@article {pmid41738567,
year = {2026},
author = {Ma, M and Liu, B and Zhou, J and Zhang, J and Zhang, Y and Li, W and Liu, X and Xu, D},
title = {Viral Community Profiling of RNA Viruses in Lesion Tissues From Hyriopsis cumingii With Epidemic Disease via Metatranscriptomics and VirID-Based RdRP Mining.},
journal = {Journal of fish diseases},
volume = {49},
number = {8},
pages = {e70143},
doi = {10.1111/jfd.70143},
pmid = {41738567},
issn = {1365-2761},
support = {2024SKLBC-KF02//National Key Laboratory of Aquatic Animal Disease Control and Healthy Aquaculture, 2024 Open Research Projects/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; *Unionidae/virology ; RNA-Dependent RNA Polymerase/genetics ; Metagenomics ; Transcriptome ; Epidemics/veterinary ; *Virome ; Hepatopancreas/virology ; },
abstract = {To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using hepatopancreas and intestinal samples from six severely infected individuals. Clinical observations were consistent with hallmark features of epidemic outbreaks. The sequencing yielded 86.2 Gb of raw data, of which 97.1% passed quality control, resulting in 77.7 Gb of high-quality clean data. Taxonomic annotation identified 182 viral species, predominantly unclassified viruses (45% Transcripts Per Million, TPM), followed by members of the phyla Lenarviricota (28%) and Uroviricota (17%). Phylogenetic analysis of RdRP sequences revealed 13 viral supergroups, with the Picorna-Calici supergroup showing the highest abundance (26.2% of annotated viruses) and reaching a prevalence of 39.3% in sample HcAV3. Notably, 89.6% of the identified viral RdRPs exhibited less than 70% amino acid identity to known viral sequences, highlighting the presence of extensive "viral dark matter" in this host species. This study establishes the first viral profile associated with epidemic disease in H. cumingii, providing a baseline for further etiological research on this high-mortality aquaculture disease.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification/physiology
Phylogeny
*Unionidae/virology
RNA-Dependent RNA Polymerase/genetics
Metagenomics
Transcriptome
Epidemics/veterinary
*Virome
Hepatopancreas/virology

@article {pmid42392820,
year = {2026},
author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY},
title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {9},
pages = {2652-2664},
doi = {10.19540/j.cnki.cjcmm.20260107.707},
pmid = {42392820},
issn = {1001-5302},
mesh = {Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; },
abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.},
}

Animals
*Drugs, Chinese Herbal/administration & dosage
*Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics
Rats
Male
Metabolomics
Metagenomics
Rats, Sprague-Dawley
*Brain Ischemia/metabolism/drug therapy/genetics
Humans
Oxidative Stress/drug effects
Blood-Brain Barrier/drug effects/metabolism
Brain/metabolism/drug effects
Gastrointestinal Microbiome/drug effects
Disease Models, Animal

@article {pmid42393176,
year = {2026},
author = {Gordon, LM and Sevigny, JL and Buck, CB and Murray, MJ and Sidor, IF and Newton, AL and Palisoul, SM and Kelly, M and Nigatu, AS and Simpson, SD and Popov, VL and Waltzek, TB and Tsongalis, GJ and Frasca, S and Thomas, WK},
title = {A novel adomavirus from proliferative skin lesions of a broadnose sevengill shark (Notorynchus cepedianus).},
journal = {Npj viruses},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44298-026-00210-8},
pmid = {42393176},
issn = {2948-1767},
support = {P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; },
abstract = {In May of 2022, an aquarium-maintained broadnose sevengill shark (Notorynchus cepedianus) developed proliferative skin lesions that prompted pathologic and molecular investigation. Histopathologic examination revealed epidermal hyperplasia consisting of proliferation of spinous epithelial cells with mild dysplasia. Metagenomic sequencing identified a novel adomavirus with an 18,834 base pair circular double-stranded DNA genome. The virus, provisionally named broadnose sevengill shark adomavirus (7AdoV), contains two bidirectionally expressed protein-coding gene sets. Genomic annotation and structural predictions of proteins were used to contextualize 7AdoV phylogenetically and functionally. Transcriptomic analysis showed that expression of the structural late gene set was higher than the replicative early gene set at the time of diagnostic sampling. In situ hybridization using RNAscope technology localized transcripts of the adomavirus Wasp gene to epithelial cells of the hyperplastic epidermis. Infection by this novel adomavirus was associated with superficial and proliferative lesions that were self-limiting and resolved in this shark.},
}

@article {pmid42393215,
year = {2026},
author = {Nthuku, S and Mordecai, J and Babajide, AA and Makoko, D and Sawadogo, Y and Awe, OI},
title = {The Kenyan Human Gut Virome Catalogue reveals extensive viral diversity and age-dependent community structure.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60183-9},
pmid = {42393215},
issn = {2045-2322},
abstract = {The human gut virome is a critical yet understudied component of the microbiome that shapes microbial community structure and host-microbe interactions. However, most existing human gut virome reference databases have been constructed predominantly from populations in high-income countries, resulting in the substantial underrepresentation of African populations. To help address this disparity, we developed the Kenyan Human Gut Virome Catalogue (KHGVC), the first comprehensive human gut virome resource for Kenya and the first country-specific human gut virome catalogue from Africa. Using a standardized viromics pipeline applied to 626 fecal metagenomes spanning infants and adults across three Kenyan counties, we reconstructed 116,968 viral operational taxonomic units (vOTUs). Cross-catalogue comparisons revealed extensive novelty where 65.6% of KHGVC's vOTUs larger than 10 kb lacked matches in five major human gut virome databases, and 95% remained unique relative to the Unified Human Gut Virome (UHGV). Temperate bacteriophages accounted for ~ 70% of vOTUs, supporting a major role for lysogeny in gut ecosystem stability. Functional annotation assigned putative roles to ~ 27% of predicted viral proteins, primarily structural and replication-associated functions. Application of KHGVC revealed pronounced age-dependent virome structuring in which infant viromes were less diverse and enriched in Bifidobacterium-infecting phages, including Bifidobacterium longum, whereas adult viromes exhibited greater diversity and expansion of Prevotella-associated phages. Together, the KHGVC substantially expands known human gut viral diversity and provides a foundational reference for Kenyan and African virome research. The KHGVC can be accessed freely through a publicly available interactive web interface (https://igmr.org/software/kenyavirocat).},
}

@article {pmid42394019,
year = {2026},
author = {Dicko, A and Barro, SG and Sombie, S and Séré, R and Bonkoungou, I},
title = {Applications of Metagenomics and Artificial Intelligence in Characterizing Antimicrobial Resistance in Livestock: A Systematic Review.},
journal = {Studies in health technology and informatics},
volume = {338},
number = {},
pages = {328-332},
doi = {10.3233/SHTI260857},
pmid = {42394019},
issn = {1879-8365},
mesh = {Animals ; *Metagenomics/methods ; *Livestock/microbiology/genetics ; *Artificial Intelligence ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Humans ; One Health ; Machine Learning ; },
abstract = {Antimicrobial resistance (AMR) is an urgent global health threat, intensified by the widespread use of antimicrobials in livestock production. This study synthesizes the current landscape of combining metagenomic sequencing with artificial intelligence (machine learning and deep learning) to characterize, surveil, and predict AMR within the One Health framework. A comprehensive multi-database literature search was conducted, and, following PRISMA guidelines, 10 peer-reviewed studies meeting the inclusion criteria were selected for full synthesis. Metagenomic shotgun sequencing significantly surpasses conventional culture-based methods by directly capturing antimicrobial resistance genes (ARGs) from complex biological communities. AI algorithms substantially outperform traditional bioinformatic tools, achieving high predictive accuracy (AUC-ROC > 0.90) and revealing consistent ARG transfer pathways that link livestock, human, and environmental compartments. Integrating metagenomics with AI delivers a paradigm shift for proactive AMR surveillance. However, standardization, interpretability, and technological adaptation to resource-limited settings-especially in sub-Saharan Africa-remain urgent priorities to inform effective public health policy.},
}

Animals
*Metagenomics/methods
*Livestock/microbiology/genetics
*Artificial Intelligence
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Humans
One Health
Machine Learning

@article {pmid42394335,
year = {2026},
author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X},
title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {55},
number = {3},
pages = {491-498},
doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019},
pmid = {42394335},
issn = {1000-8020},
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; },
abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.

METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1∶1∶1 ratio) and Mix-B group(same bacterial strains, in a 10∶1∶1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 × 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.

RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, β-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.

CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Male
Mice
Mice, Inbred C57BL
Lactobacillus acidophilus/physiology
Tryptophan/metabolism
Indoles/metabolism
Bifidobacterium animalis/physiology
Lacticaseibacillus rhamnosus/physiology
Feces/microbiology
*Microbiota

@article {pmid42394341,
year = {2026},
author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V},
title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.},
journal = {Journal of environmental quality},
volume = {55},
number = {4},
pages = {e70215},
doi = {10.1002/jeq2.70215},
pmid = {42394341},
issn = {1537-2537},
support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; },
mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; },
abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.},
}

New Caledonia
Seasons
*Seawater/microbiology
*Microbiota
RNA, Ribosomal, 16S/analysis
Bacteria/classification
Tropical Climate
*Environmental Monitoring
Archaea
Ecosystem

@article {pmid42394361,
year = {2026},
author = {Queiroz, VF and Tatara, JM and Jivaji, AM and Given, CJ and Dutra, LAL and Abbas, W and Ricky, Z and Stokke, R and Stensvåg, K and Abrahao, JS and Almeida, GMF},
title = {Isolation of a Cohort of Giant Viruses From Above the Arctic Circle in Northern Norway.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70366},
doi = {10.1111/1462-2920.70366},
pmid = {42394361},
issn = {1462-2920},
support = {311192/A65276//Tromsø Forskningsstiftelse/ ; 101150485//Horizon 2020 Framework Programme/ ; 101162830/ERC_/European Research Council/International ; 315427//Norges Forskningsråd/ ; TMS2020TMT13//Trond Mohn stiftelse/ ; },
mesh = {*Giant Viruses/isolation & purification/classification/genetics ; Arctic Regions ; Norway ; Phylogeny ; *Acanthamoeba/virology ; Mimiviridae/isolation & purification/classification/genetics ; *Seawater/virology ; Fresh Water/virology ; },
abstract = {Viruses are the most abundant biological entities on Earth. Metagenomic data indicates a higher viral abundance of viruses of unicellular eukaryotes in the polar regions, information still not matched by broad isolation efforts using samples collected in these regions. Here we describe a prospection effort using diverse samples collected above the Arctic circle, including freshwater and marine samples from urban areas, deep-sea hydrothermal vents and sea ice samples from the Nansen Basin. We isolated 10 giant viruses capable of infecting Acanthamoeba spp., five representing the Marseilleviridae family and five representing the Mimiviridae family. These viruses are the northernmost isolates found so far in the Nordic countries and consist of a unique cohort of Arctic viruses that differs geographically and temporarily from a cohort already described from the Siberian permafrost. Despite an apparent viral diversity in the samples, the uniqueness of the samples themselves and the use of additional non-amebozoan strains as hosts, our viruses are still representatives of known viral families. In conclusion, here we show the isolation of giant viruses in Northern Norway and highlight the potential host bias towards Acanthamoeba in giant virus prospection, indicating the need to break this bias to diversify the isolation of environmental viruses.},
}

*Giant Viruses/isolation & purification/classification/genetics
Arctic Regions
Norway
Phylogeny
*Acanthamoeba/virology
Mimiviridae/isolation & purification/classification/genetics
*Seawater/virology
Fresh Water/virology

@article {pmid42394639,
year = {2026},
author = {Zhu, H and Yang, P and Tu, Y and Fu, X and Yang, X and An, N},
title = {A Case Report of Meningitis with Possible Coinfection by Listeria monocytogenes and Mycobacterium tuberculosis (Detected by Metagenomic Next-Generation Sequencing) and Literature Review.},
journal = {Case reports in critical care},
volume = {2026},
number = {},
pages = {9615951},
pmid = {42394639},
issn = {2090-6420},
abstract = {RATIONALE: The study is aimed at exploring the complex clinical scenario of a patient with systemic lupus erythematosus who developed a rare coinfection with Listeria monocytogenes and Mycobacterium tuberculosis. The rationale is to highlight the diagnostic and therapeutic challenges in managing such a case, particularly in the context of immunosuppression and the need for effective antimicrobial therapy. This case underscores the importance of advanced diagnostic techniques like metagenomic next-generation sequencing in identifying coinfections and the critical balance required in treating both infections while managing the underlying autoimmune condition.

PATIENT CONCERNS: This case report presents a 58-year-old female patient who initially manifested thrombocytopenia and was diagnosed with SLE in an external hospital. After treatment, her condition did not improve. On the contrary, she developed a fever and a headache, and her disturbance of consciousness gradually worsened. The patient was admitted to our hospital with a suspected diagnosis of lupus encephalopathy and central nervous system infection.

DIAGNOSES: MRI plain scan showed linear enhancement shadows in the right temporal pole and bilateral cerebellar hemisphere regions on the fluid-attenuated inversion recovery three-dimensional volumetric fluid-attenuated inversion recovery contrast-enhanced scan. Subsequently, NGS of the cerebrospinal fluid detected L. monocytogenes and M. tuberculosis, suggesting a possible mixed infectious meningitis caused by these two pathogens.

INTERVENTIONS: The patient underwent a comprehensive treatment regimen including antiListeria and antituberculosis therapies. Unfortunately, this was followed by the development of liver failure and various other complications. In response, we administered interventions such as blood purification and liver support measures. Furthermore, we organized a multidisciplinary consultation to address the complex medical needs of the patient.

OUTCOMES: Despite aggressive medical interventions, the patient's condition deteriorated. She developed multiorgan failure, which significantly impacted her prognosis. The patient's family elected to withdraw life-sustaining treatment, and the patient passed away within 24 h after discharge.

LESSONS: This case underscores the importance of early and accurate diagnosis, particularly for immunocompromised patients with complex clinical presentations. Identifying mixed infections is crucial, and it also poses a significant challenge in selecting appropriate antimicrobial agents and conducting relevant tests.},
}

@article {pmid42394779,
year = {2026},
author = {Wishahi, M and Badawy, M},
title = {Letter to the Editor: Urinary infection in European guidelines 2025 vs microbiology culture results in the management of urinary infection.},
journal = {World journal of experimental medicine},
volume = {16},
number = {2},
pages = {115894},
pmid = {42394779},
issn = {2220-315X},
abstract = {We read with great interest the study by Yadav et al published in the World Journal of Experimental Medicine, which postulated a nomogram including patient's critical factors, other than urine sample. European Association of Urology (EAU) published the guidelines on urological infection 2025. The EAU guidelines 2025 of urinary infections (UIs) has classified in two distanced categories: Localized UTs and systemic UTs according to specific patient's symptoms and clinical signs, this new practical classification replaced previous concept of non-complicated urinary tract infection (UTI) against complicated UTI. The new EAU classification categorizes UIs as either localized or systemic, according to the presence of specific clinical signs and symptoms, this new practical classification replaced previous concept of non-complicated UTI against complicated UTI, irrespective of the results of bacteriological findings. In the new classification of UIs, the classification is based on clinical set-up on which the practitioner or urologist will manage the patient. Management of UIs is crucial to consider the urinary and gut microbiota. It was established recently that antibiotic use affects microbiota homeostasis in the gut and urinary tract that will initiate dysbiosis.},
}

@article {pmid42394824,
year = {2026},
author = {Wu, Y and Cai, H and Wu, Q and Wu, J and Hu, J and Huang, E and Li, Z and Liang, S and Hu, X and Dai, J and Liao, R},
title = {The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1873187},
pmid = {42394824},
issn = {2235-2988},
mesh = {Animals ; *CRISPR-Cas Systems ; Humans ; *Mosquito-Borne Diseases/virology ; *Epidemiological Monitoring ; *Culicidae/virology ; *Mosquito Vectors/virology ; *Viruses/genetics/isolation & purification/classification ; *Virus Diseases/virology/transmission/diagnosis ; },
abstract = {Mosquito-borne virus surveillance increasingly requires rapid, distributed detection of co-circulating pathogens, serotypes, and lineages across clinical and vector-sampling sites. CRISPR-Cas platforms offer a programmable toolkit for this purpose, but their readiness differs substantially across surveillance functions. Here, we review CRISPR-Cas methods for mosquito-borne virus surveillance across detection, tracing, and discovery-supporting targeted screening. Detection is the most advanced application: selected Cas12- and Cas13-based assays for dengue, Zika, chikungunya, West Nile, Japanese encephalitis, and related mosquito-associated viruses report sub-hour workflows, portable readouts, and targeted serotype- or lineage-marker discrimination. However, performance remains assay-, target-, and sample-matrix-dependent, and validation in pooled mosquito samples and field settings is still limited. Tracing currently relies mainly on validated portable amplicon-sequencing workflows, whereas CRISPR-aided sample-preparation methods such as DASH, FLASH, RAPID-DASH, and Cas9-targeted enrichment remain transferable opportunities for host depletion or target enrichment rather than established mosquito-borne virus genomic-surveillance workflows. For discovery-oriented surveillance, multiplex CRISPR-Cas systems such as CARMEN can support targeted screening of known or near-neighbor viruses represented by predesigned crRNAs, while metagenomic next-generation sequencing remains necessary for divergent or previously unknown viruses. Across these functions, CRISPR-Cas programmability may accelerate parts of assay redesign, but practical retargeting still requires compatible amplification primers, effector-specific target constraints, cross-reactivity assessment, and analytical revalidation. Routine surveillance use will require integrated demonstrations with clinical and pooled-vector samples, comparison against established molecular and sequencing methods, cost validation, and regulatory evidence.},
}

Animals
*CRISPR-Cas Systems
Humans
*Mosquito-Borne Diseases/virology
*Epidemiological Monitoring
*Culicidae/virology
*Mosquito Vectors/virology
*Viruses/genetics/isolation & purification/classification
*Virus Diseases/virology/transmission/diagnosis

@article {pmid42394849,
year = {2026},
author = {Ding, J and Liu, F and Zhao, Y and He, Z and Shi, Y and Shu, L},
title = {Protists show high resilience and thrive under multiple chemical stressors.},
journal = {mLife},
volume = {5},
number = {3},
pages = {388-392},
pmid = {42394849},
issn = {2770-100X},
abstract = {Protists are an underexplored but functionally important component of aerobic-activated granular sludge under pollution stress. Using metagenomics, we profiled protistan responses to ciprofloxacin, triclosan, and Cu[2+] (alone or in combination). Protists remained a stable 6.35%-7.88% of the bacterial community, and the consumers were the most abundant groups. Ciprofloxacin showed little effect on protist abundance, while Cu[2+] increased protist abundance, especially consumers. Stress conditions also strengthened predominantly positive protist-bacteria associations, suggesting cross-domain interactions that may enhance community resilience. These results demonstrate that protists are key determinants in stabilizing microbial communities under multiple stressors.},
}

@article {pmid42395046,
year = {2026},
author = {Kumar, A and Ghosh, D},
title = {Letter to the Editor: Dengue virus as an underrecognized cause of encephalitis in tropical Asia - Bridging diagnostic and surveillance gaps.},
journal = {World journal of virology},
volume = {15},
number = {2},
pages = {118082},
pmid = {42395046},
issn = {2220-3249},
abstract = {Arboviral encephalitis remains a major public health concern in tropical Asia, where the etiology of a substantial proportion of central nervous system infections remains undetermined despite endemic circulation of dengue virus (DENV) and Japanese encephalitis virus. Laboratory confirmation is frequently absent in clinically suspected encephalitis. Perera et al recently published a study in World Journal of Virology, highlight this diagnostic gap by identifying DENV infection in 6.06% of encephalitis cases, including molecular evidence of DENV-3 neuroinvasion. These findings add to the growing evidence that DENV can cause encephalitis and meningoencephalitis across age groups. However, encephalitis in endemic settings is etiologically heterogeneous, and dengue represents only one of several infectious and immune-mediated contributors. Neurological dengue is likely under-recognized due to overlapping clinical presentations and limited diagnostic capacity. The identification of DENV-3 is noteworthy given its recurrent association with neurological disease. Limited concordance between reverse transcription polymerase chain reaction and immunoglobulin M assays reflects challenges related to viral kinetics, timing of specimen collection, and flaviviral serological cross-reactivity. Strengthening surveillance through integrated molecular and serological diagnostic strategies, including multiplex polymerase chain reaction and metagenomic next-generation sequencing, is essential to reduce undiagnosed encephalitis and improve clinical management and public health preparedness in tropical Asia.},
}

@article {pmid42395425,
year = {2026},
author = {Shih, JB and Zhao, C and Pollard, KS and Lind, AL},
title = {Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.24.734308},
pmid = {42395425},
issn = {2692-8205},
abstract = {Microbial eukaryotes are prevalent members of host-associated and free-living microbial communities, but are routinely excluded from studies of these communities. Existing methods for eukaryote detection from whole metagenome sequencing are limited by contamination of eukaryotic reference genomes and incomplete taxonomic coverage. Our previously published tool EukDetect addressed these challenges using a curated database of universal BUSCO marker genes, but lacked validated quantitative abundance metrics and was built from a limited number of genomes. Here we present EukDetect2, incorporating a database containing 6,948 microbial eukaryotic genomes representing 6,594 unique species, 2,339 of which are newly added since EukDetect version 1, alongside quantitative metrics for estimating absolute and relative abundance of microbial eukaryotes. Using simulated data, we demonstrate accurate abundance estimation, no false positives from bacterial or host-derived reads, and equivalent or greater sensitivity and specificity than alternative taxonomic profiling tools across a range of microbial abundances and community compositions. Applying EukDetect2 across globally distributed human gut microbiome cohorts, we find that Blastocystis spp. and Dientamoeba fragilis are the most prevalent gut eukaryotes across cohorts, while host-associated fungi are consistently less prevalent than commensal protists. Blastocystis abundance is positively associated with a gut microbial community enriched for fiber-fermenting microbes and depleted for pro-inflammatory and industrialization-associated taxa. EukDetect2 provides sensitive, accurate, and quantitative metrics for investigating microbial eukaryotes from metagenomic samples.},
}

@article {pmid42395547,
year = {2026},
author = {Kokroko, N and Jayanti, R and Sapoval, N and Nute, MG and Nakhleh, L and Treangen, TJ},
title = {Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.22.733643},
pmid = {42395547},
issn = {2692-8205},
abstract = {MOTIVATION: Horizontal gene transfer (HGT) shapes bacterial evolution and microbial ecosystems, yet detecting HGT within microbiomes remains a challenge due to fragmented metagenomic assemblies, reference bias, reliance on gene boundaries, and limited ability to model structural mosaicism and patterns across genomes.

METHODS: We present Kente, a novel pangenome graph-based framework designed for HGT detection that aligns metagenomic assembly contigs to a curated database of >600 genus-level bacterial pangenome graphs constructed using minigraph. Kente infers local taxonomic composition along contigs using alignment evidence and classifies candidate transfers using structured clade-transition topologies (e.g., A-B-A sandwich, open tips, and mosaic patterns). A complementary intra-genus module detects inter-species transfers within a single genus graph using segment-level clade annotations.

RESULTS: Across simulated intra- and inter-genus transfer scenarios, Kente achieves higher precision and comparable recall relative to existing gene-centric microbiome HGT detection approaches while reducing false positives from fragmented assemblies. Application to real human gut metagenomes (HMP2, n = 26) demonstrates Kente's ability to detect candidate cross-lineage transfer regions in complex microbial communities. Runtime profiling shows near-linear scaling with input size, enabling efficient analysis of large metagenomic assemblies.

https://github.com/treangenlab/Kente.},
}

@article {pmid42395643,
year = {2026},
author = {Yang, S and Yu, Q and Zeng, Y and Lu, Y and Xia, C and Cheng, F and Liu, Y and Liu, M and Chen, Y},
title = {Direct viral invasion and tumor-like pulmonary nodules: A fatal case of mpox in a patient with advanced HIV disease.},
journal = {Biosafety and health},
volume = {8},
number = {3},
pages = {228-233},
pmid = {42395643},
issn = {2590-0536},
abstract = {While mpox is typically a self-limiting zoonosis, individuals with advanced human immunodeficiency virus type 1 (HIV-1) infection are at increased risk for severe visceral complications and high mortality. We report a fatal case of fulminant mpox pneumonia in a 38-year-old male with advanced HIV-1 Infection and severe immunosuppression (CD4[+] T-cell count <100 cells/µL). The patient initially presented with characteristic cutaneous lesions but rapidly progressed to dyspnea and respiratory failure. Serial chest imaging revealed diffuse, solid perivascular nodules and patchy consolidations were highly suggestive of pulmonary malignancy. While initial microbiological cultures and clinical presentation (Day 4) suggested bacterial and fungal superinfections, metagenomic next-generation sequencing (mNGS) of lung tissue biopsy identified an overwhelming burden of mpox virus (MPXV; 260,840 sequence reads), cytomegalovirus (CMV) and Epstein-Barr virus (EBV), confirming direct viral invasion of the pulmonary parenchyma. Despite comprehensive treatment with antibiotics, antifungals, CMV-targeted therapy, and mechanical ventilation (specific anti-orthopoxvirus agents were unavailable), the patient succumbed to progressive respiratory failure on Day 31. This case highlights that mpox can manifest as severe necrotizing pneumonia with tumor-like radiological features in patients with acquired immunodeficiency syndrome (AIDS). It underscores the necessity of early pulmonary imaging and molecular testing in high-risk populations to differentiate mpox pneumonia from malignancy or opportunistic infections.},
}

@article {pmid42395675,
year = {2026},
author = {Almuhanna, AA and Vatte, C and Guo, Q and Elsalamouni, TS and Al-Muhanna, FA and Aboalrihy, AM and Alhabib, HA and Almomen, MF and Alali, RA and Habara, AH and Alrubaish, MA and Alfalah, KM and Cyrus, C and Abdul-Rahman, IS and Keating, BJ and Al-Ali, AK and Wang, C},
title = {Gut microbiota in a Saudi population with chronic kidney disease.},
journal = {World journal of nephrology},
volume = {15},
number = {2},
pages = {118343},
pmid = {42395675},
issn = {2220-6124},
abstract = {BACKGROUND: The gut microbiota (GM) plays an important role in chronic kidney disease (CKD) progression, and dialysis modalities can differentially impact the GM composition and function. There is also limited information on the GM in Arab populations.

AIM: To investigate the distinct microbial profiles and functional alterations associated with hemodialysis (HD) and peritoneal dialysis (PD) in a Saudi Arabian cohort.

METHODS: We performed whole-genome metagenomic sequencing on fecal samples from 189 participants (controls and CKD, HD, and PD patients).

RESULTS: We detected distinct microbial profiles across all patient groups compared with that of the controls. Microbial risk scores derived from differentially abundant taxa accurately distinguished CKD, PD, and HD patients from controls, with area under the curves exceeding 0.9. Compared with HD patients, PD patients exhibited reduced species richness, an increased abundance of opportunistic pathogens (particularly Proteobacteria), and increased virulence. Functional analysis revealed suppressed energy metabolism and activated proinflammatory pathways in PD patients. Cooccurrence network analysis demonstrated decreased microbial community resilience in PD patients, with increased Proteobacteria interactions. Conversely, the HD group showed partial recovery of microbial balance and beneficial metabolic functions, including increased short-chain fatty acid metabolism and reduced lipopolysaccharide biosynthesis.

CONCLUSION: The findings of this study highlight the potential of the microbial profile as a robust biomarker for CKD classification and underscore the differential impacts of different dialysis modalities.},
}

@article {pmid42395905,
year = {2026},
author = {Li, H and Li, N and Wang, C and Yang, J and Dong, Z and Cai, Z and Li, J and Chen, Y and Zheng, J and Zhu, J},
title = {Dysbiosis and unsustainable delayed gut microbiota development as non-invasive biomarkers for predicting autism spectrum disorder in Chinese children.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753665},
pmid = {42395905},
issn = {1664-302X},
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social impairment, restricted interest, repetitive behavior, and stereotypical behavioral patterns. Diagnosing ASD presents considerable challenges; a previous large-sample study in children linked ASD and intestinal flora imbalances.

METHODS: To explore the composition and functional changes of the gut microbiota in children with ASD, shotgun metagenomic sequencing was used to evaluate the gut microbiota of 78 Chinese children (34 with ASD and 44 with typical development [TD] children).

RESULTS: We observed differences in the gut microbiota composition and richness between children with ASD and TD in this cohort. The α-diversity of the gut microbiota in the ASD group fluctuated more with age than that in the TD group, based on cross-sectional data. Age-related dynamic changes in the gut bacteria of TD children were not clearly observed in children with ASD. Gut microbiota of children with ASD showed a higher number of antibiotic resistance genes compared to TD. Additionally, the functional gene pathways related to carbohydrate-active enzymes and amino acid metabolism and synthesis appeared reduced in the ASD group.

DISCUSSION: This exploratory study describes key compositional and functional characteristics of the gut microbiota in Chinese children with ASD. Our preliminary findings identify differential bacterial taxa that may be considered as potential candidates for further investigation as fecal markers, and suggest differences in age-related gut microbiota patterns between ASD and TD children. However, due to the modest sample size, cross-sectional design, and lack of external validation, these results should be regarded as a preliminary exploration and require confirmation in larger, independent cohorts.},
}

@article {pmid42396176,
year = {2026},
author = {Deb, D and Liguori, F and Shuster, BM and Huang, R and Shoreibah, S and Wang, S and Rojas Ocampo, NE and Murray, KP and Danino, T},
title = {Toward development of soil-derived Bacillus isolates as lung cancer cytotoxic agents.},
journal = {Biodesign research},
volume = {8},
number = {2},
pages = {100074},
pmid = {42396176},
issn = {2693-1257},
abstract = {The wide-ranging impact of the human microbiome on health and disease has sparked growing interest in employing bacteria as live therapeutics. Natural properties of bacteria have been enhanced using synthetic biology to treat diverse diseases, from infections to inflammation and cancer. However, a major obstacle in this area is identifying specific bacterial hosts and molecular payloads that are both safe and effective for specific diseases or cancers. In this study, we explored environmental microbial diversity as a promising source of new therapeutic agents that could be engineered for bacterial drug delivery systems. We collected and characterized soil bacteria from 25 urban public parks, then evaluated their secreted metabolites for anti-cancer activity using both monolayer and three-dimensional spheroid models of lung cancer. Metagenomic analysis, toxicity profiling, and co-culture assays revealed that several Bacillus species isolated from Manhattan park soils produced compounds with strong, dose-dependent cytotoxic effects on lung cancer cells. Furthermore, we demonstrated that Bacillus subtilis-a well-characterized, gram-positive model organism-was capable of colonizing lung tumor spheroids, suggesting its potential as a safe and effective chassis for bacterial cancer therapy. Complementing these experiments, we developed a mechanistic ordinary differential equation (ODE) model of the bacteria-spheroid co-culture that is consistent with our bacterial and spheroid growth data. Overall, our findings highlight a discovery platform for the screening of environmental microbes as chassis or payload sources for microbial cancer therapies.},
}

@article {pmid42396177,
year = {2026},
author = {Ross, DAN and Lauzon, J and Makarenkov, V and Kembel, SW},
title = {Metagenome-assembled genomes from the temperate forest phyllosphere in Eastern Canada.},
journal = {Access microbiology},
volume = {8},
number = {7},
pages = {},
pmid = {42396177},
issn = {2516-8290},
abstract = {The phyllosphere is host to diverse microbial communities surviving in dynamic environmental conditions and which form important relationships with their hosts. Here, we constructed metagenome-assembled genomes (MAGs) from 25 temperate forest phyllosphere samples collected in Eastern Canada. We found 423 dereplicated MAGs with completeness ≥50% and contamination ≤10%, using a combination of co-assembly strategies. The MAGs were predominantly classified into the bacterial phyla Pseudomonadota (n=197), Actinomycetota (n=88) and Acidobacteriota (n=50) and included two archaeal MAGs in the phylum Thermoproteota. These genomes can help to improve reference database entries of phyllosphere-affiliated microbes, increasing our understanding of phyllosphere microbial phylogenomic and community dynamics and the ecological roles of phyllosphere microbiomes.},
}

@article {pmid42396572,
year = {2026},
author = {Campos, PE and Collins, PC and Ruane, A and Carlsson, JE and Carlsson, J},
title = {Instance of a Heteroplasmic Mitogenome in Alvinocaridid Shrimp Mirocaris fortunata (Martin & Christiansen 1995) Found at the Moytirra Deep-Sea High-Temperature Hydrothermal Vent Field.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73956},
pmid = {42396572},
issn = {2045-7758},
abstract = {In this study, we report the complete mitochondrial genome of the deep-sea hydrothermal vent shrimp Mirocaris fortunata (Alvinocarididae) from shotgun sequencing data on an individual tail tissue. The 15,923-bp-long sequence displays 98.72% pairwise identity with its closest relative, Mirocaris indica. A significant proportion of the mitochondrial genome (0.63%) corresponds to heteroplasmic sites that were found on 14 of the 37 genes, including cox1, though all such sites induce synonymous mutations. This level of heteroplasmy may serve as the first step for recombination of the mitogenome by paternal leakage and/or a less effective purifying selection in somatic tissues. We also take advantage of the shotgun deep sequencing strategy to assess the metagenomic composition of the sample and are able to detect other deep-sea hydrothermal vent species present at the vent system.},
}

@article {pmid42397430,
year = {2026},
author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H},
title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42397430},
issn = {1436-6215},
mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.

METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.

RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.

CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.},
}

Animals
Proto-Oncogene Protein c-ets-1/metabolism/genetics
*T-Lymphocytes, Regulatory/metabolism
Mice
*Crohn Disease/diet therapy/metabolism
*Colitis/diet therapy
Forkhead Transcription Factors/metabolism/genetics
*Interleukin-10/genetics/metabolism/deficiency
Disease Models, Animal
Cell Differentiation/drug effects
Core Binding Factor Alpha 2 Subunit/metabolism/genetics
Mice, Knockout
Mice, Inbred C57BL
Gastrointestinal Microbiome
Male

@article {pmid42397535,
year = {2026},
author = {Sharma, R and Gupta, V and Pal, V and Sen, J and Meghvansi, MK and Goel, AK},
title = {Influence of inoculum-to-substrate ratio on process stability and microbial community structure in anaerobic digestion of human faecal matter.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42397535},
issn = {1614-7499},
abstract = {Anaerobic digestion is a pivotal technology for modern sanitation. This study investigates the impact of inoculum-substrate ratio (ISR) on anaerobic digestion of human faecal matter (HFM). To determine the anaerobic digestion efficiency of HFM, the experiments were conducted using an automatic biomethane potential test system with ISRs ranging from 0.33 to 3. Higher ISRs (1, 2, and 3) resulted in improved volatile solids reduction, increased hydrolysis rates, and higher cumulative methane production compared to lower ISRs. Kinetic modelling revealed that an ISR of 3 exhibited the highest hydrolysis rate constant and shortest lag phase. Analysis of volatile fatty acids showed that higher ISRs mitigated acid accumulation and maintained pH stability. Microbial community analysis demonstrated shifts in bacterial and archaeal populations across different ISRs, with higher ratios fostering greater diversity and abundance of hydrolytic and methanogenic microorganisms. The findings offer essential insights for enhancing the anaerobic digestion of HFM, promoting sustainable waste management and renewable energy production.},
}

@article {pmid42397700,
year = {2026},
author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D},
title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001778},
pmid = {42397700},
issn = {2057-5858},
mesh = {Humans ; *Enterococcus faecium/genetics/isolation & purification/classification ; *Vancomycin-Resistant Enterococci/genetics/isolation & purification/classification ; *Metagenomics/methods ; *Gram-Positive Bacterial Infections/microbiology/transmission ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Metagenome ; },
abstract = {Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity and can miss transmission involving low-abundance and co-colonizing strains. Here, we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures obtained between 2020 and 2025 at a single hospital. GI tract populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters including 6 clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.},
}

Humans
*Enterococcus faecium/genetics/isolation & purification/classification
*Vancomycin-Resistant Enterococci/genetics/isolation & purification/classification
*Metagenomics/methods
*Gram-Positive Bacterial Infections/microbiology/transmission
Gastrointestinal Tract/microbiology
Genetic Variation
Metagenome

@article {pmid42397950,
year = {2026},
author = {Karthik, Y and Nanjareddy, K and Arthikala, MK},
title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2693436},
doi = {10.1080/15592324.2026.2693436},
pmid = {42397950},
issn = {1559-2324},
mesh = {*Glycine max/microbiology/growth & development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF & PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.},
}

*Glycine max/microbiology/growth & development/metabolism
*Rhizosphere
*Microbiota/physiology
Soil Microbiology
Plant Roots/microbiology

@article {pmid42397959,
year = {2026},
author = {Umezawa, K and Tsuji, JM and Tani, Y and Nohara, S and Amann, RI and Fukui, M},
title = {Isolation of Allocrenothrix methanica reveals distinct ecophysiologies of filamentous methanotrophs and adaptations to O2 limitation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag178},
pmid = {42397959},
issn = {1751-7370},
abstract = {Ferdinand Cohn observed abundant filamentous bacteria in drinking water wells in 1870 that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular methanotrophs, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotrophic strains of the "lacustrine Crenothrix" clade from an iron-rich wetland and reveal their unique cell biology and ecology. We demonstrate that the strains are microaerobic and grow as filaments of cells, which are connected by unidirectionally oriented structures. The strains have broad genomic repertoires for addressing O2 limitation that are uniquely associated with lacustrine Crenothrix compared to related clades based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we also detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to O2 limitation, and we propose that the strains uniquely store or share metabolic intermediates between cells in filaments to thrive under such conditions. Our cultivation-based findings for these strains, which we name Allocrenothrix methanica, provide new insights into the diversity, evolution, and ecology of filamentous methanotrophs, connecting over 150 years of microbiology research and opening vast new opportunities to investigate bacteria contributing to the global methane cycle under O2 limitation.},
}

@article {pmid42398003,
year = {2026},
author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG},
title = {Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.},
journal = {Genome biology and evolution},
volume = {18},
number = {7},
pages = {},
doi = {10.1093/gbe/evag152},
pmid = {42398003},
issn = {1759-6653},
support = {//Costco/Project Apis m/ ; 2005306//NSF IOS Collaborative Research/ ; 2022049//NSF DBI Biology Integration Institutes/ ; //Bill and Melinda Gates Foundation to Phase Genomics/ ; },
mesh = {Animals ; Bees/virology/microbiology ; *Bacteriophages/genetics ; *Host Specificity/genetics ; Genetic Variation ; Evolution, Molecular ; Genome, Viral ; Phylogeny ; Selection, Genetic ; Metagenome ; },
abstract = {Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.},
}

Animals
Bees/virology/microbiology
*Bacteriophages/genetics
*Host Specificity/genetics
Genetic Variation
Evolution, Molecular
Genome, Viral
Phylogeny
Selection, Genetic
Metagenome

@article {pmid42398208,
year = {2026},
author = {Yi, Y and Li, D and Li, Y and Wang, H and Yang, D and Yang, S and Xing, S and Wei, S and Yang, J and Guo, H and Luo, Z},
title = {Abrus cantoniensis α-glucan-like polysaccharide alleviates influenza via gut microbial acetate to activate free fatty acid receptor 2/ mitochondrial antiviral signaling protein/interferon-beta pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158533},
doi = {10.1016/j.phymed.2026.158533},
pmid = {42398208},
issn = {1618-095X},
abstract = {BACKGROUND: The gut microbiota is critical for host defense against influenza. Polysaccharides are known for their microbiota-modulating and immunomodulatory activities; however, the anti-influenza efficacy of homogeneous Abrus cantoniensis polysaccharides (ACP) remains unexplored.

PURPOSE: The present study seeks to clarify the protective role of ACP in influenza and explore its underlying molecular mechanisms.

METHODS: Initially, crude polysaccharides were extracted via ethanol precipitation and subsequently purified by gel chromatography. Systematic structural characterization of ACP was then performed using carbohydrate chemistry techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), ultraviolet (UV) spectroscopy, and nuclear magnetic resonance (NMR). The therapeutic efficacy of ACP was assessed by monitoring various indicators such as body weight, survival rate, viral load, and pulmonary pathological changes in mouse models. Furthermore, to elucidate the biological mechanism underlying ACP's anti-influenza activity via regulation of pulmonary interferon-beta (IFN-β) immune networks by intestinal acetate-producing microbiota, multi-omics analyses integrating metagenomics, metabolomics, gene knockout, immunofluorescence, and Western blot were conducted. Finally, the potential anti-influenza effects of ACP via the gut-lung axis were evaluated based on in vivo and in vitro detection of protein expression of IFN-β, free fatty acid receptor 2 (FFAR2), and mitochondrial antiviral signaling protein (MAVS), as well as antiviral interferon-stimulated genes (ISGs).

RESULTS: In this study, we purified a novel polysaccharide, ACP-A1, with a backbone of→4)-α-D-Glcp-(1→,→4)-β-D-Galp-(1→, and →4,6)-α-D-Glcp-(1→ linkages and α-D-Glcp-(1→ branches at O-6. In H1N1-infected mice, oral ACP-A1 alleviated weight loss, increased survival, and reduced lung inflammation and viral load. Metagenomic and targeted metabolomic analyses showed that ACP-A1 enriched Limosilactobacillus reuteri and elevated acetate levels. Fecal microbiota transplantation, FFAR2 inhibition, and MAVS knockout experiments demonstrated that ACP-A1 enhances the FFAR2/MAVS/IFN-β antiviral pathway via microbial-derived acetate.

CONCLUSION: Collectively, our findings elucidate that ACP mitigates influenza virus-induced lung dysfunction by promoting the proliferation of acetate-producing gut microbiota, particularly Limosilactobacillus reuteri, and activating the FFAR2/MAVS/IFN-β antiviral axis in pulmonary immune cells. These findings establish ACP-A1 as a natural polysaccharide regulating IFN-β homeostasis, highlighting its potential for influenza prevention.},
}

@article {pmid42398246,
year = {2026},
author = {Zhang, Y and Tang, Z and Shangguan, H and Zhu, R and Xie, A and Huang, Q and Su, J and O'Connor, P and Jiang, Y and Sun, X},
title = {Invasive giant African snails as potential reservoirs of antimicrobial resistance and bacterial pathogens in urban park.},
journal = {Journal of environmental management},
volume = {413},
number = {},
pages = {130396},
doi = {10.1016/j.jenvman.2026.130396},
pmid = {42398246},
issn = {1095-8630},
abstract = {Urban parks serve millions of visitors annually, yet antimicrobial resistance (AMR) surveillance programs rarely consider invasive species as environmental reservoirs. Here, we investigated antibiotic resistance genes (ARGs) and potential zoonotic pathogens in invasive giant African snails (Lissachatina fulica) across 23 urban parks in Xiamen, China, with comparative analysis of dog feces and earthworm casts collected from the same parks. Metagenomic profiling revealed that snails harbored extensive ARG diversity (1222 subtypes) comparable to dogs (1,393) and substantially exceeding earthworms (492), with 936 ARG subtypes shared between invasive snails and dogs. Invasive snails also carried substantial relative abundances of potential zoonotic pathogens (mean 15.7% relative abundance), including clinically relevant taxa such as Escherichia, Pseudomonas, and Enterococcus. Phenotypic testing of representative isolates confirmed the presence of antibiotic-resistant bacteria in snail and dog fecal samples. The convergence of broad ARG diversity, substantial potential zoonotic pathogen burdens, and coprophagous behavior suggests that invasive snails may represent previously unmonitored environmental hosts associated with AMR in urban parks. Field observations of snails consuming dog feces, together with the greater resistome similarity between snails and dogs than between snails and earthworms, are consistent with exposure to animal feces as a potential source of ARGs. This study underscores the need to integrate invasive species into One Health AMR surveillance and urban environmental management strategies.},
}

@article {pmid42398311,
year = {2026},
author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V},
title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128605},
doi = {10.1016/j.micres.2026.128605},
pmid = {42398311},
issn = {1618-0623},
abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.},
}

@article {pmid42398436,
year = {2026},
author = {Funk, T and Zaheer, R and Wobeser, B and Conrad, C and McLeod, L and Gow, S and Otto, SJG and Waldner, CL and McAllister, T},
title = {Evaluating detection of Histophilus somni immunoglobulin-binding protein A DR2 Fic: A species-specific gene target for recombinase polymerase amplification relative to long-read sequencing of respiratory samples from feedlot calves.},
journal = {Research in veterinary science},
volume = {210},
number = {},
pages = {106315},
doi = {10.1016/j.rvsc.2026.106315},
pmid = {42398436},
issn = {1532-2661},
abstract = {Histophilosis is an important cause of morbidity and mortality as well as antimicrobial use in feedlot cattle across North America. Detection of Histophilus somni by culture is challenging, and there is no standardized tool for distinguishing isolates that carry virulence factors most likely to contribute to disease. The DR2 repeat of H. somni-associated virulence factor 'immunoglobulin-binding protein A' (ibpA DR2) harbors a Fic domain that mediates host cell cytotoxicity and is essential for histophilosis. For rapid detection of ibpA DR2 in extracted DNA, we developed a real-time recombinase polymerase amplification (RPA) assay with a runtime of 24 min at 39 °C. DNA from H. somni-RPA-positive respiratory swabs (n = 73) was screened for ibpA DR2 using the novel RPA assay and long-read metagenomic sequencing, as well as nanopore whole-genome sequencing (WGS) of H. somni isolated from the same samples. IbpA DR2 was identified in 71% and 70% of tested samples using RPA and WGS, respectively, and in ≤41% of samples using metagenomic sequencing. The likelihood of detection by RPA did not differ (OR 1.1, 95% CI (0.42, 2.9), P > 0.99) from WGS; however, agreement between these assays was only fair (κ = 0.31). Conversely, RPA (OR 3.4, 95% CI (1.6, 8.2)) and WGS (OR 8.0, 95% CI (2.4, 42)) were more likely (P < 0.001) to detect ibpA DR2 than metagenomic sequencing, likely reflecting limited coverage of H. somni by metagenomics. This study demonstrated that RPA and long-read WGS detected ibpA DR2 with similar frequencies in extracted DNA and H. somni isolates, respectively. Further testing of non-target isolates confirmed the analytical specificity of ibpA DR2 to H. somni. Further investigation of the diagnostic validity for RPA-based ibpA DR2 detection is required in a larger cohort of field samples, as a rapid screening tool for H. somni most likely to contribute to disease.},
}

@article {pmid42398457,
year = {2026},
author = {Fonseca, A and Kenney, S and Bierly, S and Boney, J and Ganda, E},
title = {Assessing the impact of dietary interventions on the resistomes of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107343},
doi = {10.1016/j.psj.2026.107343},
pmid = {42398457},
issn = {1525-3171},
abstract = {Antimicrobial resistance (AMR) is a major One Health concern, and while natural feed additives such as probiotics and phytotherapeutics are increasingly used as alternatives to antimicrobial growth promoters (AGPs) in poultry production, their potential effects on the selection of antibiotic resistance genes remain poorly understood. Therefore, our objective was to characterize the effects of a probiotic and an essential oils blend on the broiler resistome. Cobb 500 1-day-old chicks (N=320) were randomly allocated in 32 cages, with eight replicates of ten broilers per cage per treatment and were raised until day 21. Treatments consisted of four diets: a basal diet (negative control), a basal diet with Bacitracin Methylene Disalicylate (BMD) at 50 g/ton, a basal diet with an essential oil blend at 100 g/ton, and a basal diet with a probiotic (Bacillus subtilis) at 226.8 g/ton. Excreta samples were collected at three-time points (1, 10, and 21 days) to characterize broilers' resistome. The DNA extracted from these samples was sequenced using shotgun metagenomics on the NovaSeq platform and statistical analyses were done using Kruskal-Wallis and PERMANOVA to assess gene diversity. Across all samples, 823 unique ARGs were identified. These genes spanned a broad spectrum of classes, including multi-compound, metals, drugs, and biocides resistance. No significant differences in alpha diversity of these genes (P = 0.51) were observed between treatment groups; however, AMR gene diversity varied by age (P < 0.001). A statistically significant difference was observed in beta diversity across ages (P = 0.001), but not between treatments (P = 0.95). While age impacted AMR gene diversity, under our experimental conditions, antibiotics or other in-feed additives did not significantly alter broiler resistomes. This study advances poultry AMR surveillance by demonstrating that resistome diversity and composition in broiler chickens are predominantly shaped by age-dependent microbial succession, while neither in-feed antibiotics nor non-antibiotic feed additives induced persistent or treatment-specific alterations in ARG profiles under the conditions tested.},
}

@article {pmid42398478,
year = {2026},
author = {Gao, Q and Hou, J and Ding, W and Qi, C and Xu, D and Zhou, C and You, G},
title = {Carbon-to-nitrogen stoichiometry shapes divergent intracellular and extracellular antibiotic resistance gene fates through a dissolved organic matter-extracellular polymeric substance-mobile genetic element cascade in cyanobacteria-bacteria co-cultures.},
journal = {Water research},
volume = {304},
number = {},
pages = {126390},
doi = {10.1016/j.watres.2026.126390},
pmid = {42398478},
issn = {1879-2448},
abstract = {The carbon-to-nitrogen (C:N) ratio constrains microbial metabolism, yet whether nutrient stoichiometry controls the differential fates of intracellular (iARGs) versus extracellular antibiotic resistance genes (eARGs) remains unknown. This study aimed to test whether C:N ratios approaching the bacterial threshold elemental ratio (TER) would maximize iARG enrichment through a dissolved organic matter (DOM)-extracellular polymeric substance (EPS)-mobile genetic element (MGE) cascade, while eARG dynamics would be governed by physicochemical processes. Cyanobacteria-bacteria co-cultures at four C:N ratios (5:1, 10:1, 20:1, 40:1) were analyzed using shotgun metagenomics, FTICR-MS, 3D-EEM, untargeted metabolomics, and EPS fractionation. C:N = 10:1 produced the highest iARG abundance (65.1 ± 17.4 TPM, mean ± SD) and a 17-fold iARG/eARG ratio, while eARG showed no significant treatment effect (Kruskal-Wallis p = 0.082, treating triplicate subsamples as observations). FTICR-MS revealed the lowest intensity-weighted O/C (0.334), most negative NOSC (-0.67), and highest molecular diversity (8029 formulas) at C:N = 10:1, indicating a uniquely reduced, aliphatic-enriched DOM pool. (Note: FTICR-MS samples were pooled from triplicate subsamples per treatment, yielding one composite per C:N level; these results are therefore descriptive and unreplicated.) EPS polysaccharide/protein ratios peaked at 2.8, correlating with iARG across treatments (ρ=0.91, p < 0.001) but inversely with eARG (ρ=-0.59, p = 0.044). Guanosine (ppGpp precursor) peaked at C:N = 10:1 (ρ=0.75 with iARG) while UDP-glucose was depleted, confirming active EPS biosynthesis. Piecewise structural equation modeling identified a pathway from C:N through DOM, EPS, and MGE to iARG (R[2]=0.78, Fisher's C p = 0.31), whereas eARG depended on eDNA physicochemical trapping (R[2]=0.41). These findings provide evidence that nutrient stoichiometry acts as a selective control on ARG partitioning, suggesting that C:N monitoring could be incorporated into eutrophic water ARG risk assessment.},
}

@article {pmid42398553,
year = {2026},
author = {Xu, J and Zhang, X and Sun, W and Zhang, X and Wu, P and Wang, A},
title = {Hydroxylamine steers nitrogen metabolism toward dissimilatory nitrate reduction to ammonium by suppressing competitive denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135307},
doi = {10.1016/j.biortech.2026.135307},
pmid = {42398553},
issn = {1873-2976},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is important for nitrogen conservation and resource recovery in wastewater treatment, but its efficiency is often limited by competition for electrons and substrates from denitrifiers. Although hydroxylamine (NH2OH) has been shown to modulate various nitrogen transformation processes, its long-term effects on DNRA systems and the underlying microbial ecological responses remain unclear. In this study, the nitrogen transformation performance, electron transfer characteristics, and microbial community succession in DNRA systems were comprehensively investigated under prolonged exposure to 0-5 mg/L NH2OH. The results demonstrated that, with increasing NH2OH concentrations, the system consistently achieved near-complete nitrate removal without nitrite accumulation, and the effluent NH4[+]-N reached up to 51.5 mg/L, indicating a substantial enhancement of DNRA ammonium production. Functional activity analyses and apparent electron-equivalent balance suggested an increased contribution of DNRA to nitrate-reduction-associated electron consumption. Metagenomic analyses further showed that NH2OH could decrease the relative abundances of denitrification-related genes, including nirS, norB, and nosZ, while increasing those of narG and the nrf gene cluster. Building upon the existing DNRA functionality, NH2OH selectively enriched a tolerant DNRA population, exemplified by Ignavibacteriota, and facilitated cross-feeding interactions and electron transfer network remodeling involving fermentative bacteria. Collectively, these findings suggest that NH2OH can weaken denitrification competition and increase the apparent contribution of DNRA to nitrate-reduction-associated electron consumption, thereby enhancing ammonium production. Moreover, these findings may provide a theoretical basis for the future development of DNRA-Anammox coupled processes for high-level nitrogen removal.},
}

@article {pmid42398606,
year = {2026},
author = {Liu, J and Liu, Y and Zheng, Y and Wang, H and Wang, J and Zhang, Y and Wang, K},
title = {Intestinal metabolic characteristics of Smilax china L. pectic polysaccharide and prediction of its gut microbiota-mediated mechanism.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153348},
doi = {10.1016/j.ijbiomac.2026.153348},
pmid = {42398606},
issn = {1879-0003},
abstract = {This study aimed to investigate the intestinal metabolic characteristics and mechanisms of the pectic polysaccharide isolated from the medicinal plant Smilax china L. (SCLP). Firstly, in vitro simulated digestion confirmed that SCLP remained stable in simulated digestive fluids. Subsequently, in vivo real-time tracking of intestinal metabolism based on fluorescent labeling revealed that SCLP maintained its prototype in the small intestine and began to be degraded into fragments (Mw < 4000 Da) upon reaching the cecum and colon, where it was retained for prolonged periods. Pseudo-sterile mouse experiments indicated the mediating role of gut microbiota in SCLP metabolism. Furthermore, metagenomic sequencing suggested that SCLP increased the proportion of polysaccharide utilization loci (PULs) from Phocaeicola vulgatus and Bacteroides uniformis, elevated the gene numbers of carbohydrate-active enzymes (CAZymes) including GHs, GTs and CBMs, and activated pathways of carbohydrate metabolism. Finally, in vitro bacterial culture study verified the degradation and utilization of SCLP by Phocaeicola vulgatus and Bacteroides uniformis. In summary, this work elucidates the intestinal metabolic profile of SCLP, providing valuable insights for its further development and utilization.},
}

@article {pmid42398615,
year = {2026},
author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J},
title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153356},
doi = {10.1016/j.ijbiomac.2026.153356},
pmid = {42398615},
issn = {1879-0003},
abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.},
}

@article {pmid42399247,
year = {2026},
author = {Liao, H and Cui, HX and Chen, LX and Duan, CS and Li, J and Zhao, S and Zhu, YG and Su, JQ},
title = {Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75234-y},
pmid = {42399247},
issn = {2041-1723},
abstract = {Glacier forelands undergo a transition from oligotrophic to eutrophic conditions during primary succession. Reduced sulfur compounds may serve as an energy source for early microbial colonizers, yet the sulfur oxidation potential and key taxa remain largely unknown. Here, we perform a multi‑omics survey across a 130‑year chronosequence on the Tibetan Plateau. Glacial retreat profoundly reshapes both viral communities (61,394 viral operational taxonomic units, vOTUs) and microbial communities (404 metagenome‑assembled genomes, MAGs). Notably, Oxidative Dissimilatory sulfite reductase (Dsr) operon‑encoding Sulfur‑Oxidizing Bacteria (ODSOB) were specifically enriched within the first 1-5 years after retreat. Their associated viruses predominantly follow a "piggyback‑the‑winner" strategy, influencing host cold shock protein evolution and potentially modulating sulfur oxidation via iron‑sulfur (Fe‑S) cluster assembly. Metatranscriptomics reveals elevated expression of the oxidative Dsr operon and Form‑I ribulose‑1,5‑bisphosphate carboxylase/oxygenase (RubisCO) in early stages, coinciding with higher sulfate, sulfite, sulfide, and dissolved inorganic carbon (DIC)‑to‑dissolved carbon ratios compared to later stages. These findings indicate that ODSOB support DIC fixation and sulfide detoxification during early ecosystem development. Collectively, this study uncovers the eco‑evolutionary dynamics between viruses and microbes in developing ecosystems and provides genomic and functional evidence for ODSOB as key drivers of soil formation and primary succession in glacial forelands.},
}

@article {pmid42399252,
year = {2026},
author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J},
title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01079-4},
pmid = {42399252},
issn = {2055-5008},
support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.},
}

@article {pmid42399304,
year = {2026},
author = {Sun, Y and Cheng, X and Zhou, J and Li, R and Wei, Y and Li, H and Qin, Y and Bao, J and Ren, X and Qu, S and Liu, W},
title = {Bio-stimulants improve tomato growth by regulating the rhizosphere microbiome involved in phosphorus and nitrogen cycling.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59808-w},
pmid = {42399304},
issn = {2045-2322},
support = {2024CXPT056//the Key R&D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; },
abstract = {Bio-stimulants are promising environment friendly alternatives to support sustainable agricultural development, capable of boosting crop growth and yield while cutting down excessive dependence on chemical synthetic fertilizers. Nevertheless, the explicit regulatory mechanisms by which bio-stimulants exert the role of growth-promoting functions still remain largely unclear and require further systematic clarification. In this study, we explored the influences of bio-stimulants (rich in humic acid) on tomato growth performance and rhizosphere microbial community assembly via greenhouse trials, and comparatively analyzed the functional differences between foliar spraying and root irrigation application modes. The results demonstrated that bio-stimulants treatment markedly improved tomato aboveground biomass, plant nitrogen and phosphorus accumulation by 17.1%, 27.4% and 22.7%, respectively. Meanwhile, bio-stimulants application effectively raised soil available nitrogen and soil organic matter levels, and further facilitated phosphorus assimilation in tomato plants. Metagenomic sequencing confirmed that bio-stimulants substantially reshaped the overall structure and composition of tomato rhizosphere microbiome. Specifically, they dramatically enriched the relative abundance of core microbial taxa responsible for soil nitrogen fixation and phosphorus solubilization. Collectively, these results clearly elaborate the underlying action mechanism: bio-stimulants optimize rhizosphere micro-ecological environment, enrich functional nutrient-solubilizing microorganisms, improve soil nutrient availability, and ultimately promote nutrient absorption and vegetative growth of tomato plants. This study confirms that bio-stimulants can serve as efficient and reliable regulators to advance green and sustainable crop production.},
}

@article {pmid42342250,
year = {2026},
author = {Baghbanzadeh, M and Mann, BT and Crandall, KA and Rahnavard, A},
title = {seqLens: Optimizing Language Models for Genomic Predictions.},
journal = {Molecular biology and evolution},
volume = {43},
number = {7},
pages = {},
pmid = {42342250},
issn = {1537-1719},
support = {2109688//National Science Foundation/ ; },
mesh = {*Genomics/methods ; *Models, Genetic ; Large Language Models ; Evolution, Molecular ; Genome ; },
abstract = {Understanding evolutionary variation in genomic sequences through the lens of language modeling has the potential to revolutionize biological research. Yet to maximize the utility of language modeling in genomics, we must overcome computational challenges in tokenization and model architecture adapted to diverse genomic features across evolutionary timescales. In this study, we investigated key elements in genomic language modeling (gLM), including tokenization, pretraining datasets, fine-tuning approaches, pooling methods, and domain adaptation, and applied the language models to diverse genomic data. We gathered two evolutionarily distinct pretraining datasets: one consisting of 19,551 reference genomes, including over 18,000 prokaryotic genomes (115 B nucleotides) and the remainder eukaryotic genomes, and another more balanced dataset with 1,354 genomes, including 1,166 prokaryotic and 188 eukaryotic reference genomes (180 B nucleotides). We trained five byte-pair encoding tokenizers and pretrained 52 gLMs, systematically comparing different architectures, hyperparameters, and classification heads. We introduce seqLens, a family of models based on disentangled attention with relative positional encoding, which outperforms relatively similar-sized models in 13 of 19 benchmarking phenotypic predictions. We further explore continual pretraining, domain adaptation, and parameter-efficient fine-tuning methods to assess trade-offs between computational efficiency and accuracy. Our findings demonstrate that relevant pretraining data significantly boost performance, alternative pooling techniques can enhance classification, tokenizers with larger vocabulary sizes negatively impact generalization, and gLMs are capable of understanding evolutionary relationships. These insights provide a foundation for optimizing genomic language models for identifying diverse evolutionary genomic features and improving genome annotations.},
}

*Genomics/methods
*Models, Genetic
Large Language Models
Evolution, Molecular
Genome

@article {pmid42386120,
year = {2026},
author = {Nancy, N and Sharma, M and Singh, K and Singh, B and Sharma, PK},
title = {Mutation T71R enhanced the structural stability and functional activity of wild type superoxide dismutase cloned from soil metagenome.},
journal = {Gene},
volume = {},
number = {},
pages = {150294},
doi = {10.1016/j.gene.2026.150294},
pmid = {42386120},
issn = {1879-0038},
abstract = {In this study, we report engineering of three mutations m1, m2, and m3 respectively in the wild type SOD, cloned form soil metagenome. Expressed proteins from wild type and mutants were purified to homogeneity using Ni-NTA affinity chromatography. Biochemical characterization of mutants demonstrated enhanced functional activity at varying pH and temperature compared to wild type and other mutant proteins. Additionally, it also showed increased specific activity of 185 ± 0.75 U/mg compared to 150 ± 0.042 U/mg and 168 ± 0.25 U/mg respectively for mutant m1, m2 and m3. Altogether, it was observed that the relative enzyme activity of mutant m1, m2 and m3 enhanced ∼ 30 %, 10 % and 17 % respectively compared to wild type. Biophysical investigation carried out employing circular dichroism and intrinsic tryptophan fluorescence also demonstrated conformational stability in the secondary and tertiary structure of mutant m1 compared to the wild type at varying pH and temperature. Interestingly, in silico molecular simulation dynamics studies carried out at 300 ns demonstrated structural stability, reduced flexibility and attainment of stable conformation in this mutant form. Molecular simulation analysis revealed that mutation T71R in m1 tends to introduce β-sheet like secondary structure at protein surface, which might enhance residue-residue interactions within this protein, leading to allover enhancement in the stability and activity of this mutant.},
}

@article {pmid42386249,
year = {2026},
author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J},
title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.},
journal = {The American journal of clinical nutrition},
volume = {124},
number = {1},
pages = {101323},
doi = {10.1016/j.ajcnut.2026.101323},
pmid = {42386249},
issn = {1938-3207},
mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; },
abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).

OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.

METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.

RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.

CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.},
}

Humans
*Endotoxemia/complications/blood
Male
Female
*Postprandial Period
*Coronary Disease/complications/blood
Middle Aged
Lipopolysaccharides/blood
Diet, Fat-Restricted
Recurrence
Diet, Mediterranean
Aged
Gastrointestinal Microbiome
*Cardiovascular Diseases/etiology

@article {pmid42387129,
year = {2026},
author = {Kumar, A and Kumar, A and Tyagi, A and Singh, R and Charaya, MU},
title = {A review of bloodstream infections-pathogens, pathogenesis, diagnostic strategies, treatment methods-challenges and future aspects.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42387129},
issn = {1435-4373},
abstract = {PURPOSE: Bloodstream infections (BSIs) remain a major cause of morbidity and mortality worldwide and continue to represent a substantial challenge to modern healthcare systems. These infections arise when pathogenic microorganisms gain access to the bloodstream, triggering systemic inflammatory responses that may progress to sepsis, septic shock, multi-organ dysfunction, and death. This review provides a comprehensive overview of the historical development, epidemiology, pathogenesis, diagnosis, treatment, and future perspectives of BSIs. The major bacterial, fungal, viral, and parasitic pathogens associated with BSIs are discussed, with particular emphasis on their virulence attributes, mechanisms of immune evasion, antimicrobial resistance, and clinical significance.

METHODS: A comprehensive literature review was conducted using peer-reviewed publications, clinical guidelines, surveillance reports, and systematic reviews published between 2010 and mid-2026. Evidence related to bacterial, fungal, viral, and parasitic bloodstream pathogens, host-pathogen interactions, diagnostic modalities, antimicrobial resistance mechanisms, and emerging therapeutic and diagnostic innovations was critically evaluated and integrated.

RESULTS: BSIs continue to impose a substantial healthcare burden, driven by increasing antimicrobial resistance, delayed diagnosis, and diverse pathogen-specific virulence mechanisms. Bacterial pathogens remain the predominant cause of BSIs, whereas Candida species represent the leading fungal agents. Advances in molecular diagnostics, metagenomic sequencing, biomarker-guided testing, and artificial intelligence-assisted analyses have substantially improved rapid pathogen detection and therapeutic decision-making. Precision medicine, genomic surveillance, and novel antimicrobial agents show considerable promise for enhancing clinical management and addressing multidrug-resistant infections.

CONCLUSION: Bloodstream infections remain a major global health challenge due to their complex pathogenesis, increasing antimicrobial resistance, and high associated mortality. Improving patient outcomes requires early and accurate pathogen identification, prompt initiation of targeted antimicrobial therapy, effective antimicrobial stewardship, and continuous epidemiological surveillance. The integration of next-generation diagnostics, artificial intelligence-assisted pathogen detection, genomic surveillance, and precision medicine has the potential to transform BSI diagnosis and management by enabling rapid, individualized therapeutic interventions.},
}

@article {pmid42387141,
year = {2026},
author = {Zou, P and Wang, X and Zhao, H and Yang, K and Ye, J and Sun, Y and Meng, X and Yi, Z and Xiong, X and Li, W},
title = {Mycobacterium Abscessus Infection after Breast Augmentation: Case Reports and Literature Review.},
journal = {Aesthetic plastic surgery},
volume = {},
number = {},
pages = {},
pmid = {42387141},
issn = {1432-5241},
abstract = {BACKGROUND: Mycobacterium abscessus (M. abscessus) infection following breast augmentation is a rare complication, yet evidence and standardized treatments remain limited. Challenges include diagnostic difficulties and prolonged treatment periods.

METHODS: We report two cases of M. abscessus infection following breast augmentation and conducted a structured narrative review of PubMed literature to explore prevention, diagnosis, and treatment strategies associated with this condition.

RESULTS: The two patients underwent different breast augmentation procedures: one received autologous fat transfer, and the other had a prosthetic implant inserted. Following confirmation of M. abscessus infection via metagenomic next-generation sequencing (mNGS), both patients underwent through surgical debridement and drainage with daily amikacin irrigation. Combination antibiotic therapy was administered, including intravenous amikacin and linezolid, plus oral azithromycin. Both patients demonstrated good tolerance to the prescribed antibiotics, achieving effective infection control without recurrence over a 12-month follow-up period. The rigorous debridement and targeted antibiotic therapy significantly enhanced treatment efficacy.

CONCLUSION: This study reports two rare cases of M. abscessus infection occurring after breast aesthetic surgery. Such infections are difficult to diagnose and are often associated with prolonged treatment courses. We successfully identified the causative pathogen through mNGS and implemented a comprehensive treatment strategy that included multiple surgical debridements, local irrigation, and combination antimicrobial therapy with azithromycin, amikacin, and linezolid, which was associated with favorable clinical outcomes. Rather than establishing a definitive management model, this study provides practical, case-based insights into the diagnosis and management of postoperative M. abscessus infections.

LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .},
}

@article {pmid42387381,
year = {2026},
author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B},
title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42387381},
issn = {1471-2180},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.

RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq. Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.

CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.},
}

*RNA, Ribosomal, 16S/genetics
*Computational Biology/methods
*Gene Library
Humans
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Sequence Analysis, DNA/methods
Metagenomics/methods
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid42387416,
year = {2026},
author = {Ishio, D and Eguchi, H and Hotta, F and Miyamoto, T},
title = {Blepharoconjunctivitis mimicking conjunctival tumor associated with Streptococcus intermedius sinusitis: case report and literature review.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13910-6},
pmid = {42387416},
issn = {1471-2334},
abstract = {Streptococcus intermedius, a commensal bacterium in the human oral cavity, can occasionally cause severe infections in deep tissues. The patient was referred because of a conjunctival tumor. She had severe nasal cavity and periocular tissue inflammation that persisted for over a year. Microbiological examination of the nasal and ocular specimens identified S. intermedius as the pathogenic strain. The inflammation and the conjunctival mass subsided after systemic and topical administration of a susceptible antibiotic. Smear microscopy of the eye and nasal discharge was useful for the differential diagnosis. 16S metagenomic analysis using MinION as an adjunctive diagnostic tool has contributed to the species identification of the pathogenic strain.},
}

@article {pmid42387479,
year = {2026},
author = {Vastolo, A and Tolone, M and Gannuscio, R and Staropoli, A and Giosa, D and Bonomo, A and Vinale, F and Cutrignelli, MI and Todaro, M},
title = {Impact of Opuntia spp. by-product silage on sheep metabolic profile, rumen fermentation and microbial communities.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05646-x},
pmid = {42387479},
issn = {1746-6148},
support = {cod. U-Gov PRJ-1776; CUP: J83C22000830005//National Recovery and Resilience Plan (PNNR) of Italy: project Biometric-Call PNNR a cascata-Università della TUSCIA/ ; },
abstract = {BACKGROUND: Prickly pear (Opuntia ficus-indica) by-products represent a promising alternative feed resource for improving the sustainability of sheep production systems in Mediterranean areas. This study evaluated the effects of prickly pear by-product (PPB) silages on rumen fermentation, metabolic profile, and rumen microbiome in lactating ewes. Twelve Valle del Belice ewes were assigned to three dietary treatments (control, CTR; prickly pear peel silage, PPP; and pastazzo silage, PPS) in a Latin square design. Blood biochemical parameters, rumen volatile fatty acids (VFA), and metagenomic profiles were analysed.

RESULTS: PPB inclusion did not induce significant changes in blood biochemical parameters, which remained within physiological ranges. Rumen fermentation parameters were significantly affected, with the PPP diet increasing total VFA concentration and promoting a more glucogenic profile through higher propionate production. The rumen microbiome was dominated by Prevotella, which showed higher relative abundance in the CTR diet. PPB supplementation was associated with shifts in microbial functional profiles, including pathways related to polyphenol degradation, vitamin K2 biosynthesis, and central carbon metabolism, partially consistent with observed changes in rumen fermentation. No significant effects were observed on methanogenesis-related pathways.

CONCLUSIONS: Prickly pear by-product silages, particularly prickly pear peel, modulate rumen fermentation and microbial functional profiles in lactating ewes without adversely affecting systemic metabolic status.},
}

@article {pmid42387526,
year = {2026},
author = {Bing, Y and Yuan, W and Liang, L and Li, J and Chen, Y and Feng, L and Li, X and Li, H and Zhong, J and Wang, L and Tong, Z and Liu, X},
title = {Alterations in the fecal virome and bacteriome-virome interplay in IPAH.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03797-x},
pmid = {42387526},
issn = {1465-993X},
support = {Nos. 82570072, 82170302//Innovative Research Group Project of the National Natural Science Foundation of China/ ; Nos. Ysbz2025004, Ysbz2025005, Ysbz2025006, Ysbz2025007//the Financial Budgeting Project of Beijing Institute of Respiratory Medicine/ ; },
abstract = {BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening cardiovascular disorder characterized by complex multisystem disturbances. Although alterations in the gut microbiota have been reported in IPAH, how the gut virome interacts with bacterial communities and host metabolism remains unclear.

METHODS: We enrolled 28 patients with IPAH and 30 age-matched healthy controls (HCs). Fecal viromes and bacteriomes were profiled by metagenomic sequencing, and serum metabolomic data were integrated to construct virus-bacterium-metabolite interaction networks. Random forest models were used to evaluate the diagnostic potential of virome features.

RESULTS: IPAH patients exhibited markedly reduced gut virome diversity (Shannon, Simpson, and Pielou indices, p < 0.05) and distinct community structures from HCs (p < 0.01). A total of 499 differential viral operational taxonomic units (vOTUs) were identified, accompanied by extensive reorganization of interaction networks. At the phylum level, Hofneiviricota was enriched and Phixviricota depleted, both correlating with clinical indicators. Virus-bacterium associations were markedly increased in IPAH (44,894 vs. 17,920, r > 0.5). Notably, vOTU2967, vOTU1924, and vOTU4522 were elevated and inversely related to Bacteroides, whose depletion was associated with increased lactic acid levels. Mediation analysis confirmed significant indirect virus-bacterium-metabolite effects (p < 0.05). Random forest models based on vOTUs or viral families effectively distinguished IPAH patients from controls, highlighting the exploratory potential of gut virome features for mechanistic insights.

CONCLUSIONS: IPAH is characterized by reduced virome diversity, altered viral taxa, and reorganized virus-bacterium-metabolite networks. These findings suggest that gut viruses may influence disease progression by modulating bacterial metabolism, providing a potential avenue for biomarker discovery and therapeutic intervention.},
}

@article {pmid42387604,
year = {2026},
author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY},
title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.},
journal = {Infectious diseases of poverty},
volume = {15},
number = {1},
pages = {},
pmid = {42387604},
issn = {2049-9957},
support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; },
mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; },
abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.

METHODS: Female BALB/c mice and Sprague Dawley rats (n = 10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.

RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P < 0.05) while Bacteroidetes increased (P < 0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P < 0.05) but decreased in rats (P < 0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P < 0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.

CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.},
}

Animals
Female
*Angiostrongylus cantonensis/physiology
Rats, Sprague-Dawley
*Strongylida Infections/parasitology/microbiology/metabolism
Rats
*Gastrointestinal Microbiome
Mice
Mice, Inbred BALB C
RNA, Ribosomal, 16S/genetics/analysis
Biomarkers
Feces

@article {pmid42388191,
year = {2026},
author = {Zhang, J and Fu, C and Tan, S and Lyu, B and Shu, G and Shi, L and Wu, Y and Guo, P},
title = {How Host Phylogeny, Diet, and Habitat Affect Gut Microbial Diversity in Wild Snakes.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73902},
pmid = {42388191},
issn = {2045-7758},
abstract = {Gut microbiota plays critical roles in host digestion, immune regulation, neurochemical signaling, and metabolic homeostasis. Based on wild snakes (73 individuals from 23 species) from China, we explored the composition, characteristics, and functions of gut microbes across different groups using fecal metagenomic samples; further we explored the relative contributions of host phylogeny, diet, and habitat to the microbial structure. Among 23 wild snake species, the dominant gut microbial phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with Bacteroides, Salmonella, Citrobacter, and Aeromonas comprising the major genera. Mantel test revealed a significant correlation (r = 0.3173, p = 0.0055) between microbial composition at the genus level and host genetic divergence (p-distance), indicating potential phylogenetic influence on gut microbial profiles. While α-diversity and principal coordinate analysis showed no marked differences across different subgroups. Linear discriminant analysis effect size demonstrated notable differences in the gut microbes of the terrestrial snakes with different diets and vertebrate-feeding snakes with different habitats. Functional annotation of microbial genes indicated enrichment in metabolic processes, as well as environmental and genetic information processing. Carbohydrate-active enzymes were predominantly from GT2, GT4, GT51, and GH23 families. Linear discriminant analysis effect size showed different diets and habitats had distinct differential taxa. Additionally, antibiotic resistance gene profiles varied across groups, with acrB, AcrF, MexB, acrD, and mdtF being most prevalent. Future studies should increase the samples and comprehensively consider different ecological factors to explore the impacts on the composition and functions of snake gut microbes on different evolutionary, which will provide a deeper understanding of the interrelationships between snake gut microbes and their hosts.},
}

@article {pmid42388299,
year = {2026},
author = {Maccario, L and Otani, S and Szarvas, J and Mortensen, LH and Elberling, B and Møller, KE and Madsen, CEK and Aarestrup, FM and Priemé, A},
title = {Microbial composition of archaeological middens: tracing human footprints through centuries in Greenland's ancient settlements.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809037},
pmid = {42388299},
issn = {1664-302X},
abstract = {The history of Greenland is marked by different waves of Paleo-Inuit immigration from North America from 2,500 BC to the 12th century and from the 10th to 15th century, Norse settlers immigrated from Northwest Europe and flourished in Southwest Greenland with the introduction of domestic livestock. The different Inuit and Norse cultures created middens by dumping and accumulating domestic waste; a latent source of microbes, including potential pathogens, that might have been preserved due to the general wet and cold conditions in the region. The aim of this study was to evaluate whether ancient Arctic settlements might be possible hot-spots for pathogenic agents that may spread to the surrounding environment because of current climate changes. Using metagenomics, we compared the microbial communities and resistomes of 78 samples from middens from different ages and locations in West and South Greenland (two Paleo-Inuit, four Norse and one early Colonial-time middens) to 143 soil samples from nearby surroundings. We found that the middens harbor a distinctive microbial signature enriched in human-associated bacteria. Those include opportunistic pathogens such as Clostridium perfringens and Paeniclostridium sordellii. In some early colonial midden layers, C. perfringens and Paraclostridium tenue together accounted for up to ~40%-50% of MetaPhlAn-derived relative abundance in individual samples. Antimicrobial resistance genes representing 17 resistance classes were detected across all sites, dominated by β-lactam and tetracycline resistance. Transect analyses across an actively eroding midden showed that midden-derived bacteria were confined to local erosion layers and were rapidly replaced by native marine communities, indicating limited environmental dispersal.},
}

@article {pmid42388302,
year = {2026},
author = {Cao, H and Wang, Q and Ren, W and Wang, A and Tian, W and Zhang, D and Chen, J},
title = {Characterization of the gastric mucosal microbiota in tumoral and peritumoral mucosa in patients with advanced gastric cancer from Northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1763714},
pmid = {42388302},
issn = {1664-302X},
abstract = {INTRODUCTION: The gastric microbiota affects tumor development and treatment response, yet the characteristics and interactions of mucosal bacteria and fungi in advanced gastric cancer (AGC) remain unclear.

METHODS: Here we analyzed 177 mucosal samples (88 peritumoral and 89 tumoral) from 91 AGC patients in Northwest China using shotgun metagenomic sequencing.

RESULTS: MetaPhlAn4 and Kaiju were used to annotate the gastric mucosal microbial composition. MetaPhlAn4 has identified 12 phyla (no phylum-level differences), 98 genera and 278 species. PERMANOVA revealed age and tumor location significantly influenced microbial composition in tumoral mucosa. Wilcoxon signed-rank test revealed that 10 species including Serratia surfactantfaciens, Pseudomonas protegens, Treponema pectinovorum, Streptococcus anginosus, Bacteroides heparinolyticus, Selenomonas sputigena, and Mogibacterium diversum were significantly enriched in tumoral tissue, whereas five species including Actinomyces graevenitzii, Gemella sanguinis, Porphyromonas pasteri, Helicobacter pylori, and Leptotrichia sp. oral taxon-215 were more abundant in peritumoral mucosa. HUMAnN4 showed tumor-enriched bacteria were involved in metabolic pathways including polysaccharide degradation, biosynthesis of fatty acids, nucleotides, and arginine/histidine/purine/pyrimidine, which were primarily linked to S. surfactantfaciens. Peritumor-enriched bacteria were associated with L-tryptophan biosynthesis, L-arginine degradation, and TCA cycle. Kaiju annotation further revealed 2,429 bacteria, 12 archaea, 74 viruses, 82 fungi, and 63 other eukaryota species, among which the majority of significantly different species were enriched in the tumoral mocusa. Mycobiome analysis revealed eight fungal phyla, 82 genera and 82 species. PERMANOVA revealed that age had a significant effect on fungal composition in peritumoral mucosa, and five species including Saccharomyces cerevisiae, Aspergillus ochraceoroseus, Aspergillus fumigatiaffinis, Mitosporidium daphniae, and Puccinia striiformis were significantly positively correlated with age. Alpha diversity using Shannon index was significantly reduced in peritumoral mucosa at both genus and species levels. Wilcoxon signed-rank test revealed that all the significantly different fungi, including eight phyla, 46 genera, and 42 species were significantly enriched in tumoral mucosa. Correlation analysis indicated tumor-enriched bacteria were positively correlated with tumoral fungi but negatively with peritumoral fungi, suggesting possible synergistic bacteria-fungi interactions.

DISCUSSION: This study comprehensively characterizes the gastric mucosal bacteriome and mycobiome in AGC, illuminates potential microbiota-mediated carcinogenic mechanisms, identifies candidate biomarkers, and fills a regional research gap.},
}

@article {pmid42388305,
year = {2026},
author = {Zhang, H and Ma, L and Jia, L and Li, Y and Wang, Y and Wang, W and Wu, W and Wang, H and Li, H and Zhang, Y and Chen, G and Hou, K and Dong, J},
title = {Multi-omics analysis reveals the potential for fermented Cordyceps militaris mushroom substrate in laying hens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807060},
pmid = {42388305},
issn = {1664-302X},
abstract = {This study examines how varying levels of fermented Cordyceps militaris mushroom substrate (CMMS) in laying hen diets affect production performance, digestive health, immunity, cecal microbiota, metabolites, and quorum-sensing functions. Fermentation reduced CMMS dry matter, NDF, and phosphorus content (p < 0.05). Replacing 30% of the diet with fermented CMMS significantly improved laying rate, egg weight, feed intake, and feed efficiency (p < 0.05), while enhancing yolk color, Haugh units, and lipase activity. A 20% substitution increased nutrient digestibility and immunoglobulin levels (p < 0.05). Metagenomic analysis revealed increased abundance of Phocaeicola, Alistipes, and Parabacteroides (p < 0.05) with enhanced energy metabolism and specific gene families. Metabolomic analysis identified 1,529 differentially expressed metabolites, with carboxylic acids being most prevalent (21.20%), and enhanced taurine/hypotaurine metabolism and GPI-anchor biosynthesis. Parabacteroides showed negative correlations with certain metabolites, while Alistipes correlated positively with PemK/MazF family genes (p < 0.001). CMMS fermented feed proportions influence cecal microbiota, their metabolites, and quorum sensing in laying hens, affecting production, digestibility, immunity, metabolism, and health, demonstrating CMMS potential as alternative poultry nutrition.},
}

@article {pmid42388398,
year = {2026},
author = {Yu, L and Chong, Z and Yanchun, L and Yingying, H},
title = {The Diagnosis of Human Neurological Infection Caused by Rabies Virus Using Metagenomic Next-Generation Sequencing: Two Case Reports.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {1910139},
pmid = {42388398},
issn = {2090-6625},
abstract = {The rabies virus (RABV) causes acute progressive and fatal encephalomyelitis. Two case studies of RABV neurological infection identified using metagenomic next-generation sequencing (mNGS) are presented in this paper. A total of 39 RABV sequences were detected using mNGS in the cerebrospinal fluid (CSF) in Case 1. The detected sequences were located in the 0%-35% range of the enriched and amplified region and had a 27 × sequencing depth. A total of 75 RABV sequences were detected using mNGS in the CSF in Case 2. These cases illustrate that mNGS use during the early diagnosis of infectious diseases is critical. They also indicate that RABV can remain latent in the human body for many years. Disease prevention education for people who have experienced bites or scratches by rabid animals is therefore crucial.},
}

@article {pmid42388653,
year = {2026},
author = {Zhang, X and Sun, E and Zhao, Z and Li, S and Shen, X and Liu, J and He, Q and Wang, Y and Zhao, F and Zhao, H and Zhang, H},
title = {Intervention With Lacticaseibacillus paracaseiPC-01 Fermented Milk Beverage Ameliorates Functional Dyspepsia and Modulates Gut Microbiome: A Pilot Study.},
journal = {Food science & nutrition},
volume = {14},
number = {7},
pages = {e71928},
pmid = {42388653},
issn = {2048-7177},
abstract = {Functional dyspepsia (FD) is a common chronic gastrointestinal disorder characterized by persistent or recurrent epigastric symptoms in the absence of detectable structural abnormalities. In this pilot study, we explored whether a Lacticaseibacillus paracasei PC-01 (PC-01) fermented milk beverage alleviates FD symptoms. Fifty-five patients with FD were randomized into an experimental group (EP, n = 37) receiving the PC-01 fermented milk beverage (5.0 × 10[8] CFU/mL, 200 mL/day) or a control group (CP, n = 18) receiving the active comparator, an acidified milk beverage (non-fermented, without PC-01) (200 mL/day). The interventions lasted 28 days, with symptom scores on the 7-point Global Overall Symptom Scale (GOSS) and Gastrointestinal Symptom Rating Scale (GSRS), and fecal samples were collected at baseline (day 0), 14, and 28. Consumption of the PC-01 fermented milk beverage in this pilot study was associated with improvements in FD symptoms, and a higher effective response rate was observed in the EP group than in the CP group (p = 0.04). Metagenomic analysis revealed that, compared with the CP group, the EP group exhibited significant enrichment of potentially beneficial bacteria (e.g., Blautia) and a reduction in potentially pathogenic bacteria (e.g., Clostridium paraputrificum), accompanied by significant downregulation of the fatty acid β-oxidation I (FAO-PWY) pathway. We acknowledge that the limitation of this pilot study is that the acidified milk beverage used as the control might also exert certain effects on gastrointestinal symptoms and gut microbiota, which could not be fully avoided due to the lack of a fully inert placebo. Collectively, the findings of this preliminary study indicate that the PC-01 fermented milk beverage may alleviate FD-related symptoms and modulate the gut microbiome and metabolic pathways, highlighting its potential in ameliorating FD-associated symptoms. Further large-sample, multi-center, and long-term clinical studies are warranted to verify these preliminary results and establish the long-term efficacy and safety of FD management.},
}

@article {pmid42388798,
year = {2026},
author = {Sen, P and Oliver, LL and Makarova, KS and Wolf, YI and Pavloudi, C and Shlafstein, M and Saw, JH},
title = {Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.716669},
pmid = {42388798},
issn = {2692-8205},
abstract = {Microbial communities of geothermal habitats are central to understanding the evolution of life on Earth. Metagenomics has provided insight into the role of viruses in shaping microbial diversity of complex environments. However, identification of novel viruses is constrained by lack of marker genes and low nucleotide similarities between related viral taxa. While microbial and viral diversity have been explored in terrestrial hot springs and hydrothermal vent systems, other volcanic features remain underexplored. Fumaroles (steam vents) are geothermal features that heat groundwater with magma, releasing steam and volcanic gases such as CO2 and H2S. Comparatively physicochemically dynamic to hot springs, fumarole temperatures and gas emissions rapidly fluctuate with volcanic activity. Here, we describe viruses identified metagenomically from microbial mats hosted near basaltic fumaroles on the Big Island of Hawaìi. To our knowledge, this is the first systematic survey of fumarole viruses. Our utilization of a sensitive profile-based approach for identification reveals high viral diversity in fumaroles, resulting in estimation of two undescribed order-level clades of Caudoviricetes (tailed phages). Viral metabolic genes provide evidence of viral-mediated adaptation of microbes to fumarole conditions. We describe patterns of viral diversity that diverge from the Bank model of viral ecology, hinting at viral dispersal between biofilms and high viral richness and evenness. Lastly, we provide a description of the first terrestrial geothermal environment dominated by Microviridae, previously only described in viral communities of deep ocean hydrothermal vents. This study offers important findings for exploration of viral ecology in extreme environments.},
}

@article {pmid42388836,
year = {2026},
author = {Liu, B and Ding, Q and Tang, S and Dong, H and Li, RJ and Gan, M and Wei, J and Zhang, N and Wu, C and Zhang, TH and Yu, HZ and Zheng, Z},
title = {Avian paramyxovirus type 1-associated severe pneumonia in humans: Molecular characterization and zoonotic transmission risk.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101501},
pmid = {42388836},
issn = {2352-7714},
abstract = {BACKGROUND: Avian paramyxovirus serotype 1 (APMV-1, Newcastle disease virus) is a major poultry pathogen. Human infections are rare and typically self-limiting, but its potential to cause severe respiratory disease and the mechanisms underlying cross-species transmission remain understudied.

METHODS: We analyzed a 65-year-old male with severe pneumonia who had contact with sick backyard feeder chickens. Immunocompetence was evaluated via routine blood tests and serum immunoglobulin levels. mNGS identified 40 APMV-1 sequence reads (50.6% microbial abundance) covering 10.78% of the genome. APMV-1 nucleic acid, antigen, and high IgG titers were detected in human specimens. High viral loads were confirmed in chicken and environmental samples. Phylogenetic analysis classified the strain as Class I genotype 1.1.2 1b, genetically identical to poultry-derived viruses, suggesting a potential avian-to-human transmission.

RESULTS: mNGS identified 40 APMV-1 sequence reads (50.6% microbial abundance) covering 10.78% of the genome. APMV-1 nucleic acid, antigen, and high IgG titers were detected in human specimens. High viral loads were confirmed in chicken and environmental samples. Phylogenetic analysis classified the strain as Class I genotype 1.1.2 1b, genetically identical to poultry-derived viruses, providing molecular clues for zoonotic infection.

CONCLUSIONS: APMV-1 Class I genotype 1.1.2 1b can cross the species barrier and cause life-threatening pneumonia in immunocompetent humans. Our findings highlight its underrecognized zoonotic potential, emphasizing the need for enhanced surveillance in avian and human populations and research into determinants of cross-species pathogenicity.},
}

@article {pmid42389124,
year = {2026},
author = {Zhou, Y and Bian, P and Yang, C and Qu, J and Wang, H and Gao, W},
title = {Differences in carbon sequestration capacity, rhizosphere microorganisms and metabolic functions among different herbaceous plants.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1849153},
pmid = {42389124},
issn = {1664-462X},
abstract = {Mitigating the rapid increase in global CO2 concentrations necessitates a deeper understanding of plant-microbe symbiotic carbon sequestration. While previous research has predominantly focused on woody plants, the carbon sequestration potential and mechanisms of herbaceous plants and their rhizosphere microbiomes remain largely underexplored. To address this gap, this study employed metagenomic technology to systematically investigate the carbon sequestration capacities and metabolic mechanisms of seven plant species and their rhizosphere soil microorganisms. Plant physiological measurements were integrated with microbial functional profiles predicted via PICRUSt2. The results show that the rhizosphere soil microbial communities generally possess functional genes for carbon decomposition and carbon fixation, providing evidence for the coupling of intracellular decomposition and synthesis metabolism in microorganisms. Notably, Spearman correlation analysis established a direct statistical link between plant physiological performance and specific microbial metabolic pathways. These findings demonstrate a functional coupling between plant physiology and rhizosphere microbial carbon metabolism. By linking plant phenotypes to microbial gene pathways, this study reveals that herbaceous plants and their rhizosphere microbiomes form an integrated carbon sequestration system. Therefore, leveraging such plant-soil interactions offers a promising strategy to enhance ecosystem carbon sinks and mitigate rising atmospheric CO2.},
}

@article {pmid42389176,
year = {2026},
author = {Ubani, O and Ngole-Jeme, VM},
title = {Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112987},
pmid = {42389176},
issn = {2352-3409},
abstract = {This article describes a long-read whole-genome shotgun sequencing dataset generated from microbial communities inhabiting industrially and municipally impacted freshwater wetlands in South Africa. Surface water samples were collected from five strategically selected sites exposed to distinct anthropogenic pressures, including industrial effluent discharge, sewage overflow, greywater inputs, informal settlement runoff, and landfill leachate to generate a unique microbial genomic data. Environmental DNA was extracted and sequenced using the PacBio Sequel IIe platform, producing high-fidelity long reads suitable for improved assembly contiguity and functional reconstruction. Post-quality control processing yielded 4.9 × 10[4] to 1.6 × 10[5] HiFi reads per sample, corresponding to 0.34-1.02 Gb of high-accuracy sequence data per site. Long-read assemblies generated between 16,080 and 54,670 predicted protein-coding genes per sample. Taxonomic classification using Kaiju assigned 94.1-99.8% of assembled sequences to reference taxa. Domain-level profiles were exclusively bacterial dominated, with few rare or undetected (0.000-0.001%) archaeal, eukaryotic, or viral representation. Phylum-level composition was strongly dominated by Pseudomonadota (83-95%), followed by Bacillota (3-10%) and Bacteroidota (1-14%), with Actinomycetota consistently below 1%. Functional annotation using the DRAM pipeline identified 9390-31,251 KEGG orthologs, 969-3039 MEROPS peptidases, 13,454-45,103 Pfam domains, and 202-776 carbohydrate-active enzyme (CAZy) genes across assemblies. Distilled metabolic modules indicated the presence of near‑complete electron transport chain complexes (I-V), denitrification-associated pathways, sulfur oxidation and dissimilatory reduction genes, and diverse carbohydrate degradation functions; methanogenesis‑associated modules were not detected among the annotated metabolic pathways recovered in this dataset. The dataset provides genomic coverage of urban wetland microbiomes shaped by mixed industrial and municipal stressors and represents one of the few long-read metagenomic resources available for southern African freshwater wetlands. The availability of assembled contigs, gene annotations, metabolic reconstructions, enables reuse for comparative environmental genomics, biogeochemical modelling, bioremediation gene discovery, resistome screening, and microbial ecology investigations. This high-fidelity long-read sequencing resource expands opportunities for structural and functional analyses of anthropogenically influenced wetland ecosystems and supports future research in environmental biotechnology, bioinformatics-driven ecosystem monitoring, and microbial adaptation to urban pollution gradients.},
}

@article {pmid42389349,
year = {2026},
author = {Iranzo, J and Wolf, Y and Koonin, E},
title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9816737/v1},
pmid = {42389349},
issn = {2693-5015},
abstract = {Background Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome? Results We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors. Conclusions Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving ground for emerging defense systems, which might eventually become cost-effective once optimized by selection.},
}

@article {pmid42389510,
year = {2026},
author = {Al Shareef, ZM and Al-Shahrabi, RM and Sharif-Askari, FS and Yener, B and Bhamidimarri, PM and Bouzid, A and Talaat, IM and Bendardaf, R and Hamoudi, RA and Mote, S and Mall, R and Castiglione, F},
title = {Microbial dysbiosis and inferred functional profiling reveals the potential role of Methylobacterium in prostate cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1760700},
pmid = {42389510},
issn = {2235-2988},
mesh = {Humans ; Male ; *Methylobacterium/genetics/classification/isolation & purification/physiology ; *Prostatic Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Retrospective Studies ; Microbiota/genetics ; Prostate/microbiology/pathology ; },
abstract = {BACKGROUND AND OBJECTIVE: Prostate cancer (PCa) is a leading malignancy in men, with a multifactorial aetiology involving genetic, hormonal, and microbial factors. Although emerging evidence implicates tumour-associated microbial communities in cancer biology, microbial signatures in PCa, particularly in Arab populations, remain underexplored. This study aimed to characterize the prostate tissue microbiota in an Arab cohort and explore associations with clinical features.

METHODS: In this retrospective study, 40 formalin-fixed paraffin-embedded (FFPE) prostate tissue samples (23 PCa and 17 benign prostatic hyperplasia [BPH]) were analysed using 16S rRNA gene sequencing. Microbial diversity, taxonomic composition, and predicted functional potential inferred from 16S data were assessed using DADA2 (v1.30.0), phyllode (v1.46.0), and PICRUSt2 (v2.5.2), with taxonomic classification based on the SILVA database (release 138). Beta diversity differences were tested using PERMANOVA (999 permutations), and differential abundance analyses were corrected using false discovery rate (FDR).

KEY FINDINGS AND LIMITATIONS: PCa tissues demonstrated higher alpha diversity than BPH samples, with greater heterogeneity in beta diversity. Among the identified genera, Methylobacterium was enriched in PCa samples and remained directionally consistent after multivariable adjustment. Exploratory analyses suggested higher abundance in advanced and deceased cases; however, survival findings were limited by sample size. Functional inference indicated enrichment of predicted pathways for carbohydrate and nitrogen metabolism.

CONCLUSIONS: This exploratory study identified Methylobacterium as a candidate microbial signature associated with PCa in an Arab cohort. Given the modest sample size and the inferential nature of functional predictions, these findings require validation in larger prospective studies using direct metagenomic and metabolomic approaches.},
}

Humans
Male
*Methylobacterium/genetics/classification/isolation & purification/physiology
*Prostatic Neoplasms/microbiology/pathology
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Retrospective Studies
Microbiota/genetics
Prostate/microbiology/pathology

@article {pmid42389512,
year = {2026},
author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Lázaro-Martínez, JL},
title = {Correction: Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1902309},
doi = {10.3389/fcimb.2026.1902309},
pmid = {42389512},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1729196.].},
}

@article {pmid42389745,
year = {2026},
author = {Ota, Y and Nukui, Y and Gu, Y and Saito, R},
title = {Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm.},
journal = {Biofilm},
volume = {12},
number = {},
pages = {100377},
pmid = {42389745},
issn = {2590-2075},
abstract = {Antimicrobial resistance (AMR), particularly among carbapenemase-producing organisms, poses a major global health threat. Although hospital wastewater is considered an AMR hotspot, its functional contribution to resistance dynamics remains poorly defined. We developed in situ biofilms in hospital wastewater and applied integrated metagenomic, metatranscriptomic, and culture-based analyses to characterize community structure and gene expression. Biofilms exhibited greater biomass and higher contamination with extended-spectrum β-lactamase-producing Escherichia coli than planktonic wastewater. Biofilms were enriched in surface-adapted Flavobacteriaceae species and a broader array of carbapenemase genes, whereas wastewater showed higher abundance of gut-associated Bacteroidaceae species and virulence factors. Mobile genetic elements linked multiple AMR genes and showed increased expression in biofilms, including bla IMP family carbapenemases. Culture confirmed bla IMP-1 in four biofilm isolates and one wastewater isolate. These findings indicate that hospital-wastewater biofilms can serve as important reservoirs that promote the persistence and potential dissemination of clinically relevant carbapenem resistance.},
}

@article {pmid42390233,
year = {2026},
author = {Peng, Y and Liu, Q and Lin, X and Xing, F and Li, S and Liu, X and Han, Y and Chen, Y and Dong, X},
title = {Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0036926},
doi = {10.1128/msphere.00369-26},
pmid = {42390233},
issn = {2379-5042},
abstract = {Salinity is a major abiotic driver of microbial diversity and metabolic function in coastal ecosystems. While its broad ecological impacts are well established, its role in shaping hydrocarbon-degrading communities and their adaptive mechanisms remains poorly understood. Here, we integrated gene- and genome-resolved metagenomics to investigate how salinity regulates the diversity, ecological interactions, and evolutionary dynamics of aerobic hydrocarbon-degrading microbes in Zhenhai Bay sediments (0.17-28.54 practical salinity units [PSU]). Across the natural salinity gradient, 10 types of hydrocarbon-degrading genes and 30 bacterial genomes spanning four phyla were identified, revealing extensive metabolic potential for the aerobic degradation of both aliphatic and aromatic hydrocarbons. The functional diversity and relative abundance of these genes increased significantly with salinity, accompanied by strong correlations with organic carbon parameters and nitrogen availability. Co-occurrence network analyses showed that hydrocarbon degraders, particularly Gammaproteobacteria, acted as key taxa maintaining community stability under saline conditions. Comparative genomics revealed that these bacteria possess multiple halotolerance strategies, including compatible solute biosynthesis and ion transport, supported by diverse energy-generating pathways. Frequent horizontal gene transfer and duplication of alkane monooxygenases (alkB and cyp153) expanded substrate ranges and enhanced functional diversity in hydrocarbon oxidation, highlighting salinity-driven evolutionary innovation. Together, these findings demonstrate that salinity governs the structure, metabolism, and evolution of hydrocarbon-degrading microbes, promoting microbial adaptation and functional diversification in coastal sediments.IMPORTANCESalinity is a defining feature of coastal ecosystems and a major regulator of microbial processes that support carbon cycling and pollutant degradation. This study highlights that salinity plays a central role in structuring hydrocarbon-degrading microbial communities and shaping their functional capacities and evolutionary trajectories in coastal sediments. By integrating osmoadaptation, metabolic potential, and community organization, our work shows that hydrocarbon degraders function as key links between environmental conditions and ecological processes. Salinity-driven shifts in microbial networks and metabolic strategies illustrate how environmental gradients can foster resilience and stability in highly dynamic coastal systems. Beyond advancing understanding of microbial responses, this study has potential implications for the rational design of bioremediation strategies targeting hydrocarbon pollutants in saline and estuarine environments.},
}

@article {pmid42390270,
year = {2026},
author = {Varona, NS and Schellenberg, L and Barnes, W and Scholten, Y and Haas, AF and Silveira, C},
title = {Bacteriophage replication strategies are associated with organic matter energy content on coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0039526},
doi = {10.1128/msystems.00395-26},
pmid = {42390270},
issn = {2379-5077},
abstract = {Bacteriophages, viruses that infect bacteria, play a crucial role in carbon cycling within marine environments. In coral reefs, dissolved organic matter (DOM) released by benthic primary producers such as algae fuels heterotrophic microbial growth, which can be detrimental to corals. This microbialization process has been associated with the abundance and replication strategies of bacteriophages, but the direct relationship between reef DOM composition and bacteriophage communities remains unclear. Here, we combine metabolomics, metagenomes, and viromes to demonstrate that phage communities have significant relationships with DOM composition on the reefs of Curaçao, Southern Caribbean. While total viral abundances did not significantly correlate with overall dissolved organic carbon (DOC) concentration on these reefs, co-occurrence networks identified thousands of statistically significant associations between free or cell-associated viruses and organic compounds. Cell-associated phages had significantly more positive associations with compounds that had a reduced nominal oxidative state of carbon (NOSC). Furthermore, temperate phages were more frequently correlated with metabolites exhibiting higher Gibbs energy than putatively lytic phages. Six of the ten viruses with the highest number of positive associations with metabolites were temperate (i.e., encoded an integrase or were identified as a prophage), despite this network consisting of approximately 90% lytic viruses. These temperate viruses were predicted to infect members of the genus Sphingobium. Together, these findings reveal a connection between phage replication strategies and DOM energy availability, with potential implications for coral reef biogeochemistry.IMPORTANCECoral reefs are highly dynamic ecosystems where microbial communities and organic matter cycles are intricately linked. This study provides new insights into how bacteriophages interact with dissolved organic matter (DOM) composition, revealing that cell-associated bacteriophages, particularly temperate phages, are associated with more energy-rich organic compounds. These findings suggest that DOM could affect the lysis-lysogeny decision of temperate phages or that lysogeny may play an underappreciated role in shaping the reef carbon cycle. Energy-rich organic compounds have generally been associated with increased algal abundances and coral decline. By demonstrating significant connections between viral infection strategies and the energy content of DOM, our results highlight the potential for phages to influence coral reef biogeochemistry and health.},
}

@article {pmid42390352,
year = {2026},
author = {Zhong, W and Zhu, Z and Zeng, Z and Wu, J and Xie, X and Li, X and Lv, Q and Li, D and Liu, M and Ward, G and Knol, J and Wopereis, H and Guyard, C and Jingjing, X and Lianyi, H and Wang, B and Li, Y and Roeselers, G and Gong, S},
title = {Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo02082h},
pmid = {42390352},
issn = {2042-650X},
abstract = {The neonatal period is a critical stage of development during which the gut microbiome profoundly influences both short- and long-term health and nutrition. Its maturation from infancy to childhood is shaped by interacting environmental factors, including feeding mode, birth mode, and geographic location. A clinical study of 445 infants and toddlers (aged 0-24 months) from six socioeconomically diverse regions in China investigated age-related trajectories of gut microbiome and metabolomic development, with a particular focus on feeding mode. The study included a breastfed reference group and a formula-fed group that received an open-label formula containing a prebiotic mixture of short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS, 9 : 1). Longitudinal fecal samples were analyzed using shotgun metagenomic and metabolomic approaches. Feeding mode was strongly associated with variations in gut microbiome structure and function, along with birth mode and geographic location. Bifidobacterium and Bacteroides were the dominant taxa in both groups and exhibited dynamic abundance trajectories over time. Increased Bifidobacterium abundance was correlated with gene functions involved in starch and fatty acid metabolism as well as the fructose-6-phosphoketolase pathway (Bifid shunt). Comparative metabolomic analyses of amino acids and bile acids revealed highly similar metabolic profiles between the two groups. These findings highlight the association between feeding mode with the developing gut microbiome and describe age-dependent trajectories in Chinese children.},
}

@article {pmid42390679,
year = {2026},
author = {Shao, Z and Zheng, F and Sun, J and Wei, H and Sun, Y and Wang, F},
title = {Response of soil microbiomes to nano-zero-valent iron and biochar in Cr(VI)-contaminated soil remediation.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {6},
pages = {},
pmid = {42390679},
issn = {1573-3017},
support = {2021CXGC011206//Major Scientific and Technological Innovation Project of Shandong Province/ ; },
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Iron/chemistry ; *Microbiota/drug effects ; *Chromium ; *Charcoal/chemistry ; *Environmental Restoration and Remediation/methods ; Bacteria/drug effects ; *Metal Nanoparticles ; },
abstract = {Both biochar and nano-zero-valent iron (nZVI) are increasingly used to remediate soils polluted with heavy metals, such as the toxic Cr(VI). However, how soil microbiomes respond to biochar and nZVI applied in Cr(VI)-contaminated soil has not yet been clarified. The current study compared the effects of bare nZVI (B-nZVI) and starch-stabilized nZVI (S-nZVI) at 100 and 1000 mg/kg on soil enzyme activity and microbial communities in Cr(VI)-contaminated soil growing mung bean amended with or without 1% biochar. High-throughput metagenomic sequencing was conducted to determine the evenness (Simpson index), diversity (Shannon index), and richness (Chao-1 index) of soil bacteria, fungi, archaea, and viruses. Soil catalase activity was inhibited by S-nZVI but stimulated by biochar. Soil phosphatase activity was stimulated by both types of nZVI, but not influenced by biochar. The combination of 1000 mg/kg nZVI and biochar decreased bacterial and fungal evenness and diversity, but did not significantly alter their richness. Archaeal communities remained relatively stable across most treatments. The evenness and diversity of viral communities increased significantly at 1000 mg/kg S-nZVI, whereas the richness decreased conversely. PCoA showed that soil microbial community structure was significantly changed by 1000 mg/kg S-nZVI, which diminished Actinobacteria but enriched Cellvibrio. Furthermore, 1000 mg/kg S-nZVI increased the abundances of some genes involved in antioxidant enzymes and the metabolism of Fe and Cr, and decreased the abundance of C-cycling genes significantly. Overall, S-nZVI caused significant perturbations in soil microbial activity and community structure, but these adverse effects were alleviated by the incorporation of biochar.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
*Iron/chemistry
*Microbiota/drug effects
*Chromium
*Charcoal/chemistry
*Environmental Restoration and Remediation/methods
Bacteria/drug effects
*Metal Nanoparticles

@article {pmid42390736,
year = {2026},
author = {Qi, M and Ye, H and Lei, D and Shao, J and Zhou, W},
title = {Metagenomic next-generation sequencing assists in identifying neurosyphilis: a case series.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42390736},
issn = {1439-0973},
support = {Y20240739//Wenzhou Science & Technology Bureau/ ; },
abstract = {BACKGROUND: Neurosyphilis is a severe manifestation of syphilis caused by Treponema pallidum and remains challenging to diagnose because of heterogeneous clinical presentations and the limited performance of cerebrospinal fluid (CSF) assays. Here, we report four neurosyphilis cases in which CSF metagenomic next-generation sequencing (mNGS) detected T. pallidum and explore its potential value as an adjunctive diagnostic tool.

METHODS: We retrospectively reviewed four HIV-negative adults treated at the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University in whom CSF mNGS detected T. pallidum and the overall clinical assessment supported neurosyphilis. Demographic data, presentations, neuroimaging, CSF parameters, serology, antimicrobial therapy, and outcomes were extracted from the medical records.

RESULTS: All patients had positive syphilis serology and inflammatory CSF profiles with lymphocytic pleocytosis (40-130 cells/µL) and elevated CSF protein (0.70-1.26 g/L). Brain magnetic resonance imaging (MRI) revealed non-specific chronic structural changes in all patients (including white matter hyperintensities, cerebral atrophy, and ventricular enlargement), with no acute ischemic, hemorrhagic, or neoplastic lesions. Bacterial cultures remained negative after 48 h. CSF mNGS detected T. pallidum in all cases (unique reads 8-135; standardized mapped reads number (SMRN) 1-53; genome coverage 0.0260-0.4945%), including three patients whose predominant presentations were neuropsychiatric. Following anti-treponemal therapy with ceftriaxone or penicillin, all patients showed clinical improvement.

CONCLUSIONS: In this case series, CSF mNGS provided direct detection of T. pallidum and supported the diagnosis of neurosyphilis in patients with diverse, often neuropsychiatric presentations when conventional microbiology was non-diagnostic. CSF mNGS may serve as a useful adjunct in selected patients, but results should be interpreted alongside clinical features and CSF inflammation rather than in isolation.},
}

@article {pmid42391470,
year = {2026},
author = {Plominsky, AM and Peoples, LM and Norenberg, M and Ramirez-Flandes, S and Podell, S and Mullane, KK and Casagrande, D and Roman, C and Pockalny, R and Smith, DC and Belser, C and Poulain, J and Allen, EE and Glud, RN and Ulloa, O and Barber, N and D'Hondt, S and Bartlett, DH},
title = {Minimising decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag064},
pmid = {42391470},
issn = {1751-7370},
abstract = {The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimising pressure and temperature effects. When compared to samples collected under pressurised conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a > 20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurised (e.g., members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g., Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.},
}

@article {pmid42391838,
year = {2026},
author = {Yu, YH and Marín Arancibia, M},
title = {Mesorhizobium bavaricum sp. nov. and Mesorhizobium monacense sp. nov., two novel Lotus-associated species harbouring symbiotic plasmids.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {5},
pages = {126739},
doi = {10.1016/j.syapm.2026.126739},
pmid = {42391838},
issn = {1618-0984},
abstract = {Legumes establish a mutualistic interaction with nitrogen-fixing rhizobia. Lotus japonicus is a model for studying this symbiosis; however, only a limited number of rhizobial species nodulating this host have been taxonomically described. Here, we characterise four Mesorhizobium strains (DC-1.1[T], Qj1B1, DC-1.5[T], and Qj2B2) isolated from root nodules of Lotus japonicus and Lotus burttii. Multi-locus phylogeny and phylogenomic analyses resolved these isolates into two well-supported monophyletic clades. Genome-based comparisons supported their classification as distinct taxa, with strains DC-1.1[T] and Qj1B1 showing 95.2% average nucleotide identity (ANI) and 62.9-63.5% digital DNA-DNA hybridisation (dDDH) values relative to Mesorhizobium newzealandense ICMP 19545[T], whereas DC-1.5[T] and Qj2B2 exhibited 92.5-92.8% ANI and 49.9-50.5% dDDH compared with Mesorhizobium waimense ICMP 19557[T]. Together with chemotaxonomic and physiological traits, these data support the proposal of two novel species, Mesorhizobium bavaricum sp. nov. (DC-1.1[T] and Qj1B1) and Mesorhizobium monacense sp. nov. (DC-1.5[T] and Qj2B2). Metagenomic analyses predicted high environmental prevalence for these novel taxa, particularly within soil habitats. Isolates DC-1.1[T], Qj1B1, and DC-1.5[T] effectively nodulated Lotus burttii and significantly promoted plant growth, whereas Qj2B2 neither nodulated nor enhanced growth. Comparative genomic analysis revealed that the nodulating isolates harbour symbiotic genes (nod, fix, and nif) on symbiotic plasmids, a rare feature in Mesorhizobium strains, whereas Qj2B2 lacks essential nod and nif genes. Consistent with these genomic features, symbiotaxonomic analysis assigned the nodulating isolates to symbiovar loti. These results highlight the potential of these isolates as models for comparative analyses of symbiotic plasmid evolution and horizontal gene transfer.},
}

@article {pmid42391940,
year = {2026},
author = {Wang, J and Guo, C and Pu, X},
title = {Metabolic filtering as a putative mechanism linking soil metabolome and microbial community assembly along a lake expansion gradient.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128601},
doi = {10.1016/j.micres.2026.128601},
pmid = {42391940},
issn = {1618-0623},
abstract = {Climate-driven lake expansion across the Qinghai-Tibet Plateau induces profound edaphic shifts, but how these abiotic changes shape soil microbial assembly remains unclear. Soil metagenomics and metabolomics were integrated along a 0-10 km spatial gradient at Gahai. Redundancy analysis (RDA) identified moisture (NDWI) and salinity (SI) as primary ecosystem drivers. Structural equation modeling (SEM) provided exploratory evidence consistent with a mediation pathway (P = 0.64, CFI = 1, RMSEA = 0), in which environmental factors potentially influenced microbial community structure indirectly, via reshaping the soil metabolome rather than through a direct path. Moisture availability exerted a strong negative effect on soil metabolic profiles (λ = -0.93), leading to a pronounced negative correlation between the metabolome and microbial community (λ= -0.97). Multi-omics integration attributed this pattern to stress-induced accumulation of defensive metabolites, including Feruloylputrescine and 3-Methylthiopropyl-desulfoglucosinolate. These compounds showed significant negative correlations with dominant genera (e.g., Candidatus Kryptobacter). This "metabolic filtering" is hypothesized to selectively limit the presence of non-adapted taxa based solely on correlational SEM and network analyses, supporting our tentative hypothesis that increasing environmental stress may promote a transition from competitive interactions toward patterns consistent with stronger deterministic filtering. Our exploratory findings suggest that the soil metabolome acts as a functional interface mediating microbial adaptation and strategic resource allocation to lake expansion in this high-altitude saline-alkali system. However, due to regional heterogeneity, these patterns provide a theoretical baseline for plateau lake ecosystems and should be applied with caution to broader geographic areas.},
}

@article {pmid42391942,
year = {2026},
author = {Castellano-Hinojosa, A and de Freitas, J and de Carvalho, DU and Monus, BD and González-López, J and Strauss, SL and Albrecht, U},
title = {Compartmental and functional responses of the citrus microbiome and resistome to the systemic delivery of oxytetracycline by trunk injection.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128613},
doi = {10.1016/j.micres.2026.128613},
pmid = {42391942},
issn = {1618-0623},
abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely limits citrus production worldwide. We investigated how oxytetracycline (OTC) trunk injection affects the citrus holobiont, examining its ability to suppress CLas and improve tree performance while assessing compartment-specific responses of the microbiome and resistome. A field experiment was conducted in CLas-infected sweet orange trees, integrating qPCR pathogen quantification, fruit yield and juice quality measurements, functional pathway analysis, and genome-resolved profiling across leaves, bark, fibrous roots, and the rhizosphere at three time points after injection. OTC reduced CLas abundance in leaves and improved fruit yield and juice quality without altering microbial diversity. No clear OTC-associated shifts in microbial functional pathways were observed in aboveground compartments, and resistome profiles were strongly compartment-dependent but showed no detectable response to OTC treatment. However, pronounced functional shifts were detected in belowground compartments, with consistent reductions in carbon-, nitrogen-, and phosphorus-related pathways and declines in several taxa and metagenome-assembled genomes associated with nutrient turnover. In contrast, stress-tolerance and xenobiotic-responsive microorganisms were enriched. In addition, these belowground responses were associated with low-abundance, rare taxa rather than by changes in alpha diversity or the dominant community, revealing a hidden functional reconfiguration that was concentrated in the root and rhizosphere compartments most relevant to nutrient cycling and long-term soil health. These findings demonstrate that systemically delivered OTC induces targeted, compartment-specific reorganization of microbiome functions rather than broad disruption. By linking physiological improvement with functional and genome-resolved microbial responses, this study highlights the broader ecological consequences of antibiotic interventions in perennial crops.},
}

@article {pmid42392368,
year = {2026},
author = {Cheng, M and Qin, X and Han, Y and Tan, F and She, M and Zhu, X and Yuan, L and Teng, M and Ou, X and Luo, S and Xiang, P and Chen, L and Yang, F},
title = {Genomic and biosynthetic landscape of high-temperature Daqu microbiome.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135297},
doi = {10.1016/j.biortech.2026.135297},
pmid = {42392368},
issn = {1873-2976},
abstract = {As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82% of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3% are novel, and 17,031 biosynthetic gene clusters, of which 62.63% are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.},
}

@article {pmid42392373,
year = {2026},
author = {Long, Y and Zhu, C and Wu, X and Hou, J and Zeng, J and Wu, SL},
title = {Magnetite-driven food waste conversion toward high-value medium-chain fatty acids production through promoted biological processes and electrochemical environment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135299},
doi = {10.1016/j.biortech.2026.135299},
pmid = {42392373},
issn = {1873-2976},
abstract = {Achieving high-value valorization of food waste (FW) into medium-chain fatty acids (MCFAs) is vital for alleviating environmental pressure and advancing carbon neutrality. However, the inherent electron transfer and metabolic bottlenecks in FW bioconversion process restrains the conversion efficiency of MCFAs. Herein, the performance and comprehensive mechanisms of Fe3O4-enhanced MCFA production were comprehensively studied through integrated batch fermentation tests, bio-electrochemical characterizations, and metagenomic analysis. Results revealed that the optimal dosage of 8 g/L Fe3O4 enhanced caproate production to 3409.32 mg COD/L (a 3.7-fold increase over the control group). Notably, this dosage drove the further elongation of carbon chains, yielding high-energy-density heptanoate (C7) and caprylate (C8), thereby elevating MCFA selectivity from 5.5 % to 38.6 %. Further analysis indicated that Fe3O4 promoted all biological processes (solubilization, hydrolysis, acidogenesis, and chain elongation). Mechanically, Fe3O4 optimized the electrochemical microenvironment, enhancing conductivity and electron transport system (ETS) activity by 32.5 % and 69.1 %, respectively. The correlation-based network analysis confirmed a strong correlation (r > 0.4) between product distribution, iron cycling (Fe[2+] concentration), and conductivity. Metagenomic analysis elucidated that by enriching core functional genera like Clostridium and Sphaerochaeta and associated functional microbial genes, Fe3O4 synergistically promoted the efficient bioconversion of FW into MCFAs. This study offers new mechanistic insights into enhancing MCFA production via magnetite-regulated electron transfer, providing a robust strategy for efficient resource recovery from complex organic wastes.},
}

@article {pmid42392375,
year = {2026},
author = {Hou, K and Yang, B and Zhao, R and Zhang, J and Duan, Y},
title = {Dose-dependent effects of biochar on low-temperature anammox: reactor performance, community variation, and functional potential.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135296},
doi = {10.1016/j.biortech.2026.135296},
pmid = {42392375},
issn = {1873-2976},
abstract = {Low temperature is a major constraint on the practical application of anaerobic ammonium oxidation (anammox). Although biochar has been reported to improve low-temperature anammox, the effect of dosage remains insufficiently understood. In this study, mature anammox sludge was amended with 0, 3, 7, and 9 g/L bamboo-derived biochar and operated under a stepwise temperature decrease from 35 to 15°C, followed by low-temperature operation for 70 d. Reactor performance, extracellular polymeric substances (EPS), microbial community composition, and metagenomic functional potential were analyzed to clarify the dose effect of biochar. Among the tested dosages, 7 g/L biochar achieved the highest nitrogen removal efficiency (48.6%) at 15°C, which was 12.8 percentage points higher than the control value of 35.8%. Biochar-amended reactors also showed higher EPS contents than the control, and the 7 g/L group better maintained the PN/PS ratio under low-temperature stress. Community analysis indicated a higher relative abundance of Candidatus Brocadia in the biochar-amended groups, especially at 7 g/L. Metagenomic analysis further showed higher abundance of genes associated with nitrogen metabolism, carbon metabolism, and EPS-related precursor synthesis in the 7 g/L group. These results suggest that an appropriate biochar dosage can improve low-temperature anammox performance and is associated with EPS stabilization, enrichment of key functional taxa, and enhanced functional potential. This study provides guidance for biochar dosage optimization in low-temperature anammox systems.},
}

@article {pmid42392574,
year = {2026},
author = {Vita, AA and Brown, J and Norby-Adams, L and Ghanem, N and Weir, TL and Goldenberg, JZ},
title = {Microbial-derived polyphenol metabolites and the gut microbiota: A scoping review of clinical studies.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101700},
doi = {10.1016/j.tjnut.2026.101700},
pmid = {42392574},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary (poly)phenols are widely recognized for their health-promoting properties, yet their bioactivity is largely contingent upon gut microbial metabolism. Individual differences in microbiome composition lead to variable production of microbial-derived (poly)phenol metabolites (MPMs) and thus contribute to divergent health outcomes.

OBJECTIVE: This scoping review aimed to systematically map the scope of clinical evidence reporting relationships between MPMs and gut microbiota composition and function, highlighting research gaps to guide future investigations.

METHODS: Using pre-defined search criteria, two reviewers identified human clinical studies reporting relationships between metabolite levels and microbiome outcomes.

RESULTS: Fifty-six studies were included. Evidence was frequently focused on phenolic acids (n=20), phytoestrogens (n=18), and urolithins (n=17), with relationships between microbiota and other MPMs only being reported in 1-2 studies. The majority of studies across MPM categories used 16S rRNA gene sequencing for identification of gut microbiota (n=42), among other methods, with only six studies using metagenomic shotgun sequencing, thus limiting taxonomic resolution and functional inference. Findings revealed recurrent associations between specific microbes and MPMs; while some reflected known producer taxa (e.g., Gordonibacter and urolithins), others may represent broader community-level interactions (e.g., Alistipes and equol). However, these results varied across (poly)phenol class, intervention type, and host-specific context.

CONCLUSION: This scoping review identified recurrent microbiota-MPM associations alongside major evidence gaps, including limited functional microbiome characterization and sparse investigation of several MPM classes/subclasses (e.g., resveratrol-, flavanone-, and flavan-3-ol-related MPMs). Future research using standardized, high-resolution multi-omics approaches is needed to improve identification of reproducible microbial signatures and mechanisms underlying (poly)phenol metabolism, and to link these features with functional health outcomes.},
}

@article {pmid42379395,
year = {2026},
author = {Mannila, E and Gómez-Gallego, C and Muluh, G and Nuotio, P and Koistinen, V and Erawijantari, P and Salminen, S and Lahti, L and Kolehmainen, M and Linderborg, KM},
title = {Oat-rich low-gluten diet modulates plasma short-chain fatty acids without significant changes in fecal microbiome or inflammatory markers - a randomized clinical trial in people with cardiometabolic risk.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101690},
doi = {10.1016/j.tjnut.2026.101690},
pmid = {42379395},
issn = {1541-6100},
abstract = {BACKGROUND: Increasingly popular low-gluten diets (LGDs) are generally low in fiber; however, it is possible to improve the LGD by using oat-based products.

OBJECTIVE: To investigate the changes in fecal microbiome, fasting plasma short-chain fatty acids (SCFAs), and inflammatory markers during a 6-week oat- or rice-rich LGD in individuals with increased cardiometabolic risk.

METHODS: The participants (n=69) were allocated into two parallel groups following a 6-week LGD with either oats or rice. Fasting plasma, stool, and dietary information were collected both at the baseline and at the end of the trial. Fecal microbial communities were analyzed by shotgun metagenomics (Novaseq X Plus) and characterized using MetaPhlAn4. Their functional potential was assessed with HUMAnN3 using the MetaCyc database. Plasma SCFAs were quantified by UHPLC-MS, and inflammatory markers were detected and quantified using a 45-cytokine panel (Olink Target). Diet-group differences over time were assessed with linear mixed-effects model.

RESULTS: Dietary information revealed high-oat and low-rice consumption at the baseline for both groups. Overall, the oat-rich LGD increased circulating SCFAs. Particularly, butyrate increased more during the oat-rich LGD than during the rice-rich LGD (ptimeXgroup=0.033). Regarding changes in the fecal microbiome, the rice group had a higher Shannon diversity index after the intervention than the oat group (ptimeXgroup=0.025), and more changes in the microbiome. This is possibly due to more substantial dietary changes from a low rice consumption compared to the habitual diet in the baseline. No significant differences between or changes within the groups in inflammatory markers were observed.

CONCLUSIONS: Changing to an oat-rich LGD increases fasting plasma SCFA concentrations without significant effects on the fecal microbiome and inflammatory markers in individuals with increased cardiometabolic risk. When there is a regular baseline consumption of oats, adopting a low-fiber rice-rich LGD may shift the microbiome towards potentially unfavorable direction.

NCT05526092, https://clinicaltrials.gov/study/NCT05526092.},
}

@article {pmid42379815,
year = {2026},
author = {Patel, I and Mammel, M and Gangiredla, J and Mukherjee, A},
title = {Targeted amplicon sequencing for enhanced detection of spiked Shiga toxin-producing Escherichia coli in ready-to-eat romaine lettuce: a proof-of-concept study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0102226},
doi = {10.1128/spectrum.01022-26},
pmid = {42379815},
issn = {2165-0497},
abstract = {The early and accurate detection of low-level pathogenic and indicator organisms in fresh produce is critical for preventing widespread foodborne outbreaks. Contamination of leafy greens with foodborne pathogens, such as Shiga toxin-producing Escherichia coli (STEC), is a significant public health issue, making rapid and sensitive detection methods critical for mitigating outbreaks. Although next-generation sequencing (NGS) is a powerful tool for pathogen identification, challenges remain in detecting low contamination levels in food products. Here, we demonstrate the use of a custom targeted amplicon sequencing (TAS) primer panel targeting species with food safety concerns, including known human foodborne pathogens, opportunistic pathogens, and indicator organisms related to food spoilage. Using a quasi-metagenomics approach, this proof-of-concept study demonstrates that, compared to whole-metagenomic sequencing (WMS), TAS is a rapid and sensitive NGS-based method for detecting low levels of pathogens. Ready-to-eat romaine lettuce was spiked with STEC and incubated in enrichment medium. DNA was isolated at 0.5, 5, and 6 h, and libraries were prepared for both WMS and TAS. The results indicated that TAS was more sensitive than WMS not only at detecting the pathogen at the species level but also at identifying key virulence markers stx1 and stx2. Overall, our targeted sequencing approach provides a rapid and sensitive molecular method to detect and identify foodborne pathogenic bacteria, demonstrating its potential for application in food safety.IMPORTANCEDetecting low-level pathogenic and indicator organisms is critical to prevent foodborne outbreaks. Conventional methods lack speed and sensitivity. While next-generation sequencing methods, such as whole-metagenomic sequencing (WMS), offer a broad microbial landscape view, detecting pathogens at low concentrations within complex food matrices remains challenging. To address this, a targeted amplicon sequencing (TAS) panel was designed to identify species of food safety concern and key indicator organisms. This study demonstrates that TAS is more sensitive than WMS. The application of this TAS assay provides an important bridge between qPCR and WMS by detecting and characterizing pathogens that might be present in low numbers and otherwise missed in an enrichment. TAS allows multiplexing and overcomes the critical limitation of sensitivity in complex samples, providing a robust tool for food safety surveillance. Our findings demonstrate the potential use of targeted next-generation sequencing (NGS)-based methods to mitigate the risk of foodborne illnesses.},
}

@article {pmid42379825,
year = {2026},
author = {Wang, S and Chen, M and Jiao, D},
title = {ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0410125},
doi = {10.1128/spectrum.04101-25},
pmid = {42379825},
issn = {2165-0497},
abstract = {UNLABELLED: Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe "identifiability limit" when disentangling highly similar genomes. Under high-noise conditions, sequencing errors, coverage overdispersion, and collinearity confound standard expectation-maximization algorithms, resulting in overfitting and spurious "ghost" strains. Here, we introduce zero-inflated latent allocation for strain reconstruction from metagenomes with adaptive sparsity regularization (ZILA-SRM) to overcome this barrier through three innovations. First, we integrate a zero-inflated Poisson mixture model to decouple "structural zeros" (true strain absence) from "sampling zeros" (stochastic dropout), addressing overdispersion in standard Poisson-based tools. Second, we impose a convex adaptive sparsity regularization penalty that leverages biological sparsity priors to shrink noise artifacts dynamically. Third, we implement a graph-theoretic refinement step using maximal clique enumeration to resolve haplotype collinearity. Benchmarking against StrainFinder and MixtureS on 702 synthetic data sets shows that ZILA-SRM achieves a 20% improvement in precision in high-complexity scenarios while maintaining over 80% recall for minor variants at 0.5% abundance. Re-analysis of deep-sequencing data from 195 Mycobacterium tuberculosis clinical samples reveals cryptic low-abundance drug-resistant variants in 12% of patients, including a minor clone carrying the rpoB S450L mutation. Furthermore, application to skin microbiome data sets further reveals a strong negative correlation between dominant Staphylococcus aureus and Staphylococcus epidermidis strains, providing genomic evidence for competitive exclusion. These findings establish ZILA-SRM as a robust tool for resolving strain-level diversity in complex metagenomes.

IMPORTANCE: Understanding microbial communities at the strain level is critical because closely related strains can differ dramatically in traits such as drug resistance, virulence, and ecological interactions. However, resolving individual strains from metagenomic sequencing data remains difficult, especially when strains are highly similar or present at low abundance. As a result, biologically meaningful diversity is often obscured or misinterpreted as noise. In this study, we introduce a new framework that improves the reliability of strain reconstruction from complex metagenomic data. By reducing false-positive strain detection while preserving sensitivity to rare variants, our approach enables more accurate characterization of microbial populations. This improved resolution reveals previously hidden subpopulations in clinical and microbiome datasets, providing clearer insights into microbial evolution, competition, and the emergence of clinically relevant traits such as antibiotic resistance.},
}

@article {pmid42380482,
year = {2026},
author = {Kang, X and He, P and Zhang, H and Lü, F},
title = {Virus-mediated prokaryotic community adaptation dynamics under thermal stress in municipal organic solid waste microbiomes.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10568-3},
pmid = {42380482},
issn = {2399-3642},
abstract = {Temperature influences microbial metabolic activity, which is crucial for biotechnological processes and bioproducts stabilization. However, temperature-driven responses of complex viruses and prokaryotic communities, and the modulatory role of viruses in prokaryotic community within environmental biotechnology systems, remain poorly understood. We developed a continuous thermal stress system with temperature gradients and high-resolution temporal sampling of metagenomics and metatranscriptomics, using municipal organic solid waste as a biological model. An optimized meta-omics pipeline integrating genomic potential and activity was applied to investigate the adaptive dynamics of complex prokaryotic and viral communities. Continuous thermal stress triggered stress responses in paired virus-hosts within the system. Thermal stress exerted distinct effects on temperate and virulent viruses. Viruses formed quasi-symbiotic alliances with their hosts to withstand thermal stress by integrating protein folding genes, stress response, and metabolic function genes, shaping host adaptability under thermal pressure. Equipped with multiple defense and counter-defense systems, viruses accelerated the accumulation of beneficial mutations under thermal stress, enabling them to escape host immunity and intensify competition with prokaryotic communities. This study demonstrates how viruses accelerated both the restructuring and adaptive responses of prokaryotic communities under thermal stress, advancing our understanding of phage-based therapeutic strategies in temperature-variable engineering applications.},
}

@article {pmid42381037,
year = {2026},
author = {Garcia-Castillo, L and Ferrero, G and Blaževitš, O and Francescato, G and Eliass, AT and Cortez, NE and Beltrà, M and Tarallo, S and Pardini, B and Costelli, P and Naccarati, A and Longo, VD and Penna, F},
title = {Fasting-mimicking diet counteracts gut microbial dysbiosis in experimental lynch syndrome.},
journal = {Cancer & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40170-026-00446-1},
pmid = {42381037},
issn = {2049-3002},
abstract = {The development of colorectal cancer (CRC) is largely influenced by hereditary factors, with up to one-third of cases linked to genetic predisposition. In parallel, environmental factors such as diet and intestinal microbiota play a significant role. Lynch syndrome (LS), the most common form of hereditary CRC, is due to mutations in DNA mismatch repair genes. Diet interventions such as calorie restriction (CR) can modify the course of the disease, altering nutrient supply and promoting beneficial microbial populations. Fasting-mimicking diets (FMD) are plant-based CR regimens that showed promise in modulating the gut microbiota and suppressing CRC progression in pre-clinical ectopic cancer models. In this study, Villin-Cre/Msh2-floxed (VCM) mice, modelling LS, were subjected to periodic FMD cycles for 10 months. FMD regimen influenced animal weight in a sexually dimorphic manner, stably reducing animal body weight only in males. Moreover, shotgun metagenomic sequencing revealed that FMD mitigated the dysbiotic longitudinal changes associated with cancer onset, preserving beneficial species, such as Lactobacillus johnsonii, and reducing adverse species, such as Escherichia coli. Metabolic pathway analysis also showed significant differences, with FMD preventing the upregulation of pathways involved in amino acid and nucleotide synthesis, potentially promoting tumour growth. Overall, the findings suggest that periodic FMD may result useful in a multimodal approach for LS management, counteracting gut microbiota alterations.},
}

@article {pmid42381048,
year = {2026},
author = {Porcel Sanchis, D and Pola, M and Engelberts, JP and Guerra-Font, O and Messer, L and Alberola-Mora, I and Escobar Sáez, L and Pérez Gómez, N and Portolés Campo, Á and Valero-Tebar, J and Naya Garmendia, LM and Preciado Barahona, JC and Gil García, R and Arnau, V and McIlroy, SJ and Džunková, M},
title = {Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02456-z},
pmid = {42381048},
issn = {2049-2618},
abstract = {BACKGROUND: Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in distinguishing true symbionts from contaminants. Here, we use metagenomics of museum specimens to uncover symbioses in endangered or difficult-to-collect animals, such as nudibranchs. To date, Doriopsilla is the only nudibranch demonstrated to harbor an uncultured symbiont involved in chemical defense, leaving it unclear whether comparable associations occur in other nudibranchs. We hypothesized that bona fide symbionts should belong to abundant, uncultured lineages consistently present across individuals of the same host taxon collected across space and time.

RESULTS: Using ethanol-preserved specimens archived for up to 30 years, we doubled the number of available nudibranch microbiome datasets and found that dominant uncultured symbionts are rare, with most nudibranchs likely relying on alternative chemical defense mechanisms. An exception were Polycera and Felimare that contained two previously unknown symbionts, Candidatus Polyceribacter and Candidatus Felimaribacter, from distinct uncultured orders that are globally rare in marine metagenomes. These symbionts encode diverse biosynthetic gene clusters exhibiting strain- and species-level microdiversity consistent with metabolites previously reported from their hosts. Their restricted host distribution, phylogenetic distinctiveness, and phylogenetic similarity to symbionts of sponges or corals that are not nudibranch prey, support long-term evolutionary specialization and functional convergence. Fine-scale diversification further suggests host-driven microbial adaptation following symbiosis establishment.

CONCLUSIONS: Overall, this study establishes museomics as a robust framework for symbiosis research and advances understanding of the evolutionary and chemical ecology of host-microbe interactions in rare marine invertebrates. Video Abstract.},
}

@article {pmid42381185,
year = {2026},
author = {Mouanes-Abelin, J and Pomares, C and Montoya, JG and Pondrom, M and Maria, L and Zimmer, AJ and Gomez, CA},
title = {Toxoplasmosis Beyond Transplantation: Diagnostic and Prevention Challenges in a Patient Receiving Targeted Immunomodulators.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70263},
doi = {10.1111/tid.70263},
pmid = {42381185},
issn = {1399-3062},
abstract = {Toxoplasmosis has long been recognized as a serious complication in immunocompromised host, particularly those with advanced HIV/AIDS, hematopoietic stem-cell transplantation (HSCT), solid-organ transplant (SOT), and hematological malignancies. The rapid expansion of targeted immunomodulators, including chimeric antigen receptor T-cell (CAR-T) therapies, monoclonal antibodies, and small-molecule inhibitors, is creating new at-risk populations beyond traditional transplant settings. We present a 9-year-old boy with high-risk B-cell acute lymphoblastic leukemia (B-ALL), who developed prolonged fever and macrophage activation syndrome (MAS). After an extensive unrevealing workup, disseminated acute toxoplasmosis was identified incidentally on bone marrow aspirate via morphologic identification of tachyzoites and confirmed by Toxoplasma gondii PCR. This case exemplifies the emerging threat of toxoplasmosis in non-transplant immunomodulated hosts and supports three core mitigation strategies. First, baseline Toxoplasma IgG and IgM serology should be obtained in all patients initiating targeted immunotherapy, recognizing that B-cell depletion or hypogammaglobulinemia may render IgG unreliable, and that IgM may be falsely negative, delayed, or persistently positive in immunocompromised individuals. Second, targeted PCR from clinically relevant compartments or metagenomic next-generation sequencing when conventional diagnostics is unrevealing should be applied early. Third, prevention requires a bundled approach: baseline screening, patient education for seronegative individuals, and trimethoprim-sulfamethoxazole prophylaxis with or without serial qPCR monitoring for seropositive patients. Toxoplasmosis is no longer a transplant-exclusive concern. As targeted immunomodulators reshape practice across rheumatology, oncology, neurology, and autoimmune disease, infectious diseases specialists must lead efforts to raise cross-specialty awareness, establish guidelines, and build registries to define the true burden of toxoplasmosis in these growing populations.},
}

@article {pmid42381379,
year = {2026},
author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA},
title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690687},
doi = {10.1080/19490976.2026.2690687},
pmid = {42381379},
issn = {1949-0984},
mesh = {Animals ; *Probiotics/administration & dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.},
}

Animals
*Probiotics/administration & dosage
Multiomics
*Saccharomyces boulardii/physiology
Receptors, Aryl Hydrocarbon/metabolism/agonists
Signal Transduction
*Gastrointestinal Microbiome
*Colorectal Neoplasms/immunology/microbiology/metabolism/therapy
Mice
Bacteria/classification/genetics/isolation & purification

@article {pmid42381607,
year = {2026},
author = {Lv, JL and Zhu, MQ and Gao, T and Pan, Y and Yu, HQ and Min, D and Xiong, YJ and Liu, DF},
title = {Profiling Active Low-Abundance Microbes in As/Sb-Contaminated Soils via d-Amino Acid-Based In Situ Labeling.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c07045},
pmid = {42381607},
issn = {1520-5851},
abstract = {Soil microbial communities play a pivotal ecological role in contaminated environments. However, conventional metagenomic approaches struggle to distinguish between "potential function holders" and "in situ metabolically active executors". Here, we employed a method combining fluorescent d-amino acid labeling, fluorescence-activated cell sorting, and metagenomics (FDAA-FACS-Metagenomics) to capture and profile active microbes in complex soils. The secondary addition of As(V) and Sb(V) enhanced the community's reductive activity toward these metalloids, reshaping the active assemblages. Clostridium was markedly enriched, and several low-abundance members were activated as true executors of the reduction process. MAGs recovered via FDAA-FACS revealed an active core community with functional partitioning: some taxa participated directly in As(V)/Sb(V) reduction, while others contributed to community stability through tolerance and metabolic support. Notably, a Desulfitobacteriaceae genome (MAG29) harbored both arrAB and anrAB gene clusters, a complete Wood-Ljungdahl carbon fixation pathway, and nitrogen fixation genes. These genomic features suggest the potential for a multifunctional metabolic lifestyle involving metalloid reduction, carbon fixation, and nitrogen transformation. Such metabolic versatility may enable MAG29 to contribute to coupled carbon-nitrogen cycling and metalloid transformation under contaminated environmental conditions. These findings emphasize the important ecological roles of rare, metabolically active microbes in metalloid transformation and soil ecosystem functioning.},
}

@article {pmid42381665,
year = {2026},
author = {Flach, CF and Berglund, F and Osena, G and Huijbers, PMC and Larsson, DGJ},
title = {Sewage surveillance for assessing clinical antibiotic resistance prevalence: Combining metagenomic and phenotypic data.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101485},
pmid = {42381665},
issn = {2352-7714},
abstract = {Surveillance of antibiotic resistance in clinical isolates is a cornerstone for the management of bacterial infections but is limited in large parts of the world, often due to lack of resources. Sewage surveillance has been proposed as a promising, resource-efficient complement to the traditional surveillance approach based on samples from many individual patients. Both phenotypic data on resistance in sewage isolates and abundance of antibiotic resistance genes in sewage have been shown to correlate with resistance prevalence in clinical isolates. Here, we aimed to directly compare and combine an isolate-based and a gene-based sewage surveillance approach to evaluate what best can reflect clinical resistance rates. The two approaches, based on susceptibility testing of collected E. coli isolates and metagenomic sequencing, respectively, were applied to municipal sewage samples collected in ten European countries. The data generated was related to available data on resistance to aminopenicillins, fluoroquinolones, third generation cephalosporins and aminoglycosides prevalence in clinical E. coli isolates using beta regression models. None of the tested individual predictors were superior across all four investigated classes of antibiotics. For modelling of aminopenicillin resistance, a clearly higher R[2] value was obtained when isolate-based and gene-based data was combined as predictors, also after adjusting for the number of included variables. We conclude that there could be a value of including both isolate- and gene-based sewage data for predictions of resistance rates in clinical isolates, while emphasizing the value of linking predictors to specific species and classes of antibiotics.},
}

@article {pmid42381921,
year = {2026},
author = {Salah, R and AbdElaal, KR and Ghonaim, L and Awe, OI and Moustafa, A},
title = {DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag166},
pmid = {42381921},
issn = {2635-0041},
abstract = {MOTIVATION: Accurate species-level classification of prokaryotic 16S rRNA sequences remains difficult: existing tools rely on exact alignment, k-mer heuristics, or phylogenetic placement and are limited by incomplete reference databases. Deep learning approaches in microbial genomics have focused largely on whole-genome metagenomics, leaving 16S taxonomy under-supported.

RESULTS: We present DeepTaxa, a hybrid CNN-BERT framework that pairs a multiscale CNN with a transformer trained from scratch on the DNABERT-2 BPE vocabulary, producing parallel rank-specific predictions across the seven Linnean ranks. On the Greengenes2 2024.09 test set, DeepTaxa achieves species-level accuracy of 92.96% and F1 of 0.9212 (3-seed mean; cross-seed standard deviation ≤ 0.0008 F1 at every rank), with F1 above 0.99 from domain through class and a species-level expected calibration error of 0.0242. DeepTaxa exceeds DADA2 (90.05%) and QIIME 2 (85.01%) at the species rank on the same held-out test set, with larger gains over the k-mer-based classifiers SINTAX and Kraken 2. Performance degrades smoothly with decreasing training-set similarity (species F1 from 0.95 to 0.45), and a dedicated V3-V4 amplicon checkpoint reaches 87.55% species accuracy from an approximately 420 bp window.

Source code, trained checkpoints for full-length 16S and V3-V4 amplicons, curated datasets, and reproducible workflows are publicly available at github.com/systems-genomics-lab/deeptaxa and huggingface.co/systems-genomics-lab/deeptaxa.},
}

@article {pmid42382111,
year = {2026},
author = {Sachula, W and Huimin, L and Yaxing, Z and Ding, Y and Shangxiong, Z and Shengli, L and Haizhou, S and Chunhua, Z},
title = {An integrative multi-omics investigation into the influence of forage type on the volatile flavor profile of Ujumqin sheep mutton.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1856240},
pmid = {42382111},
issn = {2297-1769},
abstract = {China ranks among the leading producers and consumers of mutton globally and the development of nutritional strategies to improve meat quality and sensory attributes. This study investigated the effect of three high-quality forages, i.e., alfalfa hay (ALFA), Leymus chinensis hay (LEYM) and oat hay (OATS) compared to corn stalks-based control diet (CORN) on rumen microbiota, metabolomics profiles, and muscle volatile flavor compounds in lambs through a multi-omics integration approach. Forty male lambs were randomly allocated into four dietary groups (n = 10/group) and fed a concentrated forage supplement for 91 days. From each group, six lambs (n = 6/group; totla 24) were slaughtered. Rumen fluid and longissimus dorsi muscle samples were collected for metagenomics, untargeted metabolomics, and volatile flavor analysis. Differential microbial taxa were identified using LEfSe analysis, followed by integrated Pearson correlation and MetoOrigin analysis to link microbiota, metabolites, and metabolic pathways. Associations with muscle volatile flavor compounds were also assessed. LEfSe analysis identified 4, 3, and 7 differentially abundant rumen microbial taxa in the ALFA, LEYM and OATS groups, respectively, compared to CORN. Integrated analysis showed these taxa correlated with 4, 9 and 11 rumen metabolites via 3, 11 and 7 microbial or host-microbial co-metabolic routes, respectively. These metabolic changes were strongly associated to alterations in muscle volatile flavor compounds. Particularly, the ALFA diet increased volatile compounds associated with fresh, grassy, floral, and citrus-like odors reduced mutton-related Pyrazine (2,5-dimethyl-). The LEYM diet reduced Pentaborane(9) and Pyrazine, which are associated with undesirable mutton like odors. The OATS diet increased 2-Nonanone and Phenylethyl Alcohol (fruity and floral smells), while suppressing n-Decanoic acid and n-Octanoic acid (associated with characteristic mutton aroma). These results showed that high-quality forages improve the mutton flavor by regulating the rumen micro-ecological network and associated metabolic pathways along the forage-microbiota-metabolites-muscle flavor axis. These findings provide a theoretical foundation for precise nutritional interventions aimed at enhancing meat quality in lambs.},
}

@article {pmid42382141,
year = {2026},
author = {Chigwada, AD and Tekere, M},
title = {Archaea-driven bioremediation of polyolefins and polyesters in extreme environments.},
journal = {Biodesign research},
volume = {8},
number = {3},
pages = {100092},
pmid = {42382141},
issn = {2693-1257},
abstract = {Global plastic production surpassed 436 million metric tonnes in 2023, with polyolefins, polyethylene and polypropylene, and polyesters, polyethylene terephthalate and polybutylene adipate terephthalate dominating the persistent fraction. In extreme environments, these recalcitrant polymers accumulate rapidly: hadal-trench sediments contain microplastic abundances of 71.1 items per kilogram dry weight, while bottom waters reach 2.06-13.51 particles per litre. Abiotic degradation is severely limited by hydrostatic pressure, hypersalinity, low temperature, and anaerobiosis. Although bacterial and fungal pathways have received primary attention, archaea adapted to polyextreme conditions represent an underexplored resource. Landmark discoveries include PET46, a lid-containing feruloyl esterase from uncultured Candidatus Bathyarchaeota in Guaymas Basin deep-sea sediments that hydrolyses semi-crystalline polyethylene terephthalate powder at rates comparable to established bacterial PETases while outperforming them on oligomers. Subsequent metagenomic prospecting identified GuaPA, a distinct Bathyarchaeia-derived PETase capable of film depolymerisation. Deep-sea plastispheres, hypersaline basins, and extraterrestrial analog sites further reveal archaeal colonisation and metabolic versatility. This review synthesises metagenomic, enzymatic, and community-level evidence, critically evaluates archaeal advantages relative to bacteria and fungi, addresses persistent gaps, including limited polyolefin mineralisation and cultivation bias, and outlines priorities for enzyme engineering and consortia design. The work advances sustainable bioremediation strategies aligned with climate-action goals and circular-economy frameworks in extreme and space environments.},
}

@article {pmid42382346,
year = {2026},
author = {He, B and Xiao, Z and Zou, L and Wei, J and Xiang, Z and Sang, F and Guo, X},
title = {Unveiling the unique gut microbial signatures in colorectal adenomas: establishment and validation of a cross-kingdom microbiome predictive model.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1854806},
pmid = {42382346},
issn = {1664-302X},
abstract = {BACKGROUND: Colorectal adenoma (CA), the main precancerous lesion of colorectal cancer (CRC), originates in approximately 85-90% of CRC cases. With increasing demands for early diagnosis and treatment, gut microbiome research has become a forefront area. While numerous studies have shown that gut bacteria are closely related to the development of colorectal adenomas and cancer, research on viruses, archaea, and fungi is limited.

METHODS: From January 2019 to January 2024, this study collected 296 fecal samples from multiple centers and performed metagenomic analysis using shotgun sequencing. Principal coordinate analysis (PCoA) was conducted based on Bray-Curtis distance at the species level, α-diversity was calculated, and LEfSe analysis identified differential microorganisms. A random forest model was developed to distinguish adenoma patients from healthy individuals, with performance evaluated through internal validation using Bootstrap sampling and external validation with an independent cohort.

FINDINGS: Significant differences in the relative abundance of certain bacteria (e.g., Phocaeicola_vulgatus and Prevotella_copri), fungi (Candida_albicans), archaea (Methanobrevibacter_oralis), and viruses (Streptococcus satellite phage Javan301) were observed in adenoma patients. Spearman correlation analysis revealed complex network relationships among these microorganisms. The prediction model achieved a mean AUC of 0.80 ± 0.05 and an external validation AUC of 0.75, demonstrating stability and generalizability.

CONCLUSION: This study shows significant cross-kingdom microbial signatures in colorectal adenoma patients, providing potential for developing new preventive and therapeutic methods. The predictive model, based on these differential microorganisms, exhibits robust and promising classification performance, offering potential for early adenoma detection.},
}

@article {pmid42382358,
year = {2026},
author = {Mengjia, C and Bujiang, W and Honghui, C and Qiying, H and Haojun, S},
title = {Biliary tract microbes and common bile duct stones: current status and prospects.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818256},
pmid = {42382358},
issn = {1664-302X},
abstract = {Common bile duct stones is a common digestive system disease, and about 5%-30% of patients with cholelithiasis are complicated with common bile duct stones. It poses significant challenges to clinical diagnosis and treatment. Although its occurrence is related to traditional factors such as abnormal bile composition and biliary dynamics disorders, the exact pathogenesis has not been fully clarified. In recent years, with the rapid development of high-throughput sequencing and metagenomics and other microbiome technologies, researchers have begun to pay attention to the role of biliary microbiota in the formation of common bile duct stones. More and more evidence indicates that the biliary tract microbes may has been associated with the occurrence and development of stones. This review firstly examines the literature implicating between biliary microorganisms and different types of common bile duct stones. We discuss the various mechanisms of action of biliary tract microorganisms in the occurrence of common bile duct stones. We also evaluated the specific value of microbial markers for diagnostic typing and prediction of recurrence.},
}

@article {pmid42382773,
year = {2026},
author = {Zhang, D and Song, Y and Bai, Y and Yan, J and Shen, R},
title = {Autoimmune GFAP astrocytopathy with eosinophils on cerebrospinal fluid cytology and isolated spinal cord lesions on MRI: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1865920},
pmid = {42382773},
issn = {1664-3224},
mesh = {Humans ; Female ; Adult ; *Glial Fibrillary Acidic Protein/immunology ; Magnetic Resonance Imaging ; *Astrocytes/immunology/pathology ; *Spinal Cord/pathology/diagnostic imaging/immunology ; *Eosinophils/immunology/pathology ; Biomarkers ; Autoantibodies/immunology ; },
abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy is an autoimmune inflammatory disorder of the central nervous system associated with GFAP-IgG. It most commonly presents as meningoencephalitis, myelitis, or meningoencephalomyelitis. Although MRI abnormalities in the brain and spinal cord are common, isolated spinal cord lesions without corresponding brain MRI abnormalities are uncommon and may pose a diagnostic challenge. Eosinophils identified on cerebrospinal fluid cytology have rarely been reported in this disorder.

CASE PRESENTATION: A 31-year-old woman presented with fever, headache, urinary retention, and meningeal irritation signs. Despite these findings, brain magnetic resonance imaging (MRI) was unremarkable, whereas spinal MRI revealed discontinuous patchy long-segment intramedullary lesions in the thoracic cord. Cerebrospinal fluid (CSF) analysis showed elevated opening pressure, pleocytosis, increased protein, and 10% eosinophils on cytological examination. Infectious studies, including CSF culture and metagenomic next-generation sequencing, were negative. Serum and CSF antibodies against aquaporin-4, myelin oligodendrocyte glycoprotein, and myelin basic protein were negative, whereas CSF GFAP-IgG was positive at a titer of 1:32, while serum GFAP-IgG was negative. Following high-dose intravenous methylprednisolone and an oral prednisone taper, the patient showed marked clinical, CSF, and radiological improvement, with complete resolution of thoracic cord lesions on follow-up MRI.

CONCLUSION: Isolated spinal cord lesions on MRI may represent an important clue to autoimmune GFAP astrocytopathy and should prompt consideration of this diagnosis even in the absence of brain MRI abnormalities. The presence of eosinophils on cerebrospinal fluid cytology may further suggest a distinct inflammatory profile and offer insight into the pathophysiology of the disease.},
}

Humans
Female
Adult
*Glial Fibrillary Acidic Protein/immunology
Magnetic Resonance Imaging
*Astrocytes/immunology/pathology
*Spinal Cord/pathology/diagnostic imaging/immunology
*Eosinophils/immunology/pathology
Biomarkers
Autoantibodies/immunology

@article {pmid42382960,
year = {2026},
author = {Zhang, WJ and Yang, Z and She, JQ and Wu, HL and Xia, ZY and Zhang, D and Suo, LG and Pan, Z and Zhang, Y and Wang, HZ and Hong, J and Zhang, C},
title = {Metagenomic analysis of ocular microbiome in aqueous humor from myopia, cataract, primary open angle glaucoma and Posner-Schlossman syndrome.},
journal = {International journal of ophthalmology},
volume = {19},
number = {7},
pages = {1235-1248},
pmid = {42382960},
issn = {2222-3959},
abstract = {AIM: To characterize the composition and functional features of the aqueous humor microbiome in common ocular diseases, including myopia, cataract, primary open angle glaucoma (POAG), and Posner-Schlossman syndrome (PSS).

METHODS: We performed metagenomic sequencing on 176 aqueous humor samples from patients with cataract (n=37), POAG (n=66), PSS (n=35), and myopia patients (n=38, as controls). Taxonomic profiling, functional annotation, and diversity analyses were conducted to characterize microbial communities, with adjustments for age and gender where appropriate. Associations between microbial features and clinical parameters were evaluated using correlation analyses.

RESULTS: We identified 6635 bacterial, 141 archaeal, 96 eukaryotic, and 108 viral operational taxonomic units (OTUs) in the aqueous humor. The microbiome was dominated by Actinomycetota and Pseudomonadota at the phylum level. Compared to myopia controls, POAG and PSS patients showed significantly reduced alpha diversity after age adjustment (P<0.05), whereas cataract patients showed no significant difference. Additionally, we identified disease-specific microbial signatures including enrichment of Cytomegalovirus (CMV) in PSS. Functional analysis revealed enrichment of distinct metabolic pathways. Finally, correlations were observed between microbiota/pathway abundance and clinical phenotype, though none remained significant after multiple testing correction.

CONCLUSION: This study provides a preliminary characterization of the aqueous humor microbiome in patients with POAG, PSS, cataract, and myopia controls. The identified microbial signatures and functional pathways offer new insights into potential microbiome-mediated mechanisms in ocular pathophysiology and may inform future diagnostic and therapeutic strategies.},
}

@article {pmid42383698,
year = {2026},
author = {Briggs, FB and Litwiler, J and Montini, F and Fereidan Esfahani, M and Sagen, J and McCauley, JL and Nelson, F and Gregory, S and Brambilla, R and Trapl, ES and Cooke Bailey, JN and Schwerdtfeger, LA and Cox, L and Weiner, H and Tobin, WO},
title = {Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261454207},
doi = {10.1177/13524585261454207},
pmid = {42383698},
issn = {1477-0970},
abstract = {BACKGROUND: Smokers with multiple sclerosis (MS) experience worse disease, yet underlying mechanisms remain unknown. Smoking disrupts bile acid and tryptophan metabolism in non-MS populations; both pathways involve host-microbiome co-metabolism and have been linked to MS.

OBJECTIVE: Determine whether smoking perturbs these metabolic pathways in MS and whether such alterations statistically mediate smoking's effect on MS severity.

METHODS: We analyzed serum bile acid, tryptophan, and tobacco-related metabolites across four independent MS cohorts (N = 266) using discovery-replication analyses. Mixed-effects regression assessed replicating associations with current smoking and nicotine exposure. Mediation analyses tested if replicating metabolites were potential mediators between smoking and MS severity. Hypothesis-generating metagenomic analyses explored smoking-associated gut-microbial shifts and metabolite correlations.

RESULTS: Current smokers and nicotine-exposed MS subjects had reductions in bile acids and tryptophan metabolites, notably indolepropionate, a neuroprotective, anti-inflammatory gut-microbial metabolite. Lower indolepropionate statistically mediated ~20% of smoking's adverse effect on MS severity. Metagenomic analyses identified potential smoking-enriched MS-linked taxa, and that indolepropionate broadly co-occurs with microbial networks (e.g. Lachnoclostridium appeared inversely associated with indolepropionate in smokers with MS).

CONCLUSION: Tobacco exposure disrupts host-microbiome tryptophan and bile acid metabolism in persons with multiple sclerosis, with indolepropionate depletion partially mediating disease severity, highlighting a potential mechanistic pathway warranting further investigation in MS smokers.},
}

@article {pmid42384485,
year = {2026},
author = {Crouch, AL and Rambeau, M and Li-Pook-Than, J and Snyder, MP and Henderson, JA and Yracheta, JM and Anderson, MZ},
title = {The gut microbiome of a Northern Plains tribe is in transition between global Indigenous and industrialized populations.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {116334},
doi = {10.1016/j.celrep.2025.116334},
pmid = {42384485},
issn = {2211-1247},
abstract = {The human gut is shaped by environmental factors, producing distinct microbial communities. Indigenous individuals practicing traditional lifestyles often harbor more diverse microbiota, with taxa often absent in industrialized people. However, little engagement has occurred with American Indian communities in North America who experienced forced relocation and dietary programs during colonization. Here, shotgun metagenomics profiled the gut microbiome of people from a Northern Plains tribe (NPT) reservation in comparison to 12 global populations engaged in traditional, agrarian, or industrialized lifestyles. Analysis of the 532 samples revealed that the NPT microbiota exhibited greater bacterial and archaeal diversity than industrialized populations but reduced diversity compared to global traditional and agrarian populations. Relative to the general United States population, NPT microbiomes encoded more virulence factor and microbial defense genes and fewer CAZyme-encoding genes. These findings suggest that the NPT gut microbiome is in transition between lifestyles associated with global Indigenous and industrialized populations.},
}

@article {pmid42384916,
year = {2026},
author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA},
title = {Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag422},
pmid = {42384916},
issn = {1367-4811},
abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13,897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on January 04, 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42384962,
year = {2026},
author = {Narayanan, AK and Philosof, A and Murali, R and Connon, SA and Wegener, G and Orphan, VJ},
title = {Viral communities from long-term anaerobic alkane-oxidizing enrichments encode predicted cell surface adhesion functions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag172},
pmid = {42384962},
issn = {1751-7370},
abstract = {The anaerobic oxidation of methane and higher C2+ alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free enrichments of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.},
}

@article {pmid42385223,
year = {2026},
author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A},
title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70359},
doi = {10.1002/mbo3.70359},
pmid = {42385223},
issn = {2045-8827},
mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; },
abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.},
}

*Rivers/microbiology/chemistry
*Metagenomics
Seasons
Bangladesh
*Bacteria/genetics/classification/drug effects/isolation & purification
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Metagenome
Water Quality
Shotgun Sequencing

@article {pmid42385456,
year = {2026},
author = {Hodžić, A and Cizek, V and Kunert, M and Berry, D and Collingro, A},
title = {Qualitative profiling of the gut-specific chlamydial population in Ixodes ricinus ticks.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {4},
pages = {102679},
doi = {10.1016/j.ttbdis.2026.102679},
pmid = {42385456},
issn = {1877-9603},
abstract = {Members of the phylum Chlamydiota are obligate intracellular bacteria increasingly recognized across a wide range of arthropod hosts, including ticks. In this study, we investigated the diversity and distribution of chlamydiae in Ixodes ricinus ticks and their potential association with Lyme borreliosis spirochetes. A total of 250 questing nymphal and female I. ricinus ticks were collected from three recreational sites in Vienna, Austria. Individual tick guts were screened for chlamydiae using pan-Chlamydiota PCR assays targeting the 16S rRNA gene, followed by sequencing for taxonomic identification. The presence and abundance of Borrelia burgdorferi sensu lato were quantified by specific qPCR to evaluate potential co-occurrence patterns. Chlamydiota DNA was detected in ticks from all investigated areas, with prevalence varying according to geography and developmental stage. Phylogenetic analyzes revealed high chlamydial diversity within the gut microbiome, predominantly comprising members of the metagenomic family MCF-D, followed by Parachlamydiaceae, Endochlamydiaceae, and Parasimkaniaceae. A positive, albeit not statistically significant, association between Chlamydiota and Borrelia was also observed. These findings indicate that the I. ricinus gut microbiome harbours a diverse assemblage of chlamydiae, suggesting potential ecological and functional relevance. Overall, our study highlights the importance of tissue-specific, single-tick analyzes for elucidating microbiome complexity and advances current understanding of Chlamydiota diversity in the tick vector. Further experimental and multi-omics studies are warranted to elucidate the biological roles of these bacteria in tick physiology and pathogen infection dynamics.},
}

@article {pmid42385542,
year = {2026},
author = {Zhong, X and Sun, Z and Wu, H and Li, E and Fang, G},
title = {Response of soil nitrogen-cycling functional genes and their associations to nitrogen enrichment in a typical subtropical estuary (Min River), Southeast China.},
journal = {Marine pollution bulletin},
volume = {232},
number = {},
pages = {120078},
doi = {10.1016/j.marpolbul.2026.120078},
pmid = {42385542},
issn = {1879-3363},
abstract = {Soil N-cycling functional genes are easily modified by environmental changes, but insufficient information is available regarding the response of their elaborate associations to nitrogen (N) enrichment in estuarine marsh ecosystem. In this study, a field experiment with four N enrichment levels (NN, 0.0 g N m[-2] yr[-1]; NL, 37.5 g N m[-2] yr[-1]; NM, 50.0 g N m[-2] yr[-1]; and NH, 100.0 g N m[-2] yr[-1]) was conducted in a typical Cyperus malaccensis marsh in the Min River estuary of southeastern China. After 28 and 40 months of sustained N additions (represented by T28 and T40 periods, respectively), the potential impacts of N enrichment on soil N-cycling functional genes and their associations were investigated by metagenomic sequencing. Results showed that although the composition of functional microbial communities showed causality with N enrichment levels, its variation was primarily driven by N-enriched duration as evidenced by the higher interpretability (64.7%). With prolonged the experiment, the diversity of soil N-cycling microbial communities dropped markedly while their richness showed no statistically significant alteration. Within each sampling period, the relative abundances of functional genes involved in organic N metabolism (ONM, glnB, GDH2 and GLT1), assimilatory nitrate reduction (ANRA, narB, nirA, NR and NIT-6), denitrification (nirS, norC and napB), N fixation (nifK/D, vnfH/K/G and anfG), dissimilatory nitrate reduction (DNRA, nrfA and nirB/D), N transport (nrtC/B) and nitrification (pmoB/C-amoB/C) significantly increased with increasing N additions. Compared with the T28 period, the relative abundances of genes involved in ONM (GDH2 and K00261_gdhA), denitrification (narI and nirS), N fixation (nifD/H and vnf/H/K) and N transport (NRT2 and nrtA/C) elevated significantly at T40 period, while those participated in DNRA (nrfH), nitrification (hao) and anammox (hzsB/C) declined markedly. Under N-enriched conditions, the network complexity of functional genes displayed decreases in the LN and MN treatments, followed by a significant increase in the HN treatment. With prolonged the experiment, the positive correlations among functional genes were weakened and the succession of functional microbial communities was driven in a more functionally specialized direction by a few dominant species. This paper found that sustained N enrichment drove the phased reconstruction of gene networks with a continuous weakening of positive associations among functional genes. The findings can guide the policymaking of targeted N load control and estuarine marsh conservation.},
}