@article {pmid42612378,
year = {2026},
author = {Wang, Y and Wang, C and Han, X and Ji, J and Song, J and Zhang, M and Qi, W and Peng, Y},
title = {Salinity-dependent nitrifier adaptation shapes partial nitritation resilience under dynamic saline conditions: Mechanistic insights into Nitrosomonas salt adaptation.},
journal = {Water research},
volume = {307},
number = {},
pages = {126738},
doi = {10.1016/j.watres.2026.126738},
pmid = {42612378},
issn = {1879-2448},
abstract = {Salinity stress is a promising strategy for establishing partial nitritation (PN). Nevertheless, the adaptation of nitrifiers and its implications for PN stability under dynamic saline conditions remain poorly understood. In this study, a continuous-flow self-circulating up-flow fluidized bed reactor (AOAN-Zier) was employed to systematically investigate the effects of salt loading rate (SLR) fluctuations on nitrifier functional responses and PN resilience under different salinity backgrounds. PN was rapidly established within 7 d under salt-free conditions, achieving a nitrite accumulation ratio (NAR) of 96% on day 9. Subsequent responses to SLR reduction differed depending on salinity history. At 10 g/L salinity, reduced SLR alleviated nitrite-oxidizing bacteria (NOB) inhibition and resulted in PN deterioration. In contrast, after long-term exposure to 30 g/L salinity, the system maintained an average NAR of 99% despite SLR reduction, owing to the sustained loss of NOB functional activity. Activity assays, microbial succession, and metagenomic analyses revealed that PN resilience was primarily determined by NOB absolute activity rather than the relative activity balance between AOB and NOB. Long-term saline selection promoted functional divergence among nitrifiers, with salt-adapted Nitrosomonas maintaining ammonia oxidation capacity through coordinated osmotic regulation, nitrogen metabolism, oxidative stress defense, and energy conservation. Moreover, the salt-adapted sludge retained high AOB activity after desalination under mainstream-like low-ammonium conditions. This study provides new insights into salinity-dependent nitrifier adaptation and advances the understanding of microbial mechanisms underlying PN resilience under dynamic saline conditions.},
}

@article {pmid42612504,
year = {2026},
author = {Liu, Y and Zhang, C and Zhang, Y and Pang, J and Zhang, J and Li, J and Shi, H and He, X and Kang, Y and Shen, J},
title = {Multivariable-adjusted multi-omics signatures reveal gut microbial functional alterations and metabolic dysregulation in intrinsic capacity decline.},
journal = {The journal of nutrition, health & aging},
volume = {30},
number = {10},
pages = {100945},
doi = {10.1016/j.jnha.2026.100945},
pmid = {42612504},
issn = {1760-4788},
abstract = {BACKGROUND: Intrinsic capacity (IC) decline is inherently correlated with aging, yet distinguishing specific IC-related biomarkers from general physiological aging markers remains a significant challenge. We aimed to identify multi-omics signatures associated with IC decline after adjustment for relevant covariates and to explore the functional pathways potentially involved in IC decline.

METHODS: We analyzed 110 fecal (metagenomics) and 121 serum (untargeted metabolomics) samples from older adults at Beijing Hospital. Multivariable models were applied adjusting for age, sex, Charlson Comorbidity Index (CCI), fish intake, and fruit intake frequency. Differential analyses and network-based mediation approaches were used to assess microbiome-metabolome-IC associations.

RESULTS: After multivariable adjustment, 57 bacterial species and 56 serum metabolites were associated with IC status. The normal IC group showed enrichment of multiple taxa, including Lactobacillus zeae and Paenibacillus glucanolyticus. IC decline was associated with concurrent alterations in amino acid and carnitine-related metabolic pathways, including changes in L-serine, Cysteine, N6,N6,N6-trimethyl-L-lysine, and carnitine C5-OH. Network-based mediation analysis identified overlapping associations among senescence-related metabolites (N1,N8-diacetylspermidine), dietary-derived microbial products (3-(3-hydroxyphenyl)-3-hydroxypropanoic acid), and secondary bile acids (3-epideoxycholic acid), suggesting a structured microbiome-metabolome architecture linked to IC variation.

CONCLUSIONS: This study identifies a multi-omics signature associated with IC decline after adjustment for major demographic, clinical, and dietary factors. The findings reveal concurrent alterations in circulating metabolites related to nutrient and carnitine metabolism, alongside compositional and functional differences in the gut microbiome. Together, these parallel findings characterize a multi-omics profile associated with functional decline. These results provide hypotheses for future validation in longitudinal studies.},
}

@article {pmid42612534,
year = {2026},
author = {Li, B and You, Y and Fan, Y and Wu, J and Lv, X and Ji, J and Zhang, M},
title = {Mechanism exploration of divergent partial denitrification performance under tetracycline stress: Insights from functional gene, electron transport and molecular docking.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143220},
doi = {10.1016/j.jhazmat.2026.143220},
pmid = {42612534},
issn = {1873-3336},
abstract = {Nitrates and antibiotics like tetracycline (TC) coexist in wastewater and inhibit nitrite (NO2[-]-N) accumulation during partial denitrification (PD), restricting anammox coupling. A moving bed biofilm reactor (PD-MBBR) and a sequencing batch reactor (PD-SBR) were compared under TC stress (0-8 mg/L). The PD-MBBR proved more robust, sustaining a high nitrate transformation ratio (NTR) of 95.11% and ∼53% TC removal. Metagenomic sequencing, quantitative polymerase chain reaction (qPCR), and molecular docking revealed this tolerance stemmed from physical shielding and metabolic compensation. Carrier-attached growth promoted extracellular polymeric substances (EPS) overproduction, forming a dense barrier preventing TC from binding to key denitrifying enzymes. The biofilm maintained stable nitrate reductase (NAR) activity via high narG and napA gene abundances, while nitrite reductase (NIR) was inhibited, ensuring efficient NO2[-]-N accumulation. This was supported by hyperactivated electron transport chain components, with complex III relative abundance increasing 15.08% and peak enzymatic activity reaching 149.02%. While IntI1-mediated horizontal gene transfer fortified community defense, concentrated antibiotic resistance genes (ARGs) within the biofilm pose a secondary dissemination risk. Thus, PD-MBBR provides an efficient pretreatment strategy for anammox, though downstream ARGs management is warranted.},
}

@article {pmid42612779,
year = {2026},
author = {Zhang, Q and Wang, Z and Lei, C and Xu, N and Zhang, Z and Zhou, S and Qian, H},
title = {Machine learning prediction of human antibiotic resistance risk using 16S rRNA profiles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128988},
doi = {10.1016/j.envpol.2026.128988},
pmid = {42612779},
issn = {1873-6424},
abstract = {Antimicrobial resistance poses a growing global health threat, yet large-scale surveillance and risk evaluation remain constrained by the cost and accessibility of metagenomic sequencing. Here, we demonstrate that antibiotic resistance risk, integrating gene mobility, human accessibility, clinical relevance, and host pathogenicity, can be quantitatively inferred from microbial taxonomic composition through its ecological coupling with microbial hosts. By integrating 177,134 metagenome-assembled genomes, 3,058 metagenomes, and 31,216 16S rRNA profiles, we defined a comprehensive ARG host catalogue and conserved core taxa across sequencing platforms. A machine learning model built on this framework achieved high predictive accuracy in held-out test data (R[2] > 0.96) and retained strong performance in an independent dataset with paired 16S rRNA and metagenomic profiles (Pearson r = 0.74; Lin's CCC = 0.73), supporting its robustness and cross-platform transferability. Applying this tool on a global scale, we demonstrate that resistance risk exhibits consistent structure across populations, with host-associated ecological factors explaining more variation than socioeconomic conditions, supporting the feasibility of translating taxonomic profiles into quantitative estimates of functional risk. This work establishes a scalable framework for inferring antibiotic resistance risk from 16S data, enabling equitable, large-scale surveillance of antimicrobial resistance while positioning microbiome composition as a predictive basis for functional risk and advancing a general paradigm for inferring microbial traits from community structure.},
}

@article {pmid42612844,
year = {2026},
author = {Wan, R and Zheng, K and Chen, T and Xun, Y and Lv, J and Meng, L and Yang, Y and Zhu, X},
title = {Antibiotic resistome biomarkers and determinants in lettuce planting soil amended with β-lactam pharmaceutical fermentation residues.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135608},
doi = {10.1016/j.biortech.2026.135608},
pmid = {42612844},
issn = {1873-2976},
abstract = {As nutrient-rich biosolids generated by the pharmaceutical industry, pharmaceutical fermentation residues (PFRs) pose high potential for recycling, particularly as organic soil amendments after removing drug residues. In this study, the antibiotic resistome profile of the lettuce pot experiment soil amended by two major types of β-lactam pharmaceutical fermentation residues (penicillin and clavulanic acid) and their derived high-temperature spray granulation treated PFRs was investigated using metagenomic sequencing. After treatment, penicillin and clavulanic acid removal ratios achieved 94.2% and 97.3%. The number and TPM abundance of total antibiotic resistance genes (ARGs) in soil amended by treated PFR decreased by 32.1% and 27.9%, compared to soil fertilized with raw PFR, and were not significantly different from those in the control groups (without PFR or treated PFR application). The results implied that a total of 47 ARGs (7 clinical high-risk ARGs), 32 bacterial taxa (13 potential pathogens), and 21 MGEs were identified as biomarkers by the random forest model. Biomarker MGEs (qacEdelta, tnpAB, and IS91) and bacteria (Neisseria, Staphylococcus, Stenotrophomonas, and Clostridium) were closely associated with the abundance of most biomarker ARGs, including those high-risk ARGs. tnpAB and IS91 were proposed as sentinel indicators of ARG mobility risk. Subsequent RDA analysis explored the variation of ARG biomarker determinants across different growth stages. MGEs dominated before seeding, thereafter, the bacterial community gradually became the principal contributor. Collectively, these findings may benefit the safe recycling of PFR and provide valuable theoretical data for antimicrobial risk assessment of pharmaceutical biowaste.},
}

@article {pmid42612871,
year = {2026},
author = {Bhatt, NP and Nguyen, TTH and Iacono, G and Rodriguez, GR and Anderson, CRB and Perry, A and Barlow, CK and Anderson, D and Burgio, G and Marsland, BJ and Jiang, SH and Deshpande, AV and Starkey, MR},
title = {Generation of a novel Slc7a9[G105R] mutant mouse identifies new biomarkers for cystinuria.},
journal = {Kidney international},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.kint.2026.06.050},
pmid = {42612871},
issn = {1523-1755},
abstract = {INTRODUCTION: Cystinuria is a rare inherited disease characterized by increased urinary cystine levels resulting in the formation of cystine stones in the urinary tract. Mutations in the genes encoding the cystine transporter complex, SLC3A1 and SLC7A9, are the primary drivers of the disease. Current mouse models used to study cystinuria rely on gene deficiency or spontaneous mutations in mice that do not accurately reflect the pathogenic mutations found in humans.

METHODS: We generated a novel Slc7a9[G105R] knock-in mouse model in which glycine at position 105 is replaced by arginine, recapitulating the most common pathogenic mutation in human SLC7A9. Disease onset and progression were assessed using micro-CT imaging, fecal metagenomics, and urine and serum metabolomics and proteomics.

RESULTS: Both male and female Slc7a9[G105R] mice developed a cystinuria phenotype by nine weeks of age, characterized by substantial cystine stone formation and increased urinary cystine, lysine, arginine, and ornithine. Slc7a9[G105R] mice displayed distinct serum and urinary metabolite profiles, mapped to dibasic amino acid pathways, and serum protein profiles, mapped to disease progression. Fecal metagenomics revealed that Slc7a9[G105R] mice had a heterogeneous microbiota with altered functional pathways, including increased L-cysteine biosynthesis. Antibiotic-induced depletion of the microbiota did not affect cystine stone burden but reduced urinary tract inflammation. Prophylactic or therapeutic dietary supplementation with alpha-lipoic acid reduced stone burden and inflammation, but it also caused urothelial damage. Untargeted metabolomics analysis following alpha-lipoic acid supplementation identified metabolites that can increase cystine solubility, reduce inflammation, and damage epithelial cells. Correlation analysis revealed novel serum metabolite biomarkers of stone burden, including 2-hydroxybutyric acid and 2-amino-2-thiazoline-4-carboxylic acid, which were also detected in human serum.

CONCLUSION: Collectively, the Slc7a9[G105R] mutant mouse model offers a precise, rapid-onset, and translational platform for investigating cystinuria pathogenesis and evaluating potential therapeutic strategies.},
}

@article {pmid42613887,
year = {2025},
author = {Liu, S and Luo, X},
title = {[Hemophagocytic syndrome secondary to visceral leishmaniasis: a case report].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {38},
number = {3},
pages = {330-332},
doi = {10.16250/j.32.1374.2025012},
pmid = {42613887},
issn = {1005-6661},
support = {2025ZNSFSC1560//Natural Science Foundation of Sichuan Province/ ; },
mesh = {Humans ; *Leishmaniasis, Visceral/complications/diagnosis/drug therapy ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/parasitology ; Male ; Fatal Outcome ; },
abstract = {This article presents the diagnosis and treatment of a case with hemophagocytic syndrome secondary to visceral leishmaniasis. The patient had been misdiagnosed for a long period of time, and was finally definitively diagnosed as hemophagocytic syndrome secondary to visceral leishmaniasis through laboratory tests, bone marrow smear microscopy, and metagenomics next-generation sequencing. Due to unsatisfactory therapeutic efficacy, the patient's family members decided to abandon treatment, and the patient subsequently died following discharge from hospital.},
}

Humans
*Leishmaniasis, Visceral/complications/diagnosis/drug therapy
*Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/parasitology
Male
Fatal Outcome

@article {pmid42614308,
year = {2026},
author = {Su, C and Lan, J and Chen, H and Wang, D},
title = {Gut microbiota of sprint athletes: signature microbes and dietary links.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1855417},
pmid = {42614308},
issn = {2296-861X},
abstract = {BACKGROUND: The gut microbiota has emerged as an important biological factor associated with host physiological status in athletes. However, relevant research remains limited for sprint athletes, whose physiological demands differ substantially from those of endurance athletes.

OBJECTIVE: This study aimed to characterize the gut microbiota profile of college sprint athletes, compare it with non-athletic peers, identify potential sprint-associated bacterial taxa, and explore diet-microbiota associations to propose potential nutritional hypotheses for these signature taxa.

METHODS: Fecal samples were collected from 20 college sprint athletes and 23 non-athletic college students for metagenomic sequencing. Dietary intake was assessed using a validated food frequency questionnaire. Alpha and beta diversity analyses were performed to evaluate microbial community diversity and structure. LEfSe was used to identify differentially abundant taxa. Functional annotation and enrichment were conducted using KEGG, GO, and other databases. Spearman's correlation was applied to examine diet-microbiota relationships.

RESULTS: Alpha diversity indices (Shannon, Chao1, etc.) did not differ significantly between groups. In contrast, beta diversity analysis revealed significant structural separation. LEfSe identified Segatella copri (LDA = 4.986, p = 0.017) and Bifidobacterium adolescentis (LDA = 3.154, p = 0.003) as signature taxa in athletes, both with significantly higher abundance than in non-athletes. Functional analysis showed predicted enrichment of pathways related to energy metabolism (carbohydrate metabolism, ATP binding) and amino acid metabolism in athletes. Correlation analysis indicated that S. copri abundance was nominally positively associated with dairy intake (r = 0.31, p = 0.045), while B. adolescentis was nominally associated with whole grains, soy milk/soy powder, and dairy products.

CONCLUSION: College sprint athletes possess a distinct gut microbiota structure compared with non-athletes. S. copri and B. adolescentis represent distinct microbial signatures associated with sprint athletes, accompanied by corresponding predicted functional pathway enrichment. Specific dietary patterns, including the intake of whole grains, soy milk/soy powder, and dairy products, exhibit exploratory nominal associations with the signature gut microbiota composition of sprinters.},
}

@article {pmid42614418,
year = {2026},
author = {Hong, H and Zeng, Y and Guo, Z and Yu, S and Chen, L and Lan, L and Wang, K and Xu, X and Qiu, Y and Wu, S and Zhang, Z},
title = {Application of mNGS in traceability investigation of foodborne disease outbreaks caused by Salmonella Litchfield.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1870501},
pmid = {42614418},
issn = {1664-302X},
abstract = {BACKGROUND: Salmonella is one of the most common pathogens responsible for foodborne outbreaks, posing a serious threat to public health. However, when conventional culture methods fail to isolate the pathogen from food, identifying the contamination source becomes challenging. Here, we report an investigation of a foodborne outbreak caused by Salmonella Litchfield that occurred in Xiamen,China on Sep 22, 2025. Isolation of the pathogen was successful only from clinical specimens, whereas all food and environmental samples tested negative.

METHODS: Clinical, food, and environmental surface swab samples were collected. The clinical samples were screened using the 14-plex PCR assay for rapid pathogen detection. Metagenomic sequencing (mNGS) was performed on all samples in parallel. Conventional bacterial culture was also conducted, and the obtained isolates were subjected to whole-genome sequencing (WGS). A SNP-based phylogenetic tree was constructed using WGS data from clinical isolates and reference strains from different geographical regions.

RESULTS: This foodborne outbreak was caused by Salmonella Litchfield (sequence type ST124),which was recovered from anal swabs of the six patients, including the chef. Phylogenetic analysis showed that the five patient isolates formed a distinct outbreak clone, whereas the chef's isolate belonged to a separate sublineage. No SNPs differed between the chef and four of the patients; however, the one-SNP difference observed in one patient isolate represented a microevolutionary event during transmission. The chef's isolate was closely related to a strain isolated in Hangzhou 5 years previously, with a 15-SNP difference between them. No pathogens were isolated from any food samples. cgMLSTFinder detected 2,768-2,772 core genes, with completeness >99.71%, and an average GC content of 52.25%. mNGS analysis identified high abundances of Salmonella in food samples at the genus level. Among the virulence genes detected, T3SS2 and T3SS, components of canonical virulence systems in Salmonella, were present at high abundance. Additionally, floR and tet (A) were highly abundant in food samples.

CONCLUSIONS: Our integrated approach combining culture, WGS, and mNGS proved effective for rapid outbreak traceability, suggesting that the outbreak most likely originated from a contaminated food source associated with cross-regional dissemination, although the specific vehicle and transmission route remain to be determined.},
}

@article {pmid42614438,
year = {2026},
author = {Ding, ZC and Liu, Y and Zhang, SR and Yang, YH and Jiang, JL and Jiang, L},
title = {Control efficiency and Huanglongbing resistance-related clues mediated by novel Hermetia illucens frass formulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1896630},
pmid = {42614438},
issn = {1664-302X},
abstract = {The preventive and curative management of citrus Huanglongbing (HLB) remains a major global challenge in citrus production. As an emerging microbial fertilizer rich in antimicrobial peptide mixtures, Hermetia illucens frass (HIF) exhibits promising antibacterial potential against HLB-associated pathogens. In this study, we evaluated the suppressive effects of HIF on Candidatus Liberibacter asiaticus (CLas) infection and explored the underlying physiological, metabolic, and multi-omic regulatory mechanisms in CLas-infected citrus nursery trees grown in pots. Quantitative real-time PCR analysis showed that 20 and 25 consecutive soil applications of HIF significantly reduced CLas titers by 52.61% and 61.85%, respectively, and citrus leaves with typical chlorotic and mottled symptoms gradually recovered normal green coloration after 20 rounds of treatment. Phytohormone profiling indicated that the endogenous contents of auxin, cytokinin, and salicylic acid were significantly upregulated following HIF application. Non-targeted metabolomics further revealed that HIF treatment markedly increased the accumulation of 375 and 724 differential metabolites in citrus tissues, including ketones, aldehydes, terpenoids, flavonoids, alkaloids, coumarins, steroids, and polyphenols. Transcriptomic and metabolomic analyses identified 9 significantly upregulated KEGG pathways in leaves and 26 in roots after HIF treatment. Integrated multi-omic comparisons yielded 15 co-upregulated pathways from transcriptome-metabolome pairing, 4 from transcriptome-proteome pairing, and 1 from proteome-metabolome pairing. Notably, α-linolenic acid metabolism was consistently activated across transcriptomic, proteomic, and metabolomic datasets, representing a core conserved signaling pathway responding to HIF treatment. Microbial community analysis characterized the top 10 dominant bacterial genera in both HIF material and HIF-treated citrus tissues. Furthermore, HIF contained abundant antimicrobial secondary metabolites, such as lipids, benzenoids, polyketides, and phenylpropanoids. HPLC detection confirmed the presence of the lipopeptides surfactin and iturin, and metagenomic alignment predicted a total of 467 antimicrobial peptides classified as attacin-like, defensin-like, and cecropin-like peptides. Collectively, these phenotypic, physiological, and multi-omic results provide multi-layered validation clues for research on utilizing HLF to combat Huanglongbing.},
}

@article {pmid42614800,
year = {2026},
author = {Wang, A and Reheman, H and Chen, X and Shang, M and Abulikemu, D and Wang, H},
title = {Drug-resistant tuberculosis and pulmonary co-infections in immunocompromised patients: from multi-omics to precision therapy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1893416},
pmid = {42614800},
issn = {1664-302X},
abstract = {Drug-resistant tuberculosis remains a major global health threat, with an estimated 400,000 people developing rifampicin-resistant/multidrug-resistant tuberculosis (RR/MDR-TB) worldwide in 2023, according to the WHO Global Tuberculosis Report 2024. Immunocompromised populations, including people living with HIV, transplant recipients, patients receiving immunosuppressive therapies, and individuals with chronic metabolic diseases, are at particularly high risk of severe disease and pulmonary co-infections, resulting in delayed diagnosis, increased treatment complexity, and poor clinical outcomes. Despite advances in therapeutics, management remains constrained by fragmented diagnostic pathways, limited pathogen resolution, antimicrobial toxicity, and clinically significant drug-drug interactions. Recent progress in multi-omics technologies is reshaping understanding of host-pathogen dynamics in tuberculosis and co-infection states. Whole-genome sequencing enables rapid resistance prediction and transmission tracking, whereas transcriptomic, proteomic, metabolomic, and single-cell approaches are identifying biomarkers of disease severity, immune dysregulation, treatment response, and relapse risk. Parallel advances in metagenomic diagnostics and artificial intelligence-assisted imaging offer opportunities for earlier detection of mixed infections and improved clinical triage. Therapeutic paradigms are also evolving. Shorter all-oral regimens, individualized dosing strategies, therapeutic drug monitoring, and integrated antimicrobial stewardship are improving outcomes for resistant tuberculosis. Adjunctive approaches, including host-directed therapies, immunomodulation, inhaled drug delivery systems, and data-guided precision prescribing, may further enhance efficacy while reducing toxicity in vulnerable patients with co-infections. However, implementation remains uneven, and prospective evidence in immunocompromised populations is limited. Recent advances in multi-omics technologies including whole-genome sequencing, metagenomics, transcriptomics, proteomics, metabolomics, single-cell omics, and artificial intelligence-assisted diagnostics are transforming the diagnosis, biological stratification, and clinical management of DR-TB. In parallel, precision therapeutic approaches, including individualized regimen selection, therapeutic drug monitoring, host-directed therapies, and data-guided clinical decision-making, are enabling more personalized treatment strategies. This review integrates these advances into a precision medicine framework and discusses their clinical application, current limitations, and future directions for improving outcomes in immunocompromised patients with DR-TB and pulmonary co-infections.},
}

@article {pmid42614947,
year = {2026},
author = {Wang, S and Kang, L and Li, M and Zhou, X and Li, B and Wang, F and Meng, J and Li, C and Yang, K},
title = {Comparative genomic analyses provide new insights into phylogenetic and functional diversification in genus Fenollaria.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1862120},
pmid = {42614947},
issn = {1664-302X},
abstract = {The genus Fenollaria has gained attention due to its associations with human prostate cancer, colorectal cancer and other diseases. The higher abundance of Fenollaria was believed to be associated with biochemical recurrence of prostate cancer but remission of colorectal cancer. Owing to the fastidious growth requirements of Fenollaria species in laboratory isolation and culture, the genomes of isolated strains is rarely available. Consequently, only limited comparative genomic studies have been conducted, leaving knowledge gap regarding the genomic diversity, distribution of functional genes, and evolutionary relationships, which hindered the understanding of ecological adaptation and mechanism exploration of Fenollaria. Here, a large-scaled genomic investigation of Fenollaria genus was performed using four high quality MAGs generated in this study and publicly available genomic data. The four MAGs were constructed from urine metagenome samples from bladder cancer patients, which were under conditions of oligotrophy and limited oxygen. Four mono-clades were revealed by phylogenomic analysis, representing for three previously described species (i.e., F. massiliensis, F. timonensis, and F. sporofastidiosus) as well as a novel proposed Fenollaria species. The divergences among these clades were also supported by genome-wide G + C content, ANI and AAI values. The functional difference between clades were revealed by the distribution of clade-specific genes in COG categories, as well as the biased distribution of ARGs, VFs, and CRISPR-Cas systems.},
}

@article {pmid42615606,
year = {2026},
author = {Wilson, I and Perry, T and Grutzner, F},
title = {Undergraduate student practicals generate high-quality data for microbiome research.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0003026},
doi = {10.1128/jmbe.00030-26},
pmid = {42615606},
issn = {1935-7877},
abstract = {The increasing prominence and accessibility of microbiomics has provided an opportunity for authentic research experiences in the undergraduate practical classroom. In recent years, this approach has contributed to published research projects. However, there is little information evaluating the quality of student-generated data compared to that of trained researchers. To investigate this, we designed an undergraduate practical component in which 37 final-year genetics students generated microbial profiles of 22 echidna scats using matched samples that were also profiled by an experienced researcher. DNA yield, 16S rRNA PCR success, sequencing library size, and microbial diversity were compared between the groups in order to assess both the ability and accuracy of students in characterizing fecal microbiota. Our research revealed that students were able to produce microbiome data comparable to a postgraduate researcher. Importantly, we found that students did not introduce contamination at a higher rate than the trained researcher. These findings reinforce that the undergraduate classroom is a valuable approach for microbiome research in addition to its benefits for student engagement and experience. The design and successful implementation of these practicals provide a template for a variety of research-led microbiome teaching.},
}

@article {pmid42615618,
year = {2026},
author = {Hutchinson, NT and Maino-Vieytes, CA and Valls, C and Allen, J and Rund, LA and Johnson, RW and Woods, JA},
title = {Fermentation capacity of the gut microbiota influences exercise motivation and neuroendocrine integration.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0087626},
doi = {10.1128/msystems.00876-26},
pmid = {42615618},
issn = {2379-5077},
abstract = {UNLABELLED: Physical inactivity contributes substantially to global disease burden, yet the physiological mechanisms underlying exercise motivation remain poorly understood. The gut-brain axis presents a potentially modifiable target for behavioral intervention. Emerging evidence demonstrates that the gut microbiota influences motivated behaviors, but the specific metabolic functions and physiological mechanisms mediating these effects remain poorly defined. Here, we demonstrate that the predicted fermentation capacity of the gut microbiota influences voluntary wheel running (VWR) acquisition and neuroendocrine integration during exercise in C57BL/6J mice. Antibiotic-induced microbiome depletion reduced VWR acquisition, while shifting predicted function toward aerobic respiration and away from anaerobic fermentation. Supplementation with short-chain fatty acids, the primary fermentative products, restored normal VWR activity in microbiome-depleted mice. Conversely, 4-week dietary pretreatment with 2.5% prebiotic fiber (inulin) increased predicted fermentative capacity of the microbiota and VWR activity above baseline levels. Microbiome manipulation produced bidirectional dysregulation of corticosterone responses to exercise: acute antibiotic depletion increased post-exercise concentrations, while germ-free development decreased them, despite elevated striatal catecholamines. This exercise-specific uncoupling reveals microbiome-dependent integration of metabolic demand signals in the coordination of sympathetic and hypothalamic-pituitary-adrenal axis responses. Furthermore, the inulin-induced enhancement in VWR activity was associated with increased striatal histamine concentrations following exercise, suggesting additional mechanisms of neuromodulation. These findings demonstrate that the fermentative capacity of the gut microbiota influences exercise motivation and neuroendocrine regulation, providing novel insights into dietary interventions targeting physical activity.

IMPORTANCE: Physical inactivity is a leading cause of global morbidity and mortality, and our lack of understanding of the biological forces driving motivation to exercise limits our ability to develop interventions that enhance engagement. Using a rodent model of voluntary exercise along with microbiota depletion and metabolite replacement, we uncovered that the gut microbiota and its capacity to ferment dietary components into short-chain fatty acids drive exercise habit acquisition and help facilitate coordination between neurochemical signals and systemic stress hormones during exercise. Additionally, microbiome depletion "uncoupled" these systems, resulting in dysregulated stress responses during forced exercise. Finally, we showed that enhancement of microbiota fermentation capacity via dietary addition of prebiotic fiber was able to increase exercise engagement while also enhancing concentrations of histamine, a neuromodulator that potentiates locomotor activity, in the striatum. These findings suggest that the gut microbiome is a modifiable target for behavior change that facilitates integration of metabolic demand in neuroendocrine activity. Collectively, this work provides a mechanistic foundation to support the use of dietary interventions in sedentary populations to start exercise habits.},
}

@article {pmid42615753,
year = {2026},
author = {Sillos, MD and Matsuo, JSS and Morais, MB},
title = {GUT MICROBIOTA IN INFANTS WITH COW MILK ALLERGY: A SYSTEMATIC REVIEW OF CONTROLLED STUDIES.},
journal = {Arquivos de gastroenterologia},
volume = {63},
number = {},
pages = {e25133},
doi = {10.1590/S0004-2803.24612025-133},
pmid = {42615753},
issn = {1678-4219},
mesh = {Humans ; *Milk Hypersensitivity/microbiology ; *Gastrointestinal Microbiome/physiology ; Infant ; Animals ; Immunoglobulin E/immunology ; },
abstract = {BACKGROUND: Alterations in the gut microbiota may be involved in the pathophysiology of cow milk allergy (CMA). However, whether gut microbiota abnormalities contribute to the diagnostic confirmation of CMA through specific microbiome signatures is still unknown.

OBJECTIVE: To conduct a systematic review of the literature on the gut microbiota of infants with CMA.

METHODS: This systematic review included studies on the gut microbiota of infants aged <2 years with CMA at diagnosis and at follow-up after different interventions to control clinical manifestations and compared them with that of healthy controls. The PubMed database was used for literature search. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol was applied. This review was registered on the PROSPERO platform (CRD42024574354).

RESULTS: A total of 1,096 articles were identified. After applying inclusion and exclusion criteria, 18 studies were selected for the systematic review. Clinical manifestations included infants with immunoglobulin E (IgE)-mediated CMA (n=7), those with non-IgE-mediated CMA (n=10), or both (n=1). An oral challenge test for CMA diagnosis was mentioned in 11 studies, and in seven of them, a double-blind placebo-controlled challenge test was used. Most studies (n=13) used 16S rRNA gene sequencing to investigate the intestinal microbiota, and only three studies used shotgun metagenomic analysis. There was significant heterogeneity in the expression of results on microbiota characteristics. Alpha diversity was similar in the control group in most studies. A low abundance of Bifidobacteria was observed in some studies (n=5).

CONCLUSION: The results of this systematic review did not identify a typical microbiota pattern in infants with CMA. Studies including infants before elimination diet and with a diagnosis confirmed by an oral challenge test, and studies including one group of infants of the same age on exclusive breastfeeding and another group of infants of the same age on formula feeding as a control group are needed. Therefore, currently available data do not allow CMA diagnosis through a microbiota signature.},
}

Humans
*Milk Hypersensitivity/microbiology
*Gastrointestinal Microbiome/physiology
Infant
Animals
Immunoglobulin E/immunology

@article {pmid42615833,
year = {2026},
author = {Masiá, M and Gutiérrez, F},
title = {Microbial metabolite-driven mechanisms linking the gut microbiome to atherosclerosis: multi-omic and translational perspectives.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2718621},
doi = {10.1080/19490976.2026.2718621},
pmid = {42615833},
issn = {1949-0984},
mesh = {Humans ; *Atherosclerosis/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Bacteria/metabolism/classification/genetics ; Metabolomics ; },
abstract = {Atherosclerotic cardiovascular disease remains the leading cause of mortality worldwide, and a substantial residual risk persists despite optimal management of traditional risk factors. Increasing evidence implicates the gut microbiome as a mechanistic contributor to atherogenesis, not merely through taxonomic shifts but via the production of bioactive microbial metabolites that link diet, microbial metabolism, and host vascular biology. These metabolites have emerged as central effectors of the gut-artery axis, influencing intestinal barrier integrity, systemic immunity, lipid handling, and thrombosis. Among the best-characterized pathways, trimethylamine N-oxide and phenylacetylglutamine have been robustly linked to macrophage lipid accumulation, platelet hyperreactivity, and adverse cardiovascular outcomes. More recently, imidazole propionate, a histidine-derived microbial metabolite, has emerged as a candidate mediator of vascular inflammation and plaque development through imidazoline-1 receptor-dependent activation of mTORC1 signaling, supported by mechanistic and experimental evidence. Advances in metagenomics, metabolomics, and proteomics now enable systems-level interrogation of microbiome-host interactions, facilitating causal inference through integrative metabolite-protein and pathway-level analyses. These approaches have revealed reproducible molecular networks associated with subclinical and clinical atherosclerosis, providing a framework for biomarker discovery and therapeutic targeting. People with HIV represent a particularly informative human model, in which persistent gut barrier disruption and dysbiosis sustain immune activation and confer excess cardiovascular risk, with distinct microbial and metabolite signatures linked to vascular inflammation and plaque progression. This review synthesizes current evidence linking gut microbial function to atherosclerosis, with a specific focus on metabolite-driven mechanisms, multi-omic integration, and translational relevance. We highlight emerging biomarkers and therapeutic strategies targeting microbial metabolic pathways and discuss methodological challenges that must be addressed to advance the gut-artery axis toward precision cardiovascular medicine.},
}

Humans
*Atherosclerosis/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Multiomics
Animals
*Bacteria/metabolism/classification/genetics
Metabolomics

@article {pmid42615884,
year = {2026},
author = {Van, CH and Nguyen, LV and Truong, OT and Tran, SQ and Pham, HQ and Dang, BT},
title = {Unravelling Bulk Ichthyoplankton Diversity in Vietnam: Metabarcoding Validation With Controlled Mock Samples.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70192},
doi = {10.1111/1755-0998.70192},
pmid = {42615884},
issn = {1755-0998},
support = {VINIF.2022.DA00021//Vingroup Innovation Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Vietnam ; *Biodiversity ; *Fishes/classification/genetics ; *Metagenomics/methods ; },
abstract = {The sustainability of Southeast Asian fisheries hinges on high-throughput tools for monitoring early life-stage fish biodiversity. However, applying DNA metabarcoding to hyper-diverse tropical ichthyoplankton requires rigorous calibration to ensure quantitative reliability. We systematically evaluated the metabarcoding workflow using controlled mock communities, revealing that taxonomic recovery is governed by a stochastic limit of detection at a normalised proxy biomass threshold of ≤ 0.05. Quantitative analysis confirmed a significant linear relationship between specimen size and read abundance (R[2] up to 0.817), demonstrating that biomass-driven template competition induces frequent false negatives for low-biomass taxa, a phenomenon exacerbated by increasing community complexity (ANOVA: p < 0.001). To mitigate these systemic biases, we applied a size-stratified specimen-balancing strategy intended to increase the representation of small-bodied components in natural bulk samples. Applying this optimised workflow to field samples from Khanh Hoa, Vietnam, we identified 139 species and unmasked a North-South biogeographic dichotomy (PERMANOVA: R[2] = 53%, p = 0.001) driven by transect-scale environmental gradients and local hydrography. Notably, we identified diversity hotspots requiring > 200,000 reads for saturation, suggesting these sites act as critical larval retention zones. The contrast between functional management zones was highly significant (p = 0.002), with the conservation area (Zone B) exhibiting higher alpha richness and a nine-fold increase in unique indicator species compared to high-activity areas (18 vs. 2). Our work demonstrates that comprehensive validation is vital for accurate metabarcoding, offering a robust framework to understand how ecological gradients and localised human pressures shape Vietnam's critical marine spawning sites and nursery grounds.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Vietnam
*Biodiversity
*Fishes/classification/genetics
*Metagenomics/methods

@article {pmid42615987,
year = {2026},
author = {Comba, IY and Mars, RAT and Yang, L and Dumais, M and Chen, J and Van Gorp, TM and Harrington, JJ and Sinnwell, JP and Johnson, S and Holland, LA and Khan, AK and Lim, ES and Aakre, C and Athreya, AP and Gerber, GK and O'Horo, JC and Lazaridis, KN and Kashyap, PC},
title = {Gut microbiome signatures during acute infection are associated with long COVID.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2718581},
doi = {10.1080/19490976.2026.2718581},
pmid = {42615987},
issn = {1949-0984},
mesh = {Humans ; *COVID-19/microbiology ; Female ; Longitudinal Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Post-Acute COVID-19 Syndrome ; Male ; SARS-CoV-2 ; Middle Aged ; Adult ; Machine Learning ; Metagenomics ; Acute Disease ; },
abstract = {BACKGROUND: Long COVID (LC) manifests in 10%-30% of non-hospitalized individuals post-SARS-CoV-2 infection, leading to significant morbidity. The predictive role of gut microbiome composition during acute infection in the development of LC is not well understood, partly because of the heterogeneous nature of the disease.

OBJECTIVES: To determine whether the gut microbiome composition in the acute phase of SARS-CoV-2 infection predicts subsequent LC and to investigate the role of microbiome signatures in disease subphenotypes.

DESIGN: We conducted a longitudinal cohort study involving 799 outpatient participants tested for SARS-CoV-2 due to similar symptom presentation, including 380 SARS-CoV-2 positive and 419 negative individuals. Stool samples were collected at two time points for metagenomic sequencing. Logistic regression with L1 regularization was employed to predict LC based on the microbiome and clinical metadata.

RESULTS: The individuals who developed LC harbored a distinct gut microbiome during acute infection compared to those who recovered fully and uninfected controls with similar symptomatology. However, the temporal changes in the gut microbiome between the acute (0-1 month) and post-acute (1-2 months) phases were similar across the three cohorts. Using machine learning, we showed that the gut microbiome carried a modest signal for subsequent LC, but model performance was insufficient for clinical prediction, likely reflecting the heterogeneous nature of LC. Finally, we identified four LC symptom clusters, with gastrointestinal and fatigue-only groups strongly linked to gut microbiome alterations.

CONCLUSION: The gut microbiome can potentially offer solutions for understanding the heterogeneous nature of LC. Larger cohorts and phenotype-aware computational algorithms may help overcome current model performance limitations and support the development of targeted diagnostic and therapeutic strategies.},
}

Humans
*COVID-19/microbiology
Female
Longitudinal Studies
Feces/microbiology
*Gastrointestinal Microbiome
Post-Acute COVID-19 Syndrome
Male
SARS-CoV-2
Middle Aged
Adult
Machine Learning
Metagenomics
Acute Disease

@article {pmid42616025,
year = {2026},
author = {Sasaki, Y and Kozakai, T and Inoue, M and Sakanaka, M and Katoh, T and Kaneko, H and Imai, H and Odamaki, T and Fujita, K and Katayama, T},
title = {Adaptations of gummivorous primate gut-associated bifidobacteria to type-II arabinogalactan utilisation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag210},
pmid = {42616025},
issn = {1751-7370},
abstract = {Bifidobacteria inhabiting the primate gut exhibit host-dependent genetic diversification, particularly in their gene repertoire related to carbohydrate metabolism, suggesting adaptation to host diets. However, these diverse genetic traits remain poorly associated with specific dietary components. Here, through enzymatic and genetic analyses, we demonstrate that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterised pathways for the efficient utilisation of type-II arabinogalactan (AG), the major polysaccharide component of tree gums. The assimilation pathways comprises two key components: a bifunctional β-1,3-galactanase that cleaves the AG backbone via both endo- and exo-mode actions and an ATP-binding cassette transporter that internalises the released arabinogalactan oligosaccharides (AGOs) into cells. Data mining of deposited metagenomic datasets suggested that the endo/exo-β-1,3-galactanase and the AGO transporter contribute to cross-feeding interactions within Bifidobacterium communities in the gut of gummivorous primates. Our study not only highlights molecular strategies employed by certain Bifidobacterium species to adapt to the dietary habits of a host but may also inform probiotic intervention strategies for the health and welfare of these primates in captive settings.},
}

@article {pmid42616762,
year = {2026},
author = {Liu, C and Zhang, J and Chen, R and Bi, X and Dai, W and Zhao, W and Zhang, D and Wang, Q and Wang, X},
title = {Putative anaerobic transformation pathway of microcystin-RR inferred from 15N labeling and multi-omics in an enriched shrimp pond sediment microbial community.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0355950},
doi = {10.1371/journal.pone.0355950},
pmid = {42616762},
issn = {1932-6203},
mesh = {*Microcystins/metabolism ; Anaerobiosis ; Multiomics ; Animals ; *Geologic Sediments/microbiology ; Nitrogen Isotopes ; Tandem Mass Spectrometry ; Ponds/microbiology ; Metagenomics ; },
abstract = {The degradation mechanism of MC-RR by an anaerobic degrading microbial community (ADMC), enriched from shrimp pond sediment, was investigated using LC-MS/MS, metagenomic, and metatranscriptomic analyses. Three key degradation products of 15N-labeled MC-RR were tentatively identified: Adda-Glu-Mdha-Ala (m/z 618.3216), a deamination product (m/z 600.2965), and Glu-MeAsp-Ala-Arg-CO2 (m/z 466.2233). The pathway was inferred to involve hydrolytic ring-opening at Arg-Adda or Ala-Arg bonds, followed by deamination, decarboxylation, and stepwise degradation into short peptides and amino acids. Metagenomics revealed Citrobacter amalonaticus as the core dominant species and Shewanella as a low-abundance but transcriptionally active genus. Metatranscriptomic differential expression analysis (1,648 DEGs; 460 upregulated, 1,188 downregulated) showed significant upregulation of non-canonical peptidases including U32 family (YhbU, UbiU), M23 family (MepM), and S9 family serine peptidases, suggesting the involvement of a non-canonical, mlr-independent peptidase system in MC-RR transformation. Genes of the dissimilatory nitrate reduction to ammonium (DNRA) pathway (narG-nirB-nrfA) and nitric oxide reductase (norB) were concurrently upregulated, a transcriptional pattern consistent with DNRA-linked nitrogen turnover and NO detoxification during degradation, although the corresponding nitrogen fluxes were not directly measured. Among quorum sensing (QS) systems, the AI-2 system exhibited the most pronounced transcriptional response, with AHLs, DSF, and c-di-GMP genes also concurrently upregulated, suggesting a multi-signal transcriptional response during degradation of this complex substrate. These findings provide an important theoretical reference for revealing the mechanisms of anaerobic degradation of microcystins (MCs) by complex microbial communities in situ environments, while also offering scientific data to support the targeted development of efficient MCs-degrading microbial community or specific MCs-degrading enzymes.},
}

*Microcystins/metabolism
Anaerobiosis
Multiomics
Animals
*Geologic Sediments/microbiology
Nitrogen Isotopes
Tandem Mass Spectrometry
Ponds/microbiology
Metagenomics

@article {pmid42616783,
year = {2026},
author = {Zhang, YZ and Jiang, WX and Zhao, XM and Hao, J and Lu, Y and Gao, C and Li, CY and Qin, QL and Chen, XL and Chen, Y and Li, PY},
title = {The dual-function enzyme PpLipO protects polar marine bacteria from phospholipid peroxidation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {34},
pages = {e2527470123},
doi = {10.1073/pnas.2527470123},
pmid = {42616783},
issn = {1091-6490},
support = {2024YFC2816000//MOST | National Key Research and Development Program of China (NKPs)/ ; 2022YFC2807503//MOST | National Key Research and Development Program of China (NKPs)/ ; W2441012//MOST | National Natural Science Foundation of China (NSFC)/ ; 32330001//MOST | National Natural Science Foundation of China (NSFC)/ ; 42376106//MOST | National Natural Science Foundation of China (NSFC)/ ; 32400108//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Phospholipids/metabolism ; *Lipid Peroxidation ; *Pseudoalteromonas/enzymology/metabolism/genetics ; Phylogeny ; *Bacterial Proteins/metabolism/genetics/chemistry ; Antarctic Regions ; Reactive Oxygen Species/metabolism ; Oxidation-Reduction ; Aquatic Organisms ; *Lipase/metabolism/genetics/chemistry ; },
abstract = {Membrane phospholipid peroxidation is a deleterious process in which reactive oxygen species (ROS) attack unsaturated fatty acids embedded in cell membranes, generating phospholipid hydroperoxides and triggering structural damage that can ultimately lead to cell death. While mammalian strategies to mitigate peroxidation, primarily through the combined activities of phospholipase A2 (PLA2) and subsequent reduction of resultant fatty acid hydroperoxides with glutathione peroxidases/peroxiredoxins have been well characterized for more than two decades, mechanisms by which prokaryotes contend with this oxidative challenge remain poorly understood. Here, we report a phospholipid hydroperoxide elimination strategy mediated by the bifunctional enzyme PpLipO from the Antarctic sea-ice bacterium Pseudoalteromonas prydzensis. This enzyme comprises an N-terminal lipase domain and a C-terminal lipoyl peroxidase domain. Through synergistic action of these domains, PpLipO first hydrolyzes ROS-induced phospholipid hydroperoxides into fatty acid hydroperoxides via its lipase domain, then catalyzes their reduction to hydroxy fatty acids via the peroxidase domain. Comprehensive phylogenetic and structural analyses of the C-terminal peroxidase domain revealed its unique position within a distinct clade of the Ohr/OsmC family, known for their roles in organic hydroperoxide detoxification. Functional studies of PpLipO homologs in other marine bacteria, combined with metagenomic surveys, suggest that this strategy is widespread in global oceans, particular among polar marine bacteria. Altogether, our findings identify a prokaryotic phospholipid peroxidation repair mechanism that parallels the mammalian PLA2 - peroxidase system, expanding our understanding of oxidative stress response across domains of life.},
}

*Phospholipids/metabolism
*Lipid Peroxidation
*Pseudoalteromonas/enzymology/metabolism/genetics
Phylogeny
*Bacterial Proteins/metabolism/genetics/chemistry
Antarctic Regions
Reactive Oxygen Species/metabolism
Oxidation-Reduction
Aquatic Organisms
*Lipase/metabolism/genetics/chemistry

@article {pmid42616879,
year = {2026},
author = {Zheng, L and Li, B and Xu, S and Chen, J and Liang, G},
title = {Large language models enhance annotation of enzymes in metagenomes.},
journal = {Science advances},
volume = {12},
number = {34},
pages = {eaee4389},
doi = {10.1126/sciadv.aee4389},
pmid = {42616879},
issn = {2375-2548},
mesh = {Large Language Models ; Humans ; *Metagenome ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; *Enzymes/genetics/metabolism ; Software ; Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; },
abstract = {Metagenomic data have notable biological potential, but their functional interpretation is frequently impeded by incomplete protein function annotations. Accurate enzyme annotation is essential for elucidating the metabolic capabilities of microbial communities within metagenomic datasets. To address this challenge, we developed FEDKEA, an enzyme annotation tool leveraging protein language models, and provided a web platform for its use. In addition, we designed a user-friendly, FEDKEA-based metagenomic pipeline, MEnzMap, which encompasses the entire analysis workflow-from raw data quality control to function prediction and downstream analyses. Applying MEnzMap to human gut metagenomic data from the iHMP2 project, we generated a comprehensive enzyme profile landscape for both healthy individuals and patients with inflammatory bowel diseases. These tools provide an efficient method for the functional annotation of microbial dark matter and facilitate the identification of disease-associated enzymes.},
}

Large Language Models
Humans
*Metagenome
*Molecular Sequence Annotation/methods
*Metagenomics/methods
*Enzymes/genetics/metabolism
Software
Computational Biology/methods
Inflammatory Bowel Diseases/microbiology/genetics

@article {pmid42617151,
year = {2026},
author = {Yu, Z and Meng, L and Nguyen, CH and Mamitsuka, H and Kanehisa, M and Ogata, H},
title = {DeepKOALA: a scalable deep learning framework for KEGG Orthology assignment.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
doi = {10.1093/bib/bbag445},
pmid = {42617151},
issn = {1477-4054},
support = {22H00384//JSPS/ ; 25H01144//JSPS/ ; 26K21756//JSPS/ ; //SuperComputer System/ ; //Institute for Chemical Research/ ; //Kyoto University/ ; },
mesh = {*Deep Learning ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; Sequence Alignment ; *Software ; Algorithms ; },
abstract = {The KEGG Orthology (KO) system links DNA and protein sequences to biological functions and pathways, providing a curated, fundamental, and consistent annotation framework across all domains of life. While accurate, traditional sequence alignment-based annotation methods are computationally expensive, which severely limits their application in large-scale datasets. To address this challenge, we introduce Deep KEGG Orthology and Links Annotation (DeepKOALA), a deep learning approach based on Gated Recurrent Units (GRU), which frames KO annotation as an open-set recognition task. This design reduces false positives arising from out-of-scope sequences and, together with a lightweight GRU backbone, enables high-throughput annotation. The GRU-based model was benchmarked against four other deep learning architectures and showed the best balance between speed and accuracy. We then trained a GRU-based model, DeepKOALA, and performed a cross-species evaluation against existing KO annotation tools. In this comparison, DeepKOALA achieved a F1 of 83.37%, which is comparable to existing alignment-based tools. Meanwhile, the speed of DeepKOALA was 36.5-fold faster than Blast KEGG Orthology and Links Annotation (BlastKOALA). We also provide a specialized fragment model for handling incomplete sequences and an optional multi-domain mode. Together, these features make DeepKOALA a scalable and efficient option for high-throughput function annotation.},
}

*Deep Learning
*Molecular Sequence Annotation/methods
*Computational Biology/methods
Sequence Alignment
*Software
Algorithms

@article {pmid42617270,
year = {2026},
author = {Li, Y and Li, Q and Zhang, X and Wang, Y and Gao, G and Chen, D and Qin, S and Cui, Z and Liu, L and Liu, A and Wang, H and Wang, Q and Tang, B},
title = {Microbiota contributes to regulates the external genitalia development through gut-testis axis in male geese.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107476},
doi = {10.1016/j.psj.2026.107476},
pmid = {42617270},
issn = {1525-3171},
abstract = {Geese is one of the few poultry species with complete external genitalia, and the external genitalia abnormal development has become an important factor limiting the reproductive efficiency of the goose industry. Recent studies have shown that the gut microbiota plays an important role in regulating male reproductive processes, but its regulatory mechanisms in male geese's external genitalia development remain unclear. In this study, male geese with normal development (ND) and abnormal development (AD) external genitalia were selected as the research object, and multi-omics were used to investigate the regulatory of the microbe-mediated gut-testis axis on external genitalia development. At the transcriptomic level, we identified key DEGs (KNG1, P2RY4, SSTR5, and HRH3) in the testis and external genitalia between ND and AD groups, which were significantly enriched in the neuroactive ligand-receptor interaction pathway. Metabolomics analysis revealed that DMs in the ND and AD groups were significantly enriched in pathways related to aromatic amino acid metabolism and neural signal transduction. Furthermore, metagenomic results showed that the ND group was identified key bacterial genera g_Blautia and g_Faecousia affecting external genitalia development, which were associated with SCFAs synthesis and neuroendocrine signaling regulation. Integrated with multi-omics data, it was revealed that gut-derived neuroactive metabolic signals may participate in the molecular regulation of external genitalia development in male goose by modulating GPCRs signaling. Our findings not only provide new insights into the gut-testis axis regulates the development of external genitalia in male geese, but also contribute to improving the reproductive performance of male geese.},
}

@article {pmid42617542,
year = {2026},
author = {Cui, YX and Xing, BS and Li, S and Wang, ZY and Wang, XC and Li, YY and Chen, R},
title = {Codigestion of food waste and real traditional Chinese medicine wastewater in anaerobic membrane bioreactor: Stability mechanism and microbial community dynamics.},
journal = {Water research},
volume = {307},
number = {},
pages = {126691},
doi = {10.1016/j.watres.2026.126691},
pmid = {42617542},
issn = {1879-2448},
abstract = {The treatment of real traditional Chinese medicine (TCM) wastewater still poses a major challenge. In this study, the complementary properties of TCM wastewater and food waste (FW) were exploited, and a 230-day long-term experiment using an anaerobic codigestion (AcoD) system coupled with an anaerobic membrane bioreactor was conducted, thereby aiming to systematically analyse the stability mechanism of the AcoD system. The results revealed that the AcoD system could maintain stable operation at a volume ratio of 25% TCM wastewater to 75% FW under a prolonged hydraulic retention time and a reduced organic loading rate, with a methane content of approximately 60% and a chemical oxygen demand removal efficiency exceeding 97%. Increasing the proportion of TCM wastewater to 50% induced irreversible acidification (pH<6.3) and complete system collapse. Efficient organic removal was realized via the combined effect of microbial degradation and membrane interception, whereas the accumulation of extracellular polymeric substances led to membrane fouling. The results of metagenomic analysis demonstrated that enrichment of Thermodesulfobacteriota and Nitrospirota effectively mitigated the biotoxicity of TCM wastewater. Moreover, the presence of TCM-derived antimicrobial substances resulted in an increase in the abundance of tetracycline and macrolide antibiotic resistance genes, exerting selective pressure on microorganisms and inhibiting methanogenic activity. Acetoclastic methanogenesis was identified as the dominant methanogenic pathway, which is accompanied by hydrogenotrophic methanogenesis. Notably, the addition of TCM wastewater induced microbial stress responses, thereby inhibiting biofilm formation on the membrane surface. This study provides a new perspective on membrane fouling control and a theoretical basis for the treatment of real TCM wastewater.},
}

@article {pmid42617564,
year = {2026},
author = {Zhao, L and Liu, Z and Gao, J and Yin, H and Ma, L and Xiao, N},
title = {Environmental coupling between metal resistance genes and bacterial communities in Beijing urban green-space soils.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130748},
doi = {10.1016/j.jenvman.2026.130748},
pmid = {42617564},
issn = {1095-8630},
abstract = {Urban green spaces are intensively managed ecosystems exposed to chronic, multisource, low-intensity anthropogenic inputs. These inputs may alter soil microbial communities and influence the distribution of metal resistance genes (MRGs). However, MRG distributions and their relationships with environmental conditions and bacterial communities remain unclear under the complex, non-extreme pollution conditions typical of these ecosystems. We investigated Beijing urban green spaces as a representative system using metagenomic sequencing and metagenome-assembled genome (MAG) analysis. We characterized soil MRG composition, its environmental associations, and the distribution of potential hosts. MRG composition differed significantly among ecological conservation (EC), transitional urban (TU), and central urban (CU) zones. These differences were closely associated with soil physicochemical properties and bacterial community structure. Available phosphorus (AP) was significantly associated with variation in both bacterial community structure and MRG composition. MAG-based analysis identified distinct potential-host compositions across the three functional zones. Proteobacteria were more frequently represented among dereplicated MAGs from EC soils, whereas Actinobacteria were more frequent in TU and CU soils. Heavy metal concentrations correlated with MRG composition. However, variation partitioning analysis did not identify an independent contribution from heavy metals after accounting for soil physicochemical properties and bacterial community structure. These findings indicate that urban green-space soil monitoring should incorporate environmental conditions and microbial community characteristics rather than rely solely on total metal concentrations.},
}

@article {pmid42617567,
year = {2026},
author = {Zhou, Q and Xu, X and Mi, K and Huo, M and Kou, Z and Li, G and Huang, L},
title = {Investigating AHL-associated quorum sensing impact on antibiotic-driven resistome expansion in anaerobic fermentation microbiomes: Metagenomic insights.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130711},
doi = {10.1016/j.jenvman.2026.130711},
pmid = {42617567},
issn = {1095-8630},
abstract = {Previous studies have demonstrated that quorum sensing (QS) can mitigate the impact of antibiotics on environmental microbial communities. Metagenomic analysis was used to examine AHL effects on the resistome in anaerobic fermentation microbiomes under antibiotic stress in this research. AHLs reduced ARGs, MGEs, and phage abundance compared to antibiotic-only samples following the addition of high concentrations (500 nmol/L) of AHLs. Phages and integrons played pivotal roles in shaping the resistome. Escherichia coli, Vibrio cholerae, and Pseudomonas aeruginosa were key targets affected by AHLs. Both the assembled environmental metagenomes and the complete genomes of isolated bacteria consistently support the broad potential of quorum-sensing systems in mediating the dissemination or regulation of resistome spreading. Quorum sensing systems are very likely to affect microbial community resistomes by regulating the phageome. These insights are valuable for refining fermentation and waste management processes, offering potential in environmental restoration and possibly curbing the spread of resistance genes.},
}

@article {pmid42617676,
year = {2026},
author = {Gao, Z and He, Y and Li, X and He, Z and Zhang, Q and Dzakpasu, M and Wang, XC},
title = {Hydrological seasonality shapes antibiotic resistome assembly and dissemination risk in a reclaimed-water-fed urban river.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125523},
doi = {10.1016/j.envres.2026.125523},
pmid = {42617676},
issn = {1096-0953},
abstract = {Reclaimed-water-fed urban rivers are increasingly recognized as potential hotspots for antibiotic resistance gene (ARG) dissemination; however, the combined effects of hydrological variability and habitat heterogeneity on resistome dynamics remain poorly understood. Here, paired water and sediment samples were collected from 10 sites along the Qinghe River during non-flood and flood periods and analyzed using metagenomic sequencing. By integrating ARG host identification, mobile genetic element (MGE) profiling, spatial ecological analyses, and community assembly modeling, we characterized ARG composition, host associations, spatial organization, and ecological drivers. Water harbored a more diverse resistome than sediment, while flood-period water exhibited the highest ARG abundance and diversity, including pronounced enrichment of β-lactam resistance genes. A total of 415 ARG-hosting species were identified, including 41 potential human pathogenic bacterial (HPB) species, among which Acinetobacter spp. were dominant. The abundance and diversity of HPB increased markedly during the flood period. MetaCompare analysis and ARG-MGE co-occurrence patterns further indicated that flood-period water exhibited the highest community-level ARG transmission potential (risk score = 19.32), with MGEs showing stronger associations with pathogenic hosts, suggesting elevated dissemination potential. Neutral community modeling indicated that stochastic dispersal and ecological drift were the dominant assembly processes (R[2] > 0.85), whereas partial least squares path modeling identified physicochemical conditions as the strongest deterministic drivers of ARG variation (path coefficient = 0.751, P < 0.001). Collectively, these findings identify flood-period water as the critical compartment where ARG enrichment, pathogenic host accumulation, and dissemination potential converge, providing an ecological framework for seasonally targeted antimicrobial resistance surveillance and reclaimed water management under increasing hydrological variability.},
}

@article {pmid42617678,
year = {2026},
author = {Cai, Y and Zhou, B and Liu, S and Shang, C and Yang, B and Liu, Y and Zhang, S and Fan, R and Hassan, W and Yuan, R and Chen, H},
title = {Long-term PFOA and Cadmium Co-contamination Alters Soil Carbon, Nitrogen, and Phosphorus Cycling: Insights from Metagenomics and Metabolomics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125516},
doi = {10.1016/j.envres.2026.125516},
pmid = {42617678},
issn = {1096-0953},
abstract = {The co-existence of perfluorooctanoic acid (PFOA) and cadmium (Cd) in soil poses a combined threat to microbial communities. However, the ecological effects and underlying mechanisms of their long-term combined exposure remain poorly understood. This study conducted a 90-day soil microcosm experiment to systematically investigate the effects of individual and combined effects of PFOA and Cd on microbial communities. Our results demonstrated that combined pollution of PFOA and Cd significantly affected four soil enzyme activities associated with carbon, nitrogen, and phosphorus cycling. It also influenced microbial thermal activity with an IC50 of PFOA at 0.94 mg/kg. The toxic interaction between PFOA and Cd varied with both toxicity indicators and exposure time. At the community level, PFOA and Cd synergistically reduced bacterial diversity and richness, while exerting more complex interactive effects on fungal communities. Metagenomic analysis revealed that PFOA and Cd significantly affected carbon, nitrogen, and phosphorus cycling by inhibiting inorganic phosphorus solubilization genes (gcd, pqqC) and altering key genes in carbon fixation and nitrogen transformation. Metabolomic profiling further demonstrated that PFOA disrupted membrane lipid homeostasis and amino acid metabolism. Meanwhile, the co-existence of Cd exacerbated disturbances in sugar and carbon metabolism. Our findings provide genetic-level insights into microbial responses to long-term PFOA and Cd co-contamination. These results are essential for risk assessment at such co-contamination sites.},
}

@article {pmid42617679,
year = {2026},
author = {Zhou, HZ and Sun, ZL and Xiao, YX and Xiao, W and Kang-Ma, and Zhou, CH and Ma, YH and He, T},
title = {Litter C/N ratio is associated with POC-to-MAOC transformation potential across forest types in subtropical restoration.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125520},
doi = {10.1016/j.envres.2026.125520},
pmid = {42617679},
issn = {1096-0953},
abstract = {Forest type is a critical determinant of soil organic carbon (SOC) dynamics during ecological restoration, yet how forest type shapes microbial community assembly and functional gene abundance to govern the partitioning of soil carbon into particulate (POC) and mineral-associated (MAOC) fractions remains poorly resolved. In May 2025, we collected soil samples from 12 plots representing three typical forest types (coniferous, mixed, and broad-leaved forests) in the Lingnan Nature Reserve and applied metagenomic sequencing to characterize soil microbial communities and functional processes. Following over three decades of restoration, SOC in mixed (25±1.5 g/kg) and broad-leaved forest (26±2.1 g/kg) soils increased by ∼18% and 23%, respectively, compared to coniferous forests (21±1.6 g/kg). Litter C/N was lower in mixed and broad-leaved forests, corresponding with their higher SOC. Structural equation modeling further linked litter C/N ratio to POC and MAOC accumulation via microbial biomass carbon (MBC) as a key node, with POC, MAOC, and MBC increasing by 108-134%, 20-22%, and 26-31%, respectively, in mixed and broad-leaved versus coniferous soils. At the community level, variations in forest types selectively enriched Acidobacteriota or Actinomycetota, while co-occurrence network analysis revealed a shift from predominantly negative toward predominantly positive associations among bacterial taxa in broad-leaved and mixed forests, along with enhanced cross-module metabolic flow. Functionally, compared to coniferous forests, mixed and broad-leaved forests exhibited ∼15%/38% and 21%/47% increases in RPKM values of carbon fixation/degradation gene, respectively. GO enrichment analysis further indicated that litter inputs may be converted into stable humus via glycolysis and amino acid synthesis pathways. By integrating community-level microbial ecology, co-occurrence network analysis, and metagenomic functional profiling, this study provides novel mechanistic insight into how forest type shapes soil carbon fraction dynamics during restoration. These findings indicate the gene abundance variation in POC-to-MAOC transformation might be a plausible mechanistic link in the plant-microbe-soil carbon nexus and suggest that promoting broad-leaved or mixed forest restoration may represent a potentially effective strategy for enhancing soil carbon accumulation in subtropical regions.},
}

@article {pmid42617801,
year = {2026},
author = {Schaefer, L and Cantú, JO and Demianova, EA and Scholand, KK and Pflugfelder, SC and Britton, RA and de Paiva, CS},
title = {Oral administration of probiotic Limosilactobacillus reuteri DSM 17938 suppresses dry eye disease in the desiccating stress mouse model.},
journal = {The ocular surface},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtos.2026.08.005},
pmid = {42617801},
issn = {1937-5913},
abstract = {PURPOSE: Gut dysbiosis can adversely affect the ocular surface, resulting in inflammation and dry eye. We investigated the potential of an orally administered probiotic bacteria, Limosilactobacillus reuteri DSM17938 (LR17938), on dry eye disease in the desiccating stress (DS) mouse model.

METHODS: C57BL/6J mice were treated with antibiotics (ABX) to induce dysbiosis; stools were analyzed using 16S sequencing. Mice were subjected to 5 days DS while receiving daily gavage of PBS or LR17938. Conjunctival goblet cell (GC) density was assessed in formalin-fixed histological sections. Corneal barrier function was evaluated by Oregon-Green-Dextran dye uptake. T-cells were assessed by flow cytometry. MMP-9 was visualized in corneal epithelium with immunofluorescence. LR17938 efficacy was tested in the context of human gut microbiota by using mice colonized with fecal microbes from Sjögren's disease (SjD) or healthy patients. Metagenomic sequencing was performed on stool collected before and after DS.

RESULTS: 16S sequencing confirmed profound intestinal dysbiosis after ABX treatment. LR17938 administration in ABX-treated mice exposed to DS improved corneal barrier function, preserved GC density, reduced MMP-9 in corneal epithelium, increased T-regulatory cells and decreased inflammatory T-cells in cervical lymph nodes. In mice colonized with human microbiota, treatment improved corneal barrier function and GC number regardless of microbiota source. Microbiome differences were driven by SjD disease status regardless of DS exposure or probiotic treatment. While DS caused minor shifts, probiotic treatment did not result in significant changes to the gut microbiome.

CONCLUSIONS: LR17938 is a promising complementary treatment for dry eye, showing protective effects to the ocular surface.},
}

@article {pmid42617814,
year = {2026},
author = {Qi, X and Li, T and Gao, D and Jiang, H and Zhu, G and Qiu, X and Guo, Q and Ouyang, Y and Feng, H and Xiang, H},
title = {Biodegradation and toxicity attenuation of bisphenol A by Sphingopyxis granuli XYQ201: mechanism elucidation and wastewater application.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135674},
doi = {10.1016/j.biortech.2026.135674},
pmid = {42617814},
issn = {1873-2976},
abstract = {Bisphenol A (BPA) is a widespread endocrine-disrupting contaminant in wastewater, and microbial biodegradation is a promising approach for its removal. However, BPA-degrading bacteria with clarified degradation products, reduced estrogenic activity after degradation, and demonstrated performance in real wastewater remain limited. In this study, a BPA-degrading bacterium, Sphingopyxis granuli XYQ201, was isolated from municipal wastewater and shown to utilize BPA as the sole carbon source. Strain XYQ201 completely removed 50 mg/L BPA within 38 h under laboratory conditions. Four major degradation products were identified by comparison with authentic standards, including 4-[2-hydroxy-2-(4-hydroxyphenyl)propyl]phenol, 4-[1-hydroxy-2-(4-hydroxyphenyl) propan-2-yl]phenol, 2,3-bis(4-hydroxyphenyl)propane-1,2-diol, and a previously unreported metabolite, 2,2-bis(4-hydroxyphenyl)propane-1,3-diol. Toxicological evaluation using a recombinant yeast bioreporter assay showed that the major hydroxylated metabolites had markedly lower estrogenic activity than BPA, indicating attenuation of estrogenic activity during BPA transformation. Genome analysis, quantitative PCR, and heterologous expression demonstrated that a plasmid-borne bisdAB-encoded two-component cytochrome P450 system is sufficient to initiate BPA hydroxylation and generates the mono-hydroxylated products. Public genomic and metagenomic analyses showed that putative bisdA/bisdB-like genes are phylogenetically diverse and occur in multiple natural and engineered environments. In BPA-spiked wastewater, inoculation with XYQ201 substantially enhanced BPA removal under a high-load condition. These results indicate that strain XYQ201 mediates BPA transformation through a P450-initiated hydroxylation pathway with reduced estrogenic activity of the major metabolites, and may serve as a candidate strain for bioaugmentation of BPA-contaminated wastewater.},
}

@article {pmid42617854,
year = {2026},
author = {Tian, X and Ge, Q and Li, X and Yu, Z and Fan, R and Jiang, H and Yang, Y and Han, R and Du, Q},
title = {Effects of dairy processing on antibiotic resistance genes in milk and associated changes in the murine gut resistome.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28572},
pmid = {42617854},
issn = {1525-3198},
abstract = {This study evaluated the effects of dairy processing on antibiotic resistance genes (ARGs) in milk and examined whether pasteurized milk exposure is associated with changes in the murine gut resistome. Raw milk was subjected to pasteurization (63°C, 30 min), microwave treatment, high-pressure processing, spray drying, or lactic acid fermentation. Microbial enumeration, metagenomic sequencing, and quantitative PCR were used to assess bacterial communities and ARG abundance. Mice were orally administered an ARG-carrying Escherichia coli strain or pasteurized milk for 4 weeks to determine alterations in gut microbial composition and ARG profiles. Non-fermentation processing treatments reduced culturable bacterial counts, whereas most sequencing-detected ARGs showed limited changes in relative abundance across thermal, microwave, high-pressure, and spray-dried treatments. Lactic acid fermentation increased the relative abundance of several ARGs, including Erm(K), vanT, and tetA, concurrent with dominance of fermentative taxa. In mice, administration of ARG-carrying Escherichia coli increased multiple gut ARGs, including β-lactam and quinolone resistance genes. Pasteurized milk intake was associated with changes in gut microbial composition and relative abundance of selected ARGs. These findings indicate that dairy processing reduced viable bacteria but did not fully eliminate detectable ARG signals. Pasteurized milk exposure was associated with gut resistome shifts in mice, although causality was not established.},
}

@article {pmid42605089,
year = {2026},
author = {Wang, NL and Xu, LF and Liu, XG and Wei, XX and Chen, XP and Wang, LX and Zhou, K and Lin, YQ and Gong, YP and Xie, ZD and Wang, JS and , },
title = {[Metagenomic sequencing-based pathogen analysis in pediatric severe acute non-A-E hepatitis].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {64},
number = {9},
pages = {1041-1047},
doi = {10.3760/cma.j.cn112140-20260608-00446},
pmid = {42605089},
issn = {0578-1310},
abstract = {Objective: Metagenomic sequencing was employed to analyze the pathogen detection profile in pediatric severe acute non-A-E hepatitis. Methods: Based on the platform of the China Childhood Severe Acute Hepatitis Collaborative Group, a case series study was conducted. This study enrolled 36 children with severe acute non-A-E hepatitis, who were admitted to 17 hospitals between April and July 2022. Clinical data, including etiological test results and liver function tests, were collected, and peripheral blood and nasopharyngeal swab specimens were obtained. Metagenomic next-generation sequencing (mNGS) was performed to detect potential infectious pathogens. Results: Among 36 children, there were 24 males and 12 females, with an onset age of 3.5 (1.1, 9.0) years. Common clinical symptoms were fever in 22 cases (61%), jaundice in 13 cases (36%), vomiting in 12 cases (33%), abdominal pain in 10 cases (28%), rash in 10 cases (28%), and diarrhea in 3 cases (8%). Serum alanine aminotransferase and aspartate aminotransferase levels were 950 (826, 1 404) and 811 (498, 1 295) U/L, respectively. Using PCR, plasma Epstein-Barr virus (EBV)-DNA was tested in 31 cases (86%) and plasma cytomegalovirus (CMV)-DNA in 25 cases (69%), and all results were below 5×10[5] copies/L. Plasma mNGS was performed on all 36 patients, detecting 11 viruses. These included EBV in 14 cases, CMV in 12 cases, human adenovirus in 2 cases, herpes simplex virus type 1 in 2 cases, adeno-associated virus type 2 (AAV2) in 1 case, and 6 other viruses. No patient tested positive for both human adenovirus and AAV2 simultaneously. Plasma mNGS results showed a viral read count of 4 (2, 10) per 1×10[8] reads. Nasopharyngeal swab mNGS was performed on 8 cases (22%), detecting 7 viruses. These included human herpesvirus 7 in 4 cases, EBV in 3 cases, and CMV in 3 cases, as well as 4 other viruses. Human adenovirus and AAV2 were not detected. Among the 4 children with human herpesvirus 7, 2 cases were also positive for human herpesvirus 6B, but neither virus was detected in their plasma mNGS. Conclusions: The detection rates of human adenovirus and AAV2 are both low among children with severe acute non-A-E hepatitis, and there are no cases of co-infection with both viruses.},
}

@article {pmid42605509,
year = {2026},
author = {Xiao, L and Fu, C and Santos, IR and Duarte, CM and Liu, J and Zhou, L and Zhou, M and Dang, R and Lin, J and Xiao, K and Luo, Y and Han, G},
title = {Microbial Decomposition of Lignin to Methane Reduces Net Blue Carbon Benefit Across China's Saltmarshes.},
journal = {Global change biology},
volume = {32},
number = {8},
pages = {e71059},
pmid = {42605509},
issn = {1365-2486},
support = {2022YFF0802101//National Key Research and Development Program in China/ ; U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 41991330//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Methane/metabolism ; *Lignin/metabolism ; China ; *Wetlands ; Carbon/metabolism ; *Microbiota ; Biodegradation, Environmental ; },
abstract = {CH4 emissions from mangrove, saltmarsh, and seagrass ecosystems partially offset carbon sequestration, potentially diminishing the climate mitigation capacity of these blue carbon habitats. However, a mechanistic understanding of the processes governing CH4 production potential across large spatial scales remains limited. By integrating incubation-based measurements from 116 sites, we reveal significant ecosystem-specific differences in CH4 production potential, with saltmarshes emerging as CH4 production hotspot relative to mangroves and seagrass meadows. Using an integrated analytical approach encompassing more than 30 environmental, biogeochemical, and microbial parameters, we demonstrate that CH4 production potential converges on sediment organic carbon availability, particularly plant-derived carbon, as a key regulatory axis. Additionally, metagenome-assembled genomes (MAGs) recovered from saltmarshes show a functional bias toward lignin degradation, thereby fueling downstream CH4 production via methylotrophic pathways. Lignin-addition and stable carbon isotope experiments further provide supportive evidence that lignin decomposition enhances Chinese saltmarsh CH4 production potential, revealing a pathway that may reduce net blue carbon benefit. Together, these findings underscore that saltmarsh plant-derived lignin is less stable than conventionally assumed, as microbial processing redirects stored carbon toward CH4 production, challenging current blue carbon accounting frameworks at a continental scale within China.},
}

*Methane/metabolism
*Lignin/metabolism
China
*Wetlands
Carbon/metabolism
*Microbiota
Biodegradation, Environmental

@article {pmid42606111,
year = {2026},
author = {Hua, B and Pang, S and Li, A and Hu, Z and Wu, H and Zhang, S and Fan, Y and Wu, Y and Yang, W and Zhao, Y and Guan, Y and Ji, B and Kong, D and Zhao, Y and Goncharov, AA and Korotkevich, AY and Mao, R and Zhang, Y and Zhang, X},
title = {Rainfall Shapes the Diversity of Soil Nitrogen-Fixing Microorganisms Worldwide.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77215},
pmid = {42606111},
issn = {2198-3844},
support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; //Top-Notch Young Talents Program (to Ximei Zhang) of China/ ; },
abstract = {Soil nitrogen-fixing microorganisms naturally fertilize terrestrial ecosystems, but the primary driver of their diversity across the globe and the underlying mechanisms remain unclear. We analyzed the nifH gene in 1257 (1137 publicly available + 120 self-generated) soil metagenomes from 318 terrestrial ecosystems globally. Mean annual precipitation was identified as the key factor influencing the relative abundance, richness, and composition of the potential nitrogen-fixers. Precipitation was directly associated with nitrogen-fixers (e.g., water availability) rather than indirectly via other soil variables (e.g., pH). Lower precipitation increased the contribution of deterministic processes (e.g., interspecific competition) in driving their community assembly and selected species with larger genomes, while higher precipitation increased the contribution of stochastic processes (e.g., random birth/death) and favored smaller-genome species. A multifactorial experiment further demonstrated that precipitation increase had a larger regulatory effect on the stochastic processes than other factors (e.g., climate warming). eXtreme Gradient Boosting (XGBoost) projections under future global change scenarios indicate a general increase in their relative abundance across most regions worldwide, with declines only in specific areas. These findings reveal distinct patterns and mechanisms governing the global biodiversity and biogeography of soil nitrogen-fixers, providing valuable insights for developing region-specific management strategies aimed at maintaining ecosystem productivity.},
}

@article {pmid42606386,
year = {2026},
author = {Ghisleni, G and Dow, E and Iovino, T and Colman-Vega, PJ and Dicesare, A and Guanella, E and Bacchi, YM and Colombo, A and Leccese, M and Marzucchi, M and Gorla, ME and Caracciolo, A and Sala, A and Makarycheva, P and Rubrica, SC and Ferrier, A and Armanni, A and Fumagalli, S and Wood-Charlson, E and Bruno, A},
title = {Fantastic Microbes and Where to Find Them: evaluating learning-by-doing outcomes in a crowdfunded metagenomics workshop.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag093},
pmid = {42606386},
issn = {1574-6968},
abstract = {Metagenomics offers a powerful framework for authentic, interdisciplinary learning, yet it remains underrepresented in undergraduate education due to technical and infrastructural barriers. We hypothesized that a research-based, learning-by-doing metagenomics workshop supported by accessible bioinformatics tools could enhance students' perceived skills, self-efficacy, and conceptual understanding of metagenomic analysis. To test this hypothesis, we designed and evaluated a hybrid hands-on workshop in which undergraduate and postgraduate students analyzed real environmental shotgun metagenomic datasets generated from soil samples collected during a citizen science initiative. Using the graphical workflow platform KBase, participants completed an end-to-end metagenomic analysis, from quality control and assembly to genome reconstruction, taxonomic classification, functional annotation, and scientific presentation of results. Educational outcomes were assessed through validated retrospective pre-post questionnaires, self-efficacy scales, and an open-ended conceptual understanding task. Participants showed significant increases in perceived metagenomic skills and confidence in performing metagenomic analyses, while gains in perceived learning showed a positive trend. Conceptual understanding improved across educational levels, particularly among participants with limited prior experience. Together, these findings demonstrate that authentic, data-driven metagenomics activities can effectively lower barriers to computational biology and foster meaningful learning through hands-on research experiences.},
}

@article {pmid42607773,
year = {2026},
author = {Zhao, C and Mo, J and Peng, Z and Cheng, J and Zhan, O and Gong, Y and Mao, Y and Qin, Y and Wu, W},
title = {Combined lysine and cobalt supplementation improves semi-thermophilic anaerobic digestion performance with enhanced Methanosarcina-associated methylotrophic potential.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135647},
doi = {10.1016/j.biortech.2026.135647},
pmid = {42607773},
issn = {1873-2976},
abstract = {Protein-rich food waste challenges anaerobic digestion (AD) through rapid acidification and chronic ammonia stress. Semi-thermophilic AD (STAD, 41-49℃) offers a promising balance between mesophilic stability and thermophilic conversion efficiency, but further improvement may depend on strengthening methylotrophic methanogenesis, a route better aligned with the methylamine-forming potential of this substrate. l-lysine and cobalt were therefore selected as targeted additives to support its key methyl-transfer step. Their enhancement effects were evaluated through a series of experiments. Initial tests across different temperatures showed that STAD outperformed mesophilic and thermophilic digestion in both methane production and process stability, and combined supplementation gave the strongest enhancement. Under STAD, combined addition increased methane production by 58.0%, reduced volatile fatty acids (VFAs) and free ammonia by 24.7% and 21.9%, respectively, and strengthened Methanosarcina-linked methylotrophic signatures. Further optimization under STAD showed that intermediate doses performed best, and the predicted optimum, 45 mg·L[-1]l-lysine and 3.5 mg·L[-1] cobalt, was validated in a continuous reactor. This combination increased methane yield (314.21 ± 42.35 mL·gVS[-1]·d[-1]) by 33.3%, reduced VFAs and residual soluble chemical oxygen demand, by 29.6% and 44.8%, respectively, without aggravating ammonia stress. It also showed favorable preliminary economic potential, with a benefit-cost ratio of ∼15.0 during subsequent maintenance dosing. Mechanistically, these effects were linked to enrichment of hydrolytic, fermentative, and syntrophic bacteria, reduced competition from non-methylotrophic taxa, and more favorable conditions for Methanosarcina-centered, potentially methylamine-utilizing pathways. Overall, this study provides a practical strategy with clear engineering potential to further strengthen STAD for food-waste treatment.},
}

@article {pmid42608197,
year = {2026},
author = {Rao, X and Gu, Y and Gabriella, and Ma, J and Wang, H and Zou, Y},
title = {Promises and Pitfalls of Long-Read Sequencing for Resolving Microbial Complexity.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag087},
pmid = {42608197},
issn = {2047-217X},
abstract = {Long-read sequencing (LRS) has driven a transition in microbial genomics, overcoming the assembly fragmentation inherent to short-read sequencing. This review elucidates the impact of LRS across isolate genomics, metagenomics, and multi-omics domains. By spanning extensive repetitive regions, LRS facilitates the reconstruction of circular chromosomes and precisely resolves mobile genetic elements (MGEs). In metagenomics, LRS enables strain-level resolution, the recovery of circular metagenome-assembled genomes, and the precise localization of MGEs within host replicons. Furthermore, the single-molecule, amplification-free properties of LRS provide enhanced resolution of native epigenetic modifications and full-length transcriptomes. Despite these advancements, widespread implementation remains constrained by multidimensional challenges, including stringent high-molecular-weight DNA requirements, depth deficits, and computational overhead. Nevertheless, LRS is increasingly becoming the method of choice for isolate genomics and metagenomics. As detection technologies and algorithms progress, LRS will further improve our ability to decipher the structural and functional diversity of microbial ecosystems.},
}

@article {pmid42608979,
year = {2026},
author = {Wang, P and Wang, C and Zhang, Y and Bi, L and Zhao, H and Xu, Z and Wang, Z and Sheng, Y and Cui, Y},
title = {Topical Application of Indole-3-Acetic Acid, Present in S. epidermidis Supernatant, Alleviates Atopic Dermatitis in Mice at Least via the Aryl Hydrocarbon Receptor Signalling Pathway.},
journal = {Experimental dermatology},
volume = {35},
number = {8},
pages = {e70329},
doi = {10.1111/exd.70329},
pmid = {42608979},
issn = {1600-0625},
support = {201920102303//Peking Union Medical College/ ; 2024-ZX-019//Project of Integrated Traditional Chinese Medicine Collaboration "Flagship" Department Development/ ; ZRJY2023-GG14//China-Japan Friendship Hospital Youth Science and Technology Excellence Project/ ; 2208085Y25//Outstanding Youth Project of Natural Science Foundation of Anhui Province/ ; 2022YFC3602002//China National Key R&D Program of China/ ; 2022-NHLHCRF-LX-02-03//National High-Level Hospital Clinical Research Funding/ ; },
mesh = {Animals ; *Dermatitis, Atopic/drug therapy/metabolism/microbiology ; *Indoleacetic Acids/administration & dosage/pharmacology/therapeutic use/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism/antagonists & inhibitors ; *Staphylococcus epidermidis/metabolism ; Signal Transduction/drug effects ; Mice ; Humans ; Skin Microbiome ; Skin/metabolism/microbiology ; Keratinocytes/metabolism ; Administration, Topical ; Disease Models, Animal ; Female ; Molecular Docking Simulation ; },
abstract = {Dysbiosis of the skin microbiome, characterised by Staphylococcus aureus overgrowth and imbalance of commensals such as Staphylococcus epidermidis (S. epidermidis), is closely associated with atopic dermatitis (AD). However, the therapeutic relevance of defined S. epidermidis-associated indole metabolite, especially indole-3-acetic acid (IAA), in AD-like inflammation remains incompletely characterised. Here, we investigated the role of IAA, a tryptophan-derived metabolite enriched in the culture supernatant of the tested S. epidermidis strain, in AD-like inflammation. Public transcriptomic analyses suggested impaired AHR-associated and tryptophan-metabolism signatures in AD skin, particularly in lesional skin, while human metagenomic data indicated AD-associated staphylococcal alterations. Targeted metabolomics identified IAA as an enriched indole metabolite in S. epidermidis culture supernatant. In an MC903-induced AD-like mouse model, cutaneous IAA levels and S. epidermidis abundance were reduced. Topical IAA attenuated AD-like phenotypes, improved barrier-related proteins and reduced inflammatory indices. These protective effects were diminished by the AHR antagonist CH223191. Molecular docking predicted a possible interaction between IAA and AHR, and in vitro assays showed that IAA modulated keratinocyte AHR-associated inflammatory and barrier-related responses. Together, our findings support IAA as a microbiome-associated postbiotic candidate for AD management, at least partly through AHR-associated signalling.},
}

Animals
*Dermatitis, Atopic/drug therapy/metabolism/microbiology
*Indoleacetic Acids/administration & dosage/pharmacology/therapeutic use/metabolism
*Receptors, Aryl Hydrocarbon/metabolism/antagonists & inhibitors
*Staphylococcus epidermidis/metabolism
Signal Transduction/drug effects
Mice
Humans
Skin Microbiome
Skin/metabolism/microbiology
Keratinocytes/metabolism
Administration, Topical
Disease Models, Animal
Female
Molecular Docking Simulation

@article {pmid42609044,
year = {2026},
author = {Kudureti, A and Zhao, S and Liu, X and Wang, BZ and Tian, CY},
title = {Adaptation of Soil Viruses to Salinity Stress: Insights Into Genome Size Expansion and Functional Diversification.},
journal = {Environmental microbiology},
volume = {28},
number = {8},
pages = {e70395},
doi = {10.1111/1462-2920.70395},
pmid = {42609044},
issn = {1462-2920},
support = {2024TSYCCX0056//Tianshan Talent Program of Xinjiang/ ; 2025D01D47//Natural Science Foundation of Xinjiang/ ; 31971448//Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Genome, Viral ; *Viruses/genetics/classification/isolation & purification ; *Salt Stress ; *Genome Size ; Salinity ; Soil/chemistry ; Metagenome ; Biodiversity ; },
abstract = {Viruses are important components of soil biodiversity and ecosystem functions. However, their response to soil salinity stress, including ecological patterns and functional potential, remains poorly understood. Here, metagenomic data from 84 saline soil samples were retrieved from public databases and analysed. Viral sequences were extracted from metagenomes, and auxiliary metabolic genes (AMGs) were identified. 83.34% of the vOTUs had no detectable gene-sharing links with the RefSeq Viral database, highlighting the unexplored diversity of saline soil viromes. In soils with higher salinity, viral genomes exhibited larger genome sizes and increased GC content. The diversity of temperate viruses (3.16-7.32) was significantly higher than that of lytic viruses (2.49-6.99). Although the diversity of temperate viruses decreased with increasing salinity, no significant trend was observed for lytic viruses. Viral abundance correlated positively with host abundance, consistent with the 'piggyback-the-winner' ecological coupling hypothesis. Functional potentials varied with salinity, and structural analysis showed changes in atomic interactions in key proteins (NhaA, ACAT) across salinity gradients. Significantly positive correlations were found between viral diversity and functional potential related to salt tolerance, carbon fixation, organic phosphorus mineralisation and nitrogen metabolism. These results suggest viral traits correlate with salinity gradients and provide insights into viral responses in saline soils.},
}

*Soil Microbiology
*Genome, Viral
*Viruses/genetics/classification/isolation & purification
*Salt Stress
*Genome Size
Salinity
Soil/chemistry
Metagenome
Biodiversity

@article {pmid42609251,
year = {2026},
author = {Tang, J and Deng, J and Guo, K and Song, Y and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Fang, H and Zhuge, J},
title = {The clinical application of metagenomic next-generation sequencing for invasive pulmonary aspergillosis in neutropenic patients: a multicenter retrospective study in the ICU.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1878097},
pmid = {42609251},
issn = {2235-2988},
mesh = {Humans ; *Invasive Pulmonary Aspergillosis/drug therapy/diagnosis/microbiology/mortality ; Retrospective Studies ; *Neutropenia/complications ; Female ; Intensive Care Units ; Male ; Antifungal Agents/therapeutic use ; Middle Aged ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; Treatment Outcome ; },
abstract = {BACKGROUND: Early initiation of targeted antifungal therapy is critical for improving outcomes in neutropenic patients with invasive pulmonary aspergillosis (IPA) in the intensive care unit (ICU). Although metagenomic next-generation sequencing (mNGS) is valuable for pathogen detection, its clinical value in IPA patients with neutropenia remains unclear.

METHODS: This multicenter retrospective study included patients clinically diagnosed with invasive pulmonary aspergillosis (IPA). All patients underwent both conventional microbiological tests (CMTs) and metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Based on neutrophil status, patients were stratified into neutropenic and non-neutropenic groups and further divided into mNGS-guided and CMT-guided groups according to the antifungal treatment strategy.

RESULTS: mNGS demonstrated higher pathogen detection rate than conventional microbiological tests (CMTs) in both neutropenic and non-neutropenic patients with invasive pulmonary aspergillosis (IPA). It also identified a broader pathogen spectrum and a higher proportion of mixed infections. Overall, IPA patients in the mNGS-guided group had lower 28-day mortality compared with the CMT-guided group (23.17% vs. 43.75%, P = 0.04). Multivariate analysis indicated that mNGS-guided therapy was associated with reduced 28-day mortality (adjusted OR = 0.329, 95% CI: 0.111-0.974, P = 0.045). A significant interaction between treatment strategy and neutrophil status was observed (adjusted P = 0.002). In subgroup analysis, the survival benefit of mNGS-guided therapy was mainly observed in neutropenic IPA patients, who achieved higher rates of appropriate antifungal therapy and lower mortality, whereas no significant intergroup difference was found among non-neutropenic IPA patients.

CONCLUSION: mNGS-guided antifungal therapy significantly reduced 28-day mortality in neutropenic IPA patients, whereas no clear effect was observed in non-neutropenic patients. These findings highlight the potential clinical value of mNGS in guiding antifungal therapy in neutropenic IPA patients.},
}

Humans
*Invasive Pulmonary Aspergillosis/drug therapy/diagnosis/microbiology/mortality
Retrospective Studies
*Neutropenia/complications
Female
Intensive Care Units
Male
Antifungal Agents/therapeutic use
Middle Aged
*Metagenomics/methods
Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
Aged
Adult
Treatment Outcome

@article {pmid42609329,
year = {2026},
author = {Qin, P and Tuersong, W and Tao, Z and Huang, B and Tan, L and Liu, H and Zhao, J and Hu, M},
title = {Metagenomic profiling of pathogens and antibiotic resistome in influent of six municipal wastewater treatment plants: a descriptive analysis of plant-specific microbial hazards.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780611},
pmid = {42609329},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) serve as critical nodes for monitoring urban biological hazards, yet the raw influent-the primary entry point for pathogens and antibiotic resistance genes (ARGs)-remains less characterized compared to treated effluent, particularly at the level of individual facilities, as most prior studies have pooled samples or focused on post-treatment matrices.

METHODS: In this descriptive study, we performed metagenomic sequencing on influent samples collected from six municipal WWTPs, with each plant treated as an independent unit to profile its specific microbial community, pathogen composition, and antibiotic resistome.

RESULTS: Across all samples, a total of 853 bacterial and 232 eukaryotic pathogen species were identified. An exploratory risk index, calculated by integrating species abundance with established risk group classifications, assigned the highest heuristic score to Tangxun Lake (2150), reflecting its concurrent enrichment of both enteric and respiratory pathogens. The pathogen distribution exhibited plant-specific patterns: enteric pathogens including Escherichia coli, Vibrio cholerae, and Campylobacter jejuni were predominantly detected in Huangpu road and Nantaizi Lake, whereas respiratory pathogens such as Mycobacterium tuberculosis and Legionella pneumophila were more abundant in Xinzhuang, Jinyang, and Tangxun Lake. A core set of ARGs-comprising multidrug efflux pumps, β-lactamases, and tetracycline resistance genes-was consistently present across all six facilities, collectively accounting for approximately 60% of the total ARG abundance detected. In addition, exploratory correlations between mobile genetic elements (e.g., plasmids and transposases) and clinically relevant ARGs were observed across the dataset, warranting further investigation.

DISCUSSION: By generating plant-specific hazard inventories rather than pooled averages, this study provides a descriptive baseline that enables facility-specific surveillance prioritization.},
}

@article {pmid42609485,
year = {2026},
author = {Yuan, G and Xie, X and Tang, M and Zheng, X and Luo, X and Xiong, A},
title = {Determinants of fungal infection and hospital readmission risk in interstitial pneumonia with autoimmune features: associations with vitamin D and pirfenidone.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1825951},
pmid = {42609485},
issn = {1664-3224},
mesh = {Humans ; Female ; *Pyridones/therapeutic use ; Retrospective Studies ; Male ; Risk Factors ; *Vitamin D/blood ; *Patient Readmission/statistics & numerical data ; *Lung Diseases, Interstitial/immunology/complications ; Middle Aged ; Aged ; *Mycoses ; *Autoimmune Diseases ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; },
abstract = {BACKGROUND: Fungal infections significantly compromise the prognosis of patients with interstitial pneumonia with autoimmune features (IPAF). However, the specific immune-related risk factors and their impact on clinical stability remain poorly defined. This study aimed to identify independent predictors for fungal infection and early readmission to optimize risk stratification.

METHODS: We conducted a retrospective analysis of 98 patients meeting the 2015 European Respiratory Society/American Thoracic Society (ERS/ATS) IPAF classification criteria. Fungal infections were confirmed through clinical manifestations, radiological findings, and metagenomic next-generation sequencing (mNGS). Logistic and Cox regression models were employed to identify factors independently associated with fungal infection and hospital readmission.

RESULTS: Fungal infection was identified in 40.8% of the cohort, with Candida albicans as the primary pathogen. Respiratory failure (odds ratio [OR]=3.76, 95% confidence interval [CI]: 1.24-11.38) and hypertension (OR = 2.94, 95% CI: 1.01-8.64) were independent associated with higher risks of fungal infection. Vitamin D (OR = 0.94, 95% CI: 0.89-0.99) and pirfenidone (OR = 0.17, 95% CI: 0.04-0.71) were independently associated with lower risks of fungal infection. Regarding prognosis, anti-Ro-52 (hazard ratio [HR]=2.23, 95% CI: 1.06-4.68) and anti-PL-12 (HR = 3.87, 95% CI: 1.11-13.44) antibody positivity independently predicted 3-month and 6-month hospital readmission, respectively.

CONCLUSION: Fungal infections in IPAF involve a complex interplay between clinical comorbidities and immune status. In this single-center retrospective cohort, vitamin D and pirfenidone were independently associated with lower risks of fungal infection and hospital readmission after adjustment for confounders. These findings should be interpreted as associations rather than evidence of causality and require validation through large-scale, multicenter prospective studies.},
}

Humans
Female
*Pyridones/therapeutic use
Retrospective Studies
Male
Risk Factors
*Vitamin D/blood
*Patient Readmission/statistics & numerical data
*Lung Diseases, Interstitial/immunology/complications
Middle Aged
Aged
*Mycoses
*Autoimmune Diseases
Anti-Inflammatory Agents, Non-Steroidal/therapeutic use

@article {pmid42609578,
year = {2026},
author = {Li, L and Wang, C and Liu, L and Xu, T and Nie, X and Liu, Y and Zhang, H and Yang, C and Di, J},
title = {Gut microbiota-derived imidazole propionate is associated with obesity.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1861257},
pmid = {42609578},
issn = {2296-861X},
abstract = {Obesity is a progressive metabolic disorder with some well-recognized markers, such as increased or elevated branched-chain amino acids (BCAAs). However, the role of gut microbiota-derived metabolites remains unknown in Asian populations. By employing an integrated multi-omics approach combining metagenomic and plasma metabolomic profiling in an Asian cohort alongside a longitudinal analysis of a bariatric surgery subgroup. We identified a distinct metabolic signature in obesity characterized by depleted circulating histidine and a concomitant elevation of Imidazole Propionate (ImP). The elevated ImP level not only positively correlated with the body mass index (BMI) but also increased progressively across obesity severity categories, and were associated with the taxonomic enrichment of ImP-producing species, such as Streptococcus mutans and Lactobacillus gasseri. Meanwhile, the ImP level showed rapid reduction within 3 months post-bariatric surgery. Collectively, our findings indicate that gut dysbiosis and histidine metabolism toward ImP production link with obesity and metabolic dysfunction.},
}

@article {pmid42609856,
year = {2026},
author = {Salmona, M and Benattia, A and Meignin, V and Marie Ferré, V and Jouenne, F and Lorillon, G and Le Goff, J and Mourah, S and Tazi, A},
title = {No detectable infectious agents in Langerhans cell histiocytosis with lung involvement.},
journal = {ERJ open research},
volume = {12},
number = {4},
pages = {},
pmid = {42609856},
issn = {2312-0541},
abstract = {Shotgun metagenomics of pulmonary and extrapulmonary Langerhans cell histiocytosis lesions revealed no infectious pathogens and no microbiome differences from control lung tissue, which does not support an infectious role in disease pathogenesis https://bit.ly/4liJHfO.},
}

@article {pmid42610730,
year = {2026},
author = {Sukkasam, N and Liu, TX and Dofher, K and Monshupanee, T and Hallam, SJ},
title = {Metagenome-assembled genomes for N2-fixing cyanobacterium Nostoc sp. TISTR 8405 and co-occurring microorganisms from a long-term laboratory culture.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0055326},
doi = {10.1128/mra.00553-26},
pmid = {42610730},
issn = {2576-098X},
abstract = {We report here metagenome-assembled genomes from a long-term laboratory culture of the nitrogen-fixing cyanobacterium Nostoc sp. TISTR 8405, originally sourced from a Thai freshwater lake. The community consists of two additional co-occurring microorganisms, Erythrobacter sp. THAI-01 and Allorhizobium sp. THAI-01, and contains putative plasmids associated with Nostoc and Allorhizobium, respectively.},
}

@article {pmid42610965,
year = {2026},
author = {Liu, ZT and Zhao, XD and Li, JQ and Li, SX and Tang, X and Zhang, SY},
title = {High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag212},
pmid = {42610965},
issn = {1751-7370},
abstract = {Soil organic carbon is a key determinant of microbial community structure and function, yet the role of dissolved organic matter (DOM) bioavailability in shaping the soil antibiotic resistome remains poorly understood. Here, we combined previous continental-scale field sampling across 18 provinces in China (n = 141) with additional microcosm experiments to investigate how DOM molecular weight influences soil antibiotic resistance genes (ARGs) proliferation. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic analyses, we found that soils enriched in high molecular weight (HMW) DOM harbored significantly greater ARG abundance and diversity compared to low molecular weight (LMW) DOM soils. HMW DOM intensified microbial competition, as evidenced by a higher proportion of negative correlations in the co-occurrence network and lower niche breadth, favoring the enrichment of co-hosts that simultaneously carried ARGs, carbon metabolism genes, and biosynthetic gene clusters for antimicrobial compounds. Microcosm experiments confirmed that HMW DOM (lignin) addition significantly increased ARG transcript abundance (2.4-fold) and co-host relative abundance (2.3-fold), accompanied by a concurrent increase in transcribed viral auxiliary metabolic genes (2.5-fold) involved in complex carbon degradation. Structural equation modeling revealed that HMW DOM abundance and chemodiversity exerted the strongest positive effects on ARG abundance, primarily by shaping microbial community competition and metabolic potential. Collectively, our findings establish DOM bioavailability, particularly its molecular weight, as a critical yet previously overlooked driver of soil resistome development, challenging the conventional focus on total carbon content and highlighting the potential for molecular-level organic matter management to mitigate the spread of ARGs.},
}

@article {pmid42611076,
year = {2026},
author = {Irbaz, M and Hamood, Z and Shahid, S and Ghufran, A and Ajmal, A and Rafiq, I},
title = {Bacteriophage therapy for antimicrobial-resistant, biofilm‑associated diabetic foot infection: delivery routes, phage antibiotic synergy, and practical wound‑care integration.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42611076},
issn = {1432-072X},
mesh = {*Phage Therapy/methods ; *Diabetic Foot/therapy/microbiology ; *Biofilms/drug effects/growth & development ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteriophages/physiology ; *Bacterial Infections/therapy/microbiology ; Animals ; Drug Resistance, Multiple, Bacterial ; Pseudomonas aeruginosa/drug effects/virology ; Bacteria/drug effects/virology ; },
abstract = {Diabetic foot infections (DFIs) are a significant public health problem, associated with a delayed healing process and high rates of recurrence, which culminates in amputation. Two main factors, antimicrobial resistance (AMR) and biofilm formation, are responsible for the persistence and therapeutic failure of DFIs, resulting in extended healing time, infection recurrence, and an increased risk of amputation. In addition, the emergence of multidrug-resistant (MDR) pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa has made traditional antibiotic treatment less effective, necessitating alternative or adjunctive therapy. Phage therapy is an alternative approach to treat biofilm-associated and antimicrobial-resistant DFIs. Bacteriophages, viruses that infect bacteria, are highly specific to their bacterial hosts, can disrupt biofilms, and increase the activity of antimicrobial drugs used alone or in combination. This review focuses on the therapeutic potential of phage-based interventions for AMR and biofilm-related DFIs, highlighting delivery methods, phage-antibiotic synergy (PAS), incorporation into wound care regimens, and novel translational potential. Further interest in phage-based therapeutics has grown with recent advances in engineered phages, phage-derived enzymes, and precision diagnostics. Clinical and preclinical data indicate that phage therapy may be a promising strategy to improve bacterial control in specific DFI applications. Experimental studies have shown activity against MDR pathogens and biofilm-associated infections, and early clinical reports show potential for therapeutic benefit. The evidence base is currently small and is skewed towards in vitro studies, animal models, case reports, and small clinical trials. However, significant clinical evidenceis still needed before they can be widely adopted. There are several important barriers, such as the absence of large-scale randomized controlled trials, standardized treatment protocols, manufacturing consistency, and harmonized regulatory frameworks. Rigorous clinical evaluation, enhanced diagnostics (e.g., metagenomics profiling), delivery optimization, and regulatory coordination will be the key factors for further progress. Together, these advances could facilitate the integration of phage therapy into a multidisciplinary approach to DFI treatment and improve outcomes for patients with complex biofilm-related and AMR infections.},
}

*Phage Therapy/methods
*Diabetic Foot/therapy/microbiology
*Biofilms/drug effects/growth & development
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Bacteriophages/physiology
*Bacterial Infections/therapy/microbiology
Animals
Drug Resistance, Multiple, Bacterial
Pseudomonas aeruginosa/drug effects/virology
Bacteria/drug effects/virology

@article {pmid42611116,
year = {2026},
author = {Ajagbe, MA and Ahmed, SF and Ouf, A and Abdoullateef, BMT and Abdallah, RZ and Siam, R and Elbehery, AHA},
title = {Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42611116},
issn = {1573-0972},
mesh = {*Multigene Family ; *Biological Products/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota/genetics ; Metagenomics ; Metagenome ; Archaea/genetics/classification/metabolism/isolation & purification ; Phylogeny ; Biosynthetic Pathways/genetics ; Computational Biology ; },
abstract = {The rising demand for novel therapeutics, including antimicrobial, anticancer, and anti-inflammatory agents, underscores the need for new drug discovery strategies. Microbial communities represent rich reservoirs of bioactive compounds encoded by biosynthetic gene clusters (BGCs), yet traditional approaches remain limited by the inability to culture most microorganisms and the frequent rediscovery of known metabolites. Sequence-based metagenomics provides a transformative solution by directly identifying BGCs from environmental DNA. Using NovaSeq X Plus shotgun sequencing, we explored the biosynthetic potential of microbial communities in two previously unstudied brackish springs of the Siwa Oasis, Cleopatra and Fatnas. These ecosystems were dominated by bacteria (99.2%), with archaea being nearly absent (< 0.1%), and the microbial composition consisted largely of mesophilic taxa from Pseudomonadota, Bacteroidota, Actinomycetota, and Planctomycetota, which together accounted for 98.2% of the community. Our integrated bioinformatics pipeline enabled the reconstruction of 37 medium-to-high-quality metagenome-assembled genomes (MAGs), and recovered 147 BGCs mostly from Pseudomonadota, Actinomycetota, and Acidobacteriota phyla. Terpene (n = 23) and ribosomally synthesized and post-translationally modified peptide (RiPPs; n = 22) BGCs predominated within Cleopatra Spring, whereas RiPPs (n = 20) represented the dominant class recovered from Fatnas Spring. None of the recovered gene clusters mapped to experimentally validated entries in the MIBiG database (distance > 0.4), and 96.6% displayed structural divergence from the gene cluster families catalogued in the BGC Atlas. These results highlight the Siwa Oasis as a promising reservoir of unexplored biosynthetic potential and a valuable resource for natural product discovery to address global health challenges.},
}

*Multigene Family
*Biological Products/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota/genetics
Metagenomics
Metagenome
Archaea/genetics/classification/metabolism/isolation & purification
Phylogeny
Biosynthetic Pathways/genetics
Computational Biology

@article {pmid42611121,
year = {2026},
author = {Tomar, SS and Khairnar, K},
title = {SARS‑CoV‑2 Associated Shifts in the Upper Respiratory Tract Mycobiome in Non-hospitalized Cases.},
journal = {Mycopathologia},
volume = {191},
number = {5},
pages = {},
pmid = {42611121},
issn = {1573-0832},
support = {OLP-57//CSIR-NEERI/ ; },
mesh = {Humans ; *COVID-19/microbiology ; SARS-CoV-2 ; *Mycobiome ; Male ; *Fungi/classification/genetics/isolation & purification ; Female ; India ; Metagenomics ; Adult ; Middle Aged ; *Respiratory System/microbiology ; },
abstract = {SARS‑CoV‑2 infection is associated with marked changes of the upper respiratory tract mycobiome. URT mycobiome Changes in non-hospitalized patients however, remains poorly defined. We performed shotgun metagenomic sequencing of 95 upper respiratory tract swab samples from 48 symptomatic SARS‑CoV‑2-positive individuals and 47 healthy controls from central India. Fungal diversity and community structure were compared using alpha- and beta-diversity analyses, while differential taxa were identified using prevalence-based testing and a Directional Significance Score (DSS). SARS‑CoV‑2-positive samples showed significantly higher fungal alpha diversity than controls, with increased Shannon diversity (p = 0.000319) and Simpson diversity (p = 0.017). Beta-diversity analysis showed significant separation between groups for both Bray-Curtis and Jaccard distances (PERMANOVA p = 0.001), with significant dispersion effects as well (PERMDISP p = 0.001). DSS analysis showed certain fungal taxa associated with the SARS-CoV-2 group, including enrichment of Candida orthopsilosis, Malassezia furfur, Aspergillus glaucus, Aspergillus terreus, and Aspergillus niger, while Malassezia arunalokei, Aspergillus chevalieri, and Aspergillus sydowii were enriched in controls. These findings indicate that SARS‑CoV‑2 infection is associated with URT mycobiome dysbiosis and enrichment of clinically relevant opportunistic fungi in community cases.},
}

Humans
*COVID-19/microbiology
SARS-CoV-2
*Mycobiome
Male
*Fungi/classification/genetics/isolation & purification
Female
India
Metagenomics
Adult
Middle Aged
*Respiratory System/microbiology

@article {pmid42611158,
year = {2026},
author = {Vock, I and Bargetzi, A and Weisser, M and Mueller, OK and Junker, M and Mehrkens, A and Neidhoefer, C and Hamelin, B and Hosch, S and Mertz, KD and Keller, PM and Kuehl, R},
title = {Hematogenous vertebral osteomyelitis caused by vaginal microbiota: metagenomic resolution of a polymicrobial anaerobic case.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42611158},
issn = {1439-0973},
abstract = {We describe a rare case of a 35-year-old female patient suffering from polymicrobial hematogenous vertebral osteomyelitis caused by vaginal microbiota following sexual intercourse. Anaerobic blood cultures yielded Fannyhessea vaginae and Gemelliphila asaccharolytica, and intraoperative tissue cultures from decompression surgery identified Gardnerella vaginalis. Beyond Fannyhessea vaginae and Gemelliphila asaccharolytica, 16S rRNA gene Nanopore sequencing of surgical tissue also detected high amounts of Parvimonas parva, Peptostreptococcus anaerobius, Marseillibacter massiliensis, and Gemelliphila palaticanis. Antibiotic treatment with broad anaerobic coverage resulted in complete clinical resolution. Retrospective metagenomic analysis of a cervical swab obtained 9 months earlier revealed Fannyhessea vaginae and G. vaginalis to be already present in the vaginal microbiota. This case highlights the potential for hematogenous dissemination of vaginal anaerobes after sexual intercourse and underscores the diagnostic challenges posed by fastidious anaerobic bacteria. Molecular techniques are helpful tools in uncovering pathogens that may escape conventional culture methods.},
}

@article {pmid42611234,
year = {2026},
author = {Zhu, Y and Deng, X and Wang, Q and Song, H and Wang, L and Zhou, D and Gao, C and Gardea-Torresdey, JL and White, JC and Zhao, L},
title = {SiO2@CuO Nanozyme Reinforces Plant-Microbiome Synergies for Simultaneous Yield Enhancement, Nutritional Fortification, and a Beneficial Soil Legacy.},
journal = {ACS nano},
volume = {20},
number = {32},
pages = {22762-22777},
doi = {10.1021/acsnano.6c06987},
pmid = {42611234},
issn = {1936-086X},
support = {2026ZD1211704//Jing-Jin-Ji Regional Integrated Environmental Improvement-National Science and Technology Major Project/ ; CX (23)3015//Independent Innovation Fund for Agricultural Science and Technology in Jiangsu Province/ ; },
mesh = {*Microbiota/drug effects ; *Copper/chemistry/pharmacology ; *Silicon Dioxide/chemistry/pharmacology ; Soil Microbiology ; Soil/chemistry ; *Zea mays/growth & development/microbiology/drug effects/metabolism ; Rhizosphere ; Seeds ; },
abstract = {Plant associated microbes play pivotal role in promoting host fitness and health. However, modern agricultural practices, such as agrochemicals use and domestication are eroding plant-microbe partnership. Here, we show that nanoenabled seed priming strengthens plant-microbe interactions, enhancing the plant holobiont performance. We found that SiO2@CuO nanozymes (NZs) with peroxidase (POD)-like activities, as seed priming agent, initiate earlier and stronger seed respiration and boost exudates release (sugars, amino acids, and fatty acids), creating a nutrient-rich and transiently hypoxic spermosphere microenvironment. Field trials revealed that by day 40, rhizosphere microbiome diversity increased, with enrichment of functional taxa involved in carbon and nitrogen metabolism, as determined by 16S rRNA and metagenomic sequencing. Throughout the growing season, above-ground tissues in the nanopriming group consistently outperformed the hydropriming control in photosynthetic pigment content and plant height. At harvest, without additional fertilizers or other inputs, nanopriming increased maize yield by 8.1% and improved kernel nutritional quality: starch (21.0%), protein (24.5%), and iron (24.2%). Soil nutrient availability (N, P, K, Ca) and cation exchange capacity also increased, indicating the improved soil quality. Notably, the soil from nanopriming group confers the subsequent maize crop with better drought tolerance and enhanced P uptake capacity, compared to the soil from hydropriming group, indicating beneficial legacy effect. This study demonstrates that a simple seed nanopriming can steer a positive feedback loop between plant and microbe, cascading into multifaceted holobiont benefits. This offers a sustainable strategy to harness plant microbiomes and promote sustainable and climate resilient agriculture.},
}

*Microbiota/drug effects
*Copper/chemistry/pharmacology
*Silicon Dioxide/chemistry/pharmacology
Soil Microbiology
Soil/chemistry
*Zea mays/growth & development/microbiology/drug effects/metabolism
Rhizosphere
Seeds

@article {pmid42611448,
year = {2026},
author = {Xie, L and Wang, L and Lin, D and Zhou, Y and Cai, T and Wang, Y and Zhou, X and Li, X and Zhu, D and Zhang, T},
title = {Biodegradable Microplastic Diversity Drives Soil Carbon Lability via Phage-Boosted Bacterial Degradation of Recalcitrant Compounds.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22492-22504},
doi = {10.1021/acs.est.6c04389},
pmid = {42611448},
issn = {1520-5851},
support = {2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2023S011//Ningbo Public Welfare Key Science and Technology Plan Project/ ; 41977142//National Natural Science Foundation of China (NSFC)/ ; 42595623//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Carbon ; *Bacteria/metabolism ; *Soil/chemistry ; Soil Microbiology ; Bacteriophages ; Biodegradation, Environmental ; },
abstract = {Microplastic (MP) pollution threatens soil carbon stability, yet the effects of diverse MPs, particularly biodegradable MPs, on the soil carbon cycle and the associated microbial mechanisms remain poorly understood. Here, we established a gradient of MP diversity to examine its impact on soil dissolved organic matter (DOM) chemodiversity, integrating multiomics analysis to reveal coupled bacterial and viral metabolic strategies. Our results revealed that elevated MP diversity increased the proportion of low-molecular-weight compounds among newly generated DOM, reducing DOM aromaticity and stability. The enrichment of genes related to recalcitrant organic compound degradation, coupled with decreased energy metabolism gene abundance, suggested that the bioprocessing efficiency was enhanced at the expense of bacterial proliferation, facilitating DOM conversion to bioavailable forms. Accordingly, elevated MP diversity remarkably increased the diversity of soil phages and strengthened phage-host interactions, which might reflect phage-host coadaptation. Importantly, the increased abundance of phage-encoded auxiliary metabolic genes, especially those related to recalcitrant organic compound degradation, might enhance the utilization of recalcitrant DOM by the host bacteria. Collectively, these findings advance our understanding of bacterial mechanisms underlying carbon dynamics following exposure to diverse MPs, highlighting the critical role of phage-host interactions during this process.},
}

Carbon
*Bacteria/metabolism
*Soil/chemistry
Soil Microbiology
Bacteriophages
Biodegradation, Environmental

@article {pmid42611487,
year = {2026},
author = {Chase, AB and Jayarathne, JRRN and Haghighatjoo, M and Tabor, NJ and Smits, KM},
title = {A Diffusion-Driven CH4-O2 Boundary Structures Methane Oxidation and Carbon Transformation in Upland Soils.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22397-22407},
doi = {10.1021/acs.est.6c03515},
pmid = {42611487},
issn = {1520-5851},
support = {693JK32010011POTA//Pipeline and Hazardous Materials Safety Administration/ ; NA//Southern Methodist University/ ; },
mesh = {*Methane ; Oxidation-Reduction ; *Soil/chemistry ; Carbon ; Soil Microbiology ; Oxygen ; },
abstract = {Although extensive work has characterized high-affinity atmospheric methane oxidation in upland soils and sustained oxidation in chronically methane-rich environments, shallow point-source inputs introduce transient methane pulses into otherwise aerated heterotrophic soils. Whether these pulses migrate rapidly toward the atmosphere or instead create localized redox boundaries that restructure soil carbon pools and microbial metabolism remains unclear. Here, we conducted a controlled natural gas release experiment to quantify coupled geochemical and microbial responses in near-surface soils across a methane gradient. The release produced a spatial interval where measured CH4 and reconstructed O2 availability overlapped, identifying a redox transition associated with shifts in carbon geochemistry and methane-oxidation-related functional potential. Spatially resolved δ13C and C:N measurements revealed strong 13C enrichment of soil organic carbon (SOC) at the plume center, while elevated carbonate abundance and isotope composition distinguished a geochemical transition between the methane-rich plume center and distal reference soils. Within the intermediate CH4-O2 overlap zone, methane-associated monooxygenases (MMOs) and C1 assimilation genes were coordinately enriched, supporting structured C1 metabolic potential across the redox boundary. Metagenomic assembly and reconstruction linked this methane-responsive interval to Actinomycetota-affiliated genomes encoding expanded monooxygenase repertoires, including sMMO-like systems supported by operon architecture and catalytic-subunit phylogeny. This association provides a mechanistic link between transient methane exposure, redox-boundary formation, and microbial carbon transformation in aerated soils. Together, these findings show that shallow methane inputs can generate spatially constrained biogeochemical hotspots where gas transport, carbonate accumulation, and monooxygenase-associated C1 assimilation converge, and define conditions under which soil processes may influence methane transport toward the atmosphere.},
}

*Methane
Oxidation-Reduction
*Soil/chemistry
Carbon
Soil Microbiology
Oxygen

@article {pmid42611489,
year = {2026},
author = {Yuan, J and Suo, Y and Kang, D and Shapleigh, JP and Wang, B and Du, R and Peng, Y},
title = {Genome-Resolved Metagenomics Reveals Dominant Enrichment and Metabolic Adaptations of Thauera sp. in Activated Sludge under Carbon Limitation.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22680-22691},
doi = {10.1021/acs.est.6c01742},
pmid = {42611489},
issn = {1520-5851},
support = {CSTB2024NSCQ-MSX0999//Natural Science Foundation of Chongqing/ ; U23A20675//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Sewage/microbiology ; *Thauera/metabolism/genetics ; Metagenomics ; Carbon/metabolism ; Denitrification ; },
abstract = {Partial denitrification has been proposed as an alternative route to supply nitrite for anammox bacteria. The genus Thauera is frequently dominant in this process, yet the genomic basis for its ecological success within activated sludge remains unclear. Here, genome-resolved metagenomics was used to elucidate the genomic traits favoring its dominance under carbon (acetate)-limited conditions. Stable nitrite accumulation was achieved during treatment of low-strength ammonium wastewater (∼30 mg N/L) only under carbon limitation, whereas no nitrite accumulation occurred under carbon-sufficient conditions. The dominant high-quality metagenome-assembled genomes (MAGs) differed markedly between the two reactors. A near-complete MAG, affiliated with T. aminoaromatica (98.9% completeness and 0.4% contamination), dominated the carbon-limited reactor (27.0 ± 3.2%) but was rare in the carbon-sufficient reactor (0.6 ± 0.5%). The Thauera MAG encoded 4 copies of the acetate transporter genes (actP), a complete gene set for denitrification and internal carbon synthesis. Consistently, acetate limitation significantly increased both polyhydroxyalkanoate (PHA) content and the abundance of PHA-encoding microbes. Comparative genomics with 39 Thauera reference genomes further indicated selective enrichment of narG-containing Thauera lineages associated with nitrite accumulation. This study provides genomic insights into the ecological dominance of Thauera, highlighting its metabolic versatility and adaptive advantages in low-carbon wastewater treatment systems.},
}

*Sewage/microbiology
*Thauera/metabolism/genetics
Metagenomics
Carbon/metabolism
Denitrification

@article {pmid42446945,
year = {2026},
author = {Shirai, T and Kuzuya, K and Kishi, M and Ichikawa, S and Sakakibara, S and Nakai, A and Leach, S and Liu, YC and Motooka, D and Okuzaki, D and Narazaki, M and Kumanogoh, A and Kurosaki, T and Saegusa, J and Suzuki, K},
title = {Migration-dependent extrafollicular programming of preplasmablast age-associated B cells drives lupus pathogenesis.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {16},
pages = {},
pmid = {42446945},
issn = {1558-8238},
mesh = {Animals ; *Lupus Erythematosus, Systemic/pathology/immunology/genetics ; Mice ; *Cell Movement/immunology ; Humans ; Autoantibodies/immunology ; *Precursor Cells, B-Lymphoid/pathology/immunology ; *B-Lymphocytes/pathology/immunology ; Female ; Receptors, G-Protein-Coupled/immunology/genetics ; Mice, Knockout ; *Plasma Cells/pathology/immunology ; },
abstract = {Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody production. Extrafollicular (EF) B cell responses contribute to SLE pathogenesis, with age-associated B cells (ABCs) giving rise to autoantibody-secreting plasmablasts (PBs). However, the migratory cues governing this EF trajectory remain unclear. Here, we identify a distinct ABC state with PB precursor characteristics (pre-PB ABCs) and reveal a migration-dependent program underlying their generation. Single-cell analysis of patients with SLE and model mice showed that pre-PB ABCs were enriched in autoreactive clones and poised for PB differentiation. Their frequency correlated with autoantibody titers and disease activity, underscoring their pathogenic relevance. We further demonstrated that the oxysterol receptor EBI2 directed ABCs to EF niches within splenic bridging channels, promoting pre-PB ABC formation and autoreactive PB output. This process depended on the COMMD3/8 complex, a positive regulator of chemoattractant receptor signaling. Beyond EBI2-mediated ABC migration to EF niches, the COMMD3/8 complex was also required for trafficking of autoantibody-secreting cells to the bone marrow and infiltration of ABCs into the kidney. Accordingly, COMMD3/8 complex inhibition ameliorated disease in murine SLE models. These findings define a migration-dependent mechanism driving the EF differentiation of ABCs into autoreactive PBs and shaping the tissue distribution of pathogenic B cells, highlighting this program as a potential therapeutic target in SLE.},
}

Animals
*Lupus Erythematosus, Systemic/pathology/immunology/genetics
Mice
*Cell Movement/immunology
Humans
Autoantibodies/immunology
*Precursor Cells, B-Lymphoid/pathology/immunology
*B-Lymphocytes/pathology/immunology
Female
Receptors, G-Protein-Coupled/immunology/genetics
Mice, Knockout
*Plasma Cells/pathology/immunology

@article {pmid42604162,
year = {2026},
author = {Jia, P and Zhang, W and Zhang, G and Pei, W and Wu, F and He, Z and Chen, T and Liu, G},
title = {Environmental selection shapes the ecological cascade of biofilm assembly and functional gene abundance in sandstone weathering.},
journal = {Biofilm},
volume = {12},
number = {},
pages = {100388},
pmid = {42604162},
issn = {2590-2075},
abstract = {Microorganisms are pivotal agents in the process of sandstone weathering; nevertheless, the ecological mechanisms that govern their transition from mere colonization to sustained weathering activity remain ambiguous. This study systematically elucidated microbe-mediated weathering mechanisms through amplicon and metagenomic sequencing of bacteria, fungi, and archaea across a sandstone weathering sequence-from original unweathered sandstone (OS), biofilm-covered sandstone (BS), to weathered sandstone (WS). The findings indicate that microbial communities undergo associations across a weathering gradient, with biofilms constituting a unique transitional state. Community assembly mechanisms undergo a transition from stochastic processes in original sandstone to deterministic processes during the processes of biofilm formation and weathering. Biofilm communities formed modular, tightly interconnected putative association networks enriched with keystone taxa. Metagenomic analysis revealed significant enrichment of functional pathways related to iron acquisition, organic acid metabolism, and sulfur cycling during weathering, with functional annotation directly linking these traits to pivotal microbial groups. The findings of this study, as suggested by partial least squares path modeling (PLS-PM), indicate that environmental changes are associated with deterministic processes and with increased microbial richness. These factors are further linked to the composition of putative keystone taxa along the weathering gradient. These pivotal groups subsequently influence the abundance of weathering-related functional genes, directly accelerating weathering processes. This finding unveils a distinct ecological cascade pathway, commencing with environmental selection and culminating in the enrichment of functional gene potentials. The present study proposes a universal framework demonstrating that sandstone weathering is associated with deterministic processes, putative keystone taxa, and synergistic gene networks. This mechanism is not only applicable to sandstone systems, but also offers novel insights into the understanding of microbially mediated mineral weathering in terrestrial environments. This process is fundamental in influencing global biogeochemical cycles, soil formation, and the preservation of geological and cultural heritage.},
}

@article {pmid42604235,
year = {2026},
author = {Frizzo, R and Pettenuzzo, S and Bortoletto, E and Gregori, I and Vezzi, A and Panin, M and Hemmati, S and Archetti, L and Mammi, S and Bogialli, S and Venier, P},
title = {Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt-marsh tidal creek sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag184},
pmid = {42604235},
issn = {2730-6151},
abstract = {Salt marshes are highly productive ecosystems where microbial communities drive key transformations of organic matter at rates often exceeding those of oceanic and inland environments. Viruses are recognized as important drivers and regulators of global biogeochemical cycling, yet their diversity, host range, and functional roles in salt marsh ecosystems remain largely unresolved. To address these gaps, we investigated how viral lysis and host reprogramming can affect microbe-mediated organic matter transformations in a salt marsh of the Venice lagoon (Italy). Focusing on tidal creek surface sediments, we reconstructed 311 metagenome-assembled genomes (MAGs), built corresponding genome-scale metabolic models (GEMs) individually constrained with 121 metabolites detected in the sediments, and identified 3537 viral populations (vOTUs) across 10 samples. To assess the impact of viral lysis, we inferred prokaryotic hosts for 243 vOTUs and analysed host metabolism through MAG pathway analysis and GEM flux modelling across 13 bacterial orders, thus highlighting a negative impact on polysaccharide degradation, organic nitrogen mineralization, and organosulphur mineralization/volatilization processes. For host metabolic reprogramming, we characterized a subset of 50 auxiliary viral genes (AVGs) by mapping them to GEM reactions and analysing their stoichiometry, directionality, and pathway context, outlining two dominant strategies: resource scavenging through nucleotide-sugar biosynthesis, amino acid utilization, and sulphate assimilation; functional host maintenance through cofactor biosynthesis, electron transport, and energy production through carbonyl-compound utilization. Our findings provide a mechanistic view of the viral influence on organic matter transformations in salt marsh sediments and confirm viruses as key players in salt marsh biogeochemistry.},
}

@article {pmid42604251,
year = {2026},
author = {Zhang, B and Jiang, X and Zhao, H and Wang, B},
title = {BileActome reveals community-assembled bile acid metabolism in the rumen microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag205},
pmid = {42604251},
issn = {2730-6151},
abstract = {Microbial bile acid metabolism is an important link between microbiomes and host physiology, but its genetic basis remains difficult to resolve from genome and metagenome data. This is largely because existing annotation resources are not designed for the high sequence diversity and functional complexity of microbial bile acid genes. Here we present BileActome, a reusable annotation resource developed specifically for microbial bile acid metabolism. BileActome defines 27 experimentally supported gene families, including bile salt hydrolases, bile acid-inducible operon genes, and microbial hydroxysteroid dehydrogenases. Its design prioritizes experimentally supported functional sites when available and conserved domain features otherwise, while also distinguishing key functional subtypes. We applied BileActome to 1693 high-quality rumen metagenome-assembled and isolate genomes and validated its performance using controlled in vitro rumen fermentations under three bile acid interventions. In metagenomic gene-catalog analyses, BileActome enabled pathway-level interpretation of microbial responses to bile acid exposure, with the most reproducible responses centered on Bai-associated gene families. At genome scale, it generated a phylogeny-informed map of bile acid metabolic potential that was broader and more informative than Kyoto Encyclopedia of Genes and Genomes (KEGG)-based annotation. Further analyses of genomes, local gene organization, and genome-level guilds showed that bile acid metabolism in the rumen is modular, phylogenetically structured, and distributed across different microbial members. Deconjugation and oxidation/epimerization-related functions were widespread, whereas complete bile acid-inducible systems were less common. Together, these findings support a community-assembled model of bile acid metabolism and establish BileActome as an open and reproducible framework for studying specialized microbial functions in complex ecosystems.},
}

@article {pmid42604392,
year = {2026},
author = {Wang, S and Shui, F and Zhou, Y and Wang, X and Zeng, Y and Shan, Y and Li, J and Zhang, L and Song, K and Wu, F},
title = {Unexpected novel clade III type nitrous oxide-reducing bacteria from incubated lake sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag194},
pmid = {42604392},
issn = {2730-6151},
abstract = {Nitrous oxide-reducing bacteria (N2ORB) play a pivotal role in regulating N2O emissions in aquatic ecosystems, with clade I and clade II nosZ-harboring microorganisms representing well-recognized contributors to microbial N2O consumption. Beyond conventional N2ORB, the recently identified clade III nosZ from soil may represent a previously overlooked potential N2O sink, yet the distribution and characterization remain largely unexplored in aquatic ecosystems. Here we established microcosm systems using sediments from five lakes and subjected them to warming temperature gradients to investigate the diversity and genomic characteristics of N2ORB. Hidden Markov model (HMM)-based analyses identified a total of 45 nonredundant nosZ sequences, including 12 affiliated with clade III nosZ. Clade III nosZ accounted for 10.2%-40.6% of total nosZ genes, indicating that clade III nosZ-harboring N2ORB is widespread and non-negligible. Reconstruction of metagenome-assembled genomes (MAGs) identified four phylogenetically novel clade III nosZ-harboring N2ORB, with these MAGs showing low average amino acid identity to their closest known reference genomes. These MAGs showed different denitrification gene inventories, with MAG33 lacking identifiable genes for upstream N2O-producing steps, suggesting a potential non-denitrifying N2O reducer. They also encoded oxygen-related stress-response genes, suggesting a potential ability to perform N2O respiration in the presence of oxygen. Unlike canonical clade I/II nosZ clusters, clade III nosZ-harboring MAGs lacked typical accessory genes and instead exhibited distinct neighboring transporter- and cytochrome-related genes. Together, our results provide evidence for the occurrence of clade III nosZ-harboring N2ORB in non-soil ecosystems and expand current understanding of their genomic traits.},
}

@article {pmid42604646,
year = {2026},
author = {Cai, L and Chen, J and Hu, W and Xi, M and Zhang, Y and Chen, X},
title = {Chronic Fibular Osteomyelitis Caused by Schaalia turicensis: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109064},
doi = {10.1016/j.ijid.2026.109064},
pmid = {42604646},
issn = {1878-3511},
abstract = {BACKGROUND: Schaalia turicensis (previously classified as Actinomyces turicensis) may lead to actinomycosis, typically presented as a chronic, granulomatous infection marked by suppuration and sinus tract formation, with a propensity for recurrence. This report details a rare case of chronic post-traumatic osteomyelitis attributable to S. turicensis.

CASE PRESENTATION: A 57-year-old woman was presented with a four-year history of recurrent redness, swelling, and ulceration of the left lower leg after surgical intervention. Debridement of the lesion was performed by orthopedists. Metagenomic next-generation sequencing (mNGS) analysis of intraoperative tissue samples revealed S. turicensis and penicillin therapy was initiated accordingly. Subsequent culture results identified Actinomyces species and methicillin-resistant Staphylococcus epidermidis (MRSE). The antibiotic regimen was adjusted to clindamycin, leading to clinical improvement and eventual discharge.

CONCLUSION: This case underscores the diagnostic dilemma posed by indolent pathogens like S. turicensis in chronic post-surgical osteomyelitis. mNGS provided a rapid and precise microbiological diagnosis, directly informing critical therapeutic decisions.},
}

@article {pmid42604702,
year = {2026},
author = {Liang, E and Shen, J and Song, T and Liu, X and Liu, Y and Su, J and Gu, Y and Zhao, Y},
title = {A novel in-situ sludge reduction strategy: Bio-promoter assisted low-MLVSS operation for reducing sludge production while maintaining nitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135648},
doi = {10.1016/j.biortech.2026.135648},
pmid = {42604702},
issn = {1873-2976},
abstract = {Excess sludge production and subsequent treatment remain major challenges in activated sludge-based wastewater treatment. However, biological strategies for efficient in-situ sludge reduction remain limited. In this study, a composite bio-promoter was developed to support low-MLVSS operation. At 15% lower MLVSS, the bioreactor maintained 88.37% ammonia nitrogen removal, while the observed sludge yield decreased by 19.78% within a cycle. Long-term operation showed that bio-promoter addition activated the metabolic activity and key enzyme functions, thereby reducing the net sludge increase by 13.46%. The lower sludge production response was accompanied by higher biomass-specific nitrifying activity. The specific oxygen uptake rate of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria increased by 7.39% and 11.55%, respectively. The specific activities of ammonia monooxygenase and hydroxylamine oxidase increased by 13.66% and 27.71%, respectively. Metagenomics analysis revealed that Nitrosomonas and Nitrospira became the dominant functional bacteria in the community. The relative abundance of key nitrification genes amoA and hao increased by 6.25% and 40.80%, respectively, suggesting that the bio-promoter enhanced the functional activity of retained nitrifying biomass and helped maintain nitrification under reduced sludge concentration. This study created a novel bio-promoter technology scheme for in-situ sludge reduction and provided a theoretical basis and practical strategy for achieving energy-saving and efficient operation.},
}

@article {pmid42602596,
year = {2026},
author = {Xie, Z and Liu, X and Bo, B and Wei, W and Li, C and Ye, C},
title = {Effect of phosphorus fraction in shaping bacterial and archaeal community succession in the largest hydrologically connected lake of Northeast Asia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844785},
pmid = {42602596},
issn = {1664-302X},
abstract = {Microbial beta diversity and its components are key ecological indicators for understanding community assembly in lake sediments, yet their coupling with phosphorus (P) fractions remains poorly understood in hydrologically connected lake systems. In this study, sediment cores were collected from Xingkai Lake, the largest freshwater lake in Northeast Asia with a unique twin lake structure, and were analyzed using metagenomic sequencing combined with sequential P fractionation. Results showed that total beta diversity and species turnover for bacteria and archaea increased significantly with sediment depth in both lakes, with faster turnover rates in Daxingkai Lake. Nestedness was generally not significant in Daxingkai Lake but showed a significant positive trend with depth for archaea in Xiaoxingkai Lake. The dominant P fraction in the Daxingkai Lake sediments were HCl-Pi and residual P, while NaOH-Pi dominated in Xiaoxingkai lake sediments. Organic P explained the largest proportion of bacterial beta diversity variation in Daxingkai Lake, while inorganic P was the primary driver in Xiaoxingkai Lake. Conversely, inorganic P dominated the archaeal beta diversity variation in Daxingkai, whereas organic P dominated in Xiaoxingkai. These findings demonstrate that species turnover is the dominant component of beta diversity along the sediment depth gradient. The contrasting roles of organic P and inorganic P in shaping microbial beta diversity highlight the importance of P resource partitioning in driving microbial community succession and provide a basis for developing microbial beta diversity indicators to support eutrophication assessment and sediment management in hydrologically connected lake systems.},
}

@article {pmid42602688,
year = {2026},
author = {Sheng, H and Liu, J and Yu, Q and Peng, H},
title = {Comparative Analysis of Metagenomic Next-Generation Sequencing and Conventional Culture for Pathogen Detection in 218 Patients with Pulmonary Infectious Diseases: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {625827},
pmid = {42602688},
issn = {1178-6973},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising technique, but comparative studies of mNGS and culture across different pulmonary diseases are limited.

METHODS: We retrospectively analyzed data from 218 patients who underwent BALF mNGS testing between November 2021 and April 2025, and patients were categorized into pneumonia, bronchiectasis, NTM, tuberculosis, and other groups based on discharge diagnoses. We compared detection rates, pathogen spectra, co-infection rates, and special pathogen distributions between mNGS and culture. We also assessed concordance (Kappa) and complementary rates.

RESULTS: The overall positive detection rate of mNGS was significantly higher than that of culture (95.4% vs 67.4%, P<0.001). The overall concordance rate was 71.1%, with a Kappa of 0.42. mNGS additionally detected pathogens in 84 cases (38.5%), primarily viruses (38), Nocardia (8), NTM (15), fungi (45), and Legionella (4). Culture additionally detected 23 cases (10.6%). Co-infection was detected by mNGS in 118 cases (54.1%), far higher than culture (42 cases, 19.3%, P<0.001). The bronchiectasis group had significantly higher detection of Pseudomonas aeruginosa (54.5%) and Nocardia (18.2%).

CONCLUSION: mNGS provides a higher detection rate than culture in this cohort, particularly for special pathogens, and is complementary to culture. Pathogen profiles varied across disease types; however, the clinical benefit of mNGS-guided therapy remains to be evaluated in prospective studies.},
}

@article {pmid42603397,
year = {2026},
author = {Geng, D and Ding, Y and Jiang, Y and Wang, Z and Chen, G and Chang, G and Bai, H},
title = {Multi-omics analysis of cecal microbiota-hypothalamus axis interactions in small-sized meat ducks with divergent residual feed intake.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107310},
doi = {10.1016/j.psj.2026.107310},
pmid = {42603397},
issn = {1525-3171},
abstract = {Residual feed intake (RFI) is an indicator of feed efficiency that reflects variation in nutrient utilization independent of growth. This study characterized physiological traits and multi-omics profiles associated with divergent RFI in small-sized meat ducks. From an initial population of 500 1-day-old ducks, a total of 420 healthy ducks were individually housed from 21 to 42 d to record feed intake, and ducks with low RFI (LRFI) and high RFI (HRFI) were identified for further analyses. During the experiment, 30 ducks per group for growth performance, 15 ducks per group for plasma biochemical and 5 per group for multi-omics. Compared with HRFI ducks, LRFI ducks showed lower feed intake, lower feed conversion ratio (FCR), and lower plasma triglyceride concentrations, whereas body weight gain did not differ between groups. Shotgun metagenomic analysis showed that LRFI ducks were enriched in Bacteroides-related lineages and had higher predicted capacities for complex carbohydrate degradation, lipid and energy metabolism, and cofactor synthesis, whereas HRFI ducks were enriched in taxa including Subdoligranulum variabile and Clostridioides difficile. Untargeted cecal metabolomics revealed distinct lipid- and bile acid-related metabolic profiles between the 2 groups, including differences in long-chain lipid species and bile acid-associated metabolites. Hypothalamic transcriptomic analysis identified differentially expressed genes related to neuropeptide signaling, serotonin biosynthesis, intracellular signaling, and inflammatory regulation, including NMUR2, TPH1, and PTK2B. Correlation analysis integrating microbial taxa, metabolites, and hypothalamic transcripts further revealed coordinated associations among these features in small-sized meat ducks with divergent RFI. Overall, variation in feed efficiency in ducks was associated with differences in cecal microbiota, metabolite profiles, and hypothalamic gene expression, and these results highlight candidate microbial taxa, metabolites, and genes for further validation.},
}

@article {pmid42603473,
year = {2026},
author = {Zhang, XM and Lai, CY and Men, Y and Zhao, HP},
title = {Aerobic biotransformation of 8:2 FTCA in activated sludge: Carbon source dependence and multiple transformation pathways.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143305},
doi = {10.1016/j.jhazmat.2026.143305},
pmid = {42603473},
issn = {1873-3336},
abstract = {8:2 fluorotelomer carboxylic acid (8:2 FTCA) has been detected in environmental matrices and biota, yet its aerobic biodegradation remains poorly understood. Here, 30-day activated-sludge microcosms were used to investigate the degradation kinetics, transformation pathways, and microbial responses of 8:2 FTCA (10 μM) under carbon-limited and carbon-amended conditions. Only 38 mol% removal occurred without external carbon, whereas acetate, butanol, and octane increased removal to 85-90 mol%, with octane producing the highest fluoride release (24 μM). Target and non-target analyses identified 8:2 FTUCA and 7:3 FTCA as major intermediates and revealed the accumulation of five perfluorocarboxylic acids (PFCAs). Detection of OH-8:2 FTCA and PFNA supported a potential α-oxidation pathway. Mechanistically, 8:2 FTUCA forms via HF elimination and 7:3 FTCA via H/F exchange, while hydroxylation, α/β-oxidation, and decarboxylation may have contributed to PFCAs formation. Metagenomic analysis showed that 8:2 FTCA exposure and carbon amendments selectively enriched microorganisms, including Tepidiforma, Ectorhizobium, and Actinocorallia, which harbored genes encoding dehalogenases, monooxygenases, and fluoride exporters. Collectively, these results suggest that carbon sources availability may influence 8:2 FTCA transformation, defluorination, and microbial functional profiles in activated sludge, providing additional insights into the potential aerobic biotransformation of FTCAs in multi-contaminant environments.},
}

@article {pmid42603474,
year = {2026},
author = {Zhang, C and Chen, J and Yang, W and Du, K and Tao, W and Lu, Q and Jiang, M and Hu, J and Zhu, Q and Elrys, AS and Cai, Z and Meng, L and Müller, C and Dan, X and Zhang, J},
title = {Small-sized biodegradable PLA microplastics inhibit plant nitrogen uptake by reshaping soil microbial communities and stimulating microbial metabolism.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143209},
doi = {10.1016/j.jhazmat.2026.143209},
pmid = {42603474},
issn = {1873-3336},
abstract = {The effects of microplastics (MPs) varying in polymer type and size on soil microbial community composition, metabolic functions, and nutrient cycling remain insufficiently understood. Here, we conducted a pot experiment using MPs differing in polymer type (non-biodegradable polyethylene [PE], and biodegradable polylactic acid [PLA]) and four particle sizes (1200-1400, 600-700, 120-150, and 25-38 μm), with amplicon sequencing, shotgun metagenomics, and nitrogen-15 ([15]N) tracing model. Our results showed that small-sized PLA-MPs (25-38 μm) reduced bacterial diversity, destabilized microbial networks, and shifted community assembly toward deterministic processes, whereas PE-MPs and larger-sized PLA-MPs exerted minimal effects. This shift was associated with enhanced depolymerization-related enzymatic potential, accompanied by greater dissolved organic carbon (DOC) availability. The resulting increase in C availability stimulated central C metabolism, promoting microbial resource acquisition and biomass synthesis. To maintain microbial C:N homeostasis, microbial N assimilation was stimulated through ammonium (NH4[+]) assimilation mediated by the glutamate dehydrogenase (GDH) and glutamine synthetase-glutamate synthase (GS-GOGAT) pathways and nitrate (NO3[-]) assimilation via assimilatory nitrate reduction to ammonium (ANRA). Consistently, the [15]N tracing model revealed that microbial assimilation rates of NH4[+]-N and NO3[-]-N increased by 10.5-fold and 12.7-fold, respectively, exceeding gross N mineralization rates, thereby depleting soil inorganic N pools and suppressing plant N uptake. Overall, our findings provide mechanistic insights into how PLA-MPs reshape soil functioning by reprogramming microbial communities and metabolism, thereby altering plant-microbe competition for N. These results highlight the potential risks of increasing biodegradable plastic inputs for cropland nutrient cycling and plant N acquisition.},
}

@article {pmid42603694,
year = {2026},
author = {Du, J and Liu, Y and Zuo, Z and Fan, S and Xu, X},
title = {Growth form controls the seasonal stability of nutrient-pollution mitigation by submerged macrophytes in shallow lakes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125499},
doi = {10.1016/j.envres.2026.125499},
pmid = {42603694},
issn = {1096-0953},
abstract = {Submerged macrophyte restoration is widely used to mitigate nutrient pollution in eutrophic shallow lakes, yet its effectiveness is often evaluated during peak plant growth rather than across the full growing season. This creates uncertainty about whether restored clear-water conditions can persist during late-season plant decline. Here, a mesocosm experiment compared a canopy-forming species, Hydrilla verticillata, with a rosette-forming species, Vallisneria natans, at vigorous- and late-growth stages. We measured overlying-water quality, sediment properties, extracellular enzyme activities, microbial community structure and metagenomic functional potential, and evaluated association patterns using Mantel analysis and partial least squares path modeling. Both species reduced nitrogen and chlorophyll-a during vigorous growth, indicating comparable short-term restoration effects. By late growth, however, H. verticillata showed biomass decline and rebound of total phosphorus and chlorophyll-a to levels similar to the unvegetated control, whereas V. natans maintained lower nutrient concentrations, stronger rhizosphere redox status and more persistent water-quality improvement. Under the shared seasonal background, this late-season divergence is more consistent with differences in growth-form strategy and late-stage plant condition than with seasonal forcing alone, and in H. verticillata may reflect senescence- and decomposition-associated nutrient rerelease. Sediment and metagenomic patterns indicated treatment- and niche-related differences in microbial functional potential for nitrogen and phosphorus cycling, although these abundance-based patterns should not be interpreted as direct process rates. The results show that submerged macrophyte restoration in nutrient-polluted shallow lakes should be assessed by full-season stability rather than peak-growth performance alone. Rosette-forming macrophytes may provide more reliable support for internal nutrient loading control where late-season persistence is a management priority.},
}

@article {pmid42603915,
year = {2026},
author = {Cherinet, MT and Bereded, NK and Van de Voorde, I},
title = {Traditional Ethiopian fermented condiments: a systematic review of microbial dynamics, nutritional transformations, and future perspectives.},
journal = {Journal of food science and technology},
volume = {63},
number = {9},
pages = {1637-1647},
pmid = {42603915},
issn = {0022-1155},
abstract = {UNLABELLED: Traditional Ethiopian fermented condiments, including Siljo, Datta, Awaze, Helbat, and Azo, are culturally significant and nutritionally valuable. Despite their importance, evidence on their microbial ecology, nutritional transformations, safety, and functional potential remains fragmented and insufficiently characterized. This systematic review, conducted in accordance with PRISMA 2020 guidelines, consolidates current knowledge on the microbial dynamics, nutritional changes, probiotic traits, and food safety of these traditional Ethiopian fermented condiments. A comprehensive literature search was carried out up to December 2025 across PubMed, Scopus, Cochrane Library, Epistemonikos, and Google Scholar. Studies consistently reported that lactic acid bacteria-particularly Lactiplantibacillus plantarum, Pediococcus pentosaceus, and Weissella spp.-dominate spontaneous fermentations, driving acidification to pH values typically between 3.6 and 4.5 and contributing to pathogen suppression. Fermentation also induced product-specific nutritional transformations, including changes in protein content and digestibility, mineral dynamics, and the formation of bioactive compounds. However, outcomes varied considerably depending on substrate composition, microbial consortia, and processing conditions. Data on antinutritional factor reduction (phytates, tannins, and trypsin inhibitors) were absent across all included studies, representing a critical knowledge gap. Despite these promising attributes, research on these condiments is largely limited by reliance on culture-dependent methods, heterogeneous fermentation practices, and inconsistent analytical approaches. The evidence base for some condiments, particularly Azo and Datta, is further constrained by reliance on grey literature and secondary data sources. To fully harness their microbial, nutritional, and commercial potential, future studies should employ integrated research methodologies based on standardized fermentation protocols, metagenomics, metabolomics, and comprehensive nutritional assessments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-026-06764-y.},
}

@article {pmid42604017,
year = {2026},
author = {Wu, Y and Xie, L and Li, S and Ye, J and Zhu, Z and Zhang, Y and Chen, F},
title = {Ecosystem settings and urbanization shape microbial communities and antibiotic resistance genes on coastal microplastics.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100655},
pmid = {42604017},
issn = {2666-5174},
abstract = {Coastal wetlands are increasingly contaminated by microplastics that provide long-lived substrates for microbial colonization, yet the joint effects of ecosystem settings and urbanization on plastisphere communities and their resistomes remain poorly understood. Here, we used a 2 × 2 factorial design across mangrove and sandy-beach sediments under rural and urban influence, combined with metagenomic profiling, to characterize microplastic-associated microbiota and antibiotic resistance genes (ARGs). Microbial communities on microplastics showed clear separation between mangroves and sandy shores, with additional shifts along the rural-urban gradient, indicating context-dependent plastisphere assembly. Urbanization substantially increased richness in mangrove plastispheres, whereas effects on sandy beaches were weak or inconsistent and largely confined to low-abundance taxa. In situ exposure yielded a diverse ARG repertoire (>1 000 ARGs), and ARG composition showed significant ecosystem × human-impact interactions, with urban mangrove microplastics hosting the highest ARG diversity. Genus-ARG co-occurrence networks showed denser bacteria-ARG association patterns in mangrove than in sandy-beach plastispheres, with a limited number of genera statistically associated with multiple ARGs. These results suggest that plastisphere communities and resistomes varied across ecosystem settings and urbanization contexts, with urban mangrove microplastics showing relatively higher ARG diversity and stronger bacteria-ARG co-occurrence patterns. These findings highlight the need for habitat-specific monitoring of microplastic-associated resistance.},
}

@article {pmid42599548,
year = {2026},
author = {Medeiros, WB and Hidalgo-Martinez, KJ and Penna, DDPS and Oliveira, VM},
title = {Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42599548},
issn = {1573-0972},
mesh = {Antarctic Regions ; *Microbiota/genetics ; Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.},
}

Antarctic Regions
*Microbiota/genetics
Multigene Family
Metagenome
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics
Phylogeny
Ecosystem
Drug Resistance, Bacterial/genetics

@article {pmid42599752,
year = {2026},
author = {Zhou, Y and Shao, Q and Liu, C and Tian, J and Guan, X and Zhang, X and Lu, J},
title = {Seasonal Dynamics of Community and Function of Gut Microbiome in Taihangshan Macaque (Macaca mulatta tcheliensis): Inferred From Metagenomic Data.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70163},
pmid = {42599752},
issn = {1749-4877},
support = {No.31672302;No.32070446//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a key regulator of host nutritional intake, growth, and health, playing an essential role in mediating host adaptation to environmental changes. The northernmost population of rhesus macaque, Taihangshan macaque (Macaca mulatta tcheliensis), faces severe survival challenges, such as food shortages and harsh temperatures during winter and early spring. Previous studies have shown that they cope with seasonal changes through behavioral adaptations, such as adjusting food resources and flexibly regulating macronutrient intake. However, the role of the gut microbiome in supporting the seasonal adaptation of Taihangshan macaques remains unclear. Herein, we investigated seasonal variations in gut microbiome alpha diversity, composition, and functions from fecal samples of Taihangshan macaques using metagenomic analysis. The results showed that: (1) totally 435 non-redundant metagenome assembled genomes (MAGs) were generated; (2) alpha diversity was significantly higher in spring and winter than in summer and autumn; and (3) in winter, pathways of fatty acid biosynthesis and essential amino acid (EAA) biosynthesis, as well as CAZymes (GH3 and GH5) involved in cellulose and hemicellulose degradation, were significantly enriched. In contrast, pathways related to carbohydrate, energy, and glycan biosynthesis and metabolism, along with CAZymes (GT8 and GH23) potentially facilitating fat synthesis and storage, were enriched in summer. These functional adjustments likely help the host cope with seasonal variations in food availability and environmental conditions. Overall, this study provides new insights into how the gut microbiome responds to seasonal changes in diet and environmental factors in mammals inhabiting temperate forests.},
}

@article {pmid42600417,
year = {2026},
author = {Kasaiyan, S and Mateo, J and Buzzanca, D and Chiarini, E and Alessandria, V and Caro, I},
title = {Technological and microbial changes in cooked sausages incorporating cooked chickpea as a meat replacer and powdered banana pseudostem.},
journal = {Meat science},
volume = {242},
number = {},
pages = {110204},
doi = {10.1016/j.meatsci.2026.110204},
pmid = {42600417},
issn = {1873-4138},
abstract = {This study investigated the quality and microbial dynamics of vacuum-packaged cooked pork sausages reformulated by partially replacing meat protein (13%) with cooked chickpea paste and incorporating powdered banana pseudostem (BPS; 0%-0.4%) as a fibre source. Four sausages: Control (CON), CCP without BPS (CCP-0), and CCP with low (0.2%) or high (0.4%) BPS (CCP-BL and CCP-BH) were analysed over 20 days of refrigerated vacuum storage (3-7 °C). Composition, liquid retention, texture profile, colour, and microbial counts were evaluated. High-resolution shotgun metagenomics was applied to characterize bacterial and fungal dynamics. Composition and cooking yield remained unaffected by the reformulations (p > 0.05). However, substituting meat with cooked chickpea increased centrifugation loss (2 percentage points) and decreased hardness (2-3N), chewiness (∼3 N), and elasticity (0.04-0.05 units). Incorporating BPS increased initial product pH (up to 0.1 units), while decreasing lightness (up to 4 units). Initial total mesophilic bacterial counts were about 1 Log CFU/g higher in sausages with BPS and reached levels near 7 Log CFU/g across all batches by day 10. Adding chickpea supported the growth and survival of Enterobacteriaceae during storage. Shotgun metagenomics revealed that Brochothrix thermosphacta dominated the spoilage microbiota in CON and CCP-0 batches, exceeding 80% relative abundance by day 20. Conversely, BPS inclusion introduces plant-associated taxa (Klebsiella michiganensis and Pantoea rwandensis), significantly elevating alpha diversity and reducing B. thermosphacta percentage (< 20% relative abundance). While cooked chickpeas alter sausage textural characteristics, BPS serves as a functional fibre that modulates vacuum-packaged spoilage ecology.},
}

@article {pmid42600516,
year = {2026},
author = {Hu, Q and Wan, T and Liu, Y and Zhong, H and Chen, Y and Ao, Z and Jin, X and Guo, S},
title = {A real-world retrospective cohort study reveals the clinical utility of metagenomic next-generation sequencing in lower respiratory tract infections.},
journal = {Journal of infection and public health},
volume = {19},
number = {10},
pages = {103332},
doi = {10.1016/j.jiph.2026.103332},
pmid = {42600516},
issn = {1876-035X},
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are complicated by diverse pathogens, posing challenges to traditional diagnostics. However, robust evidence on LRTI pathogen spectra and metagenomic next-generation sequencing (mNGS) clinical utility remains limited.

METHODS: A retrospective analysis was conducted among 815 patients with suspected LRTIs who underwent mNGS and conventional microbiological testing(CMT) of bronchoalveolar lavage fluid. We evaluated the pathogen spectrum, the diagnostic value of mNGS across different infection categories, and its utility in guiding antibiotic therapy.

RESULT: Following exclusions, 754 patients demonstrated 84.5% mNGS positivity. mNGS detected DNA viruses (33.85%, EBV predominating), bacteria (30.83%), fungi (23.30%), mycobacteria (9.43%), and special pathogens (2.59%). Confirmed pathogens included Mycobacterium tuberculosis (n = 124), Candida albicans (n = 118), Pseudomonas aeruginosa (n = 87), Pneumocystis jirovecii (n = 65), Haemophilus influenzae (n = 50) and Aspergillus fumigatus (n = 48). mNGS showed higher positivity than CMT (84.5% vs 53.6%, P < 0.05), with sensitivities of 90.6% (LRTIs), 73.3% (bacterial), 74.7% (fungal), and 81.9% (tuberculosis); specificities were 22.6%, 56.5%, 73.5%, and 96.4%. Its high sensitivity but modest specificity necessitates cautious interpretation. mNGS guided treatment adjustments in 48.4% of patients, with higher rates in critically ill patients (60.1% vs 45.7%, P < 0.05), though clinical improvement was lower in this group (54.7% vs 79.2%, P < 0.05).

CONCLUSIONS: mNGS comprehensively detects pathogens in LRTIs, including bacteria, fungi, mycobacteria, DNA viruses, and special pathogens. While its broad diagnostic value and treatment guidance utility are significant, integration with clinical context is essential to distinguish true pathogens from colonization.},
}

@article {pmid42600761,
year = {2026},
author = {Hong, Z and Lu, Z and Shi, R and Zheng, S and Luo, J and Chen, J and Xie, Z and Zheng, JS and Chen, YM and Zhang, Z},
title = {Prospective associations of tea consumption with skeletal muscle mass and strength: Insights from the gut microbiome and proteomics.},
journal = {Pharmacological research},
volume = {231},
number = {},
pages = {108398},
doi = {10.1016/j.phrs.2026.108398},
pmid = {42600761},
issn = {1096-1186},
abstract = {Tea consumption may be associated with skeletal muscle health, but longitudinal evidence based on repeated assessments remains limited. We examined the associations of tea intake and serum biomarkers with repeated skeletal muscle measures and explored whether these associations might be partly explained by multi-omics features. In this prospective cohort, 3408 adults were followed for approximately 12 years. Skeletal muscle mass was measured by dual-energy X-ray absorptiometry, handgrip strength by digital dynamometry, gut microbial taxonomic and functional profiles by shotgun metagenomic sequencing, serum proteins by data-independent acquisition mass spectrometry, and fecal metabolites by targeted UPLC-MS/MS metabolomics. Linear mixed-effects models examined longitudinal associations, and mediation analyses estimated indirect effects. In longitudinal analyses, higher tea consumption frequency was associated with greater appendicular skeletal muscle mass, appendicular skeletal muscle index, and handgrip strength (β: 0.037-0.140; 95% CI: 0.002-0.205). Higher circulating flavan-3-ols showed similar associations with these muscle-related outcomes (β: 0.085-0.174; 95% CI: 0.007-0.254), whereas no significant associations were observed with walking speed. Exploratory multi-omics analyses identified tea-related differences in gut microbial species and functional pathways, fecal metabolites, and circulating proteins, including Gemmiger formicilis, amino acid biosynthesis pathways, fructose 1,6-bisphosphate, VTN, CFI, CNDP1, and ITIH4. Exploratory mediation analyses identified statistical indirect associations involving multi-omics features, with estimated proportions mediated ranging from 4.5% to 19.0%. Overall, higher tea consumption and circulating biomarkers were associated with greater skeletal muscle mass and strength, accompanied by distinct multi-omics features that may provide potential biological links between tea exposure and muscle-related outcomes.},
}

@article {pmid42600856,
year = {2026},
author = {Li, Y and Chen, L and Zhang, J and Zhang, Y and Wang, M and Zhang, R and Fang, W and Zhang, P and Zhang, G},
title = {Metagenomics reveals rumen residues as a superior inoculum for volatile fatty acid production in vitro.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135627},
doi = {10.1016/j.biortech.2026.135627},
pmid = {42600856},
issn = {1873-2976},
abstract = {Rumen microbiome is widely recognized as an efficient system for lignocellulose degradation. Rumen fluid (RF) has been often used as the inoculum in previous study of bioprocesses, however, the potential of rumen solids (RS) to enhance volatile fatty acid (VFA) production remains underexplored. The anaerobic fermentation performance of RS, RF, and RF + RS mixture as inocula was compared using corn stover as substrate, with RS addition at 5%, 10%, or 20% (w/w) to corn stover and RF addition at 1:2 (v/v) to buffer solution. At a corn stover content of 2.5% (w/v, based on final working volume), the highest VFA concentration of 10.05 g/L was achieved with 20% RS as inoculum, outperforming those with both RF and RF + RS. Metagenomic analysis revealed significant differences in bacterial, fungal, and archaeal community structures with 20% RS and RF. With 20% RS, hydrolytic bacteria (e.g., Enterobacter) dominated the ecological niche, microbial co-occurrence network analysis of the 2,000 most abundant genera revealed a simpler network with fewer negative associations, and functional analysis demonstrated a notable increase in relative abundance of glycosyltransferase (GT) families within carbohydrate-active enzymes (CAZymes). With 20% RS, enrichment in glycolysis-related genes was observed, indicating a preference for carbohydrate degradation, while acid-producing pathways were enriched such as pyruvate metabolism with RF. Rumen solids, as a superior inoculum for VFA production, effectively enhanced lignocellulose bioconversion by enriching specific low-abundance microbial taxa, forming a microbial network with fewer negative associations, increasing the relative abundance of GT families, and strengthening the systemic hydrolysis capacity.},
}

@article {pmid42601406,
year = {2026},
author = {Antman, T and Lewin-Epstein, O and Yerushalmi, T and Broder, YS and Zeevi, D},
title = {Global microbial DNA signatures of temperature and nutrient limitation across ecosystems.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42601406},
issn = {2058-5276},
abstract = {Microbial genomes continuously adapt to environmental conditions, but identifying universal signatures of adaptation remains challenging. Here we show that environmental temperature can be accurately predicted across ecosystems from DNA composition alone (R[2] = 0.75), using tetranucleotide frequencies from 1,235 marine and soil metagenomes and a machine learning approach. This predictive signal was also apparent within individual taxa, consistent with a fundamental temperature-associated signature. By contrast, GC content exhibited opposite correlations with temperature in soil (positive) and marine (negative) environments. This phenomenon was probably driven by differences in nutrient availability, as GC content increases with nutrients while nutrients decrease with temperature in marine samples. By integrating these observations, we identified specific tetranucleotides, with 50% GC, that displayed consistent and robust temperature correlations across environments and may have contributed to the stability of predictions. This work highlights metagenome-wide DNA-temperature associations, relevant for understanding microbial community responses to global changes.},
}

@article {pmid42601613,
year = {2026},
author = {Lotfi, M and Jalal, D and Sayed, AA},
title = {plsMD: a plasmid reconstruction tool from short-read assemblies.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42601613},
issn = {1471-2105},
mesh = {*Plasmids/genetics ; *Software ; *Sequence Analysis, DNA/methods ; Genome, Bacterial ; Whole Genome Sequencing/methods ; },
abstract = {BACKGROUND: While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly fragmentation. Current computational tools for plasmid identification and binning have limitations in reconstructing full plasmid sequences, hindering downstream analyses like phylogenetic studies and antimicrobial resistance gene tracking.

RESULTS: We present plsMD, a tool designed for full plasmid reconstruction from short-read assemblies. plsMD integrates Unicycler assemblies with replicon and full plasmid sequence databases to guide plasmid reconstruction through a series of contig manipulations. Using two datasets - an established benchmark dataset used in previous benchmarking studies and a novel dataset consisting of newly sequenced bacterial isolates - plsMD outperformed existing tools in both. In the benchmark dataset, it achieved excellent recall, precision, and F1 scores of 91.3%, 95.5%, and 92.0%, respectively. In the novel dataset, it achieved recall, precision, and F1 scores of 77.6, 88.9 and 74.5%, respectively. plsMD supports two usage modalities: single-sample analysis for plasmid reconstruction and gene annotation, and batch-sample analysis for phylogenetic investigations of plasmid transmission.

CONCLUSIONS: plsMD represents a significant advancement in plasmid analysis, offering a robust solution for utilizing existing short-read whole genome sequencing data to study plasmid-mediated antimicrobial resistance spread and evolution.},
}

*Plasmids/genetics
*Software
*Sequence Analysis, DNA/methods
Genome, Bacterial
Whole Genome Sequencing/methods

@article {pmid42601633,
year = {2026},
author = {Albastaki, A and Naji, M and Moussa, M and Smith, J},
title = {Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70403},
doi = {10.1111/1758-2229.70403},
pmid = {42601633},
issn = {1758-2229},
mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Ecosystem ; Soil/chemistry ; Metagenomics ; Forensic Sciences ; Phylogeny ; },
abstract = {Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0-25 cm, 25-50 cm and 50-100 cm). Marine soils exhibited extreme salinity (EC 23.7-30.7 dS m[-1]) and the highest organic matter content (1.19%-1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%-96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50-100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.},
}

*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Ecosystem
Soil/chemistry
Metagenomics
Forensic Sciences
Phylogeny

@article {pmid42602060,
year = {2026},
author = {Sahu, K and Yao, Q},
title = {metaIVP: an integrative metavirome focused metagenomic processing pipeline.},
journal = {BMC methods},
volume = {3},
number = {1},
pages = {37},
pmid = {42602060},
issn = {3004-8729},
abstract = {BACKGROUND: Metagenomic studies increasingly rely on complex, multi-tool pipelines to recover and characterize viral and non-viral genomes from mixed microbial communities. While these pipelines enable high-resolution genome recovery, limited functionality in downstream post-processing workflows and insufficient logging structures often hinder reproducibility, error tracing, and selective re-analysis. These challenges are particularly critical in metaviral analyses, where viral and non-viral genomes must be processed using distinct methodologies. To address these limitations, we introduce metaIVP, a modular, integrative, and flexible framework designed to systematically manage genome content purification, re-binning, quality assessment, and downstream analyses of viral and non-viral metagenomic contexts.

METHODS: The metaIVP framework is organized into hierarchical modules, each governed by dedicated log files that explicitly control execution state and re-runnability. Contig-level and bin-level analytical and purification steps are implemented as essential modules to isolate genome contents, followed by separate viral and non-viral post-processing workflows. Viral workflows incorporate contamination detection, genome quality evaluation, host prediction, and virus-specific binning. Non-viral analyses include genome binning, alignment and mapping statistics, genome quality assessment, and replication rate estimation. Checkpoints are explicitly defined such that deletion of selected module- or sub-module-level logs enables targeted re-execution of specific analytical steps without rerunning the full pipeline. All analyses are integrated to depict a comprehensive system in the metagenomic samples, with focus on the metaviromic information.

RESULTS: The usage of metaIVP was demonstrated using both a well-controlled human gut virome dataset and a geographically structured environmental metavirome dataset, showing its broad applicability across host-associated and environmental systems. The pipeline effectively separates viral and non-viral genomic content, improves viral bin purity, and preserves sample-specific functional, taxonomic, and host-association features after virome enrichment. Compared with recent state-of-the-art approaches, metaIVP achieves comparable performance, particularly when optional re-binning with vRhyme is applied, while maintaining a higher fraction of high-confidence viral bins.

DISCUSSION: The metaIVP addresses a key gap in metavirome analysis by jointly characterizing viral and non-viral genomic components and supporting integrative downstream analyses within a single framework. Its user-friendly, modular, and controllable design allows flexible execution and provides a foundation for incorporating additional downstream analytical tools as metavirome methodologies continue to evolve.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s44330-026-00090-7.},
}

@article {pmid42602126,
year = {2026},
author = {Ortúzar, M and Formariz, V and Suescún-Sepúlveda, JA and González-Hernández, M and Riesco, R and Garrido-Oter, R and Trujillo, ME},
title = {From natural assemblages to synthetic communities in the Lupinus microbiome.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1891479},
pmid = {42602126},
issn = {1664-462X},
abstract = {INTRODUCTION: Plant roots harbour complex microbial communities that enhance nutrient acquisition, stress tolerance, and pathogen defence, yet their assembly and functional dynamics remain incompletely understood.

RESULTS: In this work, we isolated over 700 bacterial strains from wild Lupinus angustifolius across multiple compartments and soil types, capturing both dominant and rare bacterial taxa. Using co-occurrence network analysis, we selected representative strains to assemble synthetic communities (SynComs) of varying complexity, which were inoculated under sterile and non-sterile conditions. Plants were inoculated with SynComs of increasing complexity under both non-sterile soil and gnotobiotic conditions. SynCom inoculation reshaped root-associated microbiota, moderately influenced the rhizosphere, and had limited impact on bulk soil communities. Increasing SynCom complexity enhanced plant growth and triggered host transcriptional responses involving hormone signaling, defence pathways, and metabolic reprogramming.

DISCUSSION: These findings indicate that soil-driven filtering and microbial interactions govern microbiome assembly and plant responses. Incorporating taxa with distinct ecological roles, including low-abundance members, improves SynCom functionality and advances understanding of plant-microbe interactions in natural and agricultural systems.},
}

@article {pmid42602195,
year = {2026},
author = {Maitray, A and Rishi, P and Conrady, CD and Binkley, E and Williams, BK and Yeh, S and Nicola, MD and Finger, PT},
title = {Vitreoretinal Lymphoma: A Comprehensive Clinical Review and Current Standards in Management.},
journal = {Journal of vitreoretinal diseases},
volume = {},
number = {},
pages = {24741264261474159},
pmid = {42602195},
issn = {2474-1272},
abstract = {PURPOSE: To summarize current evidence on clinical features, multimodal imaging findings, diagnostic techniques, and management strategies for vitreoretinal lymphoma.

METHODS: A literature review was performed to provide updated information on available treatment options for vitreoretinal lymphoma.

RESULTS: Diagnosis of vitreoretinal lymphoma requires vitreous biopsy, with or without retinal/subretinal tissue, for cytology and immunohistochemistry, along with ancillary tests such as flow cytometry, cytokine profiling (interleukin-10/interleukin-6 ratio >1), immunoglobulin heavy chain gene rearrangement analysis, and detection of the MYD88 L265P mutation. Optical coherence tomography and other multimodal imaging techniques have become increasingly useful in raising suspicion, guiding biopsy, and monitoring treatment response. No standardized treatment protocol exists for isolated vitreoretinal lymphoma. Management options include intravitreal chemotherapy (methotrexate and/or rituximab), radiation therapy, and systemic chemotherapy, often showing a good initial response, but relapse and subsequent central nervous system (CNS) involvement are common, resulting in poor overall prognosis and survival. For vitreoretinal lymphoma with CNS disease, current strategies favor high-dose methotrexate-based systemic chemotherapy, with or without intrathecal chemotherapy; whole-brain radiation is generally reserved as rescue therapy. Emerging directions for earlier diagnosis include metagenomic deep sequencing, and chimeric antigen receptor T-cell (CAR-T) therapy has shown promise for treatment of selected relapsed/refractory cases of primary CNS lymphoma with a potential to prolong survival.

CONCLUSIONS: Treatment of vitreoretinal lymphoma requires a multidisciplinary, individualized approach that integrates multimodal imaging, cytologic and molecular diagnostics, CNS evaluation, and tailored local or systemic therapy. Prospective multicenter studies are needed to refine diagnostic algorithms and standardize management.},
}

@article {pmid42594461,
year = {2026},
author = {Lu, D and Chen, B and Nie, E and Lian, S and Li, R and Guo, R and Fu, S},
title = {Indole inhibits anaerobic digestion by disrupting AHLs-mediated quorum sensing.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143267},
doi = {10.1016/j.jhazmat.2026.143267},
pmid = {42594461},
issn = {1873-3336},
abstract = {The emerging understanding highlights indole as a disruptive factor to quorum sensing (QS) mechanisms, prompting further investigation into its role in anaerobic digestion (AD) system inhibition. However, relevant studies are still scarce and the potential mechanism linking indole and AD inhibition remains unclear. This study showed that indole (1, 2, and 3 mM) significantly reduced cumulative methane production by 8.47-51.89% and extended the lag phase by 1.34-6.68 days. Time-series AHLs quantification, metagenomics, and circular clustering heatmaps analysis revealed that indole might disrupt microbial communication between hydrolysis-acidification bacteria and acetoclastic methanogens by reducing the AHLs level (C6-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C10-HSL, and C18-HSL). Notably, indole degradation alleviated the inhibition of C10-HSL, C18-HSL, and 3-oxo-C10-HSL, which might restore hydrolysis and acidification and mitigate AD inhibition. Exogenous AHLs (1 and 5 µM) restored methane production by 48.44-55.59% in 3 mM indole-inhibited reactors (p < 0.05), while the quorum quenching agent vanillin further reduced methane production by 72.55%, suggesting that AHLs play an important role in helping microorganisms resist indole stress. These findings highlight the importance of AHLs-mediated inter-microbial communication in counteracting indole-inhibited methanogenesis inhibition, suggesting potential practical strategies to enhance AD stability and efficiency in challenging conditions.},
}

@article {pmid42595035,
year = {2026},
author = {Mao, H and Deng, Y and Wang, X and Yu, Q and Zhao, Z and Zhang, Y},
title = {Two-phase anaerobic digestion with sub-thermophilic hydrolysis: Regulating metabolites to accelerate electron transfer and enhance methanogenesis.},
journal = {Environmental research},
volume = {307},
number = {},
pages = {125448},
doi = {10.1016/j.envres.2026.125448},
pmid = {42595035},
issn = {1096-0953},
abstract = {Sub-thermophilic anaerobic digestion accelerates the hydrolysis and acidogenesis of complex substrates to improve methane production, but methanogens may be inhibited under such condition. Two-phase anaerobic digestion (TPAD) system can decouple the hydrolytic-acidogenic and methanogenic phases to optimize microbial activity in each phase. Therefore, in this study, a novel temperature-phased strategy combining a 45°C hydrolytic-acidogenic phase with a 37°C methanogenic phase (TPAD45°C/37°C) was developed to accelerate the degradation of agricultural waste and avoid the sub-thermophilic temperature-induced inhibition of methanogenesis. Results showed that 45°C hydrolytic phase increased ethanol and acetate production, and decreased propionate production compared to the 37°C control. Consequently, at a solid retention time of 20 days, the methane yield in the TPAD45°C/37°C group was 31.8% and 13.0% higher than that in the TPAD37°C/37°C and TPAD45°C/45°C groups, respectively. Mechanistically, the TPAD45°C/37°C group exhibited the highest McrA activity and coenzyme F420 content, indicating superior methanogenic activity. Furthermore, Tafel polarization and temperature-dependent conductivity analyses revealed that the higher levels of ethanol from 45°C hydrolysate provided a stronger thermodynamic driving force to minimize the energy barrier and improve intrinsic electron transfer rates, thereby enhancing methanogenesis. Additionally, the TPAD45°C/37°C group exhibited the highest overall metabolic potential. Microbial community analysis revealed that this system enriched the methanogens, which in turn promoted the degradation of complex substrates and increased methane production. This study provided an economically viable, energy-positive, and highly resilient technological strategy for the sustainable valorization of agricultural waste.},
}

@article {pmid42595117,
year = {2026},
author = {Hashimoto, M and Oki, H and Kawahara, K and Fujii, KK and Koide, T},
title = {Molecular basis of collagen triple helix recognition by VWF A-like domain 2 of collagen VII: Implications for interlaced anchoring fibril formation.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113448},
doi = {10.1016/j.jbc.2026.113448},
pmid = {42595117},
issn = {1083-351X},
abstract = {Anchoring fibrils formed by collagen VII play a critical role in stabilizing the dermal-epidermal junction. The N-terminal non-collagenous (NC1) domain of collagen VII binds firmly to basement membrane components including collagen IV and has also been reported to interact with mesenchymal fibrillar collagens via its von Willebrand factor A-like domain 2 (A2 domain). To elucidate how collagen VII recognizes fibrillar collagen, we performed yeast two-hybrid screening using a triple-helical random peptide library, which resulted in the identification of a Met-Gly-Φ (Φ; aromatic amino acid residue) motif. Biochemical analysis with synthetic triple-helical peptides revealed a binding preference of Trp > Phe as the Φ residue by the A2 domain despite Trp being absent in native collagens. The crystal structure of the A2 domain in complex with the Nle (Met surrogate)-Gly-Trp-containing peptide revealed a unique mechanism by which two distinct hydrophobic pockets of the A2 domain accommodate the Nle and Trp residues corresponding to the Met-Gly-Φ motif, engaging all three chains of the triple helix. Subsequent molecular dynamics simulations demonstrated that the A2 domain recognizes the corresponding native Met-Gly-Phe motif in a similar manner, but with lower affinity, implying a transient interaction with mesenchymal collagens. The findings obtained in this work suggest models in which transient A2-triple helix interaction promotes the recruitment of collagen I and III fibrils into the arc-shaped structure of anchoring fibrils. This also provides a foundation for linking structural understanding to skin fragility diseases caused by collagen VII dysfunction.},
}

@article {pmid42595349,
year = {2026},
author = {Yang, Z and Ramakrishnan, M and Wang, B and Wei, Q and Ahmad, Z},
title = {Optimized Controlled-Release Fertilization Improves Productivity and Reshapes the Rhizosphere Microbiome in Lei Bamboo: A Metagenomic Assessment.},
journal = {Environmental microbiology},
volume = {28},
number = {8},
pages = {e70401},
pmid = {42595349},
issn = {1462-2920},
support = {2018YFD060010403//National Key Research and Development Program of China/ ; 2021F1065-10//Special Project of Zhejiang Provincial Scientific Research Institutes/ ; },
mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Poaceae/microbiology/growth & development ; Nitrogen/metabolism ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil/chemistry ; Urea/metabolism ; },
abstract = {Intensive nitrogen fertilization in Lei bamboo (Phyllostachys praecox) plantations has increased productivity but has also reduced nitrogen-use efficiency (NUE), accelerated nutrient losses, and contributed to soil degradation. How nutrient-release strategies influence rhizosphere microbiome assembly and ecosystem functioning remains poorly understood. Here, we developed a bamboo shoot-specific controlled-release fertilizer (CRF) and evaluated different urea-CRF blending ratios to identify sustainable fertilization strategy for Lei bamboo production. Mixed CRF-urea treatments outperformed both sole-fertilizer applications and the unfertilized control. T2 (30% urea + 70% CRF) achieved the highest shoot yield, whereas T3 (50% urea + 50% CRF) enhanced NUE. Optimized fertilization improved soil nutrient availability and organic matter accumulation without significantly affecting soil pH. Metagenomic analysis revealed the enrichment of taxa associated with nutrient transformation, organic matter turnover, and plant growth. However, pathway-level analysis revealed shifts in carbon, nitrogen, and sulfur cycling activities under optimized nutrient-release regimes. Our results demonstrate that synchronizing nitrogen release with plant and microbial demand enhances rhizosphere function, productivity and NUE. T2 delivered the strongest overall agronomic performance by maximizing shoot yield while maintaining improved nutrient retention and ecological stability. These findings provide a mechanistic link between fertilization strategy, rhizosphere microbial dynamics, and ecosystem function, supporting sustainable Lei bamboo production.},
}

*Fertilizers/analysis
*Rhizosphere
*Microbiota
*Soil Microbiology
*Poaceae/microbiology/growth & development
Nitrogen/metabolism
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism
Soil/chemistry
Urea/metabolism

@article {pmid42595408,
year = {2026},
author = {McQueen, AD and Calomeni-Eck, AJ and Cicerrella, AS and Chung, SH and Malmfeldt, MP and Lindsay, DL and Gong, P},
title = {Enhancing early-season detection of harmful algal blooms caused by sediment-borne overwintering cyanobacteria using metagenomic and qPCR tools.},
journal = {Harmful algae},
volume = {158},
number = {},
pages = {103160},
doi = {10.1016/j.hal.2026.103160},
pmid = {42595408},
issn = {1878-1470},
mesh = {*Harmful Algal Bloom ; *Cyanobacteria/genetics/classification/physiology ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Seasons ; Lakes/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Polymerase Chain Reaction ; },
abstract = {To better inform adaptive management strategies for harmful algal blooms (HABs), there is a critical need to improve detection capabilities of bloom risks earlier in the growing season. Emerging molecular tools such as metagenomic Next-Generation Sequencing (NGS) and amplification-based quantitative polymerase chain reaction (qPCR) can accurately identify the taxonomy of cyanobacteria and akinetes of which the latter are particularly challenging to distinguish morphologically and estimate their abundance. This study aimed to evaluate the contribution of these advanced molecular tools to assessing the presence, density, and planktonic growth potential of overwintering cyanobacterial cells in sediments from historically HAB-impacted waterbodies in the USA. We conducted 14-day incubation experiments using field-collected lake sediments and characterized cyanobacterial taxonomy and abundance in the sediments (pre-incubation) and overlying water (post-incubation) using light microscopy, genus-specific qPCR, and 16S rRNA amplicon sequencing. By analyzing qualitative and quantitative results, we not only identified the prevailing cyanobacterial genera that moved from sediment to water column over the incubation but also determined their relative abundance and the cyanobacterial genera consistent between sediment and water column. This study demonstrated that metagenomic and qPCR tools provided additional lines of evidence to augment traditional microscopy and improved taxonomic identification and quantification. Our approach can better inform planktonic growth potential of problematic cyanobacteria to enhance early detection capabilities, and guide targeted countermeasures taken to improve preventative or remedial HAB management, reducing environmental and public health impacts.},
}

*Harmful Algal Bloom
*Cyanobacteria/genetics/classification/physiology
*Geologic Sediments/microbiology
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics/analysis
Seasons
Lakes/microbiology
Real-Time Polymerase Chain Reaction/methods
Polymerase Chain Reaction

@article {pmid42595551,
year = {2026},
author = {Wang, L and Yang, J and Li, D and Zhang, F and Yan, JA and Wang, YY and Sun, J and Cao, H},
title = {[Tremella fuciformispolysaccharide retards the progression of colorectal cancer by regulating the gut microbiota-metabolome axis].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {8},
pages = {975-982},
doi = {10.3760/cma.j.cn112152-20250925-00485},
pmid = {42595551},
issn = {0253-3766},
support = {MS2024064//Jiangsu Province Science and Technology Development Program of Traditional Chinese Medicine (General Project)/ ; YJZ202305//the Jiangnan University Affiliated Hospital Research-Oriented Hospital Medical Research Project (General Project)/ ; KX-25-C166//Wuxi City 2025 Soft Science Research Project/ ; },
mesh = {Animals ; *Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced ; Humans ; Mice ; HT29 Cells ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; NF-kappa B/metabolism ; Male ; *Basidiomycota/chemistry ; *Metabolome/drug effects ; Azoxymethane ; Apoptosis/drug effects ; Dextran Sulfate ; Cell Proliferation/drug effects ; Feces/chemistry/microbiology ; Disease Progression ; Colon/pathology/metabolism ; },
abstract = {Objective: To investigate the anti-colorectal cancer effect of tremella fuciformis polysaccharides (TFP) via the gut microbiota-metabolite axis. Methods: Colorectal cancer was induced in C57BL/6J mice using azoxymethane/dextran sulfate sodium. TFP or distilled water was administered by gavage for 3 weeks. Disease activity index (DAI), colon length, tumor burden, histopathology, gut microbiota (metagenomics), fecal metabolites (untargeted metabolomics), and colonic protein expression (Western blot) were assessed. Pyridoxic acid's effect on HT-29 cells was tested in vitro. Results: TFP significantly reduced DAI [2.0(1.8, 3.3) vs. 3.5(2.8, 4.5), P＜0.01], increased colon length [(7.2±1.1) vs. (5.5±0.5) cm, P＜0.05], lowered pathological score [6(3, 8) vs. 9(8, 10), P＜0.05], and decreased tumor number [2(1, 3) vs. 4(3, 4), P＜0.05] and volume [(11.02±7.88) vs. (24.99±3.38), P＜0.01]. Metagenomics revealed that TFP significantly reshaped gut microbiota (R[2]=0.173, P=0.027), enriching Candidatus Amulumruptor, Helicobacter, and Akkermansia. Metabolomics showed distinct profiles (R[2]=0.159, P=0.004), with pyridoxic acid elevated 1.20 fold (P＜0.001). Pyridoxic acid suppressed HT-29 cell viability and migration, and correlated positively with several upregulated bacteria, suggesting a microbiota-metabolite axis underlying its anti-tumor effect. TFP downregulated nuclear factor-κB (NF-κB) (P＜0.01) and upregulated phosphorylated AMP-activated protein kinase alpha (p-AMPKα) (P＜0.001), BAX (P＜0.001), and cleaved caspase-3 (P＜0.05). Conclusion: TFP inhibits colorectal cancer progression by modulating gut microbiota, elevating pyridoxic acid, suppressing NF-κB, and activating AMPK-mediated apoptosis.},
}

Animals
*Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced
Humans
Mice
HT29 Cells
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Polysaccharides/pharmacology
NF-kappa B/metabolism
Male
*Basidiomycota/chemistry
*Metabolome/drug effects
Azoxymethane
Apoptosis/drug effects
Dextran Sulfate
Cell Proliferation/drug effects
Feces/chemistry/microbiology
Disease Progression
Colon/pathology/metabolism

@article {pmid42595815,
year = {2026},
author = {Vasquez, YM and Nardi, T and Terasaki, GM and Byl, P and Brůna, T and Villada, JC and Romero-Gutiérrez, MF and Mock, T and James, TY and , and Woyke, T and Schulz, F},
title = {Genomic catalogue of giant viruses reveals expanded diversity and functional potential.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42595815},
issn = {2058-5276},
support = {Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727 GVMAGs, a sixfold increase from the previous giant virus phylogenetic frameworks. Phylogenomics revealed 712 previously undescribed genera, 13 previously unknown viral families and an order we propose named Mycodnavirales. By accounting for alternative and custom genetic codes, we improved gene calling in over 1,300 GVMAGs, enabling more accurate identification of protein-coding genes. Database mining uncovered putative endogenous viral elements in hosts spanning algae, fungi and parasitic protists, highlighting that giant virus integration is widespread and evolutionarily persistent. Protein-level analysis revealed enriched genes for pollutant degradation in Algavirales and widespread biosynthetic gene clusters linked to antimicrobial-like and antibiotic resistance gene-like activity. This public resource will serve as a foundation for expanding giant virus diversity, uncovering virus-host interactions and exploring viral evolution.},
}

@article {pmid42595818,
year = {2026},
author = {Cumbo, F and Blankenberg, D},
title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42595818},
issn = {1546-1696},
support = {U24HG006620//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U24CA231877//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Accurately characterizing metagenome-assembled genomes remains a substantial challenge due to the presence of sequencing errors, incomplete assembly and contamination. Here, we present MetaSBT, a tool for organizing, indexing and characterizing microbial reference genomes and metagenome-assembled genomes, demonstrated in this study using viruses. MetaSBT identifies clusters of genomes across all seven taxonomic levels using the Sequence Bloom Tree data structure, which relies on Bloom filters to index large amounts of genomes based on their k-mer composition. We built an initial set of databases composed of over 190,000 viral genomes from public sources, grouped into sequence-consistent clusters at different taxonomic levels. We defined over 40,000 candidate species, ~80% of which, to our knowledge, do not match viral species in reference databases to date. Furthermore, we showed that our databases are useful to existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. The open-source framework and databases are fully integrated into the Galaxy platform.},
}

@article {pmid42595876,
year = {2026},
author = {Knuth, D and Mäder, P and Boekhorst, J and Poll, C and Kandeler, E and Alaoui, A and Pasković, I and Polić Pasković, M and Baldi, I and Bureau, M and Alcon, F and Contreras, J and Glavan, M and Abrantes, N and Campos, I and Norgaard, T and Huerta Lwanga, E and Geissen, V and Harkes, P},
title = {Beneath the surface: non-target effects of multiple pesticides on the soil microbiome in organic and conventional agricultural European fields.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42595876},
issn = {1614-7499},
support = {862568//HORIZON EUROPE Framework Programme/ ; },
abstract = {Previous studies have shown that diverse cocktails of pesticide mixtures are omnipresent in agricultural soils yet miss a clear link to the effects on the soil microbiome. In this study, we linked the occurrence of pesticides in conventional and organic agricultural soils of the SPRINT (Sustainable plant protection transition) projects' Case Study Sites to the composition and function of soil microbial communities. Metagenomic sequencing, phospholipid fatty acids analysis and enzyme activity measurements were used to characterize the soil microbiome and effects of site-specific parameters such as pH and SOC, and pesticide residues. Differences in the soil microbiome were strongly influenced by the geographic origin of the samples, with the pH value as dominant driver. Against our hypothesis, effects of the investigated management systems were limited, yet significant at the European level. Notably, an association between some pesticides could still be observed after accounting for the variation explained by the environmental factors. Among these, especially fungicides, with modes of action that aim to interfere with processes in microorganisms, seemed to affect the soil microbiome. This might occur either by directly affecting these processes in non-target organisms or by changing co-dependencies between fungi and bacteria. Next to fungicides, aminomethylphosphonic acid showed a significant effect on the soil microbial composition and an interactive, possibly synergistic effect with the persistent pesticide hexachlorobenzene. The latter raises concerns about a possible interaction of recently applied pesticides and persistent "legacy" pesticides. This work highlights that even though environmental parameters can overshadow the effects of pesticides, especially the identity of the pesticides present, can have an influence on the soil microbiome.},
}

@article {pmid42597171,
year = {2026},
author = {Wang, T and Liang, H and Wu, Y and Zhang, X and Zhang, S and Wei, Z and Li, W and Song, W and Luo, Z and Al-Dalali, S},
title = {Multi-omics profiling of microbial ecology and non-volatile compounds across fermentation stages of spontaneous litchi (Litchi chinensis Sonn.) fermented vinegar-like beverage.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1908193},
pmid = {42597171},
issn = {2296-861X},
abstract = {INTRODUCTION: Litchi fruit vinegar-like beverages (LVBs) are notable processed products derived from litchi fruit, yet few studies have focused on the systematic characterization of microbial and metabolic dynamics during their natural fermentation process.

METHODS: This work employed a comprehensive methodology integrating metagenomics and untargeted metabolomics based on UHPLC-MS/MS (Orbitrap Q Exactive HF-X) to elucidate the dynamic profiles of the microbial community and non-volatile metabolites, as well as their interrelations, across the various spontaneous fermentation stages of LVBs.

RESULTS: Metagenomic analysis indicated reduced microbial diversity and substantial structural changes within the community. Bacteria dominated the fermentation, accounting for 69.16 - 99.04% of the microbial community based on the taxonomically classified reads at the kingdom level. During the preliminary stage, Leuconostoc, Enterobacter, and Klebsiella were the prevalent genera. During the mid-fermentation stage, Komagataeibacter and Lactiplantibacillus emerged as the predominant genera in acid production. In the final stage, the microbial community was dominated primarily by Zymomonas and the Acetobacteriaceae family, including Acetobacter and Komagataeibacter. The non-targeted metabolomics study identified 2,382 metabolites through comprehensive database matching (in-house library, HMDB, KEGG, and metDNA algorithm) and stringent quality filtering (identification score > 0.5 and QC CV < 0.5), which were categorized into 20 distinct groups. Thirty seven metabolites, including amino acids, organic acids, and benzene derivatives, were identified as probable distinct differential metabolites based on a p-value threshold of p < 0.05, VIP > 1.0, and a fold change (FC ≥ 2 or ≤ 0.5) between consecutive fermentation stages in pairwise OPLS-DA of litchi vinegar-like beverage fermentation. Spearman correlation analysis revealed a highly organized ecological interaction network among dominant bacteria, physicochemical parameters, and non-volatile taste metabolites in the LVB fermentation system. Zymomonas mobilis, Acetobacter pasteurianus, Leuconostoc suionicum, and Lactiplantibacillus plantarum facilitated fermentation through metabolic synergy. Meanwhile, stage-specific enrichment of distinct Enterobacteriaceae species (Enterobacter hormaechei, and Enterobacter quasiroggenkampii) reflected species-level niche differentiation and resource competition, rather than a unified family-wide competitive behavior.

DISCUSSION: These findings provide a theoretical framework for engineering synthetic consortia and bioaugmentation approaches, informing the selection of starters and co-cultures to enhance LVB sensory and bioactive properties, alongside facilitating sfruit valorization.},
}

@article {pmid42597276,
year = {2026},
author = {Ding, Y and Li, Q and He, F and Zheng, Q and Zhao, G and Wan, J and Fang, Y and Yang, T and Zou, L and Yu, W and Dai, J},
title = {The Impact of Human Immunodeficiency Virus Co‑Infection on the Pathogen Spectrum and Outcomes of Severe Community‑Acquired Pneumonia: Insights from Metagenomic Next‑Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {599541},
pmid = {42597276},
issn = {1178-6973},
abstract = {PURPOSE: Severe community-acquired pneumonia (SCAP) causes high morbidity and mortality. Metagenomic next-generation sequencing (mNGS) data comparing pathogen profiles in SCAP between people living with human immunodeficiency virus (HIV) (PLWH) and HIV-uninfected individuals remain scarce.

PATIENTS AND METHODS: We retrospectively enrolled 72 SCAP patients at Kunming Third People's Hospital. We compared alpha diversity of respiratory microbiota, pathogen spectrum and healthcare resource utilization (HRU) between the two groups. We also assessed whether HIV infection was an independent risk factor for 30-day mortality.

RESULTS: mNGS detected pathogens in 70 of 72 patients (97.2%). PLWH showed higher detection rates of Pneumocystis jirovecii (p < 0.001), Human gammaherpesvirus 4 (EBV) (p = 0.013), and Human betaherpesvirus 5 (CMV) (p < 0.001). Among the 54 SCAP patients who survived 30 days, HRU metrics did not differ between groups. Elevated D-dimer level was an independent risk factor for 30-day mortality in SCAP patients (hazard ratio [HR]: 1.02, 95% confidence interval [CI]: 1.004-1.030; p = 0.0127).

CONCLUSION: HIV co‑infection in SCAP patients is associated with a distinct pathogen spectrum but does not affect HRU or 30‑day mortality. Elevated D‑dimer level is an independent risk factor for 30‑day mortality in SCAP patients.},
}

@article {pmid42597328,
year = {2026},
author = {Wu, B and Lu, S and Liu, H},
title = {Precision diagnostics in bronchiectasis: current advances in imaging, microbiology, biomarkers, and digital health.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1907636},
pmid = {42597328},
issn = {2296-858X},
abstract = {Bronchiectasis is a complex, chronic airway syndrome driven by a vicious cycle of irreversible bronchial dilatation, impaired mucociliary clearance, recurrent infection, and tissue-destructive inflammation. Reflecting its profound clinical heterogeneity, patients with identical structural damage on high-resolution computed tomography (HRCT) often exhibit divergent profiles in airway microbiology, inflammatory endotypes, exacerbation frequencies, and therapeutic responses, indicating that static anatomical classification fails to capture disease complexity. Sole reliance on visual CT inspection, standard sputum cultures, and subjective symptom tracking misses the driving mechanisms of individual disease progression. Emerging modalities-artificial intelligence (AI)-driven quantitative imaging, molecular microbiology, high-throughput biomarker profiling, and digital remote monitoring-aim to address these gaps. Our analysis shows that while these tools cannot substitute for bedside clinical acumen, they clarify obscure phenotypes, expose actionable treatable traits, and enable earlier, preemptive strategies. This review evaluates these contemporary diagnostic frameworks in non-cystic fibrosis bronchiectasis, dissecting their clinical utility, evidentiary maturity, and the economic and logistical barriers to routine adoption. Given that current evidence remains fragmented, advancing the field demands standardized imaging protocols, transparent algorithmic pipelines, clinically actionable metagenomic reporting, and robust validation in underrepresented Asian and Chinese cohorts. The real challenge lies not in generating more data, but in integrating these heterogeneous, high-dimensional datasets into pragmatic, point-of-care decision pathways that improve patient outcomes without widening disparities in global healthcare delivery.},
}

@article {pmid42597565,
year = {2026},
author = {Okonta, EO and Nnadi, CO and Paul-Chima, UO},
title = {The gut microbiome as a plausible but unproven moderator of cinnamon trial outcomes in type 2 diabetes: toward phytochemical standardization and precision nutraceuticals.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1874182},
pmid = {42597565},
issn = {2296-861X},
abstract = {Cinnamon (Cinnamomum spp.) has been widely investigated as an adjunctive nutraceutical for glycemic management in type 2 diabetes mellitus, yet clinical findings remain inconsistent. This variability is commonly attributed to differences in cinnamon species, dosage, intervention duration, baseline glycemic status and phytochemical standardization, alongside methodological factors such as trial quality, dietary patterns, medication use, adherence and endpoint selection. One potential contributor that has received limited attention is the gut microbiome. We propose a testable hypothesis that a substantial proportion of the marked inter-trial heterogeneity observed in cinnamon meta-analyses (I[2] > 75%) may reflect underlying gut-microbial metabotypes differing in their ability to convert cinnamon polyphenols and procyanidins into bioactive metabolites. Type 2 diabetes is associated with altered microbial composition, reduced butyrate-producing taxa and disrupted metabolic pathways. Cinnamon phytochemicals, including polyphenols, cinnamaldehyde, procyanidins and coumarin, undergo microbial biotransformation that may influence their bioavailability and metabolic effects. Because cinnamaldehyde is rapidly absorbed in the proximal gastrointestinal tract, colon-targeted delivery systems may be required to rigorously evaluate microbiome-mediated mechanisms. No randomized controlled trial has directly examined whether microbiome composition modifies cinnamon's glycemic effects in type 2 diabetes. Future studies should therefore incorporate microbiome-informed designs, including phytochemical fingerprinting, safety monitoring and, where feasible, metagenomic and metabolomic profiling, to distinguish true biological non-response from intervention heterogeneity and advance precision nutraceutical approaches for diabetes management.},
}

@article {pmid42597686,
year = {2026},
author = {Annaswamy, V and Mikesh, M and Dinkeloo, K},
title = {The Microbiome of Nurdles: Life on the Primary Microplastics of the Texas Gulf Coast.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42597686},
issn = {2578-9430},
abstract = {Nurdles are small, pre-production plastic pellets. Globally, nurdles are the second largest source of microplastic pollution due to release during manufacture and transport. As these nurdles persist in the environment, they undergo weathering-a process that significantly increases surface area and colonization by microbes. To gain an understanding of the composition of the microbiome found on nurdles, full-length 16S targeted metagenomic sequencing was performed on DNA extracted from nurdles collected from the Texas Gulf Coast. Sequencing data showed a greater amount and diversity of microbes found to be associated with nurdles than with the sand from which the nurdles were collected.},
}

@article {pmid42597889,
year = {2026},
author = {Ren, S and Ren, S and Chen, H and Zhang, W and Zhang, T and Chong, H and Wang, Z and Cao, W and Yong, X and Zhou, J},
title = {SuSha: A multi-model ensemble learning framework for predicting microbial salinity adaptation.},
journal = {Engineering microbiology},
volume = {6},
number = {3},
pages = {100292},
pmid = {42597889},
issn = {2667-3703},
abstract = {Current research on microbial salinity adaptation faces substantial challenges, including the limited predictive accuracy of traditional single-gene models and difficulty in dissecting systemic biological responses to salinity stress in complex natural habitats. To overcome these bottlenecks, the multi-model ensemble learning tool SuSha, which leverages genome-wide amino acid composition features, was developed. By extracting features from the whole-genome data of 123 bacterial and archaeal species with well-defined salinity adaptations, a 24-dimensional feature vector was constructed, comprising the frequencies of 20 standard amino acids and four aggregated functional categories. Based on this, an ensemble model was developed by integrating algorithms such as random forest, bagging, and extra trees. Five-fold cross-validation demonstrated that this 24-dimensional feature-based ensemble model achieved a global accuracy of 0.765 and an area under the curve of 0.941, significantly outperforming individual baseline models. Furthermore, the model was externally validated using 2678 metagenomic samples from six global regions, encompassing freshwater, marine, and hypersaline habitats. SuSha exhibited high robustness, ecological consistency across diverse salinity gradients, and a classification accuracy of over 90% for extreme halophiles, particularly within the extreme halophilic range. By enabling high-precision genotype-to-phenotype predictions using a habitat-adaptive algorithm-switching strategy, SuSha provides a robust computational framework for inferring the physiological potential of uncultivated microorganisms and mining microbial resources in extreme environments.},
}

@article {pmid42598143,
year = {2026},
author = {Mollick, SA and Khual, GK and Ghosh, A and Patel, SK and Bhattacharyya, S and Roy, CS and Maile, A and Nagarajaram, HA and Longkumer, M and Babu, MN and Kundapur, AR and Uniyal, S and Chattterjee, A and Mitra, M and Sikdar, M and Urade, BP and Pulamaghatta, VN},
title = {Gut microbial diversity and candidate keystone taxa in Indian tribes: Insights across lifestyle-ecological continuum and health associations.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100650},
pmid = {42598143},
issn = {2666-5174},
abstract = {Despite the critical role of the gut microbiome in host physiology and health, it remains poorly characterized in Indigenous populations undergoing rapid acculturation. This study presents high-resolution, whole-genome metagenomic profiling of gut microbiota from five Particularly Vulnerable Tribal Groups (PVTGs) of Southern India, Irula, Jenu Kuruba, Kurumba, Chenchu, and Konda Savara, spanning distinct ecological zones and cultural transitions. Using an ecology-lifestyle continuum framework, we investigated taxonomic and functional diversity with a focus on identifying computationally inferred candidate keystone taxa, defined by their association with variation in community ordination structure. A leave-one-taxon-out ordination framework identified 121 candidate keystone taxa, many of which were population-specific and have not been widely reported. Functional analyses revealed a conserved core of metabolic pathways, including glycolysis and folate biosynthesis, alongside group-specific enrichment in xenobiotic degradation, amino acid biosynthesis, mucin metabolism, and lipid processing, associated with differences in dietary and environmental exposures across populations. Large-scale disease-association mapping (n = 5,625) linked 50 candidate keystone taxa to 14 conditions, with 44 associated with health and 6 with disease. While Fusicatenibacter saccharivorans and Alistipes shahii were enriched in healthy states, Ruminococcus gnavus, Bifidobacterium longum, Flavonifractor plautii, and Blautia wexlerae were enriched in disease-associated profiles. Cross-cohort validation against an independent set of traditional metagenomes (n = 119) further showed that a subset of Indian tribal core candidate keystone taxa was consistently identified across geographically distinct populations, with partial conservation of community associations and health associations, indicating reproducible context-dependent microbial association patterns across traditional populations. Alpha diversity was highest in minimally acculturated groups, with higher degrees of acculturation associated with reduced microbial diversity and greater enrichment of disease-associated taxa. Overall, this study provides a context-aware framework for understanding gut microbiome dynamics in culturally transitioning populations, emphasizing the conservation of microbial heritage and informing population-specific microbiome-based interventions.},
}

@article {pmid42598172,
year = {2026},
author = {Udahemuka, JC and Cassidy, H and Schuele, L and Uwibambe, E and Ngabo, MG and Masirika, LM and Sindayiheba, R and Otani, S and Gashegu, M and Twizere, JC and Aarestrup, F and Ndayisenga, F and Oude Munnink, BB and Koopmans, MPG and Ndishimye, P},
title = {Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101529},
pmid = {42598172},
issn = {2352-7714},
abstract = {Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade. In this study, we investigated whether these outbreaks resulted from repeated introductions or sustained local circulation. We generated RVFV whole-genome sequences from livestock samples collected between 2022 and 2025 using Nanopore sequencing. Genomic analyses indicated the outbreaks resulted from sustained local circulation of lineage C rather than repeated introductions, suggesting ongoing transmission likely driven by sporadic spillover. This study underscores the importance of continuous genomic One Health surveillance in endemic settings.},
}