functionality across diverse chemical environments highlights their robustness for biotechnological use. Notably, UvsXt enhances loop-mediated isothermal amplification of viral RNA by stabilizing ssDNA intermediates. These findings expand the repertoire of thermostable recombinases with potential utility in diagnostic applications.}, }
@article {pmid41667306, year = {2026}, author = {Tong, Y and Chen, Y and Dong, Y and Chen, K and Yang, J and Dong, X and Wan, X and Luo, Z and Fang, J and Liu, Y and Li, W and Wang, Z and Gu, X}, title = {Characterization of the oral microbiota of Kawasaki disease patients by metagenomic analysis: A pilot study.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2026.01.007}, pmid = {41667306}, issn = {1995-9133}, abstract = {BACKGROUND: Kawasaki disease (KD) is an acute febrile systemic vasculitis characterized by vascular inflammation. Its pathogenesis has been linked to the infiltration of IgA[+] plasma cells within the respiratory tract, suggesting the upper airway may act as a potential portal of entry. However, evidence connecting respiratory infections to KD remains limited. This study aimed to explore the relationship between oral microbiota and KD development.
METHODS: Oral swab samples were collected from 25 KD patients before and after intravenous immunoglobulin (IVIG) treatment, as well as from 25 healthy controls. Metagenomic sequencing was performed to characterize overall microbial composition and identify potential microbial markers associated with KD.
RESULTS: Significant alterations in oral microbiota composition were observed between KD patients and healthy controls. The diversity of oral microbiota in KD patients was markedly lower than that in healthy controls, and exhibited an upward trend following IVIG treatment. Elevated levels of Streptococcus, Prevotella, and Veillonella, along with reduced levels of Haemophilus, Neisseria, and Rothia, were closely associated with KD development. Putative novel pathogen Abiotrophia defectiva was significantly enriched in patients with KD. Correlation analysis revealed that the relative abundances of several Haemophilus species were positively correlated with albumin levels in KD patients before IVIG treatment. Additionally, the anti-inflammatory bacterium Rothia mucilaginosa may play a protective role against the development of coronary artery lesions in KD.
CONCLUSION: These findings provide new evidence that distinct alterations in the oral microbiome are associated with KD development. Oral microbiota-based biomarkers may represent a potential strategy for KD therapy.}, }
@article {pmid41667397, year = {2026}, author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E}, title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2627692}, pmid = {41667397}, issn = {1949-0984}, mesh = {Humans ; *Ceftriaxone/therapeutic use/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy ; Aged ; *Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification ; Genetic Variation ; Adult ; Rectum/microbiology ; }, abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.}, }
@article {pmid41667950, year = {2026}, author = {Rodrigues, GVP and Ferreira, LYM and Aguiar, ERGR}, title = {ViralQuest: a user-friendly interactive pipeline for viral-sequences analysis and curation.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41667950}, issn = {1471-2105}, support = {Financial Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {BACKGROUND: High-throughput sequencing (HTS) has become an essential, unbiased tool in virology for identifying known and novel viruses. However, analyzing the large and complex datasets generated by HTS presents significant bioinformatics challenges. The process of accurately identifying and characterizing viral sequences from assembled contigs remains a bottleneck, often requiring specialized expertise and involving non-standardized parameters. There is a pressing need for robust, user-friendly, and reproducible pipelines to streamline this post-assembly analysis.
RESULTS: To address these challenges, we developed ViralQuest, a bioinformatics tool that automates the in-depth characterization of viral sequences from pre-assembled contigs. The pipeline integrates multiple lines of evidence for robust identification, using Diamond BLASTx against the Viral RefSeq database and pyHMMER searches against the RVDB, Vfam, and eggNOG profile HMM databases. For detailed characterization, ViralQuest performs taxonomic classification based on the ICTV nomenclature and functional annotation via Pfam domain analysis. Novel features of ViralQuest include an AI-powered summarization module that uses a Large Language Model (LLM) to generate contextual narratives for key viral findings and a comprehensive confidence score to rank putative viral contigs. All results are consolidated into a single, interactive HTML report that includes dynamic visualizations of contigs, ORFs, and protein domains, alongside detailed data tables that are exportable in TSV and SVG formats.
CONCLUSION: ViralQuest provides an accessible and comprehensive solution for the post-assembly analysis of viral metagenomic data. By combining rigorous bioinformatics methods with novel AI-driven features and an intuitive reporting interface, it streamlines the complex process of viral identification and characterization. The tool enhances the interpretability and reliability of results, making in-depth virome analysis more accessible to the broader research community. ViralQuest is available on GitHub at https://github.com/gabrielvpina/viralquest/.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-026-06391-6.}, }
@article {pmid41668110, year = {2026}, author = {Fujii, H and Sato, M and Nguyen, HAT and Vu, HTT and Kakiuchi, S and Dhoubhadel, BG and Nakamura, S and Motooka, D and Ogura, Y and Nakano, S and Parry, CM and Morimoto, K and Yoshida, LM and Anh, DD and Hayashi, T and Iida, T and Ariyoshi, K}, title = {Genomic analysis of the genetic background underlying Streptococcus pneumoniae beta-lactam nonsusceptibility in central Vietnam: increased beta-lactam nonsusceptibility and dynamics of the pbp2x gene.}, journal = {Tropical medicine and health}, volume = {54}, number = {1}, pages = {}, pmid = {41668110}, issn = {1348-8945}, support = {2014-Ippan-10, 2015-Ippan-25//Institute of Tropical Medicine, Nagasaki University/ ; }, abstract = {BACKGROUND: We previously reported alarmingly high carriage rates of Streptococcus pneumoniae (SP) serotype 19F and serogroup 6 isolates, which were not susceptible to multiple beta-lactams among children under five years of age in Vietnam. Multilocus sequence typing analysis revealed the predominance of two major lineages, ST320 and ST13223, among serotype 19F and serogroup 6 isolates, respectively. Investigating the association between nonsusceptible genotypes and clinical outcomes could help optimize patient care or lead to the development of new diagnostic tests.
METHODS: We performed WGS on SP isolates randomly selected from the two major lineages and their related strains. FASTQ quality control and de novo assembly were performed using CLC Genomics Workbench ver. 7.5.1. Draft genome sequences were annotated using DFAST (DDBJ Fast Annotation and Submission Tool), which revealed the serogroups/serotypes and the sequences of the three major penicillin-binding protein genes and the sequence types. Draft sequences were aligned using MUMmer ver. 3.23, and putative recombination events and phylogenetic relationships excluding recombination regions were identified using Gubbins ver. 2.4.1. Finally, the association between a detected nonsusceptible genotype and the duration of hospital stay was evaluated in patients with acute respiratory infection.
RESULTS: WGS analysis (serotype 19F/ST320, n = 22; serogroup 6/ST13223, n = 13; and isolates closely related to ST13223, n = 4) revealed substantial differences in genomic diversity and antimicrobial susceptibility between serogroup 6/ST13223 and serotype 19F/ST320 isolates, particularly the recombination-prone nature of serogroup 6/ST13223. Among the 23 recombination events observed in serogroup 6/ST13223, only those spanning the pbp2x region (15.5 kb and 6.4 kb) were associated with high MICs for multiple beta-lactams. A subset of ST13223 isolates and all ST320 isolates carried the identical pbp2x allele 16, which was significantly associated with a lack of susceptibility to the combination of penicillin, cefotaxime, and meropenem (p < 0.0001; odds ratio 11.5; 95% confidence interval [CI] 3.35-39.3). No significant association was demonstrated between the presence of this pbp2x allele and prolonged hospitalization (p = 0.6123).
CONCLUSIONS: We revealed that the widespread nonsusceptibility to multiple beta-lactams among SP isolates circulating in central Vietnam was primarily driven by the dynamics of the pbp2x gene. However, the nonsusceptible pbp2x allele had little effect on clinical outcome.}, }
@article {pmid41668124, year = {2026}, author = {Zhang, R and Debeljak, P and Gadegaonkar, SS and Baudet, C and Ringard, A and Blain, S and Obernosterer, I}, title = {Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41668124}, issn = {2049-2618}, support = {202006220057//China Scholarship Council/ ; ANR19-CE01-0012//Agence Nationale de la Recherche/ ; }, mesh = {*Membrane Transport Proteins/genetics/metabolism ; *Seawater/microbiology/chemistry ; *Bacteria/genetics/metabolism/classification ; *Trace Elements/metabolism ; Indian Ocean ; *Metals/metabolism ; *Bacterial Proteins/genetics/metabolism ; Metals, Heavy/metabolism ; Homeostasis ; Iron/metabolism ; }, abstract = {BACKGROUND: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean.
RESULTS: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses.
CONCLUSIONS: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.}, }
@article {pmid41668418, year = {2026}, author = {Moguel, B and Carrillo Olivas, L and Guerrero-Osornio, MG and Herrera Paredes, S}, title = {Recent Microbial Evolutionary Insights From Metagenomics.}, journal = {Genome biology and evolution}, volume = {18}, number = {3}, pages = {}, pmid = {41668418}, issn = {1759-6653}, support = {2022-000002-01NACF-03333//DGAPA-PAPIIT/ ; 2023-000002-01NACF-03323//SECIHTI/ ; IN212524//SECIHTI/ ; //DGAPA-PAPIIT/ ; }, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Evolution, Molecular ; Humans ; *Biological Evolution ; Phylogeny ; }, abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.}, }
@article {pmid41668536, year = {2026}, author = {Wei, H and Guo, S and Ding, W and Yang, Y and Hu, X and Aili, A and Chen, X and Xue, X and Pan, L}, title = {Altered gut microbial dynamics and the antivascular remodeling effect of carnosine in hypobaric hypoxic pulmonary hypertension rats.}, journal = {Acta biochimica et biophysica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.3724/abbs.2025237}, pmid = {41668536}, issn = {1745-7270}, abstract = {Exposure to chronic hypobaric hypoxia provokes marked alterations in the gut microbiota and its metabolome, yet the functional significance of histidine-derived metabolites in hypobaric hypoxic pulmonary hypertension (PH) remains underexplored. Here, we employ 16S rDNA, metagenomic, and untargeted metabolomic sequencing to characterize longitudinal shifts in the fecal microbiota and metabolites during hypobaric hypoxic PH development in Sprague-Dawley rats. Fecal carnosine levels and the abundance of its producer, Ruminococcus bromii, both decrease significantly over 28 days of hypobaric hypoxia (P < 0.05). Spearman correlation shows that carnosine is inversely correlated with the percentage of pulmonary arteriole media thickness (MT%; r = -0.8741, P < 0.001). Therapeutic supplementation with carnosine restores systemic and pulmonary antioxidant defenses and attenuates vascular remodeling without altering right ventricular pressures. In vitro, carnosine inhibits hypoxia-induced pulmonary artery smooth muscle cell (PASMC) proliferation and migration and suppresses nuclear factor erythroid 2-related factor 2 (Nrf2) accumulation. These findings reveal dynamic gut-lung crosstalk in hypobaric hypoxic PH and nominate carnosine as a metabolite-based intervention to mitigate hypoxia-driven pulmonary vascular remodeling.}, }
@article {pmid41668731, year = {2025}, author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C}, title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1745848}, pmid = {41668731}, issn = {2235-2988}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Culex/microbiology/genetics/physiology ; Metagenomics ; *Smell/genetics ; Gene Expression Profiling ; Arthropod Antennae/metabolism ; Transcriptome ; Computational Biology ; Multiomics ; }, abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.
METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.
RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that the gut microbial richness of male individuals was significantly higher than that of females, and the β-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.
DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.}, }
@article {pmid41668733, year = {2025}, author = {Sui, Q and Yu, J and Cui, S}, title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1707599}, pmid = {41668733}, issn = {2235-2988}, mesh = {Humans ; Middle Aged ; Male ; Female ; Aged ; Retrospective Studies ; *Atherosclerosis/microbiology/diagnosis ; *Microbiota ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Risk Factors ; Bacteria/classification/genetics/isolation & purification ; *Cardiovascular Diseases/microbiology/diagnosis ; Metagenomics ; }, abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.
METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).
RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.
CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.}, }
@article {pmid41668735, year = {2025}, author = {Cao, Y and Wang, C and Yin, H and Xu, D and Li, W and Yuan, Z and Xu, W and Song, Z and Pang, F and Wang, D}, title = {Establishing hospital-specific background microbial libraries to reduce false positives in mNGS diagnosis of periprosthetic joint infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1668697}, pmid = {41668735}, issn = {2235-2988}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Hospitals ; False Positive Reactions ; *Bacteria/genetics/classification/isolation & purification ; Computational Biology ; }, abstract = {BACKGROUND: Due to the high sensitivity of metagenomic next-generation sequencing (mNGS), trace amounts of nucleic acid contamination can lead to false positives, posing challenges for result interpretation. This study is the first to experimentally identify and establish background microbial libraries (BML) related to periprosthetic joint infection (PJI) across different medical institutions, aiming to demonstrate the necessity of institution-specific BMLs to improve mNGS diagnostic accuracy.
METHODS: Samples were taken from 3 different acetabular reamer for hip arthroplasty in 7 different hospitals. The whole process was strictly aseptic, mNGS was performed according to standard operating procedures. The sterility of instruments was confirmed by culture method. The sequencing results of specimens from different hospitals were compared to analyze the difference of background bacteria. Bioinformatics analysis and visualization were presented through R language.
RESULTS: A total of 26 samples (24 instrument swabs and 2 negative controls) generated 254 million reads, of which 1.13% matched microbial genomes. The proportion of microbial reads (1.13%) falls within ranges typically observed for contamination in low-biomass metagenomic sequencing studies. Among these, bacteria accounted for 87.48%, fungi 11.18%, parasites 1.26%, and viruses 0.06%. The most abundant bacterial genera included Cutibacterium, Staphylococcus, and Acinetobacter. Principal component analysis revealed distinct bacterial compositions among the seven hospitals, and clustering analysis showed significant inter-hospital variation (p < 0.05). Liaocheng People's Hospital exhibited the highest species richness (340 species), followed by Guanxian County People's Hospital (169 species).
CONCLUSIONS: The composition and abundance of residual bacterial DNA vary markedly among institutions, underscoring the necessity of establishing hospital-specific BMLs. Incorporating such libraries into clinical mNGS interpretation can effectively reduce false positives and enhance the diagnostic accuracy of PJI. arthroplasty, bacterial culture, next-generation sequencing, joint replacement, periprosthetic joint infection, background microbial libraries.}, }
@article {pmid41668736, year = {2025}, author = {Wang, Q and Ding, H and Hao, Z and Liao, G}, title = {Metagenomic next-generation sequencing enhances diagnosis of fungal infections in kidney transplant recipients: a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1667475}, pmid = {41668736}, issn = {2235-2988}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Female ; Male ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Transplant Recipients ; *Fungi/genetics/classification/isolation & purification ; Adult ; *Mycoses/diagnosis/microbiology ; Aged ; }, abstract = {BACKGROUND: Although fungal infections are relatively rare, they have low detection rates and high mortality rates. The value of metagenomic next-generation sequencing (mNGS) in kidney transplant patients with fungal infections remains insufficiently explored, especially regarding diagnosis and antimicrobial stewardship.
METHODS: From September 2021 to August 2023, 234 kidney transplant patients were enrolled, with detailed data collected on 66 patients suspected of fungal infections. The pathogen detection performance of mNGS and conventional microbiological tests (CMTs) was compared. The impacts of mNGS and CMTs on treatment adjustment were also assessed. Finally, the value of mNGS in detecting donor-derived infections was investigated.
RESULTS: Among 66 patients, 21 fungal species were identified: 18 species detected by mNGS and 10 by CMTs. The overall positive rate of mNGS was significantly higher than culture (90.67% vs. 26.67%), especially for multiple fungal infections (9vs0). mNGS identified more Candida (26vs12), Pneumocystis jirovecii (14vs0), Aspergillus (10vs4), Mucor (6vs2) organisms compared with CMTs. Donor-derived fungi were identified in 11 (6.7%) patients, including 10 cases of Candida spp. and 1 case of Mucor spp. Anti-infection therapies were adjusted in 28 (24.4%) cases based on mNGS.
CONCLUSION: The mNGS technique showed distinct advantages in detecting fungal infections in kidney transplant patients, facilitating informed anti-infection strategies and enhanced graft protection. Moreover, it provides effective identification of fungal infections originating from donor sources.}, }
@article {pmid41669395, year = {2025}, author = {Criollo Delgado, L and Zewude, D and Karzhaev, DS and Polev, DE and Potokina, EК}, title = {Identification of CtE1 gene nucleotide polymorphisms and development of SNP-based KASP markers in guar (Cyamopsis tetragonoloba (L.) Taub.).}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {25}, number = {8}, pages = {1246-1254}, doi = {10.18699/vjgb-25-134}, pmid = {41669395}, issn = {2500-0462}, abstract = {Guar (Cyamopsis tetragonoloba (L.) Taub), is an important short-day legume crop, whose cultivation is limited at high latitudes due its photoperiod sensitivity, that negatively impacts flowering and maturation of this industrial-oriented crop. In its close relative, soybean, the E1 gene has been highly associated with the regulation of flowering time under long-day conditions. In this study we investigated the natural diversity of the E1 homologue gene (CtE1) in a panel of 144 guar accessions. For this purpose, the CtE1 gene was amplified and sequenced using Illumina. As a result, five novel SNPs were identified in the 5'-untranslated region, coding region, and 3'-untranslated region of the CtE1 gene. One non-synonymous SNP was located in the coding region causing a conservative Arg→Lys substitution. Based on the identified SNP, five KASP markers linked to polymorphism in the target gene were developed and tested in the guar collection. No significant associations were detected between discovered SNPs and available data on variability in flowering time or vegetation period length in the cohort of 144 accessions. These findings suggest that natural variation of the CtE1 gene in the studied germplasm collection has minimal effect on flowering or maturation. The limited functional allelic diversity observed in the CtE1 gene of guar compared to the E1 gene in soybean likely reflects differences in their evolutionary histories, domestication bottlenecks, and selection pressures.}, }
@article {pmid41669550, year = {2026}, author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A}, title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20648}, pmid = {41669550}, issn = {2167-8359}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Nutrients ; *Stress, Physiological ; Phylogeny ; Biodegradation, Environmental ; }, abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.}, }
@article {pmid41669552, year = {2026}, author = {Hearne, G and S Refahi, M and Duan, HN and Brown, JR and Rosen, GL}, title = {Normalized compression distance for DNA classification.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20677}, pmid = {41669552}, issn = {2167-8359}, mesh = {Humans ; *Data Compression/methods ; Algorithms ; *Genomics/methods ; *Sequence Analysis, DNA/methods ; Open Reading Frames ; Neural Networks, Computer ; *DNA/classification/genetics ; }, abstract = {Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.}, }
@article {pmid41669888, year = {2026}, author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T}, title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.}, journal = {Journal of hypertension}, volume = {44}, number = {4}, pages = {673-681}, pmid = {41669888}, issn = {1473-5598}, mesh = {Humans ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; Cohort Studies ; }, abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.
AIM: This study assessed the association between gut microbiome and incident hypertension.
METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74 years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.
RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.
CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.}, }
@article {pmid41670185, year = {2026}, author = {Sampara, P and Tomatsu, A and Malmstrom, RR and Ziels, RM}, title = {Quantitative DNA Stable Isotope Probing Identifies Active Microorganisms Assimilating Volatile Fatty Acids in Full-Scale Enhanced Biological Phosphorus Removal Processes.}, journal = {Environmental science & technology}, volume = {60}, number = {7}, pages = {5570-5583}, doi = {10.1021/acs.est.5c14266}, pmid = {41670185}, issn = {1520-5851}, mesh = {*Phosphorus ; *Fatty Acids, Volatile/metabolism ; Bacteria/metabolism ; Anaerobiosis ; }, abstract = {Enhanced biological phosphorus removal (EBPR) systems often rely on exogenous carbon sources, such as volatile fatty acids (VFAs), to achieve higher P removal. Here, we employed DNA quantitative stable isotope probing (qSIP) using two VFAs, acetate and propionate, in cyclic anaerobic/aerobic incubations to assess their effects on P cycling and microbial activity with biomass from two full-scale EBPR water resource-recovery facilities that utilize VFA addition. We found that anaerobic VFA uptake preferences differed within known groups of PAOs, such as Candidatus Accumulibacter and Tetrasphaera-affiliated members (e.g., Ca. Phosphoribacter), between the two biomasses. The combination of qSIP with metagenomics identified isotopically labeled phages that were linked to active PAOs, highlighting their potential roles in modulating EBPR community composition and activity. The highest levels of anaerobic labeling from acetate were in genomes belonging to Saccharimonadales and Rickettsiales, which are generally host-associated with bacteria and eukaryotes, respectively. This finding highlights the possibility of cross-feeding between PAO hosts and their parasites or predators, as well as the role of so-far uncharacterized organisms participating in carbon cycling under EBPR conditions. Collectively, these results expand our understanding of the ecological interactions involved in communities anaerobically uptaking VFAs and cycling P that are central to EBPR.}, }
@article {pmid41670373, year = {2026}, author = {Pham, S and Sharma, N and Sankaran, B and Nguyen, J and Estes, MK and Hyser, JM and Prasad, BVV}, title = {Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases.}, journal = {Journal of virology}, volume = {100}, number = {3}, pages = {e0217625}, pmid = {41670373}, issn = {1098-5514}, support = {P01 AI057788/AI/NIAID NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Norovirus/enzymology/drug effects ; *Antiviral Agents/pharmacology/chemistry ; *Protease Inhibitors/pharmacology/chemistry ; Phenylalanine/analogs & derivatives/pharmacology/chemistry ; Valine/analogs & derivatives ; *Peptide Hydrolases/chemistry/metabolism ; Pyrrolidinones/pharmacology/chemistry ; *Caliciviridae/enzymology/drug effects ; *Viral Proteins/chemistry/metabolism/antagonists & inhibitors ; Animals ; Drug Evaluation, Preclinical/methods ; Models, Molecular ; Isoxazoles ; }, abstract = {Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.IMPORTANCEHuman noroviruses (HuNoVs) are a significant cause of sporadic and epidemic gastroenteritis worldwide. There are no vaccines or antiviral drugs currently available to treat infections. Our work here demonstrates the potential of the Tulane virus cell culture system as a surrogate for screening small-molecule inhibitors of the human norovirus proteases.}, }
@article {pmid41670415, year = {2026}, author = {Hasegawa, T and Iwai, S and Ikeda, HO and Miyaoka, D and Sato, N and Fujimoto, K and Wei, X and Kusaka, M and Miyata, M and Numa, S and Otsuka, Y and Imoto, S and Uematsu, S and Tsujikawa, A}, title = {Increased Gut Microbiota Diversity in Patients With Retinitis Pigmentosa and Implications for Disease Phenotypes and Progression.}, journal = {Investigative ophthalmology & visual science}, volume = {67}, number = {2}, pages = {27}, pmid = {41670415}, issn = {1552-5783}, mesh = {*Gastrointestinal Microbiome/genetics/physiology ; Animals ; Humans ; *Retinitis Pigmentosa/microbiology/physiopathology ; Mice ; Female ; Male ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Disease Models, Animal ; Phenotype ; Adult ; Feces/microbiology ; Electroretinography ; Anti-Bacterial Agents/pharmacology ; Tomography, Optical Coherence ; Aged ; Mice, Inbred C57BL ; *Bacteria/genetics/isolation & purification ; }, abstract = {PURPOSE: Inflammation is often present in retinitis pigmentosa (RP) and is reported to affect visual outcome. Gut microbiota plays a crucial role in inflammatory diseases. This study aimed to elucidate the relationship between the gut microbiota and RP.
METHODS: The 16S rRNA gene sequencing analysis was performed on stool samples collected from 103 patients with RP and 64 healthy individuals. The α and β diversities of gut microbiota, along with relative abundances, were compared between patients and healthy individuals, as well as between patients with or without cystoid macular edema (CME). The RP model rd10 mice were treated with or without antibiotics starting at 7 days of age. Retinal structure and function were evaluated.
RESULTS: Gut microbiota diversity was higher in patients with RP than in healthy individuals (P < 0.001). Moreover, patients with CME had greater diversity than did those without CME and showed a higher abundance of Romboutsia and Ruminococcus (P < 0.05). Antibiotics-treated rd10 mice showed suppressed apoptosis, attenuated decrease of photoreceptors, and a significantly lower incidence of retinal detachment. Retinal function was significantly preserved in mice treated with antibiotics. In antibiotics-treated mice, the expression of Il-1β, Nlrp3, Caspase-1, pNFkb, pJNK, and pCREB1 was downregulated, suggesting suppression of the NLRP3 inflammasome.
CONCLUSIONS: Patients with RP exhibited distinct gut microbiota characteristics compared to that of healthy individuals. Treatment with antibiotics attenuated disease progression in the RP model mouse. Modifying the gut microbiota may be a potential therapeutic strategy for modifying disease progression in RP in future investigations.}, }
@article {pmid41670507, year = {2026}, author = {Xing, Y and Chen, M and Shen, M and Zhong, Q}, title = {A Case of Rare Facial Infection Caused by Mycobacterium scrofulaceum.}, journal = {Clinical laboratory}, volume = {72}, number = {2}, pages = {}, doi = {10.7754/Clin.Lab.2025.250549}, pmid = {41670507}, issn = {1433-6510}, mesh = {Humans ; Male ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Tomography, X-Ray Computed ; Face/microbiology ; }, abstract = {BACKGROUND: In July 2024, our hospital confirmed a rare case of facial infection with Mycobacterium scrofulaceum. The patient visited our hospital due to pain and pus discharge from the right orbital incision for one month. The patient suffered multiple facial fractures due to trauma three months ago. He underwent systemic anti infection treatment and open reduction and internal fixation surgery at an external hospital. After the surgery, there was repeated swelling around the orbit, and the patient did not fully recover. One month ago, the infraorbital area was swollen again, locally ruptured, and purulent discharge was visible. After self-flushing and dressing change, the condition improved. Recently, there has been swelling around the eye socket again. In order to seek further treatment, he came to our hospital for treatment. Outpatient diagnosis: 1. Multiple space infections in the right orbit, temporal region, and skull base; 2. Postoperative open facial bone fracture.
METHODS: CT (skull and neck), facial wound pus: bacterial culture and identification, acid fast staining, Gram staining, T-SPOT tuberculosis infection detection, identification of Mycobacterium species (DNA microarray chip method), Metagenomic Next-generation Sequencing (mNGS). Other related auxiliary examinations included blood routine, urine routine, liver function, kidney function, electrocardiogram, etc. Results: CT (skull and neck) results: 1. After multiple fractures of the maxillofacial bone and anterior skull base, there is abnormal enhancement density shadow in the right maxillofacial region, indicating infection. Clinical laboratory tests: blood routine + high-sensitivity CRP (whole blood): white blood cell count 9.66 x 109/L, total neutrophil count 6.87 x 109/L, whole blood high-sensitivity C-reactive protein 46.21 mg/L, coagulation function: fibrinogen detection 6.61 g/L, D-dimer determination 1,231.52 FEU/L, inflammatory markers: interleukin-6 15.48 pg/mL, procalcitonin 0.037 ng/ml; Liver function test: total protein 85.2 g/L, globulin 44.4 g/L, aspartate aminotransferase 12.8 U/L. Facial wound pus examination: T-SPOT tuberculosis infection test: positive, with 40 antigen stimulated pore spots. Bacterial Gram staining: A small amount of Gram positive bacilli were found. Acid fast staining: acid fast bacilli detected ++: bacterial culture + identification: growth of mycobacteria ++, identification of mycobacterial species (DNA microarray method): Mycobacterium scrofulaceum, identification of Metagenomic Next-generation Sequencing (mNGS): Mycobacterium scrofulaceum. Clinical treatment plan: Chlorpheniramine 200 mg/d, Clarithromycin 0.5 g/d; Moxifloxacin 0.4 g/d, locally applied with 3% boric acid solution wet compress to enhance local wound dressing change. After 2 months of hospitalization, the patient's orbital swelling significantly improved, no obvious purulent discharge was observed locally, and the infection indicators significantly decreased. The patient improved and was discharged from the hospital.
CONCLUSIONS: This article reports a rare case of facial infection caused by Mycobacterium scrofulaceum. Mycobacterium scrofulaceum was quickly and accurately identified through mycobacterial strain identification (DNA microarray chip method) and mNGS. Reasonable treatment measures were adopted clinically, and the patient improved and was discharged. We hope that in the future, this study can provide assistance for the clinical diagnosis and treatment of Mycobacterium scrofulaceum infection.}, }
@article {pmid41671148, year = {2026}, author = {Buczek, DJ and Kabir, W and Lindstedt, K and Mäklin, T and Thorpe, HA and Suzuki, Y and Corander, J and Samuelsen, Ø and Sundsfjord, A}, title = {Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools.}, journal = {Microbial genomics}, volume = {12}, number = {2}, pages = {}, pmid = {41671148}, issn = {2057-5858}, mesh = {*Klebsiella pneumoniae/genetics/classification/isolation & purification ; *Computational Biology/methods ; *Metagenome ; Humans ; Whole Genome Sequencing ; Phylogeny ; Klebsiella Infections/microbiology ; Genome, Bacterial ; }, abstract = {Klebsiella pneumoniae is a major cause of human infections and is frequently associated with antimicrobial resistance (AMR). Carriage of K. pneumoniae in the gut is a major risk factor for infection and a reservoir for the spread of high-risk clonal lineages and associated AMR determinants. Accurate detection of K. pneumoniae at the subspecies level is therefore essential to better understand K. pneumoniae gut colonization ecology and clonal dissemination. We analysed two recently developed bioinformatic tools, mSWEEP and StrainGE, for sequence type (ST) detection of K. pneumoniae in culture-enriched sweep metagenomes compared to single-colony whole-genome sequencing (WGS). We show that both mSWEEP and StrainGE perform highly accurate ST detection, concordant with culture in 46/49 and 44/49 samples with WGS-detected single STs, respectively, as well as in 2/3 samples with two WGS-detected STs. Within-sample ST diversity was detected in 19 and 15 samples by mSWEEP and StrainGE, respectively, highlighting a major advantage of these tools over conventional single-colony WGS. StrainGE could also reconstruct accurate phylogenetic relationships between strains of the same ST for 2/3 different STs tested. Additionally, assembly of the genomes provides better resolution of ST detection by mSWEEP. Together, our results show that both mSWEEP and StrainGE are accurate tools for the detection and analysis of K. pneumoniae STs from mixed bacterial samples.}, }
@article {pmid41671170, year = {2026}, author = {Chettleburgh, C and Chiappe, C and Davidson, H and Taggar, G and Zhao, A and Habash, M and Landgraff, C and Parreira, VR and Lévesque, RC and Goodridge, L}, title = {Coffee cartridge filtration: a rapid, inexpensive, and easy method to concentrate nucleic acids from pathogens and fecal biomarkers in wastewater.}, journal = {Journal of applied microbiology}, volume = {137}, number = {2}, pages = {}, doi = {10.1093/jambio/lxag037}, pmid = {41671170}, issn = {1365-2672}, support = {//INSPIRE/ ; CBRF2-2023-00008//Canada Biomedical Research Fund Stage 2/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Canopy Canadian One Health Training Program on Emerging Zoonoses/ ; }, mesh = {*Wastewater/virology/microbiology/parasitology ; *Filtration/methods/economics/instrumentation ; *Feces/microbiology/virology ; Humans ; *Nucleic Acids/isolation & purification ; Coffee ; Norovirus/isolation & purification/genetics ; Ontario ; Giardia/isolation & purification/genetics ; *Viruses/isolation & purification/genetics ; Biomarkers/analysis ; Hepatitis A virus/isolation & purification/genetics ; Water Microbiology ; }, abstract = {AIMS: We propose coffee cartridge filtration as an alternative method for the concentration of nucleic acids from microorganisms in wastewater.
METHODS AND RESULTS: In this study, coffee cartridge filtration was directly compared with PEG precipitation through mass balance analysis. The utility of coffee cartridge filtration was further demonstrated through a 10-month longitudinal analysis of Giardia, human norovirus genogroup I and II, and hepatitis A virus in 45 wastewater samples from Guelph, Ontario, Canada. Fourteen of these wastewater samples were enriched with the Illumina Viral Surveillance Panel v2 and sequenced with the Illumina NextSeq 1000. PEG precipitation was more efficient at concentrating nucleic acids from all microorganisms and viruses, but all endogenous targets were detected following coffee cartridge filtration. Hepatitis A was detected in four wastewater samples and best correlated with four clinical cases when a 1-week wastewater lead time was applied. HuNoV-GI and HuNoV-GII were detected within the RT-qPCR linear dynamic range in 44/45 samples. Nucleic acids from the Polyomaviridae, Astroviridae, and Caliciviridae families were most identified in coffee cartridge-filtered wastewater samples.
CONCLUSIONS: Coffee cartridge filtration is an effective method to concentrate nucleic acids from microorganisms in wastewater in resource-limited settings.}, }
@article {pmid41671795, year = {2026}, author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B}, title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134181}, doi = {10.1016/j.biortech.2026.134181}, pmid = {41671795}, issn = {1873-2976}, mesh = {*Denitrification/drug effects ; *Sulfamethoxazole/pharmacology ; *Ammonium Compounds/metabolism ; Oxidation-Reduction/drug effects ; Anaerobiosis/drug effects ; Nitrogen/metabolism ; Bioreactors/microbiology ; Microbiota ; }, abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.}, }
@article {pmid41671813, year = {2026}, author = {Wang, N and Jin, M and Zhu, Z and Wang, Y and Li, X and Xu, J and Cheng, S and Zhu, Y and Wang, R and Xu, T and Yin, F and Li, X and Ke, Y and Yue, H}, title = {Ecological distribution and functional characterization of polyethylene-degrading enzymes from diverse metagenomes.}, journal = {The Science of the total environment}, volume = {1018}, number = {}, pages = {181486}, doi = {10.1016/j.scitotenv.2026.181486}, pmid = {41671813}, issn = {1879-1026}, mesh = {*Polyethylene/metabolism ; Biodegradation, Environmental ; *Metagenome ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {Polyethylene (PE), the most widely produced synthetic polymer, is highly resistant to degradation and poses long-term ecological risks due to its accumulation in terrestrial and aquatic ecosystems. Although biological degradation pathways have been investigated, research has primarily concentrated on heavily polluted environments, leaving the ecological distribution of PE-degrading enzymes largely unknown. In this study, we systematically screened more than 4.57 billion metagenomic sequences from diverse ecological sources-including farmland soils, Przewalski's horse gut microbiota, insect symbionts, and human oral microbiomes-for homologs of known PE-degrading enzymes. A total of 701 candidate sequences were identified using an integrated pipeline combining sequence homology, structural modeling, and molecular docking. Thirty-two representative enzymes were heterologously expressed and tested on pristine PE films and microspheres, among which 25 exhibited measurable activity, inducing surface erosion, up to ∼1.5% mass loss (w/w) of PE films over 30 days, and oxidative modifications. These degradative effects were validated by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), and stable carbon isotope (δ[13]C) analysis, collectively supporting molecular-level oxidation and early-stage carbon turnover associated with enzymatic PE degradation. Notably, PE-degrading activity was observed in microbiomes from relatively minimally disturbed environments, suggesting that microbial communities may adaptively evolve plastic-degrading capabilities in response to chronic, low-level exposure. These findings expand our understanding of plastic pollution's ecological footprint and highlight naturally occurring enzymes as promising candidates for sustainable bioremediation.}, }
@article {pmid41671864, year = {2026}, author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H}, title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141429}, doi = {10.1016/j.jhazmat.2026.141429}, pmid = {41671864}, issn = {1873-3336}, mesh = {Dogs ; Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; *Pets/microbiology ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; Male ; Female ; Acinetobacter baumannii/genetics/drug effects ; Enterococcus faecium/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.}, }
@article {pmid41671957, year = {2026}, author = {Wu, J and He, C and Wu, K and Feng, W and Yang, Y and Zhou, Q and Mao, P and Xiao, X}, title = {Silver sulfide nanoparticles amplify earthworm gut denitrification and elevate N2O emissions in subtropical forest soils under nitrogen deposition.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119853}, doi = {10.1016/j.ecoenv.2026.119853}, pmid = {41671957}, issn = {1090-2414}, mesh = {Animals ; *Oligochaeta/drug effects/metabolism ; *Denitrification/drug effects ; Forests ; Soil/chemistry ; *Nitrogen/metabolism/analysis ; *Nitrous Oxide/metabolism/analysis ; *Silver Compounds/toxicity ; *Metal Nanoparticles/toxicity ; *Soil Pollutants/toxicity/metabolism ; Nitrification/drug effects ; Soil Microbiology ; }, abstract = {Silver sulfide nanoparticles (Ag2S-NPs), commonly introduced into forest soils via sewage sludge, may disrupt nitrogen (N) cycling under elevated N deposition. This study examined how Ag2S-NPs and earthworms (Eisenia fetida) interact to influence N2O emissions in subtropical forest soils subjected to long-term simulated N deposition. A 60-day incubation was conducted using soils treated with low (1 mg Ag kg[-1]) and high (30 mg Ag kg[-1]) Ag2S-NP doses. Nitrogen deposition alone suppressed N2O emissions by acidifying soil and inhibiting nitrification. In contrast, earthworm activity enhanced emissions by stimulating organic matter turnover and N-cycling gene expression. Under N deposition, Ag2S-NPs significantly increased N2O emissions in a dose-dependent manner, with the high dose raising emissions by 68 % compared to earthworm-only treatments. Metagenomic analysis revealed that this effect was driven by increased gut-associated denitrification, with notable enrichment of narG/H/I and nirK/S genes, and denitrifiers such as Microbacterium and Bacillus. Conversely, soil nitrification declined, as reflected by reduced NO3[-] levels and amoA gene abundance. Multivariate models identified gut denitrification genes as key predictors of N2O flux. These findings highlight the synergistic impact of Ag2S-NPs and earthworms on greenhouse gas emissions in N-deposited soils and underscore the importance of considering nanomaterial-fauna-microbe interactions in forest ecosystems.}, }
@article {pmid41671964, year = {2026}, author = {Zhao, G and Chen, W and Zhang, W and Zhang, R and Huang, X}, title = {Unveiling the environmental fate and risks of non-heterocyclic sulfacetamide: From a novel degradation mechanism to microecological effects.}, journal = {Water research}, volume = {294}, number = {}, pages = {125520}, doi = {10.1016/j.watres.2026.125520}, pmid = {41671964}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; }, abstract = {The presence of sulfonamides (SAs) in the environment has been demonstrated to be a significant factor in pollution. Despite extensive research on heterocyclic SAs, the degradation mechanisms and ecological effects of non-heterocyclic sulfacetamide (SA) remain poorly understood. Our previous study isolated a challenging-to-culture strain, Leucobacter sp. HA-1, known for its SAs-degrading capacity, contains the conserved gene sadA. However, SA was not detected within the degradation spectrum linked to monooxygenase SadA activity. This indicates that other genes may be involved in SA degradation in strain HA-1. In this study, two adjacent and functionally similar amidohydrolases, SamA1 and SamA2, were identified from strain HA-1 as initiators of SA degradation to sulfanilamide (SN). The amino acid sequence similarities of SamA1 and SamA2 with reported enzymes were 39.44% and 34.54%, respectively. The combined expression of SamA1 and SmaA2 had a synergistic effect in enhancing the degradation and resistance of SA. The molecular mechanism behind strain HA-1's SA degradation was elucidated through microscopic analysis combining enzyme characterization with toxicological assessments and comparative genomics. An artificial bioremediation microecosystem targeting SA was established, notably, adding HA-1 enhanced bioaugmentation efficacy for SA elimination significantly. Metagenomic analyses revealed dynamic changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and potential functional enzymes related to SA biodegradation within these microecosystems. Under our experimental conditions, bioaugmentation with HA-1 showed potential as a strategy for SA removal and reduced the accumulation or spread risk of ARGs and MGEs. This study revealed the fate mechanisms and microecological effects of non-heterocyclic sulfacetamide SA, which are different from typical SAs, and contributes to the further promotion of the elimination of the negative environmental and ecological impacts of antibiotics.}, }
@article {pmid41671965, year = {2026}, author = {Niu, L and Pan, Y and Li, Y and Chen, X and Liu, X and Chen, Y and Wang, L and Zhang, W}, title = {WWTP effluents influence prokaryotic viral diversity and interaction with hosts: Regulating the virus-mediated nitrogen-cycling processes in river sediments.}, journal = {Water research}, volume = {294}, number = {}, pages = {125519}, doi = {10.1016/j.watres.2026.125519}, pmid = {41671965}, issn = {1879-2448}, mesh = {*Rivers ; *Geologic Sediments ; *Wastewater ; *Nitrogen Cycle ; Viruses ; Nitrogen ; }, abstract = {As an important water replenishment measure for urban rivers, the input of wastewater treatment plant (WWTP) effluents can change both the nutrient loading and the microbial community diversity of receiving rivers. However, our knowledge of the characteristics of viral communities and virus-mediated nitrogen-cycling processes in WWTP effluents-receiving rivers remains very limited. In this study, the prokaryotic virus, host and non-host communities in sediments were detected via metagenome and virome methods, to explore the variation characteristics of viral communities, interactions with hosts and virus-mediated nitrogen-cycling processes along the upper reference reach (UR), middle receiving reach (MR) and lower recovery reach (LR) of a typical WWTP effluents-receiving river. The results showed that compared to the non-hosts, viruses and hosts were much more sensitive to the influence of WWTP effluents. Among the three reaches, viruses and hosts showed more obvious spatial variability in community diversity and structures than those of non-hosts. Compared to UR, viruses in MR displayed the highest community diversity and virus-to-host abundance ratio, while viruses in LR maintained the high abundance ratio. Co-occurrence network analysis indicated the more important central roles of viruses than those of prokaryotes in bridging species or groups within the virus-host-prokaryote communities, especially in MR and LR. Functional gene analyses revealed that viral communities might potentially regulate nitrogen cycles in MR and LR via two pathways: directly carrying more abundant nitrogen-related auxiliary metabolic genes (N-vAMGs) and indirectly regulating hosts involved in nitrogen transformations (N-hosts) via enriched viruses, which showed strong responses to nitrogen loadings (TN and NO3[-]-N) in rivers. Both N-vAMGs and virus-enrichment N-hosts, dominantly involved in denitrification, dissimilatory nitrate reduction to ammonium, and organic degradation and synthesis processes, significantly increased in MR and LR, which highlighted a long-term regulation potential of viral communities to WWTP effluents-receiving rivers. Together, these findings provided a new insight into the nonnegligible ecological role of viruses in influencing biogeochemical cycles in WWTP effluents-receiving urban rivers.}, }
@article {pmid41671969, year = {2026}, author = {Fan, B and Peng, H and Ran, J and Yao, H and Luo, W and Hong, B}, title = {Environmental and microbial regulation of multi-temporal scale methane flux dynamics in a shallow karst lake.}, journal = {Water research}, volume = {294}, number = {}, pages = {125511}, doi = {10.1016/j.watres.2026.125511}, pmid = {41671969}, issn = {1879-2448}, mesh = {*Methane/analysis/metabolism ; *Lakes/microbiology/chemistry ; Seasons ; Temperature ; Carbon Isotopes ; }, abstract = {Lakes are increasingly recognized as hotspots for methane (CH4) emissions, yet high-frequency (hourly-scale) measurements of CH4 fluxes throughout all seasons and a clear understanding of their underlying environmental control mechanisms are still lacking. Here, we explore the dynamics of CH4 flux and its hydrological and biogeochemical mechanisms in a karst shallow lake ecosystem, based on eddy covariance (EC), stable carbon isotope, and metagenomic sequencing techniques. Our 13-month EC monitoring shows that the lake was a CH4 source to the atmosphere, with average emission rate being 2.07 ± 1.20 mmol CH4 m[-2] d[-1], with the highest emissions in autumn (3.63 ± 0.5 mmol m[-2] d[-1]), accounting for more than twice those of winter. Seasonal CH4 flux variations were primarily driven by water temperature, water level, and electrical conductivity. Elevated temperature stimulated methanogenesis, water level changes altered redox gradients shaping methanogen activity, and electrical conductivity regulated substrate availability favoring acetoclastic methanogens. At the diurnal scale, CH4 emissions were higher at night than during the day, with diel flux variations were mainly controlled by water temperature, which enhanced methanogenesis while suppressing oxidation. These environmental controls on CH4 flux are consistent with the structure of the methanogenic community and support the dominance of acetoclastic methanogenesis. Methanothrix was found to be the dominant (∼65%) methanogenic microbe in this carbonate-rich alkaline karst lake. Additionally, the dominant pathway of CH4 production in the lake was acetoclastic methanogenesis, with the apparent fractionation factor of δ[13]C-CH4 being 1.041 ± 0.002. We emphasize the importance of integrating physicochemical variability with microbial functional potential to advance understanding of biogeochemical feedbacks in carbonate-rich karst systems and improve the accuracy of CH4 emission estimates across scales.}, }
@article {pmid41672081, year = {2026}, author = {Miller, KJ and Wolff, IM and Montes de Oca Valeriano, LA and Soto-Giron, MJ and Jangi, S and Schott, EM and Charbonneau, MR and Ballok, AE and Toledo, GV}, title = {Targeted detection of microbes in synbiotic medical foods SBD111 and SBD121 to evaluate gut persistence: a randomised, open label trial.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-13}, doi = {10.1163/18762891-bja00109}, pmid = {41672081}, issn = {1876-2891}, abstract = {The viability and persistence of orally administered microbes in the human gut are essential to their biological function. We previously described the development of two synbiotic medical foods, SBD111 and SBD121, each comprising four food-derived microbial strains and prebiotic fibres for the dietary management of postmenopausal bone loss and rheumatoid arthritis, respectively. Here, we report a randomised, open-label clinical study examining gut persistence of SBD111 and SBD121 microbes by testing faecal samples from healthy adults following administration for seven days. Thirty-eight participants, aged 18-64 years with a body mass index (BMI) of 18.5-35 kg/m2, were randomised to receive one of the two synbiotic medical foods daily for one week, followed by a four-week monitoring period. Employing quantitative PCR (qPCR), shotgun metagenomics, and culture-based assays, we evaluated the presence and viability of the microbial strains comprising each synbiotic medical food during and after administration. SBD111 and SBD121 were well-tolerated with minimal adverse events reported. Strains were detected in over 80% of participants during the administration period, with strain abundance peaking in the first week. Persistence in the follow-up period varied by strain and detection method. The microbial strains were detected by qPCR and metagenomic sequencing for a median of seven days and three days during the follow-up period, respectively. However, Bacillus amyloliquefaciens was consistently detected for seven days by both methods. Culture-based assays confirmed the presence of viable strains from both synbiotic medical foods in stool samples up to one-week post-consumption. Faecal metagenome diversity and metabolic functional potential remained stable throughout the administration and follow-up periods. Collectively, these results establish that SBD111 and SBD121 deliver viable microbes that transiently persist in the gut, reinforcing their promise for safe and targeted dietary interventions and highlighting the value of multi-platform detection strategies for comprehensive microbial persistence assessment. This trial, funded by Sōlarea biō, is registered at ClinicalTrials.gov (NCT06614166).}, }
@article {pmid41672314, year = {2026}, author = {Gao, C and Sui, Q and Tang, Q and Zhang, J and Yan, B and Yu, D and Zuo, F and Gui, S and Liu, Z and Hu, X and Wei, Y}, title = {Integration of real-time NH4[+]-N control and spatial microbial engineering achieves high removals of nitrogen and carbon in a sequence anoxic-oxic-anoxic (SAOA) system.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134189}, doi = {10.1016/j.biortech.2026.134189}, pmid = {41672314}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Carbon/isolation & purification/metabolism ; Wastewater/chemistry ; Nitrification ; Swine ; Bioreactors/microbiology ; Biomass ; Anaerobiosis ; Animals ; Ammonia/metabolism ; Water Purification/methods ; *Ammonium Compounds/metabolism ; Bacteria/metabolism ; }, abstract = {The imbalance among nitrite supply, nitrate accumulation and aeration demand poses significant challenges in single-stage partial nitrification-anammox (PN/A) systems for stably treating high-strength anaerobically digested swine wastewater (ADSW) at low C/N ratio. Here, we propose a novel process that integrates real-time NH4[+]-N control with a floc-granule partitioned biomass architecture in a sequence anoxic-oxic-anoxic (SAOA) system to dynamically modulate free ammonia (FA) concentration while preventing free nitrous acid (FNA) inhibition. By maintaining an NH4[+]-N endpoint of 50 mg/L, FA was stabilized at 5.2 mg N/L, and FNA was effectively suppressed. Thus, the SAOA system achieved 94.14% TN removal at a loading rate of 0.24 kg N/(m[3]·d) and 92.71% COD at low influent COD/TN ratio of 1.71, respectively. Metagenomic and enzymatic profiling revealed a distinct ecological stratification: floccular biomass was enriched with Candidatus Kuenenia, whereas granular microenvironments favored ammonia-oxidizing bacteria (AOB), accompanied by the upregulation of key nitrification and anammox genes. Kinetic analysis of COD and NH4[+]-N removals revealed a stage-specific metabolic transition from carbon-driven to autotrophic nitrogen-dominated removal. This study provides mechanistically robust and scalable control paradigm for advancing simultaneous, high-efficiency nitrogen and carbon removal from nitrogen-rich and carbon-limited wastewater.}, }
@article {pmid41672322, year = {2026}, author = {Gu, JJ and Mao, BD and Dou, XX and Zhang, BX and Xu, JW and Fu, CW and Lan, BJ and Zhang, XJ and Xu, Z and Gao, F}, title = {Unveiling the mechanisms of mechanical stirring for enhanced performance and stability of algal-bacterial flocs treating low C/N synthetic wastewater.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134175}, doi = {10.1016/j.biortech.2026.134175}, pmid = {41672322}, issn = {1873-2976}, mesh = {*Wastewater/chemistry/microbiology ; *Nitrogen/analysis ; *Microalgae/metabolism ; *Water Purification/methods ; *Carbon/analysis ; *Bacteria/metabolism ; Biological Oxygen Demand Analysis ; Biomass ; Flocculation ; Symbiosis ; }, abstract = {Algal-bacterial symbiotic systems (ABS) represent an environmentally sustainable wastewater treatment technology with significant application potential, though achieving stable and efficient operation remains a critical research challenge. This 180-day comparative study systematically investigated the performance differences and underlying mechanisms between mechanically stirred and aerated algal-bacterial symbiotic flocs (ABF) cultured in low C/N ratio wastewater. The results demonstrate that mechanical stirring enhances symbiotic interactions between microalgae and bacteria, leading to significantly improved performance metrics including higher biomass concentration (3.5 g/L), elevated dissolved oxygen levels (10.3 mg/L), increased lipid content (58.4%) and lipid productivity (9.3 mg/L/d), along with superior settling characteristics as evidenced by the reduced sludge volume index (80.7 mL/g). During Phase Ⅳ, the stirred ABFs exhibited exceptional contaminant removal efficiencies, achieving 98.2% ammonium nitrogen, 83.2% total nitrogen, and 89.7% chemical oxygen demand removal. Extracellular polymeric substance (EPS) analysis revealed stimulated secretion under stirring conditions (222.3 mg/g), with tight-bound EPS (TB-EPS) predominating, significantly enhancing floc structural stability. Metagenomic analysis demonstrated that stirring enriched functional genera like Thauera and Rubrivivax, strengthening denitrification and organic degradation capacities, while activating key pathways such as the TCA cycle and nitrogen metabolism, upregulating the abundance of EPS synthesis-related genes (e.g., galU), elucidating the molecular mechanisms underlying efficient nutrient removal and floc stability. This study presents an optimized strategy for establishing high-performance ABS in low C/N ratio wastewater treatment, offering both environmental sustainability and economic viability.}, }
@article {pmid41672331, year = {2026}, author = {Yu, J and Allela, OQB and Alkhazali, WH and Bishoyi, AK and Oweis, R and Varma, P and Kashyap, A and Panigrahi, R and Chauhan, AS and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M}, title = {The gut microbiome as a modulator of antibiotic resistance: Mechanisms, dynamics, and therapeutic interventions.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108357}, doi = {10.1016/j.micpath.2026.108357}, pmid = {41672331}, issn = {1096-1208}, abstract = {The gut microbiome is increasingly recognized as a critical factor in the dynamics of antibiotic resistance, influencing the acquisition, persistence, and dissemination of antibiotic resistance genes (ARGs) among both commensal and pathogenic bacteria. This research focuses on elucidating the mechanisms by which the gut microbiome modulates the horizontal gene transfer (HGT) of ARGs, a key driver of the global antibiotic resistance crisis. By employing advanced metagenomic sequencing and functional assays, this study aims to identify specific microbial species, genetic elements, and metabolic pathways that either facilitate or inhibit the transfer of ARGs within the gut environment. Particular attention is given to the role of microbial metabolites, interspecies interactions, and environmental factors that shape the resistome the collection of all resistance genes within the microbiome. Additionally, this research explores innovative microbiome-based interventions, such as the use of probiotics, prebiotics, and bacteriophage therapy, to disrupt the transmission of ARGs and restore microbial balance. These interventions are designed to target the gut microbiome as a reservoir of resistance genes, offering a novel approach to curbing the spread of antibiotic resistance. The significance of this work lies in its potential to provide actionable insights into microbiome-mediated resistance mechanisms and to develop targeted strategies that complement traditional antibiotic therapies. By addressing the gut microbiome as a modifiable factor in the resistance landscape, this research could contribute to mitigating the global burden of antibiotic resistance, preserving the efficacy of existing treatments, and improving public health outcomes in the face of this pressing challenge.}, }
@article {pmid41672407, year = {2026}, author = {Furst, AJ and Johnson, KE and Nagel, EM and Yerabandi, N and Kats, AM and Gallagher, TT and Gale, CA and Palmsten, K and Pierce, S and Hoffman, S and Jacobs, K and Fields, DA and Isganaitis, EM and Bode, L and Demerath, EW}, title = {Gestational diabetes, human milk oligosaccharide concentrations, and their links to infant weight gain and the gut microbiome in a United States observational cohort.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {4}, pages = {101235}, doi = {10.1016/j.ajcnut.2026.101235}, pmid = {41672407}, issn = {1938-3207}, support = {R00 HD113834/HD/NICHD NIH HHS/United States ; R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; }, abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) increases offspring obesity risk, but whether this occurs via changes in human milk composition, including alterations in human milk oligosaccharides (HMOs), is unknown.
OBJECTIVES: This study aimed to identify differences in HMO concentrations in mothers with and without GDM and test whether GDM-associated HMOs are associated with infant growth, body composition, and fecal microbiome characteristics over the first 6-mo of life.
METHODS: Human milk was collected at 1-mo postpartum from 337 females (49 with GDM) who fed their infants breastmilk exclusively. HMOs were quantified by high-performance liquid chromatography and multivariate regression models were used to test differences in HMO concentrations by GDM status (false discovery rate adjustment for multiple testing set at q < 0.05). HMOs associated with GDM were then tested for associations with infant growth, body composition, and 1 and 6-mo infant fecal microbial abundances measured by metagenomic whole-genome sequencing.
RESULTS: Participants with GDM had ∼1 SD higher milk 6'sialyllactose (6'SL) {[β (95% confidence interval): 0.58 (0.20, 0.96)] and lacto-N-fucopentaose III (LNFP III) III [95% CI: 0.55 (0.16, 0.94)]} compared with those without GDM and 6'SL concentration was also positively associated with weight and length gain. Although infants of mothers with GDM had lower 1-mo fecal α-diversity and altered abundances of 6 of 56 microbial species detected compared with those without GDM, microbial features were not associated with the concentration of either 6'SL or LNFP III and evidence for mediation of GDM-growth and GDM-microbiome by HMOs was not found.
CONCLUSIONS: Mothers with a GDM diagnosis had higher milk concentrations of LNFP III and 6'SL, and 6'SL was in turn associated with increased infant growth rate, but neither HMO was associated with differential infant gut microbial abundances. The results suggest that the link between 6'SL and faster infant growth, if causal, occurs via mechanisms independent of the infant gut microbiome. This study was registered at clinicaltrials.gov as NCT03301753.}, }
@article {pmid41672513, year = {2026}, author = {Nishijima, S and Hattori, M and Nagata, N}, title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {102}, number = {2}, pages = {82-103}, pmid = {41672513}, issn = {1349-2896}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Japan ; *Health ; *Disease ; East Asian People ; }, abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.}, }
@article {pmid41673004, year = {2026}, author = {Niu, M and Fu, L and Yan, Q and He, Z and Li, D and Zhen, Y and Wang, M and Li, C}, title = {35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41673004}, issn = {2052-4463}, mesh = {*Metagenome ; Metagenomics ; *Microbiota ; *Geologic Sediments/microbiology ; Bacteria/classification/genetics ; }, abstract = {The hadal trench is the deepest part of the global ocean and harbors highly abundant microbial cells. However, the diversity and function of the majority of microbial communities in this part of the ocean are still unclear. Here, we collected 35 metagenomes from three push cores across different sites in both the northern and southern Yap trench to construct a comprehensive gene and genome dataset. A total of 32 million non-redundant genes were predicted from the whole metagenome datasets, with 63% assigned to known functional groups based on currently available databases. A total of 404 metagenome-assembled genomes (MAGs) with completeness >50% and contamination <10% were retrieved, and their taxonomy was highly diverse across 26 phyla. Alpha- and Gammaproteobacteria, Phycisphaerae, Nitrospiria, and Dehalococcoidia were dominant classes across all samples. The nonredundant gene and MAG datasets are valuable resources for advancing our understanding of the diversity, composition, and functions of microbiota in the sediment of the hadal trench.}, }
@article {pmid41673107, year = {2026}, author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG}, title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41673107}, issn = {2045-2322}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/pathology/immunology/genetics/microbiology ; *Inflammation/pathology/genetics ; Mice, Knockout ; Disease Models, Animal ; Dysbiosis ; Autoimmunity ; Mice, Inbred C57BL ; }, abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.}, }
@article {pmid41673333, year = {2026}, author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z}, title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41673333}, issn = {1432-184X}, support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Carbon/metabolism/analysis ; *Bacteria/genetics/metabolism/classification/enzymology ; *Fungi/genetics/metabolism/enzymology/classification ; Carbon Cycle ; Metagenomics ; Hydrology ; Carbon Sequestration ; Rivers/microbiology ; Metagenome ; }, abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.}, }
@article {pmid41673414, year = {2026}, author = {Salokas, J and Sofieva-Rios, S and Paatero, J and Asmi, E and Karppinen, A and Sofiev, M}, title = {Evaluation of commercial kits and purification approaches for DNA extraction from atmospheric samples for 3rd generation sequencing without amplification.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41673414}, issn = {2045-2322}, support = {101086109//HORIZON EUROPE Research Infrastructures/ ; 479507//Research Council of Finland/ ; 337552//Research Council of Finland/ ; 318194//Research Council of Finland/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Environmental Monitoring/methods ; *DNA/isolation & purification ; Sequence Analysis, DNA/methods ; Finland ; *Atmosphere ; }, abstract = {We present a DNA extraction protocol for atmospheric bioaerosol samples collected on glass-fiber filters widely used in air quality monitoring. The protocol produces high-quality molecules suitable for third-generation sequencing and other applications. The initial protocol was developed and applied in a Bioaerosol campaign performed in Finland and Lithuania in 2021 using low-volume air samplers, which posed stringent requirements to the method sensitivity. The protocol included a phenol-chloroform step for DNA purification, thus involving aggressive reagents; it was also quite time consuming and laborious. The present study advances this protocol to exclude the use of hazardous chemicals by using the SPRI paramagnetic bead technology for DNA purification and compares it to several commercial extraction methods. Despite trailing in efficiency to the initial method, the new development proved to be more efficient than several column-based commercial kits. The updated protocol was effective for a relatively high mass ratio of biological material to filter material: 70 nanograms of potential DNA on the filter to one milligram of filter fiber, as detected with the initial phenol-chloroform-based method. However, the new approach was not effective for a mass ratio lower than 15 nanograms of potential DNA per milligram of the filter material. The applicability of the new protocol for preparation of samples for the 3rd generation sequencing was confirmed by subsequent processing of the samples with the Oxford Nanopore (ONT) GridION sequencer.}, }
@article {pmid41673713, year = {2026}, author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ}, title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {65}, pmid = {41673713}, issn = {2049-2618}, support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Biofilms/growth & development ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Droughts ; *Microbiota ; *Rivers/microbiology ; Metagenomics/methods ; Metagenome ; Switzerland ; Diatoms/genetics ; Viruses/classification/genetics/isolation & purification ; Cyanobacteria/genetics/classification ; }, abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.
RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.
CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.}, }
@article {pmid41673851, year = {2026}, author = {Zhu, Z and Kang, J and Song, M and Liu, Y and Dong, H and Wang, L and Fu, M and Ma, C and Guo, Q and Liu, Q}, title = {Early diagnosis of extranodal NK/T lymphoma presenting with oral ulcer and lip swelling by metagenomics next-generation sequencing: a case report.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41673851}, issn = {1472-6831}, mesh = {Humans ; Male ; Adult ; *Lymphoma, Extranodal NK-T-Cell/diagnosis/virology/pathology ; *Oral Ulcer/virology/diagnosis/etiology ; *High-Throughput Nucleotide Sequencing ; Herpesvirus 4, Human/genetics ; *Metagenomics/methods ; Epstein-Barr Virus Infections/diagnosis ; *Lip Diseases ; Early Diagnosis ; *Lip Neoplasms/diagnosis ; }, abstract = {BACKGROUND: Extranodal natural killer/T-cell lymphoma, is a rare, aggressive lymphoma strongly associated with Epstein-Barr virus infection. Its clinical manifestations are often non-specific, and atypical presentations outside the nasal cavity, such as lip swelling or oral ulcers, can mimic benign oral conditions, leading to delayed diagnosis. Histological variability and tissue necrosis further hinder early diagnosis. Metagenomic next-generation sequencing (mNGS) has emerged as a useful adjunct for detecting pathogen-specific nucleic acids when conventional pathology is inconclusive.
CASE PRESENTATION: A 39-year-old man presented with a one-month history of recurrent upper lip swelling and a persistent labial and hard palate ulcer. Examination revealed firm swelling of the upper lip, a U-shaped ulcer on the upper labial mucosa, and an ulcer on the right hard palate. Laboratory tests were normal. Considering the patient's recollection of a prior fish bone injury to the oral mucosa, we performed mNGS on biopsy tissue in addition to routine histopathology. mNGS revealed a high load of Epstein-Barr virus DNA, prompting targeted immunohistochemistry and in situ hybridization, which confirmed the presence of Epstein-Barr virus-encoded RNA in atypical lymphocytes, establishing the diagnosis of extranodal NK/T-cell lymphoma. PET/CT showed a hypermetabolic upper-lip mass without systemic spread. The patient was classified as Ann Arbor stage IE, group A. Treatment with two cycles of pegaspargase, gemcitabine, and oxaliplatin resulted in complete healing of oral lesions, followed by localized radiotherapy. No recurrence was observed at the eight-month follow-up.
CONCLUSIONS: This case illustrates that extranodal NK/T-cell lymphoma can present with isolated oral lesions, posing significant diagnostic challenges. Incorporating mNGS into the evaluation of suspicious or infection-like oral lesions expedite Epstein-Barr virus detection, guide targeted pathological workup, and reduce diagnostic delays, ultimately improving patient outcomes.}, }
@article {pmid41673994, year = {2026}, author = {Lin, C and Wang, J and Chai, S and Yan, Y and Cao, D and Guo, Y and Xu, M and Zhang, Y and Yuan, Z and Shi, Y and Liu, GR and Luo, LJ and Deng, S and Zhao, Y and Zhang, XH and Kang, X and Wei, J and Zhang, Z and Yang, J and Liu, SL and Liu, H}, title = {Enterolactone and THBS1-3TSR synergistically inhibit ovarian cancer and suppress angiogenesis in the tumour microenvironment.}, journal = {British journal of pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1111/bph.70327}, pmid = {41673994}, issn = {1476-5381}, support = {CYCX24017//Heilongjiang CHUNYAN Innovation Team Program/ ; 82104217//National Natural Science Foundation of China/ ; 82020108022//National Natural Science Foundation of China/ ; LH2024H028//Heilongjiang Provincial Natural Science Foundation/ ; YJSCX2025-18HYD//Postgraduate Research & Practice Innovation Program of Harbin Medical University/ ; 2018M630380//China Postdoctoral Science Foundation/ ; LBH-Q21139//Heilongjiang Postdoctoral Financial Assistance/ ; LBH-Z18198//Heilongjiang Postdoctoral Financial Assistance/ ; 2019QD0026//Merit-based Funding for Returned Oversea Students in Heilongjiang Province/ ; 2019-YQ-08//Harbin Medical University Excellent Young Talents Funding/ ; 6101020101//Special Fund of Harbin Medical University/ ; XSTS2025164//Academic Enhancement Support Program of Hainan Medical University/ ; }, abstract = {BACKGROUND AND PURPOSE: Ovarian cancer is a highly malignant disease with poor prognosis due to its insidious occurrence, early metastasis and high rate of recurrence after treatment. Enterolactone (ENL) has previously been reported to inhibit ovarian cancer in positive correlation with THBS1 expression, but the involved molecular events remain unknown. In this study, we looked into interactions between ENL and THBS1 to elucidate the mechanisms underlining their joint inhibitory effects on ovarian cancer.
EXPERIMENTAL APPROACH: We observed the suppressive effect of ENL on ovarian cancer cells by cell counting kit-8, wound healing, transwell, western blot and immunohistochemistry assays. The binding of ENL to THSB1 was assessed by molecular docking and microscale thermophoresis assays. Inhibition of malignant angiogenesis by ENL was inspected by tube formation assay and zebrafish experiment. The in vivo anticancer abilities of ENL were investigated by xenograft and allograft ovarian cancer animal models, and the fecal microbiota was analysed by metagenomics.
KEY RESULTS: This study demonstrated potent inhibitory effects of ENL on ovarian cancer by both in vitro and in vivo experiments. Analysis of 61 clinical samples showed a correlation between poor prognosis and low THBS1 expression. ENL affected the expression of THBS1 and other proteins such as CD36. ENL through binding with the 3TSR domain of THBS1 inhibited malignant angiogenesis and suppressed cancer progression. ENL administration could also ameliorate gut dysbacteriosis.
CONCLUSIONS AND IMPLICATIONS: ENL has potent inhibitory effects on ovarian cancer and suppresses malignant angiogenesis by binding to THBS1-3TSR. ENL ameliorates gut dysbacteriosis.}, }
@article {pmid41674065, year = {2026}, author = {Jo, S and Seo, H and Lee, KA and Kim, S and Rahim, MA and Barman, TI and Kim, HS and Song, HY}, title = {Skin Microbiome Profiling in Patients with Primary Sjögren Disease Compared to Healthy Individuals.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510010}, pmid = {41674065}, issn = {1738-8872}, mesh = {Humans ; *Sjogren's Syndrome/microbiology ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Female ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification ; Adult ; DNA, Bacterial/genetics ; Aged ; Biodiversity ; Case-Control Studies ; Sequence Analysis, DNA ; Skin Microbiome ; }, abstract = {Primary Sjögren disease (SjD) is a systemic autoimmune disease characterized by inflammation of exocrine glands, most commonly leading to dry mouth and dry eyes. Although the etiology of SjD remains unclear, emerging evidence suggests that the microbiome modulates immune homeostasis. This study aimed to compare the skin microbiomes of SjD patients with those of healthy controls (HCs) using 16S rRNA gene sequencing. Taxonomic composition, alpha and beta diversity, and predicted functional profiles were evaluated. We observed a significant depletion of Cutibacterium and a marked reduction in microbial diversity in SjD patients. Beta diversity analyses revealed distinct clustering among groups. Functional prediction suggested the downregulation of metabolic pathways associated with microbial homeostasis. Our findings propose that alterations in the skin microbiota may contribute to SjD pathogenesis and serve as potential biomarkers or therapeutic targets.}, }
@article {pmid41674105, year = {2026}, author = {Song, B and Zeb, J}, title = {The midgut of Aedes albopictus shapes its bacteriome but not its mycobiome.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70505}, pmid = {41674105}, issn = {1526-4998}, support = {//City University of Hong Kong/ ; }, abstract = {BACKGROUND: Midgut microbiota consists mainly of bacteria and fungi and can interact directly or indirectly with ingested pathogens. However, both the specific microbes that stably colonize the mosquito midgut and how the midgut shapes their microbiome remain poorly understood. In this study, we analyzed the midgut microbiome of the insect vector Aedes albopictus at three different developmental stages collected from the field. Additionally, we reared field-collected larvae under laboratory conditions, using either field water from the breeding habitat or sterilized water, to track the linear evolution of the microbiome from larvae to adulthood.
RESULTS: Our metagenomic analysis revealed that the mosquito host selected specific bacterial species, while the mycobiome remained virtually identical to that of the surrounding water. We identified 42 core bacterial species that form a highly interactive network, as well as two core fungal species, both of which were consistently more abundant in the mosquito gut than in the surrounding water across all life stages in both laboratory and field conditions. Furthermore, we successfully assembled 271 bacterial genomes de novo, 14 of which belonged to core species. These 14 bacterial genomes were enriched in genes associated with antioxidant function and cAMP metabolism.
CONCLUSION: This study uncovers fluctuating bacterial dynamics alongside conserved fungal communities in the mosquito gut, suggesting distinct mechanisms that shape the bacteriome and mycobiome. This study highlights the antioxidant function in stabilizing bacteria in Aedes albopictus. © 2026 Society of Chemical Industry.}, }
@article {pmid41674268, year = {2026}, author = {Zaccaria, T and Beblo-Vranesevic, K and de Jonge, MI and Netea, MG and Rettberg, P}, title = {Survival limits of psychrotolerant microorganisms with relevance for planetary protection of the icy moons.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {384}, number = {2314}, pages = {}, doi = {10.1098/rsta.2024.0435}, pmid = {41674268}, issn = {1471-2962}, support = {//Deutsches Zentrum für Luft- und Raumfahrt/ ; //Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; /ERC_/European Research Council/International ; }, mesh = {*Extraterrestrial Environment ; *Moon ; Spacecraft ; *Microbial Viability ; Arctic Regions ; }, abstract = {Investigating the survival limits of extremophilic microorganisms exposed to simulated space conditions can shed light on the ability of terrestrial microorganisms to survive and propagate on other planetary bodies. Although microbes can be found in all environmental niches on Earth, this study focuses on psychrophilic and psychrotolerant microorganisms (prokaryotes and eukaryotes) which have been isolated from locations of interest such as icy moon analogue environments (e.g. Canadian high arctic, Antarctica) and cleanrooms, which might be relevant for forward planetary protection. Our research aimed to reproduce conditions for microorganisms on spacecraft travelling to the outer solar system which could contaminate the icy moon's subsurface oceans. The microorganisms were grown under oligotrophic conditions in minimal media supplemented with only a single carbon source and exposing them to extreme conditions, in terms of temperature fluctuations, in terms of freeze and thaw cycles, and radiation, as they occur during the space travel to the outer solar system. Our results in combination with future metagenome data and phenotype prediction tools will allow the identification of planetary protection relevant microorganisms in spacecraft assembly cleanrooms and on spacecraft and support the development of a target-oriented planetary protection constraints for missions to the icy moons. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.}, }
@article {pmid41674272, year = {2026}, author = {Macey, MC and Mahnert, A and Stephens, BP and Kucukkilic-Stephens, E and Olsson-Francis, K}, title = {An ensemble binning approach to identify functional diversity in cleanroom environments.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {384}, number = {2314}, pages = {}, doi = {10.1098/rsta.2024.0438}, pmid = {41674272}, issn = {1471-2962}, support = {//UK Space Agency/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Metagenome ; *Environment, Controlled ; Spacecraft ; }, abstract = {Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilization protocols to minimize microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high-quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity, temperature and alkalinity. Growth rate index (GRiD) analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.}, }
@article {pmid41674474, year = {2026}, author = {Sun, Y and Shuai, X and Sheng, Q and Lu, Y and Wu, Z and Sun, Y and Wu, D and Guo, X}, title = {Torque Teno Virus or Herpesviruses Detection By Metagenomic Next-Generation Sequencing Predicts In-Hospital Major Adverse Events in Critically Ill Patients With Severe Infections.}, journal = {Journal of medical virology}, volume = {98}, number = {2}, pages = {e70840}, pmid = {41674474}, issn = {1096-9071}, support = {//Zhongguancun Precision Medicine Foundation/ ; }, mesh = {Humans ; Critical Illness ; *Torque teno virus/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Aged ; *Herpesviridae/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; *Cross Infection/virology/epidemiology ; *Metagenomics/methods ; Adult ; *DNA Virus Infections/virology ; Risk Factors ; *Herpesviridae Infections/virology/diagnosis ; China/epidemiology ; Intensive Care Units ; }, abstract = {Viral detection occurs frequently in critically ill patients. Patients with multiple viremic events had a higher ICU mortality. The highly sensitive mNGS technology has significantly enhanced viral pathogen detection rates. We enrolled 134 critically ill patients with severe infections who underwent mNGS testing during January 2019 to December 2021, at Qilu Hospital (Qingdao) of Shandong University. Viral pathogens were identified in 78 cases (58.2%). Torque teno virus (TTV) or herpesviruses (HVs) showed the highest detection rates (23.1% and 29.9%, respectively). The incidence of major adverse events (MAEs) in the hospital was 53.0%. Patients with TTV or HVs detection had more secondary nosocomial infections and stress ulcers, and the incidence of MAEs showed an increasing trend. Multivariate Logistic regression analysis showed that APACHE II score (OR: 1.10, 95%CI: 1.02-1.19, p = 0.018) and TTV or HVs detection by mNGS (OR: 2.40, 95% CI: 1.05-5.50, p = 0.038) were independent risk factors for MAEs. This study advocates the use of mNGS for detecting viruses in critically ill patients with severe infections, as it serves as a predictor for heightened risk of in-hospital MAE.}, }
@article {pmid41674563, year = {2025}, author = {Lyu, W and Chen, L and Li, DF and Li, SY and Dai, Q and Zhou, HL and Liu, YY and Zhou, JY and Liang, XJ and Wang, L}, title = {Lactobacillus johnsonii-FM1 modulates gut microbiota and secretes anticancer metabolite vanillic acid to inhibit colorectal tumorigenesis.}, journal = {iMetaOmics}, volume = {2}, number = {3}, pages = {e70050}, pmid = {41674563}, issn = {2996-9514}, abstract = {During colorectal cancer (CRC) progression, probiotics support gut microbial balance, enhance intestinal barrier integrity, and exert antioxidant and anti-inflammatory effects. Such supplementation may slow tumor growth and serve as an adjunctive therapy for CRC. In this study, we evaluated the impact of Lactobacillus johnsonii-FM1 in Apc [Min/+] and azoxymethane/dextran sulfate sodium-induced CRC mouse models. Our results demonstrate that L. johnsonii-FM1 markedly reduces tumor number, size, and volume in both models. Shotgun metagenomic sequencing showed that L. johnsonii-FM1 increases the abundance of potentially beneficial taxa while decreasing opportunistic pathogens, thereby preserving gut barrier function. Moreover, untargeted metabolomics paired with liquid chromatography-tandem mass spectrometry identified vanillic acid (VCA) as a key bioactive metabolite produced by L. johnsonii-FM1. In vitro, VCA inhibits CRC cell line proliferation, diminishes colony formation, induces cell-cycle arrest, and promotes apoptosis. Mechanistically, VCA attenuates CRC progression by suppressing Wnt/β-catenin signaling. Our findings suggest a promising probiotic-based adjunctive strategy for CRC prevention and treatment.}, }
@article {pmid41674575, year = {2025}, author = {Zhang, Z and Xu, Y and Pang, K and Wu, C and Zhao, C and Lei, T and Zhang, J and Hai, T and Zhao, F and Zhao, Y}, title = {Microbiota humanization drives human-like metabolic and immune transcriptomic shifts in pigs.}, journal = {iMetaOmics}, volume = {2}, number = {3}, pages = {e70034}, pmid = {41674575}, issn = {2996-9514}, abstract = {Pigs are increasingly recognized as promising candidates for clinical xenotransplantation and as large-animal models for biomedical research; however, interspecies differences in gut microbiota, immune function, and metabolism remain major barriers. To address this, we established gut microbiota-humanized (GMH) pigs by transplanting human fecal microbiota into antibiotic-treated pigs. We systemically evaluated alterations in microbiota composition, serum metabolites, and immune cell profiles using integrated metagenomic, quasi-targeted metabolomic and single-cell transcriptomic (scRNA-seq) analyses. Metagenomic profiling revealed a shift in the intestinal microbiota of GMH pigs toward a human-like composition, characterized by enrichment of Bacteroidia and depletion of Bacilli. Metabolomic analysis showed that GMH pigs exhibited serum metabolite profiles more closely resembling those of humans. Among 423 detected serum metabolites, 136 that were lower in control pigs than in humans were upregulated in GMH pigs, whereas 79 that were elevated in control pigs decreased post-transplantation. Notably, pathways related to tryptophan metabolism, bile acid biosynthesis, and fatty acid metabolism were enhanced in GMT pigs, while carbon-related and glycolytic pathways were attenuated, indicating partial convergence toward human metabolic phenotype. Integration of microbial and metabolite data identified 20 and 33 metabolites associated with Bacteroidia and Bacilli, respectively. scRNA-seq profiling of peripheral blood mononuclear cells demonstrated transcriptional and compositional remodeling of T cells, monocytes, and B cell subsets in GMH pigs. These findings demonstrated that human fecal microbiota can reshape both systemic metabolic and immune artitecture in pigs, offering a robust large-animal platform for studying host-microbiota interactions and advancing translational application in xenotransplantation and microbiome-based therapeutics.}, }
@article {pmid41674603, year = {2026}, author = {Agudelo, C and Nsereko, M and Ainebyona, A and Andama, A and Castro, R and Leung, SRM and Nakafeero, J and Nannyonga, G and Nolan, K and Teran, L and Wambi, P and Young, MG and Kato-Maeda, M and Cattamanchi, A and Jaganath, D and Wobudeya, E and Wolf, AR}, title = {Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.29.26345155}, pmid = {41674603}, abstract = {BACKGROUND: Stool-based molecular tests are a noninvasive option for pediatric tuberculosis (TB) diagnosis, but have lower sensitivity compared to sputum-based tests. Untargeted metagenomic sequencing (mNGS) on stool could improve sensitivity and identify new gene targets for molecular testing.
METHODS: We performed shotgun mNGS on DNA isolated from stool samples of children undergoing assessment for pulmonary TB in Uganda. We defined the performance of mNGS to identify Mycobacterium tuberculosis (Mtb) against a microbiological reference standard (MRS, TB if sputum Xpert Ultra or culture positive) and a composite reference standard (TB if confirmed or unconfirmed TB). We also compared accuracy of mNGS against the stool-based Xpert Ultra test. Finally, we identified enriched genomic loci among Mtb classified reads.
RESULTS: We analyzed 176 stool samples of children with a median age of 3.6 years (IQR, 1-6 years). !"#$%&'(')*(+,-. (')*(&*%&$'$/$'$*&(01(234-(5$')(60&$'$/*(78(9*1$%*9(as ≥ 1, 2, or 5 sequence fragments were 35.5% (95% CI 19%:;;<=.(>;?@<(AB>< : 45%), and 19.4% (13%-25%) respectively, and specificities 92.64% (87%-96%), 97% (93%-99%), and 99.3% (96%-100%). Stool Xpert Ultra had similar sensitivity (22.6%) to stool mNGS considering all samples tested. In a head-to-head comparison, stool mNGS had lower sensitivity than stool Xpert Ultra (38.5% vs. 53.8%, difference -15.3%, 95% CI 14-68 to 25-81). mNGS utilized rRNA, virulence proteins and membrane proteins not targeted in current PCR-based platforms.
CONCLUSIONS: Metagenomic sequencing of stool DNA did not increase sensitivity of TB detection, but identified novel targets for molecular testing that may support development of more sensitive tests.}, }
@article {pmid41674628, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during autologous stem cell transplantation and are associated with dose-dependent microbiome modulation: Results from a pilot clinical trial.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.02.26345403}, pmid = {41674628}, abstract = {Plant-based dietary strategies may offer a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked to infectious complications and inferior survival. We conducted a single-arm study to test the feasibility and biological activity of a high-fiber, plant-based, whole-food meal delivery intervention during the peri-transplant period. Adults with multiple myeloma (n = 22) received fully prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting consumption of nutrient-dense, high-fiber foods despite transplant-related symptoms that often limit oral intake. The primary endpoints were feasibility and tolerability, defined by successful enrollment, adherence to study procedures, and patient-reported intake of study meals; diet was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming at least some proportion of delivered meals and with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. Larger randomized trials are warranted to determine whether microbiome-targeted nutrition can reduce transplant-related toxicities, enhance immune recovery, and improve disease control in multiple myeloma. The trial is registered at ClinicalTrials.gov (NCT06559709).}, }
@article {pmid41674736, year = {2026}, author = {Mukenschnabl, K and Humpel, O and Abdalla, TE and Wood, E}, title = {An Unusual Case of Unexplained Infertility: Co-colonization of the Uterus and Seminal Fluid.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e101251}, pmid = {41674736}, issn = {2168-8184}, abstract = {Chronic endometritis (CE) is defined as a persistent, mild inflammation of the endometrium induced by intrauterine bacterial infection. CE has been associated with infertility in patients with recurrent in vitro fertilization (IVF) failure. We report an unusual case of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility. A 35-year-old woman presented to the office for infertility evaluation after 16 months of inability to conceive naturally using ovulation kits. Initial workup revealed adequate ovarian reserve with an anti-Müllerian hormone (AMH) level of 4.8 ng/mL, tubal patency on hysterosalpingogram, and normal semen analysis. The patient and her partner failed to conceive following three cycles of ovulation induction with intrauterine insemination (IUI). In preparation for IVF, an endometrial biopsy (EMB) was performed, and five CD138+ plasma cells per 10 high-power fields suggested CE. The patient underwent antibiotic therapy, yet EMB remained positive. At this time, the partner's semen culture was positive for Enterococcus faecalis and Escherichia coli. Endometrial microbiome metagenomic analysis (EMMA) and analysis of infectious chronic endometritis (ALICE) demonstrated co-colonization with the same bacteria seen on her partner's semen culture. Both the patient and her partner required multiple rounds of antibiotic therapy before successful conception via IVF. This case demonstrates an unusual occurrence of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility, suggesting a potential pathway for CE development from bacteriospermia. The patient's EMMA/ALICE tests and the partner's semen cultures revealed the presence of the same bacteria. While current literature does not identify the development of CE from the bacteria in a partner's semen, there is an association between bacteria in semen and infertility. In couples with unexplained infertility, thorough evaluation for CE with EMB and EMMA/ALICE can be performed in conjunction with a semen culture on the partner to explore potential co-colonization and guide dual-partner treatment.}, }
@article {pmid41674838, year = {2026}, author = {Berta, J and Rowe, L and Garry, B}, title = {Catching the Mardi Gras fever: Quantifying the impact of mass gathering tourism on local bacterial prevalence and community diversity in municipal wastewater.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41674838}, issn = {2693-5015}, support = {U01 AI151812/AI/NIAID NIH HHS/United States ; }, abstract = {We employed 16S metagenomic analysis to measure the impact of Mardi Gras tourism on the bacterial ecology found in New Orleans' municipal wastewater. Throughout the peak of the 2023 Carnivale season, species turnover was significantly higher in New Orleans than it was in our control site. Alpha diversity metrics peaked 2-to-3 weeks after Mardi Gras Day, increasing between 65% and 1967% over Carnivale. We also found that human pathogens and microbiota had significantly stronger, more positive correlations with the rise in Mardi Gras tourism than did environmental control species. These changes in wastewater abundance for two species - S. enterica and E. coli - mirrored the concurrent clinical isolate data from the same region for Salmonella spp. and STEC. We also found that multiple alpha and beta diversity measures correlated strongly with increases in tourism during the peak of Carnivale season.}, }
@article {pmid41674903, year = {2025}, author = {Ding, Z and Ren, K and Xu, Y and Feng, T and Cui, K and Liu, Q and Liao, C}, title = {Disease-driven restructuring of the gut microbiome underlies inflammatory bowel disease dysbiosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1744574}, pmid = {41674903}, issn = {1664-302X}, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent intestinal disorder with rising global incidence, yet its complex pathogenesis remains poorly understood, underscoring the need to clarify the microbial mechanisms underlying intestinal inflammation. IBD is associated with a profound imbalance of the gut microbial ecosystem. However, the ecological and functional remodeling of the gut microbiota during IBD progression remains unclear. This study used metagenomic sequencing to investigate microbial composition, functional capacity, and ecological interactions in the gut microbiota of IBD patients compared with healthy individuals.
RESULTS: The IBD group exhibited significantly reduced microbial diversity and a distinct community structure compared with healthy controls. Pro-inflammatory genera such as g_Fusobacterium (p < 0.001) and g_Morganella (p < 0.001) were enriched, whereas short-chain fatty acid producing bacteria, including g_Ruminococcus (p < 0.0001) and g_Agathobacter (p < 0.0001), were markedly depleted. Functional annotation revealed decreased abundance of carbohydrate-active enzymes (GH3, GH44, GH53, and GH77; all p < 0.05) associated with polysaccharide degradation, together with enrichment of pathways related to immune activation and inflammation, such as the JAK-STAT and chemokine signaling pathways (p < 0.05). Co-occurrence network analysis further showed that IBD-associated microbes formed positively correlated clusters dominated by inflammatory taxa, whereas healthy microbiota were organized around SCFA-producing commensals.
CONCLUSION: Compared with healthy individuals, the gut microbiota of IBD patients undergoes functional reprogramming characterized by loss of metabolic versatility and enrichment of inflammation-related pathways. These findings provide new insights into the ecological and metabolic mechanisms through which the gut microbiota contribute to intestinal inflammation and disease progression.}, }
@article {pmid41674905, year = {2025}, author = {Díaz-Santiago, E and Sadio, TD and Diéme, JS and Hurtado-Martínez, M and Kindler, C and Manrique, E and Pugnaire, FI}, title = {Soil microbial communities in contrasting environments show a common core of species linked to Maytenus senegalensis shrubs.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1699694}, pmid = {41674905}, issn = {1664-302X}, abstract = {INTRODUCTION: The existence of a core microbiota specific to a plant species, or the set of microorganisms shared by all plant individuals of the species, is of utmost importance because of its many conceptual and practical consequences. The core microbiota is assumed to gather the most ecologically and functionally relevant microorganisms associated to a plant in a given environment, presumably establishing positive feedbacks that support its persistence and performance in a plant community.
METHODS: We tested the existence of a potential core microbiota in Maytenus senegalensis shrubs in two contrasted, distant ecosystems; a dry environment (Almeria, Spain) and a relatively wetter ecosystem (Dakar, Senegal).
RESULTS: Soil microbial community structure widely differed between sites influenced by soil and climate. However, a subset of microbial phylotypes appeared consistently associated to all M. senegalensis plants across our two disparate ecosystems while they were absent in the surrounding soil, suggesting the presence of a core microbiota in M. senegalensis.
DISCUSSION: Microbiota had an effect on germination that differed between sites, perhaps due to climatic constrains. We show that the assembly of understory microbial communities depends on the plant's sorting effect on the surrounding soil microbiota, plus some other taxa likely transferred by seeds; this assembly mechanism is relevant for the coevolution of plants and microorganisms, and critical for potential community responses to environmental changes.}, }
@article {pmid41675149, year = {2025}, author = {Shen, H and Du, C and Jiang, S and Dong, W and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Native synthetic microbial communities enhance zha-chili by boosting the fermentation capacity of indigenous microorganisms.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70009}, pmid = {41675149}, issn = {2996-9514}, abstract = {Fermented foods are a crucial part of the global diet, accounting for one-third of global food intake. Traditional fermented foods often rely on natural fermentation, leading to safety risks. The construction of synthetic microbial communities (SynComs) tailored for fermented foods is a key strategy to solve these issues. Here, we designed and constructed SynComs consisting of two bacterial and three fungal species, utilizing the study model of zha-chili. Using various high-throughput sequencing technologies, the dynamic alternations of microorganisms during the fermentation process were investigated, and the impact of SynComs on the fermentation process was evaluated. SynComs reduced fermentation time by approximately 15 d, increased flavor yields (8% for ethyl lactate and ethyl acetate), and greatly improved the quality of the zha-chili. Meanwhile, SynComs altered the succession of the fungal community so that Pichia became the dominant microorganism throughout the fermentation process, and the pattern of fungal community succession was brought closer to the null model. Metagenomic annotation results showed notable changes in functional genes, especially in glycoside hydrolases family. SynComs enhanced the positive correlations between indigenous microorganisms and flavor compounds while increasing other community microorganisms' contribution to flavor production. These findings provide a new approach to improve the quality of zha-chili and other traditional fermented foods through natural fermentations. We proposed that SynComs enhanced fermented foods by boosting the fermentation capacity of indigenous microorganisms.}, }
@article {pmid41675151, year = {2025}, author = {Skoog, EJ and Kebabonye, K and Klempay, B and Gondwe, M and Makati, K and Babayani, N and Jongman, M and Bowman, J and Aluwihare, L}, title = {Viral metagenomics of Okavango Delta water pans reveal novel insights into wildlife disease potential.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70018}, pmid = {41675151}, issn = {2996-9514}, abstract = {Botswana's Seronga region saw a mass elephant die-off potentially linked to water sources. This study analyzes Okavango Delta metagenomes, uncovering a diversity of viruses and harmful pathogens. Findings highlight the importance of understanding viral ecology in these waters and support One Health's objective in protecting human, animal, and ecosystem health.}, }
@article {pmid41675153, year = {2025}, author = {Ye, L and Hu, Q and Zang, T and Wang, Y and Heng, H and Chan, EWC and Chen, S}, title = {Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70004}, pmid = {41675153}, issn = {2996-9514}, abstract = {The pork microbiome was investigated using an integrated approach combining isolation and metagenomic sequencing methods to comprehensively analyze the pathogens and resistome on pork surfaces. The study revealed a large number and diversity of pathogens and resistance genes, potentially originating from air, transportation, water, or cross-contamination. These findings underscore the importance of implementing multifaceted food surveillance strategies to monitor and mitigate these risks effectively.}, }
@article {pmid41675165, year = {2025}, author = {Liu, S and Ye, Y and Guo, B and Hu, Y and Jiang, K and Liang, C and Xia, S and Wang, H}, title = {ViOTUcluster: A high-speed, All-in-one pipeline for viromic analysis of metagenomic data.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70023}, pmid = {41675165}, issn = {2996-9514}, abstract = {ViOTUcluster is a user-friendly, high-speed, accurate, All-in-one solution that streamlines the entire viromic analysis workflow-from raw reads to the generation of viral operational taxonomic units tables, as well as other key viromic analysis tasks.}, }
@article {pmid41675545, year = {2024}, author = {Huang, L and Luo, S and Liu, S and Jin, M and Wang, Y and Zong, X}, title = {Comparative multiomics analyses reveal the breed effect on the colonic host-microbe interactions in pig.}, journal = {iMetaOmics}, volume = {1}, number = {1}, pages = {e8}, pmid = {41675545}, issn = {2996-9514}, abstract = {Dysregulation of the gut microbiota often leads to immune-related disorders, indigestion, or diarrhea. Here, Jiaxing Black (JXB) pig, a local Chinese pig breed known for its great tolerance and digestibility of nutrients, was employed for a metagenomic and transcriptomic integrative analysis to reveal the gut microbiota-genes and gut microbiota-pathway interactions. A total of 452 differentially expressed genes, and 174 phyla were found between the JXB and the Duroc × Landrace × Yorkshire (DLY) pigs. Detailed analysis revealed that the differences in colon gene expression signatures between the JXB and DLY are mainly enriched in metabolic and inflammatory responses, with Lactobacillus and Lachnospiraceae enriched in DLY and JXB, respectively. Notably, Pacebacteria, Streptophyta, and Aerophobetes were found to participate in the PI3K-Akt mediated immune response in both pig breeds; however, they only accelerated the metabolism in the intestines of JXB pigs. Moreover, the host could regulate microbe metabolism and immune response by Ig-like domain-containing protein and ITIH2, PAEP, and TDRD9, respectively. Taken together, our results revealed both common and breed-specific regulations of host genes by gut microbiota in two pig breeds.}, }
@article {pmid41675707, year = {2025}, author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L}, title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.}, journal = {iMetaOmics}, volume = {2}, number = {1}, pages = {e62}, pmid = {41675707}, issn = {2996-9514}, abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.}, }
@article {pmid41675709, year = {2025}, author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y}, title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.}, journal = {iMetaOmics}, volume = {2}, number = {1}, pages = {e51}, pmid = {41675709}, issn = {2996-9514}, abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.}, }
@article {pmid41676059, year = {2026}, author = {Li, X and Yi, H and Wu, G and He, A and Li, R and Long, Y and Lin, C and Jiang, Z}, title = {Neutrophil CD64 index for rapid diagnosis of Pneumocystis jirovecii pneumonia in malignancy patients requiring mechanical ventilation: a retrospective analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1706786}, pmid = {41676059}, issn = {1664-302X}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) incidence and associated mortality have risen significantly in non-HIV immunocompromised patients, highlighting the urgent need for rapid, non-invasive diagnostics. Current methods face limitations including invasiveness, prolonged processing, or inadequate specificity. The neutrophil CD64 (nCD64) index emerges as a promising novel biomarker. Here, we conducted this study to evaluate the diagnostic performance of nCD64 index for PJP and further assess the predictive value of its longitudinal changes for 28-day mortality.
METHODS: This retrospective cohort study (July 2022-March 2025) analyzed mechanically ventilated malignancy patients with unexplained diffuse pulmonary infiltrates at a tertiary intensive care unit (ICU). PJP diagnosis required predefined clinical, radiological, and bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF mNGS) criteria. The nCD64 index was measured via flow cytometry at ICU admission and serially after ≥3 days of anti-PJP therapy. Diagnostic performance for PJP and prognostic value for 28-day mortality were assessed.
RESULTS: Among 28 PJP and 38 non-PJP patients, nCD64 index was significantly higher in PJP (13.33 vs. 2.84, p < 0.001). Receiver operating characteristic (ROC) curve analysis showed an area under the curve (AUC) of 0.846 (95% CI: 0.736-0.932) for PJP diagnosis, with sensitivity 89.3% and specificity 71.1% at cutoff ≥7. Multivariate analysis confirmed nCD64 index as an independent PJP predictor (OR = 1.097, 95% CI: 1.026-1.173; p = 0.007). Post-therapy nCD64 index elevation predicted 28-day mortality with high sensitivity (81.8%) and specificity (86.7%).
CONCLUSION: The nCD64 index functions as a dual-purpose biomarker for malignancy patients with respiratory failure requiring mechanical ventilation: it provides a rapid, non-invasive diagnostic tool for PJP and dynamically stratifies mortality risk. Moreover, dynamic tracking offers a real-time window into treatment response, guiding therapeutic decisions.}, }
@article {pmid41676099, year = {2026}, author = {Zheng, H and QuBie, X and Wang, J and Liu, P and Zhang, W}, title = {Clinical features and chest CT findings of Chlamydia pneumoniae pneumonia.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1717744}, pmid = {41676099}, issn = {2296-858X}, abstract = {OBJECTIVE: This study aimed to investigate the clinical features and chest computed tomography (CT) findings in 42 patients with Chlamydia pneumoniae pneumonia, as confirmed by metagenomic next-generation sequencing (mNGS).
METHODS: We conducted a retrospective analysis of clinical data and chest CT findings (both at disease onset and within 1 month thereafter) in 42 patients diagnosed with Chlamydia pneumoniae pneumonia by mNGS at our hospital between August 2022 and August 2025.
RESULTS: Of the 42 patients, 25 (59.5%) presented with fever, 26 (61.9%) with sore throat, 30 (71.4%) with cough, 27 (64.3%) with expectoration, 11 (26.2%) with myalgia, 10 (23.8%) with general fatigue, and 10 (23.8%) with neurological symptoms such as headache and dizziness. Laboratory tests revealed that 12 patients (28.6%) showed a mild increase in white blood cell count, 10 (23.8%) had elevated neutrophil counts, 21 (50.0%) exhibited elevated C-reactive protein (CRP) levels, and 6 (14.3%) had CRP levels exceeding 100 mg/L. In the early stage, chest CT demonstrated a lobular pneumonia pattern in 16 patients (55.2%), involvement of a single lung lobe in 20 (69.0%), predominant lower-lung distribution in 19 (65.5%), and a nodular-patchy pattern in 8 patients (27.6%) with a nodular-patchy pattern. The main accompanying features included a halo sign in 25 patients (86.2%), centrilobular nodules in 23 (79.3%), and bronchial wall thickening in 20 (69.0%). In the mid-to-late stage, chest CT revealed a lobular pneumonia pattern in 23 patients (76.7%), single-lobe involvement in 23 (76.7%), and predominant lower-lung distribution in 20 (66.7%). The major concomitant features were a halo sign in 21 patients (70.0%), centrilobular nodules in 20 (66.7%), and bronchial wall thickening in 24 (80.0%).
CONCLUSION: Chest CT findings of Chlamydia pneumoniae pneumonia are predominantly characterized by a lobular pneumonia pattern, lower-lobe distribution, and associated features such as bronchial wall thickening, centrilobular nodules, and a peripheral halo sign. Certain imaging differences exist between early and middle-to-late stages, with the nodular-patchy pattern potentially representing an ultra-early imaging marker, which may provide clues for early clinical intervention.}, }
@article {pmid41676115, year = {2024}, author = {Zhou, Y and Zheng, J and Song, W and Yan, X and Du, L and Ma, Z and Fu, Y and Ouyang, Z and Xiao, Y and Liu, Z and Tian, F and Wong, JWH and Shih, JHD and Liang, S and Tian, H and Liu, L and Wei, K and Zhang, C and Li, J and Wang, X}, title = {OUTPOST: A comprehensive analysis software for whole-metagenome shotgun sequencing incorporating group stratification.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e29}, pmid = {41676115}, issn = {2996-9514}, abstract = {The whole metagenOme shotgun seqUencing sTream Pipeline that is cOmprehensive and uSeful for mulTi groups experiments (OUTPOST) is a comprehensive analysis software for whole-metagenome shotgun sequencing incorporating group stratification, which encompasses 14 modules and boasts over 50 functions, distinguishing itself for its comprehensiveness when compared with 17 existing whole-metagenome shotgun sequencing (WMGS) tools. OUTPOST introduces innovative methods for multi-group experimental designs and meta-analysis-based biomarker identification.}, }
@article {pmid41676117, year = {2024}, author = {Shi, P and Xu, S and Yang, Z and Wang, L and Wu, Y and Li, Y and Zhu, Z}, title = {Harnessing gut microbiota for longevity: Insights into mechanisms and genetic manipulation.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e36}, pmid = {41676117}, issn = {2996-9514}, abstract = {The gut microbiota is pivotal in maintaining health, with most microorganisms being beneficial, except for a few pathogens. Emerging evidence suggests a link between the gut microbiome and aging, hinting at its potential role in longevity. However, understanding the relationship is challenging due to the microbiota's complexity. This perspective summarizes the mechanisms by which gut microbes regulate host lifespan and explores genetic manipulation strategies to promote healthy aging in the elderly.}, }
@article {pmid41676120, year = {2024}, author = {Ling, Y and Liu, Z and Han, S and Wu, H and Mu, C and Zhu, W}, title = {Integrated omics revealed the altered colonic microenvironment after inhibition of peripheral serotonin synthesis by LP533401.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e34}, pmid = {41676120}, issn = {2996-9514}, abstract = {Gut-derived 5-hydroxytryptamine (5-HT), known as serotonin, plays a crucial role in regulating gastrointestinal functions. However, the impact of disruptions in gut-derived 5-HT synthesis on the early gut microbiome and intestinal microenvironment remains unclear. In this study, LP533401, an inhibitor targeting peripheral 5-HT synthesis, was administered orally to neonatal rats starting at 4 days post-birth. By day 11, inhibition of gut-derived 5-HT resulted in altered colonic morphology, characterized by increased crypt depth and reduced myenteric thickness. To investigate the mechanisms underlying these alterations, we employed a combination of metagenomics, mucosal transcriptome, and untargeted metabolomics on colonic samples. Metagenome profiling revealed an upregulation in the microbial two-component system (ko02020) and tyrosine metabolism (ko00350), with minimal effects on taxa abundances. Transcriptome profiling analysis indicated the discriminant expression of genes enriched in pathogen infection-responsive signaling (e.g., Salmonella and Yersinia infection) and the Wnt signaling pathway that affected stem cell proliferation. Consistent with increased crypt depth, marker genes related to cell proliferation were excessively activated. Metabolomics analysis indicated lower ascorbate level and higher succinic acid level, correlating with 5-HT concentrations and increased crypt depth. Additionally, altered metabolic pathways (e.g., nucleotide metabolism, signal transduction, metabolism of cofactors and vitamins) suggested an impact on the colonic function. In summary, early inhibition of gut-derived 5-HT may unfavorably reshape the colonic microenvironment, affecting gut morphology, microbial function, stem cell proliferation, and mucosal metabolism.}, }
@article {pmid41676124, year = {2024}, author = {Xie, Y and Xu, S and Xi, Y and Li, Z and Zuo, E and Xing, K and Bai, L and Li, K}, title = {Global meta-analysis reveals the drivers of gut microbiome variation across vertebrates.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e35}, pmid = {41676124}, issn = {2996-9514}, abstract = {Shifts in gut microbial diversity and structure are one route by which vertebrate hosts adapt to local environmental conditions. However, recent studies have mostly been limited to a single species, small sample sizes, or restricted geographic ranges. Therefore, drawing a global picture of vertebrate gut microbiome diversity, community structure, and determinants for their adaptive shifts remains to be elucidated. We here collected 6508 samples from 113 vertebrate species covering diverse classes, feeding behaviors, and host habitats based on 16S rRNA gene sequencing. The results showed that host diet pattern had a significant impact on gut microbiome variation, which might drive taxonomic and functional contents of gut microbiome across vertebrates. Of note, the phylum Fusobacteria were enriched in carnivorous vertebrate gut while herbivorous vertebrate gut selectively increased the abundance of Verrucomicrobia. Also, climate factors were strongly associated with gut microbiome variation across vertebrates. Interestingly, we found that the abundance of microbiota belonging to Bacteroidetes increased gradually while the members from Proteobacteria showed a decreasing trend from high- to low-latitude zones, potentially contributing to vertebrate adaptation to local climate condition. Additionally, we comprehensively deciphered the common antibiotic resistomes and their potential mobility between terrestrial vertebrate gut microbiome (n = 487) and their sympatric soil biological environment samples (n = 203) by integrating metagenomic sequencing datasets. Particularly, potential horizontal antibiotic resistance genes (e.g., bacA) transfers were detected between vertebrates gut microbiome and their sympatric soil biological environment. Together, our findings provide new evidence of how external environmental factors affect vertebrate gut microbiome variation.}, }
@article {pmid41676125, year = {2024}, author = {Xia, JJ and Zhong, Q and Li, ZM and Wei, QZ and Jiang, LY and Duan, C and Jia, HJ and Tan, YM and Han, LY and Krutmann, J and Wang, J and Liu, X}, title = {Culture dependent and independent approaches reveal the role of specific bacteria in human skin aging.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e26}, pmid = {41676125}, issn = {2996-9514}, abstract = {Skin aging is a dynamic process involving a spectrum of phenotypic changes, making it an attractive model for studying microbiome-phenotype interactions. Therefore, 822 facial microbial samples and 14 skin phenotypes from corresponding areas were assessed in a Chinese cohort. Porphyrins and the chronological age exhibited the most significant microbial variability. We further profiled the dynamics of the skin microbiome associated with age and aging phenotypes. Using a multiple linear regression model, we predicted premature/delayed aging-related microbial species, mainly Moraxella osloensis and Cutibacterium acnes. We also validated the biological functions of the host-microbe interactions in vitro. Moraxella osloensis isolated from healthy skin regulates collagen metabolism and extracellular matrix assembly, and promotes cell senescence in human keratinocytes and fibroblasts, making it potentially applicable in the development of antiaging interventions.}, }
@article {pmid41676130, year = {2024}, author = {Yousuf, S and Luo, H and Zeng, M and Chen, L and Ma, T and Li, X and Zheng, M and Zhou, X and Chen, L and Xi, J and Lu, H and Cao, H and Ma, X and Bian, B and Zhang, P and Wu, J and Gan, R and Jia, B and Sun, L and Ju, Z and Gao, Y and Malik, WA and Ma, C and Lyu, H and Li, Y and Hou, H and Zhou, Y and Bai, D and Wang, Y and Yang, H and Xun, J and Du, S and Zhang, T and Wan, X and Peng, K and Xu, S and Wen, T and Chen, T and Liu, YX}, title = {Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e42}, pmid = {41676130}, issn = {2996-9514}, abstract = {The advent of next-generation sequencing has revolutionized microbiome research, enabling in-depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high-throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user-friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon).}, }
@article {pmid41676189, year = {2026}, author = {Zhang, G and Fang, X and Yang, H and Zhu, Y}, title = {Severe empyema caused by mixed oral anaerobic bacterial infection: a case report.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {28}, pmid = {41676189}, issn = {2523-1995}, abstract = {BACKGROUND: Empyema is a life-threatening pleural infection that can result from various bacterial sources. While oral anaerobic bacteria are recognized as potential pathogens, severe empyema caused by mixed oral anaerobic bacterial infection remains clinically rare. Recent advances in metagenomic next-generation sequencing (NGS) have improved the etiological diagnosis of complex infections. This case demonstrates the clinical significance of NGS technology and oral health in preventing systemic infections.
CASE DESCRIPTION: An 80-year-old male with poor oral hygiene and multiple dental caries presented with acute onset of left-sided chest pain, chills, and fever. Physical examination revealed diminished breath sounds over the left lung. Imaging studies confirmed left-sided empyema. Pleural fluid NGS identified mixed oral anaerobic bacteria including Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Finegoldia magna. The patient underwent thoracoscopic empyema debridement, with postoperative tissue pathology showing suppurative inflammation with fibrinous necrosis. Surgically excised tissue NGS additionally detected Finegoldia magna along with Epstein-Barr virus and human herpesvirus 6. Following targeted anti-infective therapy with meropenem and metronidazole, the patient recovered successfully.
CONCLUSIONS: This case highlights the critical role of NGS technology in identifying mixed oral anaerobic pathogens and guiding precision-targeted treatment of empyema. The atypical presentation of empyema caused by oral anaerobic bacteria warrants early surgical intervention combined with appropriate antimicrobial therapy. Our findings emphasize the importance of oral health maintenance in preventing life-threatening systemic infections and broaden our understanding of oral-systemic disease relationships.}, }
@article {pmid41676216, year = {2026}, author = {Dang, Y and Deng, Z and Wang, K and Luo, J and Wang, C and Long, F and Kong, J}, title = {Cystic fibrosis complicated by allergic bronchopulmonary aspergillosis in a Chinese adolescent: a case report and literature review.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {43}, pmid = {41676216}, issn = {2523-1995}, abstract = {BACKGROUND: Cystic fibrosis (CF) predisposes patients to allergic bronchopulmonary aspergillosis (ABPA). The objective of this study is to enhance the recognition of CF-related ABPA (CF-ABPA) in adolescents through a detailed case study. A multidisciplinary management approach is essential. Early diagnosis and intervention could substantially improve outcomes, warranting further longitudinal research on optimized treatment protocols.
CASE DESCRIPTION: A 15-year-old patient presenting with persistent respiratory symptoms underwent a series of diagnostic tests, including serum immunoglobulin E (IgE) testing, chest computed tomography (CT), bronchoscopy, bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), and whole-exome sequencing to identify CFTR mutations. The diagnostic findings revealed markedly elevated serum IgE levels (2,359.0 IU/mL), the presence of bronchiectasis with mucus plugging on CT imaging, and mNGS detection of Aspergillus fumigatus with an abundance of 97.28%. The diagnosis of CF-ABPA was confirmed by identification of a pathogenic CFTR mutation. Later antifungal therapy and corticosteroids produced notable clinical improvement.
CONCLUSIONS: CF was under-recognized historically, but this case shows that it is a clinically important cause of bronchiectasis and ABPA in Chinese adolescents. The identification of Aspergillus was accurate with the mNGS. Genetic test confirmed that the subject is a CF patient with compound heterozygous mutations in CFTR gene. The finding urges the clinician to have a high index of suspicion for the CF-ABPA in those with asthma-like refractory symptoms with structural lung disease. When diagnosed early and accurately, antifungal therapy and inhaled corticosteroids can be administered timely. The patient experienced a notable improvement both clinically and radiologically, as well as functionally. The future work should promote awareness of this clinical entity and systematic screening of similar patients in China. Further multicenter studies are necessary to formulate diagnostic and therapeutic guides for CF-ABPA in Asia.}, }
@article {pmid41676438, year = {2025}, author = {Liu, Y and Ise, Y and Takami, H and Urakawa, R and Tateno, R and Toyoda, A and Ohte, N and Shi, W and Jiang, L and Isobe, K}, title = {Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70054}, pmid = {41676438}, issn = {2996-9514}, abstract = {Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene- or taxon-specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium-related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and [[15]]N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation-that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower-pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher-pH range but diminished within the lower-pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher-pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower-pH soils were enriched in stress-adaptive functions, which promoted ammonium retention and limited N transformations-thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium-related N cycling processes across forests under varying environmental conditions.}, }
@article {pmid41676442, year = {2025}, author = {Chaboy-Cansado, R and Talavera-Marcos, S and Gallego-Simón, R and Cobeta, P and Roscales, G and Rastrojo, A and de Cárcer, DA}, title = {Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70037}, pmid = {41676442}, issn = {2996-9514}, abstract = {Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research.}, }
@article {pmid41676447, year = {2025}, author = {Deng, F and Han, Y and Li, M and Peng, Y and Chai, J and Yang, G and Li, Y and Zhao, J}, title = {HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70041}, pmid = {41676447}, issn = {2996-9514}, abstract = {Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively compares PacBio High-Fidelity (HiFi) sequencing-based metagenome-assembled genomes (MAGs) against Illumina MAGs, Oxford Nanopore Technologies (ONT) MAGs, and isolate whole-genome sequencing genomes from the same sample. HiFi sequencing yielded 31 high-quality MAGs, including 10 complete circular genomes. HiFi MAGs demonstrated significantly higher completeness, continuity, and lower contamination than Illumina or ONT MAGs (p-adj < 0.05). Crucially, HiFi MAGs exhibited closer genomic proximity to corresponding isolates at both single-nucleotide polymorphism and gene presence/absence levels. This benchmarking establishes HiFi as a robust approach for generating MAGs rivaling isolated genome quality, providing critical insights for accurate microbial genomic studies.}, }
@article {pmid41676450, year = {2025}, author = {Zhang, L and Liu, Y and Wang, S and Ching, JY and Tam, WH and Leung, TF and Leung, TY and Chan, PKS and Mak, JWY and Cheung, CP and Tun, HM and Chang, EB and DeLeon, O and Huang, Q and Chen, X and Huo, H and Miao, Y and Cheong, PK and Ip, KL and Yeung, YL and Chang, MK and Lyu, C and Yang, H and Li, B and Fan, Y and Sun, Y and Jiang, S and Ng, SC and Chan, FKL}, title = {MOMMY study profile: An integrative early-life multi-omics cohort in China.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70068}, pmid = {41676450}, issn = {2996-9514}, abstract = {Large-scale, prospective birth cohorts capturing the complex interplay between the gut microbiome, host biology, and environmental exposures are crucial to understanding early-life health but remain scarce, particularly within Asian populations. To address this gap, we established the MOMMY cohort (The MOther-infant Microbiota transmission and its link to long terM health of babY), a large, prospective birth cohort uniquely designed to investigate maternal-paternal-infant microbiota transmission and its impact on child health within the understudied Chinese population. MOMMY aims to recruit 20,000 families from three geographically and economically diverse regions across China. This cohort prospectively follows pregnant mothers, fathers, and their infants, with children up to 7 years of age. Since September 2019, we have systematically collected a comprehensive repository of longitudinal biospecimens-including maternal and infant stool, breast milk, cord blood, and parental blood-stored in an accredited biobank. This is complemented by extensive data on environmental exposures, diet, and health outcomes gathered through validated questionnaires and physician assessments. The MOMMY cohort's unique value lies in its unprecedented scale, geographic diversity, and its integrative multi-omics design, which will combine metagenomic, metabolomic, immunologic, and epigenetic data. By creating this unique resource, MOMMY will elucidate how early-life microbial and molecular trajectories, shaped by genetic and environmental factors, influence child development and disease risk, thereby filling a critical gap in global microbiome research.}, }
@article {pmid41676497, year = {2026}, author = {Lindstedt, K and Wheelock, A and Samutela, M and Kabir, W and Chasaya, M and Namuziya, N and Marsden, EJ and Kapasa, M and Mumba, C and Mulenga, B and Nkole, L and Pieciak, R and Mudenda, V and Chikoti, C and Ngoma, B and Chimoga, C and Chirwa, S and Pemba, L and Nzara, D and Lungu, J and Forman, L and Simulundu, E and MacLeod, W and Moyo, C and Somwe, SW and Holt, KE and Sundsfjord, A and Gill, CJ}, title = {Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41676497}, issn = {2692-8205}, support = {T32 HL125232/HL/NHLBI NIH HHS/United States ; }, abstract = {Klebsiella pneumoniae (Kp) is a leading cause of neonatal and infant deaths in sub-Saharan Africa and frequently associated with antimicrobial resistance. Previously, we identified Kp as a major cause of fatal community-associated lower respiratory infections among infants and children under five years in Lusaka, Zambia, using postmortem tissue sampling and pathogen specific multiplex qPCR. In this follow-up study, we employed a novel culture-independent RNA-probe hybridization-capture metagenomic sequencing approach, targeting Kp pan-genome core and accessory genes, to perform in-depth genomic analysis of Kp from eleven post-mortem lung biopsy samples from seven of these children. Analysis detected Kp in all cases except one, which identified Klebsiella quasipneumoniae subspecies similipneumoniae. Core-genome multi-locus sequence typing (cgMLST) revealed six clonal groups (CG607, CG1123, CG10072, CG280, CG3648, and CG10344) belonging to five sublineages (SL607, SL17, SL280, SL37, and SL10072), with perfect concordance between paired samples from the same case. Two infants sampled the same month harbored SL607 lineages sharing 621 out of 629 cgMLST alleles, suggesting clonal spread. Kp capsule (K) loci were detected in all but one case and included potential vaccine targets KL25, KL23, and KL122. Antimicrobial resistance genes were widespread among samples, particularly encoding resistance toward aminoglycosides, β-lactams, sulphonamides, tetracyclines, and trimethoprim. Extended spectrum β-lactamases were identified in four cases, three of which were bla CTX-M-15. The acquired Kp sideophore yersiniabactin (lineage ybt14) was identified in both cases associated with SL607, and the acquired siderophore aerobactin (lineage iuc5) was identified in one of these, suggesting possible convergence of antimicrobial resistance and hypervirulence. The detection of Kp with extensive antimicrobial resistance causing fatal community acquired pneumonia signals a deeply concerning epidemiologic shift from a largely nosocomial pathogen. This calls for urgent epidemiological investigations to better understand the burden, transmission dynamics, antimicrobial resistances, and potential vaccine targets for Kp in other community settings across sub-Saharan Africa.}, }
@article {pmid41676723, year = {2026}, author = {Kafer, LA and Escapa, IF and Boyd, AI and Tostado, AR and Kambal, A and Blutt, SE and Avadhanula, V and Piedra, PA and Lemon, KP}, title = {Streptococcus pneumoniae colonization modulates human nasal epithelial responses to respiratory syncytial virus infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41676723}, issn = {2692-8205}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; }, abstract = {Respiratory syncytial virus (RSV) is a major cause of morbidity and mortality in infants globally. Specific nasal bacterial genera are differentially associated with RSV severity in infants: Haemophilus and Streptococcus with more severe disease and Dolosigranulum with healthy controls or milder outcomes. We hypothesized these differential bacterial effects begin at the epithelial level. Therefore, we established human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) as a model system to assess effects of individual nasal microbionts on the epithelial response to subsequent RSV infection and of RSV on those microbionts. Infant-derived HNO-ALI were monocolonized with either Streptococcus pneumoniae, nontypeable Haemophilus influenzae, or Dolosigranulum pigrum one day before viral infection. RSV reduced colonizing S. pneumoniae and D. pigrum levels without affecting H. influenzae. S. pneumoniae precolonization uniquely reduced RSV levels during infection. S. pneumoniae precolonization also modulated the epithelial transcriptional response to RSV infection more so than H. influenzae or D. pigrum, with a pronounced effect on genes involved in immune response, cell cycle, stress, and growth signaling. Gene set enrichment analysis showed S. pneumoniae precolonization blunted RSV-induced increase in inflammatory and immune responses, consistent with S. pneumoniae also modulating RSV-induced cytokine production. Furthermore, S. pneumoniae precolonization blocked RSV-mediated dysregulation of cell-cycle genes, consistent with preventing arrest. Bacterial rescue of cell-cycle progression is a potential mechanism for reduced infectious virion production, since cell-cycle arrest enhances RSV replication. HNO-ALI facilitated elucidation of bacterial-viral-epithelial interplay at a frequent site of viral infection, directly linking nasal bacterial colonization to RSV infection dynamics.}, }
@article {pmid41677194, year = {2026}, author = {Simm, NM and Williams, GM and Fowler, S and Barlow, K and Carter, B and Talley, NJ and Keely, S and Duncanson, K and Hoedt, EC}, title = {A Scoping Review of Methods Used to Investigate Relationships between Dietary Intake and the Gastrointestinal Microbiome.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuaf306}, pmid = {41677194}, issn = {1753-4887}, support = {//Australian Government Research Training Program Scholarship/ ; //Australian NSW Health Round 5 Early-Mid Career Grant/ ; }, abstract = {The gastrointestinal (GI) microbiome is intrinsically linked to human health and disease, with dietary intake being a major modifiable variable contributing to microbial colonization and fermentation. Diet-microbiome studies are heterogeneous in the methods used to assess and record dietary intake, to sequence the microbiome data, and to analyze associations. To capture the extent of these inconsistencies, we performed a systematic scoping review to synthesize the information on methods used to assess and compare relationships between diet and the GI microbiome in human studies. Our search identified papers with metrics of both dietary intake and the GI microbiome (using either 16S rRNA or metagenomic shotgun sequencing) and specific diet-microbiome associative analysis. The databases searched were MEDLINE, EMBASE, CINAHL, Cochrane, and Google Scholar, and the search produced 22, 228 unique records after de-duplication. After full-text screening, 1,262 articles were selected for full extraction. A subset of 295 studies captured whole dietary intake and investigated associations with the GI microbiome. This subset assessed diet using 84 different food frequency questionnaires, 12 alternative surveys, and 4 types of diet recalls or diaries ranging from 1 to 14 days. Fifty-five percent (n = 163) of studies investigated habitual dietary intake, 35% (n = 101) investigated recent dietary intake, and 10% (n = 30) used methods to assess both. Eighty-one percent of studies employed 16S rRNA sequencing, with wide variation in extraction, sequencing, pre-processing, and annotation methods. Gaps in the reporting of the methods for each step of the sequencing and analysis process were evident, limiting future comparison of study outcomes. Microbiome-specific statistical methods were used in 11% of the subset-predominantly correlational methods that are not recommended for microbiome data. In conclusion, this review revealed extensive inconsistencies within the exploratory diet-microbiome studies, despite the existence of recommendations to assist researchers. Collaborative efforts to develop consensus in methods and reporting are needed to substantially progress the obtaining of high-quality evidence and meta-analysis in the diet-microbiome research field.}, }
@article {pmid41677732, year = {2026}, author = {Dos Santos, LCRM and de Almeida, JDR and de Sousa, NSO and Fernandes, FDS and Ennes, JFV and Frickmann, H and de Souza, JVB and de Souza, ÉS}, title = {Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials.}, journal = {Biology}, volume = {15}, number = {3}, pages = {}, pmid = {41677732}, issn = {2079-7737}, support = {EDITAL N. 020/2024 - PRODUTIVIDADE EM CT&I//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; CNPq/MCTI Universal Call No. 10/2023//National Council for Scientific and Technological Development/ ; }, abstract = {The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches-culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses-discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota.}, }
@article {pmid41678125, year = {2026}, author = {Hou, Y and Sun, H and Meng, S and Xu, W and Yu, Y and Wang, W and Liu, D and Jia, H and Wang, Y and Chu, H and Sun, Z}, title = {Deciphering the different Mycobacterium avium complex infections of HIV and non-HIV patients by bacterial GWAS and immune cells flow cytometry.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41678125}, issn = {1435-4373}, support = {82272347//National Natural Science Foundation of China/ ; 2022-1G-2161//Capital Health Research and Development of Special Fund/ ; }, abstract = {PURPOSE: Pulmonary diseases caused by Mycobacterium avium complex (MAC) show species-specific epidemiology: M. avium predominates in HIV-positive patients, while M. intracellulare mainly affects immunocompetent hosts. This study aimed to elucidate the bacterial and host mechanisms underlying these differences.
METHODS: We integrated clinical metagenomic next-generation sequencing (mNGS), k-mer-based bacterial genome-wide association study (GWAS) of clinical isolates, peripheral blood immunophenotyping of 175 patients, and mouse infection models with or without CD4 depletion.
RESULTS: K-mer GWAS identified lipid metabolism and transport genes (notably mce) enriched in isolates from hosts with different HIV statuses. Immunophenotyping showed that in HIV-negative patients, M. intracellulare infection elicited higher NKT cell frequencies than M. avium, a difference absent in HIV-positive hosts. In mice, anti-CD4[-]/M. intracellulare infection showed steadily increasing bacterial burden with time (ρ = 0.824), whereas M. avium exhibited no such trend. Early after infection (weeks 1-2), anti-CD4[-]/M. avium group had higher bacterial burden and NKT levels than anti-CD4[-]/M. intracellulare, but by week 4 the pattern reversed (all p < 0.05). CD4 depletion eliminated species-specific differences in NKT activation, and at both weeks 2 (p < 0.05) and 4 post-infection (p > 0.05), the anti-CD4[+]/M. avium groups carried a higher bacterial burden than the anti-CD4[+]/M. intracellulare groups.
CONCLUSION: MAC species exhibit fundamentally divergent infection dynamics driven by differential NKT cell activation, likely shaped by species-specific lipid antigens. This lipid-NKT axis explains contrasting clinical patterns of M. avium and M. intracellulare and highlights a potential target for host-directed interventions.}, }
@article {pmid41678126, year = {2026}, author = {Yao, Y and Lai, Y and Wu, Q and Xu, W}, title = {Targeted next-generation sequencing improves diagnosis and antimicrobial stewardship in Chlamydia psittaci pneumonia.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41678126}, issn = {1435-4373}, support = {20231001//Changning District Medical Key Specialty/ ; 20231001//Changning District Medical Key Specialty/ ; }, abstract = {UNLABELLED: PURPOSE : Chlamydia psittaci pneumonia (CPP) remains underdiagnosed due to nonspecific clinical manifestations. This study assessed the clinical utility of targeted next-generation sequencing (tNGS) in optimizing CPP diagnosis and antimicrobial stewardship, with a focus on empirical quinolone efficacy.
METHODS: We conducted a retrospective cohort study of 35 CPP patients (November 2022-October 2023) diagnosed by tNGS of respiratory specimens (8 sputum/27 bronchoalveolar lavage fluid [BALF]). Data included epidemiological history, laboratory findings, imaging features, therapeutic interventions, and clinical outcomes. Statistical comparisons between severe and non-severe CPP were performed using Student's t-test and Mann-Whitney U tests.
RESULTS: Median diagnostic delay post-admission was 4 days (IQR:3-5). Fever predominated as initial presentation (97.1%), with 45.7% reporting avian contact. Leukocyte counts were normal/mildly elevated,, yet neutrophil ratio (83.86 ± 6.17%) and D-dimer (1.31 ± 0.86 mg/L) were notably increased. All patients showed elevated CRP (175.52 ± 87.62 mg/L) and ESR (70.00 ± 22.62 mm/h). Severe CPP cases (n = 8) exhibited higher CRP (p = 0.041) and procalcitonin (p = 0.013) than non-severe cases. Common comorbidities included hepatic dysfunction (68.6%) and pleural effusion (34.3%). Polymicrobial co-infections occurred more frequently in severe CPP cases than in non-severe cases (OR = 21.07, 95% CI:1.11-402.30). tNGS-guided diagnosis prompted antibiotic adjustment in 60.0% of patients (21/35) to targeted quinolone, tetracycline, or combination therapy. Clinical recovery was achieved in 97.1%, with 2.9% mortality.
CONCLUSIONS: tNGS enhances early CPP diagnosis and targeted antimicrobial adjustment. Quinolones demonstrate high efficacy as empirical treatment. The strong association between severe CPP and polymicrobial co-infections necessitates comprehensive pathogen screening. Study limitations include a single-center design and a small sample size, warranting validation through prospective multicenter studies.}, }
@article {pmid41678593, year = {2026}, author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH}, title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.}, journal = {Circulation research}, volume = {138}, number = {4}, pages = {e326978}, pmid = {41678593}, issn = {1524-4571}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; }, abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.}, }
@article {pmid41679088, year = {2026}, author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW}, title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {2}, pages = {126697}, doi = {10.1016/j.syapm.2026.126697}, pmid = {41679088}, issn = {1618-0984}, mesh = {*Phylogeny ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; Microbiota/genetics ; Biodiversity ; DNA, Bacterial/genetics ; *Alphaproteobacteria/classification/genetics ; Lichens/microbiology ; Bacteria/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.}, }
@article {pmid41679417, year = {2026}, author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J}, title = {Female reproductive microbiome in fertility care.}, journal = {Fertility and sterility}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fertnstert.2026.02.015}, pmid = {41679417}, issn = {1556-5653}, abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. Although conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of the methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multiomics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads vs. relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches on the basis of clinical context and discuss emerging technologies, including multiomics integration for implementing microbiome assessment in fertility care.}, }
@article {pmid41679496, year = {2026}, author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y}, title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {123973}, doi = {10.1016/j.envres.2026.123973}, pmid = {41679496}, issn = {1096-0953}, mesh = {*Microplastics/toxicity ; *Rivers/microbiology ; *Seawater/microbiology ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects ; Bacteria ; Environmental Monitoring ; Biofilms ; *Water Microbiology ; }, abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.}, }
@article {pmid41679688, year = {2026}, author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM}, title = {Modulation of host proteostasis by Prevotella corporis via induction of the heat shock response.}, journal = {Cell stress & chaperones}, volume = {31}, number = {2}, pages = {100150}, pmid = {41679688}, issn = {1466-1268}, support = {R01 AG077534/AG/NIA NIH HHS/United States ; }, mesh = {*Proteostasis ; Animals ; Caenorhabditis elegans/metabolism/microbiology ; *Prevotella/physiology/metabolism ; *Heat-Shock Response ; Gastrointestinal Microbiome ; Humans ; HSP70 Heat-Shock Proteins/metabolism ; }, abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, whereas the mechanisms by which commensal microbes confer proteoprotection have received comparatively little attention. We previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates from the Human Microbiome Project on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to Prevotella corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.}, }
@article {pmid41679750, year = {2026}, author = {Lamont, RF and Jørgensen, JS}, title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1471-0528.70173}, pmid = {41679750}, issn = {1471-0528}, abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.
METHODOLOGY: A narrative review.
RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.}, }
@article {pmid41679819, year = {2026}, author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M}, title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124886}, doi = {10.1016/j.carbpol.2026.124886}, pmid = {41679819}, issn = {1879-1344}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation & purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; }, abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.}, }
@article {pmid41679837, year = {2026}, author = {Sacco, O and Johansen, EL and Tian, Y and Holck, J and Kirkensgaard, JJK and Blennow, A and De Lise, F and Shaikh-Ibrahim, A and Moracci, M and Curci, N and Svensson, B and Cobucci-Ponzano, B and Wang, Y}, title = {Biochemical characterisation of the 4-α-glucanotransferase from the hyperthermophilic archaeon Pyrobaculum arsenaticum and its formation of high-amylose resistant starch.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124919}, doi = {10.1016/j.carbpol.2026.124919}, pmid = {41679837}, issn = {1879-1344}, mesh = {*Glycogen Debranching Enzyme System/metabolism/chemistry ; *Amylose/chemistry/metabolism ; *Pyrobaculum/enzymology ; *Starch/chemistry ; Hot Temperature ; Hydrolysis ; Hydrogen-Ion Concentration ; }, abstract = {High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85 °C, pH 5.5; Naples, Italy), showed highest activity at 100 °C and pH 5.5, and specific activity of maltotriose disproportionation at 75 °C of 1170 U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75 °C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.}, }
@article {pmid41680314, year = {2026}, author = {Alrasheed, AS and Zawawi, AM and Alsulami, LM and Alghirash, FA and Alsalmi, SO and Alhalal, IA}, title = {Clinical utility of metagenomic next-generation sequencing in diagnosing spinal infections: a systematic review and meta-analysis.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {41680314}, issn = {1432-0932}, }
@article {pmid41680318, year = {2026}, author = {Choudhary, S and Kanaujia, R and Bahadur, R and Angrup, A}, title = {The role of metagenomic next-generation sequencing in spinal infections: a systematic review and meta-analysis.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {41680318}, issn = {1432-0932}, }
@article {pmid41680567, year = {2026}, author = {Chen, L and Hong, C and Xie, Y}, title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {76}, pmid = {41680567}, issn = {1720-8319}, mesh = {Humans ; *Sarcopenia/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; Aged ; Muscle Strength ; }, abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.}, }
@article {pmid41680579, year = {2026}, author = {López-Guzmán, SF and Sánchez-Jasso, DE and Hernández-Sánchez, J and Oviedo, N and Bermudez-Cruz, RM}, title = {Molecular Characterization of the Murine Catsper4 Promoter and its Regulation by CREMτ.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {33}, number = {2}, pages = {411-423}, pmid = {41680579}, issn = {1933-7205}, support = {IMSS R-2023-785-056//Instituto Mexicano del Seguro Social/ ; }, mesh = {Animals ; *Promoter Regions, Genetic ; *Cyclic AMP Response Element Modulator/metabolism/genetics ; Male ; Mice ; *Calcium Channels/genetics/metabolism ; *Gene Expression Regulation ; Mice, Inbred C57BL ; }, abstract = {Cation channel sperm-associated protein 4 (CATSPER4) is a subunit of the sperm-specific cation/calcium channel, CatSper, located in the principal piece of the sperm flagellum. It is expressed during the late stages of spermatogenesis, and disruption of the gene encoding this protein leads to male infertility. Mutations in Catsper4 are linked to asthenozoospermia. However, the molecular mechanisms regulating Catsper4 expression remain unclear. Here, we present a detailed molecular characterization of the Catsper4 promoter in mice, focusing on the role of the cAMP-responsive element modulator isoform τ (CREMτ) in its transcriptional regulation. Analysis of publicly available metagenomic chromatin immunoprecipitation-sequencing (ChIP-seq) data revealed the presence of activation histone marks-H3K4me3, H3K4me1, and H3K27ac-within a region corresponding to the 631 bp predicted promoter, suggesting an active promoter region. Although the predicted Catsper4 promoter showed minimal activity, a 65 bp deletion at the 3'-end of the promoter significantly enhanced the transcription. Moreover, removal of the 239 bp in the 5'-flanking region also increased the transcriptional activity, indicating that the