@article {pmid42276012,
year = {2026},
author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T},
title = {IgG4-related disease has a specific intestinal microbiota signature.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106326},
pmid = {42276012},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; *Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology ; Middle Aged ; Flow Cytometry ; Aged ; Immunoglobulin G ; Adult ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; },
abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.

METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).

FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.

INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.

FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.},
}

Humans
*Gastrointestinal Microbiome
Female
RNA, Ribosomal, 16S/genetics
Male
*Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology
Middle Aged
Flow Cytometry
Aged
Immunoglobulin G
Adult
Cross-Sectional Studies
Feces/microbiology
Metagenomics/methods

@article {pmid42413090,
year = {2026},
author = {Hidalgo, M},
title = {From microscopy to metagenomics: Evolution and challenges in clinical microbiology.},
journal = {Biomedica : revista del Instituto Nacional de Salud},
volume = {46},
number = {Sp. 1},
pages = {5-7},
doi = {10.7705/biomedica.8421},
pmid = {42413090},
issn = {2590-7379},
}

@article {pmid42414278,
year = {2026},
author = {Zhao, C and Li, Z and Liu, M and Bao, L and Yuan, C and Zhao, Y and Wu, K and Qiu, M and He, Y and Zhang, N and Hu, X and Zhang, Y and Han, F and Fu, Y},
title = {Dissection of mammary cell landscape in ruminal dysbiosis-induced mastitis by single-cell RNA sequencing.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01076-7},
pmid = {42414278},
issn = {2055-5008},
support = {32402956//National Natural Science Foundation of China/ ; 32422086//National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
abstract = {Growing evidence has underscored the contribution of gastrointestinal dysbiosis to the onset of mastitis, however, the local cellular changes responsible for the pathological processes of ruminal dysbiosis-induced mastitis (RDIM) are still unclear. Here, we profiled mammary single-cell transcriptomes in goats with RDIM, complemented by ruminal metagenomic and untargeted metabolomic analyses of rumen fluid and serum. Our results indicated that compromised lactation and barrier integrity in LumSec were linked to RDIM. Increased inflammatory macrophages and DCs, γδT and CD4[+] TH cell populations, along with reduced Tex/Treg and B cells were implicated in RDIM. Fibroblasts exhibited increased gene expression related to the extracellular matrix, while lymphatic endothelial cells and Vas-venous structures displayed elevated inflammatory gene expression. Tight junction integrity and apelin signaling pathways were compromised in Vas-capillary during RDIM. Notably, metagenomic analysis indicated that RDIM correlated with reduced ruminal microbial diversity and shifts in microbial community composition. Key metabolic pathways including microbial tryptophan metabolism, secondary bile acid biosynthesis, and vitamin metabolism were significantly diminished during RDIM. Furthermore, tryptophan-induced AHR signaling and secondary bile acid receptor GPBAR1, primarily expressed in vascular endothelial cells and macrophages, respectively, which were reduced during RDIM. Collectively, our study provides a comprehensive atlas of mammary cell landscapes in RDIM, which may enhance the understanding of mastitis pathogenesis.},
}

@article {pmid42415156,
year = {2026},
author = {Houvessou, GM and Antonieta Alfane, NW and Mahoche, M},
title = {Dynamic, transition and variation of cervicovaginal microbiome and HPV infection and cervical dysplasia and cancer: a systematic review.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-026-00777-0},
pmid = {42415156},
issn = {1750-9378},
abstract = {BACKGROUND: Cervical cancer is the fourth most common malignancy in women worldwide, with approximately 660,000 new cases and 350,000 deaths annually. The burden falls disproportionately on low- and middle-income countries. Although persistent infection with high-risk HPV (hrHPV) is the necessary cause, most infected women clear the virus spontaneously, implicating additional cofactors, including the cervicovaginal microbiome in determining oncogenic outcomes.

METHODS: PubMed was searched through September 10, 2024, to identify longitudinal studies assessing cervicovaginal microbiota in relation to HPV infection or cervical lesion outcomes at two or more time points. Methodological quality was evaluated using the Newcastle-Ottawa Scale (NOS). Given the substantial heterogeneity, a structured thematic synthesis was performed across three predefined domains: (a) baseline microbiome composition and clinical outcomes; (b) community state type (CST) dynamics and temporal stability; and (c) microbiome changes following treatment.

RESULTS: Twelve studies enrolling 1,663 women across 11 countries met inclusion criteria. NOS scores ranged from 4 to 9. Lactobacillus-dominated CSTs at baseline were consistently associated with HPV clearance and CIN regression, while Lactobacillus-depleted states showed higher transition rates and unfavourable outcomes. Prior L.iners (CST III) dominance was repeatedly linked to favourable outcomes, although evidence on this species remains conflicting. Cervicovaginal dysbiosis frequently preceded HPV persistence or lesion progression.

CONCLUSION: Sustained Lactobacillus-dominated CST stability, rather than dominance by any single species, is the most consistent microbiome factor associated with favourable HPV and cervical lesion outcomes. Standardized longitudinal designs incorporating metagenomic sequencing, frequent sampling intervals, and rigorous confounder adjustment are needed to advance mechanistic understanding.

Not applicable.},
}

@article {pmid42415193,
year = {2026},
author = {Lechleiter, N and Wedemeyer, J and Junker, J and Sehl-Ewert, J and Homeier-Bachmann, T},
title = {Gastrointestinal parasites of red and roe deer investigated via metagenomics and histology.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42415193},
issn = {1756-3305},
support = {Grant No. 28KIDA001//Federal Ministry of Agriculture, Food and Regional Identity (BMLEH) - Germany/ ; },
mesh = {Animals ; *Deer/parasitology ; *Metagenomics/methods ; Feces/parasitology ; *Gastrointestinal Tract/parasitology/pathology ; *Parasites/genetics/isolation & purification/classification ; Seasons ; Animals, Wild/parasitology ; *Intestinal Diseases, Parasitic/veterinary/parasitology ; },
abstract = {BACKGROUND: Some of the most common pathogens in wildlife are parasites. Since wild cervids are phylogenetically close to a lot of our livestock species, disease dynamics can arise, for example, through shared parasites. Insight into regional patterns, shaped by ecosystems and cross-species relationships, is only slowly emerging and the species-specific knowledge about lifecycle and ecology of parasites is often based on cross-sectional studies and therefore limited. Possibilities for broad and easy investigation of parasites could be the key to widen our understanding of these systems and processes.

METHODS: Here, shotgun metagenomics were investigated as a method for parasite detection in fecal samples of wild ungulates. The results were further validated by histopathological examination of gastrointestinal tissues.

RESULTS: The results from the two methods are in line with similar studies, and while not being identical, complement each other.

CONCLUSIONS: This investigation revealed parasite composition and seasonal dynamics in two species of wild cervid red deer (Cervus elaphus) and roe deer (Capreolus capreolus).},
}

Animals
*Deer/parasitology
*Metagenomics/methods
Feces/parasitology
*Gastrointestinal Tract/parasitology/pathology
*Parasites/genetics/isolation & purification/classification
Seasons
Animals, Wild/parasitology
*Intestinal Diseases, Parasitic/veterinary/parasitology

@article {pmid42415408,
year = {2026},
author = {Li, J and Liu, P and Zhang, Q and Zhao, R and Zhang, J and Zheng, X and Li, B and Zhang, XX},
title = {Temperate Phages Mediate Dual Adaptive Mechanisms That Enhance Microbial Resilience in Antibiotic-Contaminated Wastewater Treatment Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c07049},
pmid = {42415408},
issn = {1520-5851},
abstract = {Temperate phages play crucial ecological roles in engineered microbial communities, yet their adaptive strategies under antibiotic stress remain unclear. Here, metagenomic analysis was used to investigate how temperate phages facilitate host adaptation in activated sludge acclimated to chloramphenicol (CAP). Antibiotic stress markedly reshaped bacterial and temperate phage communities, with dominant degraders (e.g., Sphingomonas and Caballeronia) reaching relative abundances of 6.5-42.0%. Temperate phages exhibited specific adaptive responses by significantly enriching antibiotic resistance genes, including multidrug (arlR and mtrA) and peptide (bcrA) resistance genes, resulting in a 1.56-4.15-fold increase in the phage-derived resistome relative to the control. They also mediated general adaptive responses by encoding auxiliary genes involved in oxidative stress mitigation, DNA repair, biofilm formation, and antiviral defense. Host-phage linkage prediction identified 1045 phage-bacteria interactions, including 11 ARG-harboring viral operational taxonomic units associated with dominant CAP-degrading hosts. Collectively, our findings reveal that temperate phages facilitate microbial resilience in antibiotic-stressed environments by delivering mutualistic genetic traits, encompassing both specific (antibiotic resistance genes) and general (antiviral defense, metabolic, and stress mitigation) adaptive responses, highlighting their ecological significance and potential for enhancing the stability and performance of wastewater treatment systems under pharmaceutical stress.},
}

@article {pmid42415516,
year = {2026},
author = {Zhou, G and Liu, J and Liu, F and Xiao, Y and Graham, EB and Kuzyakov, Y and Ye, M and Xin, X and Chen, L and Zhang, C and Ma, D and Wu, Z and Zhou, Z and Zhou, J and Liang, Y and Zhang, J},
title = {Resource-Dependent Metabolic and Biogeochemical Consequences of Viruses in Agricultural Soils.},
journal = {Global change biology},
volume = {32},
number = {7},
pages = {e70994},
doi = {10.1111/gcb.70994},
pmid = {42415516},
issn = {1365-2486},
support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; SKLSSA2501//Major Program of State Key Laboratory of Soil and Sustainable Agriculture/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; DE-AC05-76RL01830//Department of Energy, Office of Science, Biological and Environmental Research program and by Pacific Northwest National Laboratory/ ; },
mesh = {*Soil Microbiology ; Agriculture ; *Soil/chemistry ; Carbon/metabolism ; *Viruses/genetics/metabolism ; Metagenome ; Fertilizers ; },
abstract = {Soil viruses are crucial for microbial life, biogeochemical cycles of carbon and nutrients, and for microbial necromass formation. We hypothesized that the effects of viruses on these processes depend on organic matter and nutrient availability in soils. Here, we combined a 34-year long-term fertilization trial, 150 sequenced soil metagenomes, and microcosm experiments to explore how viruses modulate carbon and nutrient dynamics depending on resource availability. We uncovered 2789 viral populations (vOTUs) grouping into 301 viral clusters, 91% of which were previously unknown. Organically fertilized soils harbored most lytic viruses carrying diverse element cycling-related auxiliary viral genes (AVGs) acquired through co-evolution and horizontal gene transfer. Synthesis and heterologous expression assays further indicated that four AVGs (i.e., cbhA, pel, wbpD, GT2) had higher transcript levels in Escherichia coli under nutrient rich than nutrient poor conditions. Addition of virus particles to soils raised microbial carbon use efficiency (CUE; biomass production relative to carbon uptake) and accelerated microbial turnover leading to boosted microbial necromass formation by 14%. Conversely, in soils without organic fertilizers, viruses facilitate bacterial adaptation to stress (e.g., defense system and interference competition) and accelerate microbial decomposition of organic matter. 35 days after virus addition, CO2 and N2O emissions increased by 41% and 52%, respectively. Finally, we propose the Viral Entombing-Priming (VEP) framework to describe the contrasting roles of viruses in carbon and nutrient dynamics depending on soil fertility. This work reveals the viral "Matthew effect" (the rich get richer and the poor get poorer) in resource-rich and resource-poor soils and could unlock nature-based pathways to raise carbon and nutrient retention for sustainable agriculture.},
}

*Soil Microbiology
Agriculture
*Soil/chemistry
Carbon/metabolism
*Viruses/genetics/metabolism
Metagenome
Fertilizers

@article {pmid42415518,
year = {2026},
author = {Dolivet-Maréchal, M and Palacin-Lizarbe, C and Siljanen, HMP and Paul, D and Delort, A and Gervaix, J and Creuzé des Châtelliers, C and Schmidt, S and Cognat, M and Sebag, D and Taugourdeau, O and Schübert, C and Labourdette, N and Bertrand, I and Rossi, LMW and Le Roux, X and Richaume, A and Florio, A},
title = {Vegetation Increases CH4 Emissions and Methanotroph Diversity in Marine Sediments.},
journal = {Global change biology},
volume = {32},
number = {7},
pages = {e70989},
doi = {10.1111/gcb.70989},
pmid = {42415518},
issn = {1365-2486},
support = {101037097//EU Horizon2020/ ; ANR-17-EURE-0018//Graduate School H2O'Lyon/ ; },
mesh = {*Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; France ; *Zosteraceae/microbiology/metabolism ; },
abstract = {Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH4) emissions, whose microbial and environmental descriptors in Zostera noltii meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH4 fluxes, CH4-producing and consuming microbial communities and sediment physicochemical parameters in Z. noltii meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH4 fluxes were measured at low tide during daytime conditions, providing standardized estimates of peak emissions. Microbial communities were characterized using targeted metagenomics of three functional genes (mcrA, mmoX, pmoA) and quantitative PCR. CH4 fluxes were higher in vegetated than bare sediments (24.4 ± 2.6 vs. 9.4 ± 0.7 μmol m[-2] day[-1]). Mixed linear models and random forest analyses identified C accumulation rate and CO2 flux as the strongest positive descriptors of CH4 fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera (mcrA-Methanolobus, mmoX-Methylocella, pmoA-Methylococcus, Methyloglobulus) emerged as abundant, seagrass-associated, correlated with CH4 fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH4 fluxes than gene abundance or a specific genus. Findings indicate Z. noltii meadows enhance C burial and CH4 emission, with methanotroph diversity potentially mitigating CH4 emissions. Our results provide the first integrated assessment of CH4 fluxes and their descriptors in Z. noltii meadows, based on limited temporal coverage capturing the daytime peak emission conditions, highlighting the intertwined nature of C burial and CH4 emissions and the need to account for both in blue C climate assessments.},
}

*Methane/metabolism/analysis
*Geologic Sediments/microbiology/chemistry
France
*Zosteraceae/microbiology/metabolism

@article {pmid42415914,
year = {2026},
author = {Zhang, M and Jiang, J and Yang, B and Zhao, W and Zhang, J and Ma, T and Wang, H},
title = {Integrated multi-omics analysis reveals distinct microbiota-metabolite signatures and a novel HCN2-2-hydroxybutyric acid interaction in inflammatory bowel disease.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1843166},
pmid = {42415914},
issn = {2296-861X},
abstract = {INTRODUCTION: Gut microbiota-derived short-chain fatty acids (SCFAs) exert critical regulatory functions in inflammatory bowel disease (IBD). However, integrated profiling of fecal SCFA signatures alongside gut microbiota composition in ulcerative colitis (UC) and Crohn's disease (CD) remains insufficiently characterized. Furthermore, the molecular mechanisms through which microbiota metabolites engage host protein targets warrant systematic investigation.

METHODS: This study enrolled 30 patients with UC, 20 with CD, and 30 healthy controls, with paired fecal collection. Gut microbiota composition was analyzed by deep metagenomic sequencing, and SCFA concentrations were quantified by gas chromatography-mass spectrometry. Multi-omics integration, correlation network analysis, and Bayesian kernel machine regression were employed to resolve microbiota-metabolite associations. An integrated computational pipeline incorporating molecular dynamics simulations was constructed to evaluate the thermodynamic stability and binding modalities of metabolite-protein interactions.

RESULTS: Both UC and CD patients exhibited significantly reduced gut microbial α-diversity and characteristic community structure alterations. Fecal metabolomic profiling revealed synchronous elevation of 2-Hydroxybutyric acid (2-HB) and isocaproate in both patient groups, whereas butyrate reduction was restricted to UC. Multi-omics correlation analysis identified significant associations between 2-HB and unclassified Veillonella species as well as specific functional modules. Molecular dynamics simulations with an aggregate sampling time of 100 ns revealed a structural basis for the formation of a stable complex between 2-HB and the hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2). This interaction was primarily mediated by electrostatic interactions involving Arg659, Arg618, and Arg617 residues alongside hydrophobic contacts, suggestive of potential allosteric modulation.

CONCLUSIONS: This study identifies 2-HB and isocaproate as shared fecal metabolic markers across IBD and provides a structural rationale for the interaction between 2-HB and HCN2. The druggability profile of HCN2 supports its prioritization for mechanistic investigation, with the caveat that functional validation is prerequisite to any inference of therapeutic relevance.},
}

@article {pmid42416069,
year = {2026},
author = {Wang, J and Lin, K and Zhong, Y and Wu, Z and Lu, T and Lu, W and Wang, W and Ma, C},
title = {Disseminated Mycobacterium kansasii infection with osseous involvement in anti-interferon-γ autoantibody-associated adult-onset immunodeficiency: a case report and literature review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1841472},
pmid = {42416069},
issn = {1664-3224},
mesh = {Humans ; Male ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/immunology/diagnosis/drug therapy ; *Mycobacterium kansasii/immunology ; *Interferon-gamma/immunology ; *Autoantibodies/immunology ; *Immunologic Deficiency Syndromes/immunology/complications/diagnosis ; },
abstract = {BACKGROUND: Anti-interferon-γ autoantibody-associated adult-onset immunodeficiency is a rare acquired immunodeficiency that predisposes patients to recurrent or disseminated opportunistic infections, particularly nontuberculous mycobacterial (NTM) infections. Disseminated Mycobacterium kansasii infection in this setting is uncommon and may radiologically mimic malignancy, leading to diagnostic delay.

CASE PRESENTATION: A 53-year-old Chinese man with untreated chronic hepatitis B virus (HBV) infection presented with cough, chest pain, and back pain. Chest computed tomography and ^18F-FDG PET/CT revealed a left hilar mass, mediastinal and hilar lymphadenopathy, and extensive FDG-avid skeletal lesions, initially suggesting lung cancer with bone metastases. However, repeated pathological examinations, including bronchoscopic brushing, endobronchial ultrasound-guided transbronchial needle aspiration, and cervical lymph node aspiration, failed to confirm malignancy. Targeted next-generation sequencing of bronchoalveolar lavage fluid and metagenomic next-generation sequencing of vertebral tissue both identified Mycobacterium kansasii, supporting disseminated infection with pulmonary and skeletal involvement. Subsequent immunologic testing demonstrated elevated anti-IFN-γ autoantibodies, supporting a clinical diagnosis of AIGA-associated disseminated M. kansasii infection. Antimycobacterial therapy was initiated, but further treatment was complicated by postoperative cholestatic jaundice and high-level HBV viremia, which precluded immediate escalation to immune-directed therapy.

CONCLUSIONS: AIGA-associated disseminated Mycobacterium kansasii infection can closely mimic lung cancer with bone metastases. In patients with tumor-like pulmonary and skeletal lesions but repeatedly nondiagnostic pathology, early integration of pathogen detection and anti-IFN-γ autoantibody testing may help shorten diagnostic delay.},
}

Humans
Male
Middle Aged
*Mycobacterium Infections, Nontuberculous/immunology/diagnosis/drug therapy
*Mycobacterium kansasii/immunology
*Interferon-gamma/immunology
*Autoantibodies/immunology
*Immunologic Deficiency Syndromes/immunology/complications/diagnosis

@article {pmid42416141,
year = {2026},
author = {Chen, D and Li, X and Wang, Z and Huang, L and Qin, L},
title = {Complementary mNGS and traditional testing for bloodstream infections.},
journal = {Open medicine (Warsaw, Poland)},
volume = {21},
number = {1},
pages = {20261494},
pmid = {42416141},
issn = {2391-5463},
abstract = {Bloodstream infections (BSIs) require rapid and accurate etiological diagnosis to guide timely antimicrobial therapy. Conventional diagnostic approaches, particularly blood culture, remain indispensable for antimicrobial susceptibility testing; however, they are limited by prolonged turnaround time and reduced sensitivity, especially following prior antibiotic exposure. Metagenomic next-generation sequencing (mNGS) has emerged as a culture-independent and hypothesis-free diagnostic tool capable of detecting a broad spectrum of pathogens directly from clinical samples. This approach is particularly advantageous for identifying rare, fastidious, and polymicrobial infections, as well as infections in immunocompromised patients. However, its clinical application remains constrained by challenges in distinguishing infection from colonization, interpreting antimicrobial resistance signals, and variability in bioinformatics pipelines. Thus, in the era of integrated diagnosis, mNGS does not replace but powerfully complements traditional methods. Furthermore, we propose a dynamic evidence-weighted integrated diagnostic framework to guide real time clinical decision and improve the clinical applicability of mNGS in bloodstream infections.},
}

@article {pmid42416274,
year = {2026},
author = {Dang, Y},
title = {How mNGS transforms care for non-verbal elderly stroke patients with pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1814320},
pmid = {42416274},
issn = {2235-2988},
mesh = {Humans ; Aged ; Retrospective Studies ; *Stroke/complications ; Female ; Male ; Sputum/microbiology/virology ; Aged, 80 and over ; *Pneumonia/diagnosis/microbiology/etiology/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Bacteria/isolation & purification/genetics/classification ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {BACKGROUND: Stroke-associated pneumonia (SAP) is a severe complication in non-verbal elderly stroke patients, with diagnosis hindered by the low sensitivity and slow turnaround of conventional microbial culture.

METHODS: A single-center retrospective cohort study was conducted on 64 non-verbal elderly SAP patients (≥65 years) admitted to Guangxi Jiangbin Hospital from 2018 to 2022, divided into an mNGS group (n=30, sputum/BALF tested by metagenomic next-generation sequencing) and a control group (n=34, conventional culture). Propensity score matching (1:1) was used to balance baseline characteristics, and clinical outcomes and pathogen detection efficiency were compared between groups. Multivariable Cox regression adjusted for hypoalbuminemia, electrolyte disturbance and stroke severity.

RESULTS: mNGS detected more bacterial pathogens (37 vs.27 in sputum, 37 vs.21 in BALF) and identified 3 viral and 2 atypical pathogens undetectable by culture, with a negative rate of 13.3% (vs.20.0% for sputum culture, 43.3% for BALF culture). 73.3% of mNGS group patients received antimicrobial therapy adjustment. After adjustment, the mNGS group had notably higher 28-day (96.7% vs.76.5%; adjusted HR = 0.32, P = 0.032) and 90-day survival (76.7% vs.44.1%; adjusted HR = 0.41, P = 0.024), lower invasive mechanical ventilation rate (40.0% vs.64.7%, P = 0.048), shorter median antibiotic duration (14 vs.21 days, P = 0.016) and lower median hospitalization costs (¥32,450 vs.¥89,310, P < 0.001).

CONCLUSION: mNGS enables more comprehensive pathogen detection in non-verbal elderly SAP patients, guides targeted antimicrobial therapy, and is associated with improved survival and reduced healthcare resource consumption. However, large-sample multicenter prospective studies are needed to validate these findings due to the study's limitations.},
}

Humans
Aged
Retrospective Studies
*Stroke/complications
Female
Male
Sputum/microbiology/virology
Aged, 80 and over
*Pneumonia/diagnosis/microbiology/etiology/drug therapy
Bronchoalveolar Lavage Fluid/microbiology/virology
Bacteria/isolation & purification/genetics/classification
Anti-Bacterial Agents/therapeutic use
High-Throughput Nucleotide Sequencing
Metagenomics

@article {pmid42416386,
year = {2026},
author = {Wicaksono, WA and Köberl, M and White, RA and Jansson, JK and Jansson, C and Cernava, T and Berg, G},
title = {Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface.},
journal = {Plant and soil},
volume = {523},
number = {2},
pages = {811-825},
pmid = {42416386},
issn = {0032-079X},
abstract = {AIMS: Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere.

METHODS: The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing.

RESULTS: We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific.

CONCLUSIONS: The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-024-07097-5.},
}

@article {pmid42416834,
year = {2026},
author = {Zhao, Z and Lu, M and Ying, Y},
title = {Full-term pregnancy after severe gestational psittacosis: a case report and literature review.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1836961},
pmid = {42416834},
issn = {1663-9812},
abstract = {Gestational psittacosis is a rare but high-risk infection caused by Chlamydia psittaci, often leading to severe maternal complications and adverse fetal outcomes. We report a unique case of a 30-year-old woman at 22 + 5 weeks of gestation who presented with acute high fever and respiratory failure following bird exposure. The diagnosis of C. psittaci infection was rapidly confirmed via blood metagenomic next-generation sequencing (mNGS). Following multidisciplinary consultation involving obstetricians, infectious disease specialists, intensivists, respiratory physicians, clinical pharmacists, and neonatologists, an individualized management plan was established to balance maternal infection control, respiratory support, fetal monitoring, and medication safety during pregnancy. The patient was treated with intravenous azithromycin combined with corticosteroids, and her clinical condition stabilized within 2 weeks. Notably, the pregnancy continued to term, resulting in the delivery of a healthy male infant. To our knowledge, this represents the first reported case worldwide of a successful full-term delivery following gestational psittacosis. This case underscores the critical importance of early mNGS-based diagnosis, multidisciplinary collaboration, and appropriate antimicrobial therapy in optimizing maternal and neonatal outcomes, providing a valuable clinical reference for managing this life-threatening zoonosis during pregnancy.},
}

@article {pmid42417135,
year = {2026},
author = {Walker, WB and Neven, LG},
title = {eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/jisesa/ieag062},
pmid = {42417135},
issn = {1536-2442},
support = {//Washington State Department of Agriculture Specialty Crops Block/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA, Environmental/analysis ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Sequence Analysis, DNA ; Insecta/genetics/classification ; Extrachromosomal DNA ; },
abstract = {Timely identification of biological species is often needed for various purposes, including economic reasons, and advances in DNA sequencing technologies have greatly augmented the ability to identify species through the application of DNA barcoding. One such method examines environmental DNA (eDNA) to sample the presence of organisms in an environment without necessarily having direct access to the whole organisms. In recent years, multiple high-throughput sequencing platforms have emerged, and there are differences in the efficiency, effectiveness, and economics across these platforms. In this report, we examine the application of two platforms, from PacBio and Oxford Nanopore Technologies, to sequence COI amplicons from nine barcoded yard waste samples that we previously studied for a different purpose. Here, we observed consistencies across the platforms in the identification of operational taxonomical units (OTUs) from broad swaths of life, most prominently including Bacteria, Amoebozoa, Fungi, Arthropoda, Nematoda, Spiralia, and Viridiplantae. Other taxonomical groupings were also tentatively identified. However, limitations in coverage of the diversity of COI sequences in the public databases rendered species-level identification impossible for many of the OTUs. Insect species were the best represented across all barcoded samples, and both sequencing platforms regarding percentage identity to the best BLAST hits in the databases. Following this, we took an in-depth look at the knowledge of the presence of highly matched species in the locality from where the eDNA samples were derived. Strengths and limitations of this approach in the analysis of eDNA are discussed.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*DNA, Environmental/analysis
High-Throughput Nucleotide Sequencing/methods
Biodiversity
Sequence Analysis, DNA
Insecta/genetics/classification
Extrachromosomal DNA

@article {pmid42417706,
year = {2026},
author = {Oliveira, MEAS and Lucino, D and Garcia, GJY and Bertozzi, BG and Bassinello, PZ and Colombari Filho, JM and Piler de Carvalho, CW and Góes-Neto, A and Rocha, LO and Kabuki, DY and Freitas Silva, O and Takeiti, CY},
title = {Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c02819},
pmid = {42417706},
issn = {1520-5118},
abstract = {Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.},
}

@article {pmid42417716,
year = {2026},
author = {Wang, Y and Luo, X and Ji, Y and Zhu, T and Zhao, Y and Tong, Y and Ni, BJ and Liu, Y},
title = {1,3-Dichloro-5,5-dimethylhydantoin (DCDMH)-Driven Sludge Pretreatment for Organic Carbon Valorization: Mechanistic Insights into Controlled Oxidative Disruption and Hormesis-Mediated Metabolic Reshaping.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16484},
pmid = {42417716},
issn = {1520-5851},
abstract = {Organic carbon valorization via anaerobic sludge fermentation is intrinsically constrained by biopolymer recalcitrance and methanogenic diversion. We introduced 1,3-Dichloro-5,5-dimethylhydantoin (DCDMH) pretreatment leveraging controlled oxidative disruption and microbial metabolic regulation to boost short-chain fatty acid (SCFA) production. At optimal dosage (0.025 g/g TSS), SCFA yield increased by 192.1%, driven by enhanced substrate liberation and biochemical conversion. Molecular docking and 2D-COS FTIR analyses collectively indicate that the N-Cl moiety of DCDMH preferentially oxidized hydrophobic proteins within extracellular polymeric substances, while the derived HClO could penetrate cells to damage intracellular components. This dual action disrupted structural integrity, accelerating macromolecular substrate release and conversion, and enriching stress-tolerant hydrolytic/acidogenic bacteria. Sustained HClO release established oxidative stress wherein reactive oxygen species (ROS) functioned as metabolic signals beyond mere damage indicators. Moderate intracellular ROS stress stimulated substrate acidogenesis while suppressing methanogenic carbon sinks, and enhanced the gene abundances associated with antioxidant defenses and acidogenic pathways. Crucially, this work reveals for the first time the hormetic effect of DCDMH-derived HClO on acidogenic metabolism, providing a new insight into the application of chlorine-containing disinfectants in related fields.},
}

@article {pmid42417728,
year = {2026},
author = {Välikangas, T and Fritze, H and Pitkänen, JM and Peltoniemi, K and Järvi-Laturi, E and Christensen, TR and Väisänen, M and Lämsä, J and Paavola, R and Hultman, J},
title = {Environmental variation structures northern peatland soil microbiome composition and function in a reindeer herding area exclosure experiment.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag072},
pmid = {42417728},
issn = {1574-6941},
abstract = {Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect soil microorganisms involved in methane (CH4) cycling and nitrous oxide (N2O) production/reduction. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH4 flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH4 fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.},
}

@article {pmid42417745,
year = {2026},
author = {Antunes, TPB and Antunes, E},
title = {Next-generation molecular tools in veterinary parasitology: advances, challenges, and perspectives in the diagnosis of emerging parasites.},
journal = {Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria},
volume = {35},
number = {2},
pages = {e016525},
doi = {10.1590/S1984-29612026023},
pmid = {42417745},
issn = {1984-2961},
mesh = {Animals ; *Parasitic Diseases, Animal/diagnosis/parasitology ; *Parasitology/methods/trends ; *Communicable Diseases, Emerging/diagnosis/veterinary/parasitology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Advances in molecular technologies have revolutionized veterinary parasitology, providing highly sensitive and specific tools for the detection, characterization, and surveillance of parasites in domestic and wildlife species. Approaches such as next-generation sequencing, metabarcoding, and metagenomics have significantly enhanced the ability to identify previously unknown or uncultivable species, detect complex coinfections, and deepen our understanding of parasite genetic diversity, evolution, and population dynamics. Beyond their impact on laboratory diagnostics, these tools have proven essential for the early detection of zoonoses, environmental monitoring, and the development of integrated surveillance systems under the One Health framework. This review synthesizes the major technological advances and their practical applications in both global and Latin American contexts, particularly Brazilian, highlighting how the incorporation of these tools has the potential to transform strategies for surveillance, prevention, and response to emerging and re-emerging parasitic diseases. Challenges related to standardization, cost, infrastructure, and technology transfer are also discussed, along with future perspectives for large-scale implementation aimed at strengthening diagnostic capacity and epidemiological surveillance in the face of increasing parasitic threats in a rapidly changing world.},
}

Animals
*Parasitic Diseases, Animal/diagnosis/parasitology
*Parasitology/methods/trends
*Communicable Diseases, Emerging/diagnosis/veterinary/parasitology
High-Throughput Nucleotide Sequencing

@article {pmid42417967,
year = {2026},
author = {Lin, Z and Ma, Y and Wu, H and Lu, Z and Zhuang, X and Zhao, M and Peng, S and Lin, F and Zheng, K and Li, Z},
title = {Effects of lemongrass (Cymbopogon citratus) on slaughter performance, meat quality, and intestinal health in Muscovy ducks.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/00071668.2026.2670474},
pmid = {42417967},
issn = {1466-1799},
abstract = {1. This study tested the effects of dietary lemongrass (LG) supplementation on production performance, meat quality and intestinal health of Muscovy ducks. A 42 d feeding trial used four treatment diets (0%, 2%, 4% or 6% LG) fed as part of a commercial diet after 20 d rearing from day old on a basal diet.2. The results revealed that 6% LG supplementation significantly improved slaughter performance, notably increasing full eviscerated weight (p < 0.05).3. Meat nutritional quality was enhanced by higher amino acids (cysteine and methionine in breast muscle; tyrosine in leg muscle) and beneficial polyunsaturated fatty acids (PUFA) including C22:6n3 (DHA) and C20:5n3 (EPA; p < 0.05).4. Intestinal health was improved, with LG which enhanced duodenal morphology manifested as increased villus length and villus-to-crypt ratio. There was up-regulated gene expression for intestinal barrier proteins (ZO-1, Claudin-1), immune factors (sIgA, IFN-γ) and antioxidant enzymes (SOD, GSH-Px; p < 0.05).5. Metagenomic and metabolomic analyses revealed a restructured caecal microbiota, characterised by increased commensal Ligilactobacillus spp. inhibited pathogenic Burkholderia spp. and increased production of beneficial metabolites, including butyric acid (p < 0.05), which acts as an energy source for enterocytes.6. This trial demonstrated that LG can enhance both growth performance outcomes and meat quality in Muscovy ducks through gut health modulation, supporting its application in sustainable poultry farming.},
}

@article {pmid42417977,
year = {2026},
author = {Yu, SJ and Stanley, D and Van, TTH and Steel, JC and Bajagai, YS},
title = {Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13948-1},
pmid = {42417977},
issn = {1432-0614},
support = {PRO-017656//AgriFutures Australia/ ; PRO-017656//AgriFutures Australia/ ; },
abstract = {Integrating human, animal, and environmental health is crucial for combating infectious diseases, as an estimated 60 to 75% of emerging infectious diseases originate from zoonotic sources globally. In this study, we analysed 1274 shotgun metagenomic faecal samples of humans, pigs, and chickens collected across multiple countries to estimate levels of microbial sharing at the species-level genome bins (SGBs) resolution. We confirm that host species, rather than geography, significantly structures the gut microbial community, as shown by alpha and beta diversity analyses. Despite this high host specificity, we identified substantial cross-host sharing of SGBs, including taxa recognised as pathogens such as Escherichia coli, Clostridium perfringens, Clostridium innocuum, Clostridium disporicum, Enterococcus species, and Streptococcus alactolyticus. Core taxa were predominantly host-specific, while non-core taxa were more frequently shared across humans, pigs, and chickens. LEfSe analysis identified distinctive microbial signatures for each host, further supporting differences in community composition. These findings demonstrate that unrelated and geographically distant humans and livestock can harbour highly similar microbial populations with pathogenic potential. This work provides molecular evidence supporting the need for integrated One Health surveillance to better detect, manage, and prevent zoonotic and reverse zoonotic transmission events across interconnected human, animal, and environmental systems. KEY POINTS: • There is substantial cross-host sharing of species-level genome bins, including potential pathogens • Core taxa are predominantly host-specific • Non-core taxa are more likely to be shared across humans, pigs, and chickens.},
}

@article {pmid42418234,
year = {2026},
author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC},
title = {Evolving strategies for virus discovery.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001785},
pmid = {42418234},
issn = {2057-5858},
mesh = {*Viruses/genetics/isolation & purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.},
}

*Viruses/genetics/isolation & purification/classification
Genome, Viral
*Metagenomics/methods
*Virome/genetics
Artificial Intelligence
Computational Biology/methods

@article {pmid42418242,
year = {2026},
author = {Robinson, JM and Guentas, L and Breed, MF},
title = {A microbial mirage: when microbiome metrics may obscure ecological meaning.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001777},
pmid = {42418242},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Ecology ; },
abstract = {Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.},
}

*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Ecology

@article {pmid42418263,
year = {2026},
author = {Bai, W and Huang, G and Rao, X and Li, H and Zhou, T and Yang, Y and Wei, W},
title = {Efficacy, Safety, and Mechanism of the Qi-Lian-Xiao-Pi Prescription (WW-1) for Chronic Atrophic Gastritis After Helicobacter Pylori Eradication: Protocol for a Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e90965},
doi = {10.2196/90965},
pmid = {42418263},
issn = {1929-0748},
mesh = {Humans ; *Gastritis, Atrophic/drug therapy ; *Helicobacter Infections/drug therapy ; Double-Blind Method ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; *Helicobacter pylori/drug effects ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; Female ; Male ; Treatment Outcome ; },
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is widely recognized as one of the precancerous lesions of gastric cancer. Helicobacter pylori is one of the important risk factors for CAG and gastric cancer. However, a large proportion of patients with CAG cannot avoid developing gastric cancer even after eradicating H pylori. It is necessary to find a safe and effective treatment to suppress this "inflammation-cancer" progression. The Qi-Lian-Xiao-Pi prescription (WW-1), a traditional Chinese medicine (TCM), has been reported to be effective in the treatment of CAG. However, the evidence is subject to methodological limitations.

OBJECTIVE: This study aimed to evaluate the efficacy, safety, and mechanism of the WW-1 in patients with CAG following successful H pylori eradication.

METHODS: This study is a rigorous parallel-arm, randomized, placebo-controlled, multicenter, double-blinded trial. A total of 110 eligible participants with a confirmed diagnosis of CAG after H pylori eradication are being enrolled and randomly assigned in a 1:1 ratio to either the intervention group (WW-1) or the control group (WW-1 placebo). Key eligibility criteria include confirmed CAG by histopathology, documented successful H pylori eradication, and compliance with predefined inclusion and exclusion criteria. The treatment duration is 24 weeks. Blinded histopathological assessments using the Operative Link on Gastritis Assessment and Operative Link on Gastric Intestinal Metaplasia Assessment staging systems will serve as primary outcomes. Secondary outcomes include improvement rates of gastric mucosal gland atrophy and intestinal metaplasia, as well as TCM syndrome scores. Safety will be assessed through monitoring vital signs, adverse events, blood, urine, and stool tests, liver and kidney function, and electrocardiography. Additionally, gastric mucosal DNA methylation and metagenomic sequencing of digestive tract microbiota (including saliva, tongue coating, gastric, and intestinal samples) will be analyzed to explore potential mechanisms of WW-1.

RESULTS: The funding began in November 2023. The study was officially initiated on April 20, 2025, with the enrollment of the first participant. The final study results, including efficacy outcomes, safety profiles, and mechanistic insights, are expected to be released in October 2026 after comprehensive data analysis and verification.

CONCLUSIONS: This study is designed to determine whether WW-1 can improve CAG by modulating gastric mucosal DNA methylation and the digestive tract microbiota. It represents a prospective clinical trial in TCM that aims to evaluate therapeutic effects on CAG through the regulation of microbiota homeostasis and epigenetic mechanisms. The findings of this study are expected to provide evidence regarding the efficacy and safety of WW-1 and contribute to the development of therapeutic strategies and future drug research for CAG.

DERR1-10.2196/90965.},
}

Humans
*Gastritis, Atrophic/drug therapy
*Helicobacter Infections/drug therapy
Double-Blind Method
*Drugs, Chinese Herbal/therapeutic use/pharmacology
*Helicobacter pylori/drug effects
Randomized Controlled Trials as Topic
Multicenter Studies as Topic
Female
Male
Treatment Outcome

@article {pmid42418319,
year = {2026},
author = {Li, Z and Chi, B and Ruan, C and Song, L and Dong, L and Li, A and Zheng, T and Wang, L and Huang, Y and Huang, J and Du, H and Zheng, X and Du, W and Dong, Z and Liu, Y and Huang, L and Dai, X},
title = {A deep-sea rare bacterium exhibits extraordinary metabolic versatility.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {117671},
doi = {10.1016/j.celrep.2026.117671},
pmid = {42418319},
issn = {2211-1247},
abstract = {The rare biosphere harbors immense microbial diversity, yet most low-abundance taxa remain uncultured and functionally enigmatic. Here, we isolated strain D14[T] from deep-sea water, and propose to classify it as a novel species, Metabolovarius oceani sp. nov., within the novel family Metabolovariaceae fam. nov. M. oceani represents the first cultivated member of the candidate family NORP267, a globally distributed but elusive alphaproteobacterial lineage known only from metagenome-assembled genomes. It possesses broad metabolic capabilities, including CO2 fixation, polyhydroxyalkanoate biosynthesis, complete denitrification and thiosulfate oxidation, and is capable of aerobic growth under both heterotrophic and autotrophic conditions and of anaerobic autotrophic denitrification via thiosulfate oxidation. Despite its versatile metabolic repertoire and global distribution, Metabolovariaceae remains consistently low in abundance across diverse habitats. The isolation of M. oceani permits direct experimental insights into the evolutionary adaptations, physiological resilience, and potential ecosystem roles of rare but metabolically versatile microorganisms within the microbial dark matter.},
}

@article {pmid42418574,
year = {2026},
author = {Caceres, C and Krasovec, M and Crispi, O and Gourbiere, S and Piganeau, G},
title = {Effect of cellular nutrient economy on the evolution of genome size in phytoplankton.},
journal = {Science advances},
volume = {12},
number = {28},
pages = {eaee2207},
doi = {10.1126/sciadv.aee2207},
pmid = {42418574},
issn = {2375-2548},
mesh = {*Phytoplankton/genetics/metabolism ; *Genome Size ; Selection, Genetic ; *Evolution, Molecular ; *Nutrients/metabolism ; Genetic Drift ; INDEL Mutation ; Models, Genetic ; },
abstract = {The origin of genome size variation remains a central question in evolutionary biology. While energetic costs have been proposed to influence genome size through selection on insertions and deletions (indels), nutrient availability may be a more relevant constraint in primary producers such as phytoplankton. We derived an expression for the selection coefficient of indels based on the phosphorus and nitrogen costs of nucleotides and the cellular nutrient requirements. Selection coefficient estimates indicate that natural selection dominates over genetic drift and favors the fixation of mutations that reduce genome size in phytoplankton with low nutrient requirements. Model predictions are supported by comparative genomics and metagenomic analyses. Together, this model provides a rigorous quantitative framework for understanding genome size evolution, particularly in small cells and oligotrophic environments, highlighting how nutrient limitation drives genome streamlining.},
}

*Phytoplankton/genetics/metabolism
*Genome Size
Selection, Genetic
*Evolution, Molecular
*Nutrients/metabolism
Genetic Drift
INDEL Mutation
Models, Genetic

@article {pmid42418675,
year = {2026},
author = {Zhang, M and Cao, Y and Yao, F and Lin, W and Lan, X and Sun, X and Wang, Y and Tan, Z and Ren, Y and Huang, Y and Sun, W},
title = {Antimonate Reduction Coupled to Anaerobic Ammonium Oxidation in Paddy Soil: Process Evidence and a Putative Syntrophic Microbial Model.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c00276},
pmid = {42418675},
issn = {1520-5851},
abstract = {The coupling of metal(loid) (e.g., Fe(III) and As(V)) reduction with anaerobic ammonium oxidation (anammox) is emerging as a critical process impacting the fate of N and metal(loid)s. Despite the chemical analogs of As and Sb, Sb(V) reduction exhibits different thermodynamics from As(V) reduction, which may constrain its coupling with anammox (termed "Sbammox") and impose stricter limitations on the metabolic pathway. To determine the occurrence and mechanism of Sbammox, Sb-contaminated paddy soil was used to establish the microcosms. Using [15]N isotope tracing, we confirmed the existence of Sbammox with the synchronous [15]N-N2 and Sb(III) productions and their concurrent suppressions by the inhibitor acetylene (C2H2). In contrast to the single-species-driving Asammox and Feammox, a tripartite syntrophic consortium was proposed to mediate Sbammox by DNA-stable isotope probing (SIP) combined with amplicon sequencing and metagenomic analysis. In this consortium, Ramlibacter and Candidatus Brocadia are proposed as the candidate Sb(V) reducer and ammonium oxidizer, respectively, with Geobacter hypothesized to mediate interspecies electron transfer. This distinct microbial strategy suggests that the specific thermodynamic constraints of Sb(V) necessitate a cooperative strategy rather than a solitary metabolic pathway. These findings are essential for understanding the divergent biogeochemical behaviors of As and Sb and underscore a critical dual risk in exacerbating nitrogen loss and Sb toxicity in agro-ecosystems.},
}

@article {pmid42418904,
year = {2026},
author = {Yu, J and Wan, Y and Peng, Y and Liang, S and Chan, FKL and Ng, SC and Tun, HM},
title = {Multi-cohort evidence for impaired microbial support of the methionine cycle in children with autism spectrum disorder.},
journal = {Psychiatry research},
volume = {364},
number = {},
pages = {117317},
doi = {10.1016/j.psychres.2026.117317},
pmid = {42418904},
issn = {1872-7123},
abstract = {The contribution of gut microbiota to outcomes of autism spectrum disorders (ASD) has been increasingly appreciated in recent years. With the accumulating evidence on ASD-driven alterations of the gut microbiota, heterogeneities arise across different reports. To account for variabilities in gut microbiota, clinical representations of ASD and data processing approaches, as well as limitations in sample sizes among the existing gut microbiota studies for ASD, the present multi-cohort analysis applied a standard bioinformatic and statistical pipeline on the publicly available gut metagenomic sequencing data for 674 samples, including 326 TD and 348 ASD individuals, collected from eight studies across three main geographical regions. Throughout the analysis, we identified taxonomic profiles of the gut microbiota exhibited more pronounced dysbiosis associated with ASD and between-study variations compared to functional profiles. Differentially abundant taxonomic and pathway markers were identified and validated for their consistent response to ASD across different studies. Co-occurring deficits in microbial pathways for salvaging adenosylcobalamin and S-adenosyl-L-methionine and biosynthesis of methionine in children with ASD point to a reduced microbial support for the host methionine cycle. Species from Faecalibacterium, Bacteroides, Blautia and Bifidobacterium were identified as microbial contributors to ASD-deficient microbial pathways, particularly those related to the methionine cycle. Therefore, the generalisable ASD-deficient contributors to the methionine cycle, such as Blautia wexlerae, Bacteroides stercoris and Streptococcus thermophilus, could be further investigated for their role in therapeutic applications for ASD.},
}

@article {pmid42418982,
year = {2026},
author = {Zhai, Y and Wang, X and Deng, X and Li, X and Hu, B and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M},
title = {Metagenomic insights into microbial drivers of organic micropollutant removal in wastewater-impacted riverbank filtration.},
journal = {Water research},
volume = {305},
number = {},
pages = {126421},
doi = {10.1016/j.watres.2026.126421},
pmid = {42418982},
issn = {1879-2448},
abstract = {Organic micropollutants (OMPs) in wastewater treatment plant (WWTP) effluent pose persistent risks to aquatic ecosystems and drinking water sources. Riverbank filtration (RBF) is a nature-based treatment process, yet the compartment-specific roles of riverbed sediment and downstream soil in OMP attenuation remain poorly resolved under wastewater-impacted conditions. Here, we combined targeted chemical analysis, OMP property compilation, shotgun metagenomics, EnviPath-based biotransformation annotation, and exploratory network analysis to investigate OMP attenuation in a laboratory-scale RBF system treating real WWTP effluent for 10 months. Nineteen OMPs were monitored along a sequential sediment-soil filtration pathway. Sediment preferentially attenuated hydrophilic or charged compounds, including lidocaine, amantadine, and sotalol, whereas soil contributed more strongly to the attenuation of naproxen, atenolol, and losartan. Metagenomic profiling revealed distinct microbial communities and functional gene repertoires between sediment and soil after long-term operation. Sediment harbored higher relative abundances of genes associated with oxidative xenobiotic transformation, including cytochrome P450-related enzymes, demethylases, dehydrogenases, oxidases, and aromatic compound degradation pathways. An exploratory Spearman network further identified associations among microbial genera, EnviPath-annotated candidate biotransformation genes, and OMP removal rates, including 17 KO-OMP links supported by both correlation and pathway annotation. These findings indicate that sediment and soil develop complementary microbial functional potentials that may support compound-specific OMP attenuation. This study provides a mechanistic basis for optimizing sediment-soil configurations in wastewater-impacted RBF systems and for improving nature-based barriers against diverse OMP mixtures.},
}

@article {pmid42418983,
year = {2026},
author = {Huang, Y and Liu, P and Wu, J and Li, J and Tuo, J and Zhang, Q and Zhang, XX},
title = {Diverse and ultraviolet-inducible phage-associated antibiotic resistance genes in wastewater treatment plants.},
journal = {Water research},
volume = {305},
number = {},
pages = {126419},
doi = {10.1016/j.watres.2026.126419},
pmid = {42418983},
issn = {1879-2448},
abstract = {Phage-mediated transduction is an underappreciated route of antibiotic resistance gene (ARG) dissemination in wastewater treatment plants (WWTPs), yet the diversity and fate of phage-associated ARGs remain poorly resolved. Here, a 5-year monthly metagenomic survey of 538 influent, activated sludge, and effluent samples from two municipal WWTPs in Nanjing, China, was combined with laboratory-scale UV dose-response experiments to profile the phage-encoded resistome and its fate along the treatment train. A total of 168 phage-associated ARG subtypes spanning 23 drug classes were recovered, approximately 1.7-fold more than catalogued for comparable environments in IMG/VR, with multidrug- and diaminopyrimidine-resistance genes dominating the catalogue and efflux pumps constituting the major resistance mechanism; 64.9 % of subtypes were WWTP-exclusive, highlighting pronounced habitat specificity. Caudoviricetes overwhelmingly carried the ARGs and were primarily putatively linked to Gammaproteobacteria, Betaproteobacteria, and Actinobacteria. Biological treatment markedly restructured the phage-associated resistome (PERMANOVA R[2] = 0.19-0.34, p = 0.001), whereas conventional UV disinfection produced no significant bulk abundance reduction (p > 0.05). Dose-response experiments across 0-80 mJ/cm[2] revealed a biphasic pattern: low-to-moderate doses (10-20 mJ/cm[2]) induced prophages and transiently elevated phage-fraction ARG concentrations by 0.3-0.8 log10 copies/L (≈2- to 6-fold), whereas higher doses (≥40 mJ/cm[2]) drove progressive inactivation. These findings expose a previously underappreciated paradoxical release of phage-associated ARGs within the operational UV window of Chinese municipal reactors and argue for coupling UV with complementary barriers to curb transduction-mediated resistance dissemination.},
}

@article {pmid42419029,
year = {2026},
author = {Elmaghrabi, MM and Alghamdi, S and Alzeer, S and Magrashi, AM and Bakheet, RH and Alabden, DZ and Alshuhri, S and Abouelhoda, MM and Alrashaid, BA and Tayeb, HT},
title = {Metagenomic investigation of VIM-type metallo-β-lactamase-producing multidrug-resistant Pseudomonas aeruginosa associated with a hospital outbreak across multiple hospital units in Saudi Arabia.},
journal = {Journal of infection and public health},
volume = {19},
number = {8},
pages = {103299},
doi = {10.1016/j.jiph.2026.103299},
pmid = {42419029},
issn = {1876-035X},
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) represent a public health challenge, particularly when associated with VIM-type metallo-β-lactamases (MBLs), which limit therapeutic options. Conventional microbiological methods may underestimate resistance determinants and transmission dynamics. Long-read metagenomic sequencing is a promising approach for Pathogen detection, resistome characterization, and genomic surveillance.

OBJECTIVES: The study's objectives were to characterize the resistome, including detection of the blaVIM gene, assess genomic relatedness and potential transmission dynamics, and evaluate the diagnostic value of metagenomics compared with conventional microbiological approaches.

METHODS: This retrospective infection control investigation included seven hospitalized patients from multiple hospital units. Clinical specimens included blood, respiratory specimens, surgical tissue, and device-associated material. Conventional microbiological investigations included bacterial culture, identification, and antimicrobial susceptibility testing (AST) using the VITEK 2 automated system. Carbapenemase genes were detected using Xpert Carba-R. Long-read metagenomic sequencing was conducted using Oxford Nanopore Technologies (ONT) on the GridION platform. Bioinformatic analysis was performed using the CosmosID platform for taxonomic profiling, antimicrobial resistance gene detection, and genomic relatedness assessment.

RESULTS: Conventional microbiological methods identified carbapenem-resistant Pseudomonas aeruginosa (CRPA) in five cases, whereas ONT sequencing detected the blaVIM gene in all seven samples, demonstrating superior diagnostic sensitivity. A highly conserved resistome profile was identified across all investigated cases, including multiple β-lactamase and aminoglycoside, fluoroquinolone, and polymyxin-associated resistance determinants. Genomic relatedness analysis demonstrated close clustering patterns with minimal genomic variability, suggesting possible circulation of closely related MDR strains.

CONCLUSION: These findings highlight the added value of ONT sequencing in identifying concealed resistance determinants and improving transmission tracking compared with conventional diagnostic approaches. Future investigations involving larger sample sizes and environmental surveillance are needed to further clarify transmission dynamics and potential reservoirs of VIM-producing P. aeruginosa.},
}

@article {pmid42419186,
year = {2026},
author = {Liu, H},
title = {Computational strategies for uncovering bacterial biocatalysts in the biodegradation of persistent organic pollutants.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 2},
pages = {109222},
doi = {10.1016/j.compbiolchem.2026.109222},
pmid = {42419186},
issn = {1476-928X},
abstract = {The rapid accumulation of persistent organic pollutants (POPs) in soil, sediment, and aquatic environments presents a critical global challenge that demands sustainable and efficient remediation strategies. In this context, computational enzymology has emerged as a powerful framework for accelerating the discovery, validation, and optimization of pollutant-degrading enzymes. However, prior POP-biodegradation reviews have typically treated enzymes, docking, molecular dynamics (MD), metagenomics, and artificial intelligence (AI) as separate topics (e.g., docking-focused reviews (1), metagenomics-focused reviews (2), and structural-mechanism-focused reviews (3) rather than as parts of a single bacterial-enzyme discovery pipeline. This review fills that gap by focusing specifically on bacterial biocatalysts and by integrating structure prediction, docking, MD, metagenomic mining, and machine learning-guided design into one workflow. Its main contribution is a unified framework that links sequence discovery to structural screening, dynamic validation, and experimental prioritization. This work provides a comprehensive synthesis of molecular docking, molecular dynamics (MD) simulations, and integrative artificial intelligence (AI)-driven approaches applied to biodegradation research. We highlight how molecular docking functions as a high-throughput, structure-based filter for prioritizing enzyme-pollutant interactions, while MD simulations supply the essential temporal and mechanistic resolution required to evaluate enzyme flexibility, substrate access pathways, and catalytic competence under realistic environmental conditions. Case studies across diverse pollutant classes including polycyclic aromatic hydrocarbons, organochlorine pesticides, polychlorinated biphenyls, and plastic additives demonstrate that workflows combining docking with microsecond-scale MD and MM-PBSA/GBSA free-energy calculations show markedly higher experimental reproducibility than static docking alone. Beyond individual methods, this article emphasizes the growing importance of integrative computational strategies that unite metagenomics, AI-based structure prediction, enhanced-sampling MD, and machine learning-guided directed evolution within a closed-loop Design-Build-Test-Learn (DBTL) paradigm. Such pipelines enable systematic navigation of vast biological sequence space while simultaneously balancing enzyme stability, conformational flexibility, and catalytic efficiency. Finally, we discuss prevailing challenges encompassing computational cost, structural uncertainty in apo-state predictions, force-field limitations for halogenated substrates, and the translational gap between in silico predictions and environmental field deployment, and outline future directions toward scalable, low-energy, and environmentally robust bioremediation technologies. Collectively, these advances position computational modeling as a cornerstone of next-generation, eco-friendly enzyme discovery.},
}

@article {pmid42419222,
year = {2026},
author = {Liang, Y and Gao, H and Chen, F and Sun, J and Sun, G and Wang, Z and Li, Y and Liu, H and Geng, M and Li, J and Zhang, Y},
title = {Bilateral intranigral α-synuclein seeding in A53T transgenic mice drives early Parkinsonism and concurrent gut dysbiosis.},
journal = {Biochemical and biophysical research communications},
volume = {830},
number = {},
pages = {154244},
doi = {10.1016/j.bbrc.2026.154244},
pmid = {42419222},
issn = {1090-2104},
abstract = {Heterozygous A53T α-synuclein transgenic mice (M83 line) typically exhibit late-onset Parkinson's disease (PD) symptoms. This study established an accelerated PD model via bilateral intranigral injection of α-synuclein preformed fibrils (PFF) to characterize central and peripheral pathologies. Three-month-old heterozygous A53T mice received bilateral substantia nigra injections of α-synuclein PFF or PBS. Motor function was assessed monthly. Following the onset of motor deficits, the substantia nigra was harvested for immunohistochemistry and colons were harvested for H&E, transcriptomic analysis and western blotting, while gut microbiota composition was assessed using metagenomic sequencing. Three months post-injection, PFF-treated mice exhibited significant motor deficits, dopaminergic neuron loss, and nigral α-synuclein aggregation, with no sex differences. Peripherally, mice displayed increased α-synuclein in colon, impaired gut motility, reduced Occludin expression indicating barrier damage, and colonic inflammation. Metagenomics identified gut dysbiosis characterized by a skewed Bacillota/Bacteroidota ratio, Lactobacillus depletion, and enrichment of inflammation-associated taxa. Bilateral intranigral α-synuclein PFF injection in A53T mice successfully induces an early-onset, progressive PD phenotype encompassing motor impairments, nigrostriatal neurodegeneration. Crucially, the model recapitulates key peripheral manifestations, including gastrointestinal dysfunction and microbial dysbiosis. These findings provide compelling evidence for a descending brain-to-gut pathological axis where central α-synuclein pathology drives distal gut alterations. This optimized model offers a valuable platform for investigating multi-system PD progression and bidirectional brain-gut communication mechanisms.},
}

@article {pmid42419237,
year = {2026},
author = {Li, T and Xu, J and He, S and Zhao, Q and Liu, J and Shi, Y},
title = {Salinity of oxidation pond effluent regulates the fate of antibiotic resistance genes in the soil-leachate continuum by selecting a salt-adaptive resistome.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142854},
doi = {10.1016/j.jhazmat.2026.142854},
pmid = {42419237},
issn = {1873-3336},
abstract = {Oxidation pond effluent (OPE) reuse can introduce antibiotic resistance genes (ARGs) into agricultural soils. Yet, how OPE salinity regulates ARG fate across the soil-leachate continuum remains poorly understood. Soil column experiments were conducted using three OPE salinity levels with electrical conductivities of 4.35, 8.24, and 13.17 dS/m, combined with high-throughput quantitative PCR and metagenomics. Results showed that although increasing OPE salinity reduced the mean ARG abundance across the soil-leachate continuum, its effects were clearly depth dependent, with slight ARG enrichment of 10.78%-17.26% in surface soil (0-30 cm), a unimodal response in the 30-60 cm layer, and marked reduction of 24.17%-42.60% in deeper soil (60-90 cm) and leachate. More importantly, increasing OPE salinity reduced total ARG abundance by about 14.13% in OPE, but ARG abundance still increased in surface soil after irrigation. Metagenomic analyses showed increasing OPE salinity selectively enriched ARGs related to antibiotic efflux and antibiotic inactivation, indicating that salt-adaptive ARG enrichment better explained topsoil ARG accumulation than total ARG input load alone under OPE irrigation. In addition, surface ARG enrichment was linked to the selection of bacterial groups capable of maintaining ARGs under saline conditions, and the co-localization of salt-tolerance genes, ARGs, and MGEs. In deeper soil and leachate, ARG attenuation was driven mainly by reduced bacterial abundance under continued salinity accumulation. These findings provide a new perspective on ARG risk under saline wastewater irrigation by showing that salinity-driven reshaping of the introduced resistome and salinity accumulation regulate ARG fate and downward transport potential.},
}

@article {pmid42419245,
year = {2026},
author = {Han, Z and Zhang, Y and Luan, X and Feng, H and Wang, Y and Deng, Y and Hu, C and Yang, M},
title = {Clinically prevalent transposons contribute to erm gene dissemination in the field soil under pseudo-persistent erythromycin contamination.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142927},
doi = {10.1016/j.jhazmat.2026.142927},
pmid = {42419245},
issn = {1873-3336},
abstract = {Clinically relevant antibiotic resistance genes (ARGs) or their ancestral genes are widespread in natural soil microbiome at ultralow abundance. Whether and how long-term antibiotic pressure in soil accelerate dissemination of these ARGs remain unclear. Here, annual cycle of erythromycin exposure at levels around 5-20 μg∙kg[-1] was conducted in previously undisturbed field soil for consecutive five years, to simulate the pseudo-persistent characteristic of antibiotic contamination in soil environment. The primary clinically relevant macrolide resistance genes, rRNA methyltransferase genes (erm genes), were initially rare but gradually enriched, exhibiting a 37.8-fold increase after five years, which was greatly higher than macrolide efflux pump genes and inactivation genes (less than 2.3-fold). Among diverse mobile genetic elements, transposase gene tnpA exhibited potential association with the horizontal transfer of erm genes during long-term erythromycin exposure. From genetic and statistical evidence, enriched erm genes were presumed to locate on Bacilli with mobile transposable elements Tn554 and Tn551, which were clinically prevalent gene clusters in pathogens-Enterococcus and Staphylococcus. Thus, there may be a historical contribution of long-term erythromycin contamination to erm-carrying clinical transposable elements in soil microbiome. Our findings also demonstrated soil erythromycin exposure at levels much lower than laboratory-determined minimal selective concentrations (MSCs) still exhibits long-term effects on erm genes. Taking pseudo-persistent characteristic of antibiotic contamination, we further proposed long-term in-situ assessment with endpoint of clinically relevant ARGs to obtain a real-world MSC in the future studies.},
}

@article {pmid42419262,
year = {2026},
author = {Gelsinger, DR and Wang, HH},
title = {Toward precision microbiome therapeutics: From black box to blueprint.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1157-1161},
doi = {10.1016/j.chom.2026.06.014},
pmid = {42419262},
issn = {1934-6069},
mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/physiology/genetics ; Bacteria/genetics ; Animals ; Gene Editing ; *Precision Medicine/methods ; Microbiota ; },
abstract = {The gut microbiome influences human health, yet microbiome-mediated therapies have lagged as metagenomics identifies gut-colonizing microbes without clarifying functional networks. Prior microbiome "reset" approaches improved clinical outcomes despite limited mechanistic understanding. We argue a critical field inflection point: in situ genome editing of native bacteria enables mechanism-driven, programmable, species-specific therapeutics.},
}

Humans
Metagenomics
*Gastrointestinal Microbiome/physiology/genetics
Bacteria/genetics
Animals
Gene Editing
*Precision Medicine/methods
Microbiota

@article {pmid42419272,
year = {2026},
author = {Crysler, A and de la Fuente-Nunez, C},
title = {Mining the code of life for new antibiotics.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1273-1284},
doi = {10.1016/j.chom.2026.06.007},
pmid = {42419272},
issn = {1934-6069},
mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Discovery/methods ; Antimicrobial Peptides/pharmacology ; Humans ; Drug Resistance, Bacterial ; Bacteria/drug effects/genetics ; Generative Artificial Intelligence ; Machine Learning ; },
abstract = {Antimicrobial resistance (AMR) is outpacing antibiotic development, creating an urgent need for discovery strategies that are faster, broader, and more systematic. Here, we review the transition from classical "dirt mining" and phenotypic screening toward digital discovery approaches that treat chemical structures and biological sequences as searchable, engineerable substrates for antibiotic innovation. Modern extensions of conventional screening, including in situ cultivation, co-culture, and microfluidics, have broadened access to previously uncultured microbes. Computer-aided approaches spanning virtual screening, molecular networking, and deep learning have enabled identification of unconventional antibacterial scaffolds from ultra-large chemical libraries. Mining genomes, proteomes, and metagenomes has uncovered antimicrobial peptides, encrypted peptides, and biosynthetic gene clusters encoding novel small-molecule antibiotics. Generative AI now enables design of peptides and small molecules under multiobjective constraints, including potency, toxicity, stability, and resistance risk. Together, these advances point toward discovery platforms that improve novelty, hit rates, and long-term durability in the face of AMR.},
}

*Anti-Bacterial Agents/pharmacology/chemistry
*Drug Discovery/methods
Antimicrobial Peptides/pharmacology
Humans
Drug Resistance, Bacterial
Bacteria/drug effects/genetics
Generative Artificial Intelligence
Machine Learning

@article {pmid42419418,
year = {2026},
author = {Lin, YR and Tseng, HY and Lai, ZL and Hsueh, PR},
title = {Metagenomic next-generation sequencing facilitates the diagnosis of disseminated Mycobacterium tuberculosis infection in a patient with complex sepsis.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107918},
doi = {10.1016/j.ijantimicag.2026.107918},
pmid = {42419418},
issn = {1872-7913},
}

@article {pmid42419508,
year = {2026},
author = {Hering-Peter, C and Schulz, R},
title = {Physiological responses of floc-forming microalgae-bacteria consortia to environmental perturbations.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135341},
doi = {10.1016/j.biortech.2026.135341},
pmid = {42419508},
issn = {1873-2976},
abstract = {Fast-sedimenting microalgae-bacteria consortia (MBC) offer a cost-efficient pathway for biomass harvesting while remediating polluted water bodies in chemostatic photobioreactors. Understanding how abiotic parameters affect floc morphology, sinking properties and metagenomic species composition remains critical for optimization of these specific bioreactors. This study investigated whether fast-sedimenting MBC maintain structural resilience under moderate stress but lose stability beyond critical physiological tipping points. By investigating the physiological boundaries of five environmental factors, we identified clear operational thresholds. Moderate perturbations including light intensities up to 1500 µmol m[-2] s[-1], salinities from 0 to 35 PSU and low antibiotic concentrations showed no statistically significant impact on settling efficiency. In contrast, extreme pH at 12 and temperatures at 45 °C reduced recovery rates by more than 50 % compared to controls maintaining above 87 % efficiency. The surface charge decreased from -27.94 mV to -4.83 mV under acidic conditions at pH 3, indicating electrostatic destabilization of the floc matrix. Dominance of the cyanobacterium Thermoleptolyngbya spp. persisted above 70 % abundance across all treatments. These findings define a safe operating envelope between pH 6-9 and temperatures from 15 to 35 °C necessary to maintain gravity-driven sedimentation. This work provides quantitative boundaries where biological buffering fails, enabling predictive reactor design that avoids biomass washout in continuous cultivation systems.},
}

@article {pmid42419510,
year = {2026},
author = {He, J and Liu, Y and Zhao, Y and Wei, T and Gong, Z and Wu, Y and Kang, X and Zhang, W and Ma, J and Chu, Z and Wang, R},
title = {Metagenomic insights into the mechanisms of heteroatom-doped, iron-loaded biochar in enhancing anaerobic digestion of waste activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135349},
doi = {10.1016/j.biortech.2026.135349},
pmid = {42419510},
issn = {1873-2976},
abstract = {Anaerobic digestion is a crucial technology for resource recovery from waste activated sludge. Enhancing its methane production efficiency using conductive materials is a key research objective. This study aimed to elucidate the mechanisms by which conductive materials promote this process. Three types of biochar(FeS@BC300, FeP@BC600, and FeP@BC900) were prepared by doping bamboo powder with N, P, S and iron salts under pyrolysis conditions at 300-900 °C, and their physical and chemical properties were characterized, including surface functional groups, specific surface area, capacitance, electrical resistance, electron-accepting capacity (EAC), and electron-donating capacity (EDC). These analyses assessed the influence of synthesis parameters. These materials were subsequently introduced into the anaerobic digestion of thermally hydrolyzed sludge to evaluate their impacts on methanogenic performance, microbial community structure, and metabolic pathways. The results show that the FeP@BC600 material, which exhibited the highest EDC, substantially increased microbial cytochrome c production (by 29.2 % compared to the control). This enhancement improved interspecies electron transfer, stimulated ATP synthesis (increased by 41.5 %), and reinforced both hydrogenotrophic and acetoclastic methanogenic pathways, ultimately elevating methane production by 55 %. Integrated analysis of metagenomic data, material properties, and performance metrics revealed that the key mechanism by which FeP@BC600 promotes methanogenesis is through the enrichment of cytochrome c-encoding genes, thereby facilitating direct interspecies electron transfer (DIET) and augmenting ATP synthesis. This study provides a foundation for the subsequent application of conductive materials to enhance anaerobic digestion and offers guidance for the optimized design of such materials.},
}

@article {pmid42419591,
year = {2026},
author = {Kim, S and Seo, H and Jo, S and Rahim, MA and Hossain, MS and Shuvo, MSH and Jeong, SY and Lee, MY and Kim, KH and Lee, N and Won, JH and Song, HY and Yoon, SY},
title = {Oral Sodium Butyrate Supplementation, Gut Microbiome Modulation, and Reduced Acute Graft-versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.07.006},
pmid = {42419591},
issn = {2666-6367},
abstract = {BACKGROUND: Acute graft-versus-host disease (aGVHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Disruption of the gut microbiome during transplantation has been implicated in the pathogenesis of aGVHD, yet clinically applicable strategies to modulate the microbiome in immunocompromised patients remain limited.

OBJECTIVES: To evaluate the association between oral sodium butyrate supplementation and the incidence and severity of aGVHD, and to investigate its impact on gut microbiome recovery following allo-HSCT.

STUDY DESIGN: In this prospective, single-center study, 39 consecutive patients undergoing allo-HSCT received oral sodium butyrate (1,200 mg/day) from neutrophil engraftment to day +100. Outcomes were compared with 18 historical controls treated at the same institution without butyrate supplementation. The primary endpoint was the cumulative incidence of grade II-IV aGVHD by day +100. Secondary endpoints included lower gastrointestinal aGVHD and microbiome characteristics assessed using shotgun metagenomic sequencing. Competing risk analyses were performed to account for death as a competing event.

RESULTS: Butyrate supplementation was associated with a lower incidence of grade II-IV aGVHD (30% vs 53%, p=0.028) and grade III-IV aGVHD (5% vs 34%, p=0.002). Lower gastrointestinal aGVHD occurred in 5% of the butyrate group compared with 40% of historical controls (p<0.001). In multivariable competing risk analysis, butyrate supplementation remained independently associated with reduced grade II-IV aGVHD (adjusted HR 0.31, 95% CI 0.11-0.89; p=0.029) and lower gastrointestinal aGVHD (adjusted HR 0.07, 95% CI 0.02-0.30; p<0.001). Microbiome analysis demonstrated improved recovery of gut microbial diversity at day +100 in the butyrate group, with enrichment of commensal taxa and restoration of fecal butyrate levels.

CONCLUSIONS: Oral sodium butyrate supplementation was associated with reduced incidence and severity of aGVHD, particularly involving the gastrointestinal tract, along with improved microbiome recovery. These findings suggest a potential role for postbiotic-based microbiome modulation in GVHD prevention and warrant validation in randomized controlled trials.},
}

@article {pmid42410232,
year = {2026},
author = {Li, Y and Li, J and Wang, H and Fan, J and Tang, K and Yan, G and Dong, W and Lan, T},
title = {Ischial tuberculosis: MRI and mNGS enable early diagnosis in the largest reported case series of twenty two patients.},
journal = {International orthopaedics},
volume = {},
number = {},
pages = {},
pmid = {42410232},
issn = {1432-5195},
support = {PYZ24154//The Scientific Research Cultivation Fund of Capital Medical University/ ; SKLSIM-2024108//The 2024 Youth Project of the Open Research Fund of the State Key Laboratory of Neurology and Oncology Drug Development/ ; },
abstract = {PURPOSE: To analyze the clinical features, diagnosis, treatment, and prognosis of ischial tuberculosis (IT), and to evaluate the diagnostic value of MRI and mNGS in the largest reported case series to date.

METHODS: Data from 22 patients with confirmed IT treated between January 2013 and January 2023 were retrospectively reviewed. Diagnosis was based on histopathology, microbiology, and molecular tests.

RESULTS: The mean age was 31.6 years (11 to 67). Common symptoms included gluteal pain (100.0%), sitting-induced pain (81.8%), and local swelling (59.1%). Computed tomography (CT) revealed lesions in 86.4% of patients, while magnetic resonance imaging (MRI) showed abnormalities in all 18 patients examined. The ischial tuberosity was the most common site of involvement (63.6%). The T-cell spot test for tuberculosis infection (T-SPOT.TB), Xpert Mycobacterium tuberculosis/rifampicin resistance assay (Xpert MTB/RIF), and metagenomic next-generation sequencing (mNGS) showed positivity rates of 83.3%, 83.3%, and 100%, respectively. Histopathological granulomas were observed in 77.3%. Overall, 68.2% underwent surgical debridement. All patients achieved clinical cure with no recurrence at a mean follow-up of 34.7 months.

CONCLUSION: IT has an insidious onset. MRI (100% sensitivity) is valuable for early diagnosis, and molecular tests, particularly mNGS (100% detection rate), enhance pathogen detection. Surgical debridement combined with standard chemotherapy achieved clinical cure in all patients, but comparative studies are needed to confirm its superiority over conservative treatment.},
}

@article {pmid42410336,
year = {2026},
author = {Xie, Y and Cidan, Y and Sun, F and Renqing, C and Cisang, Z and Wang, D and Cideng, D and Basang, W and Zhu, Y},
title = {Bacillus-based probiotic supplementation reshapes rumen bacterial and fungal communities and enhances carbohydrate-degrading functional capacity in weaned yaks.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05372-2},
pmid = {42410336},
issn = {1471-2180},
support = {XZ202401YD0012//Central Government-Guided Local Science and Technology Development Project, Mining and Application of Functional Microorganisms and Enzyme Resources for Efficient Cellulose Degradation in Yaks/ ; CARS-37//Modern Agricultural Industry Technology System for Beef and Yak/ ; QYXTZX-LS2020-01//Breeding and Efficient Propagation of Yaks in Gesangtang of Linzhou County/ ; },
abstract = {This study evaluated the effects of dietary supplementation with Bacillus-based probiotics on growth performance, nutrient digestibility, rumen fermentation, and microbial functional capacity in weaned yaks. Twenty animals were randomly assigned to a basal diet (control group, CON) or the same diet supplemented with Bacillus subtilis and Bacillus licheniformis (probiotic group, PRO) for 90 days. Probiotic supplementation increased average daily gain (P < 0.05) and tended to increase dry matter intake (P = 0.059). In addition, neutral detergent fibre and acid detergent fibre digestibility were improved (P < 0.05), suggesting improved degradation of structural carbohydrates. Rumen fermentation was altered, with increased concentrations of butyrate and isovalerate and reduced ammonia nitrogen, suggesting improved fermentation efficiency and nitrogen metabolism. Microbial analysis showed that probiotics reshaped both bacterial and fungal community structures without affecting α-diversity, indicating selective modulation of key microbial taxa. Notably, the relative abundance of carbohydrate-degrading genera, including Xylanibacter, was increased. Metagenomic analysis further demonstrated changes in microbial functional capacity, as evidenced by increased abundance of carbohydrate-active enzymes and genes associated with cellulose, hemicellulose, chitin, lignin, and starch degradation. These results indicate that Bacillus-based probiotics were associated with improved growth performance and enhanced rumen microbial functional potential related to carbohydrate degradation.},
}

@article {pmid42410398,
year = {2026},
author = {Xiang, X and Zhu, Y and Wang, T and Cheng, K and Ming, Y},
title = {Association between salivary microbiota-related amino acid metabolic dysregulation and tacrolimus-induced gingival overgrowth following kidney transplantation.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-09004-z},
pmid = {42410398},
issn = {1472-6831},
support = {81771722//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Kidney transplant (KT) recipients require lifelong immunosuppressive therapy to prevent allograft rejection. Drug-induced gingival overgrowth (DIGO) is a notable adverse effect of tacrolimus, for which effective preventive or therapeutic strategies are lacking. Dysbiosis of the oral microbiota has been implicated as a major risk factor for DIGO. However, its mechanistic role remains poorly understood.

RESULTS: Twenty KT recipients with newly diagnosed DIGO while receiving tacrolimus were enrolled, along with 20 matched controls with stable graft function. Salivary samples were collected and subjected to metagenomic and untargeted metabolomic profiling. Taxonomic analysis revealed greater microbial heterogeneity in DIGO patients compared to more interconnected communities observed in controls. Periodontitis-associated taxon, including Porphyromonas gingivalis, were enriched in the DIGO group. Multiple differentially expressed microbial genes and metabolites were identified, predominantly enriched in disordered amino acid metabolic pathways. Key metabolites-such as L-proline, carnosine, choline, 5-aminolevulinic acid, and spermidine-showed strong associations with DIGO-related taxon.

CONCLUSION: A strong association was observed between salivary microbial composition, metabolic profiles, and DIGO. The identified microbiota and metabolite alterations suggest a potential link between amino acid metabolic dysregulation and gingival fibroblast-related pathways in DIGO. These findings provide new insights into the biological features of DIGO and offer a foundation for future mechanistic and therapeutic studies.},
}

@article {pmid42410808,
year = {2026},
author = {Wang, Y and Yang, X and Wang, Q and Shen, T and Wang, W and Qiu, J},
title = {Microbial flora and antimicrobial resistance in dental unit waterlines of Chongqing: An observational cross-sectional laboratory study.},
journal = {Medicine},
volume = {105},
number = {27},
pages = {e49461},
doi = {10.1097/MD.0000000000049461},
pmid = {42410808},
issn = {1536-5964},
mesh = {China ; *Water Microbiology ; Cross-Sectional Studies ; *Dental Equipment/microbiology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/isolation & purification/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; },
abstract = {To identify pathogenic bacteria in dental water systems and assess microbial diversity and resistance genes, we collected water samples from 35 dental facilities in Chongqing, China. Using the VITEK 2 COMPACT system, we identified 26 strains and 13 species of opportunistic pathogens in 23 samples exceeding the standard limits. In addition, metagenomic sequencing was performed to investigate microbial diversity and resistance genes. Among the 170 collected samples, 78.2% qualified, with no significant variation across samples. However, there was a statistically significant difference in qualifying rates between hospitals of different levels (χ2 = 7.696, P = .021). Most bacteria (80.8%) were Gram-negative and non-Enterobacteriaceae, with only 1 type belonging to the Enterobacteriaceae family. Notably abundant resistance genes included bacA, adeC, mexT, mdfA, adeJ, mdtK, emrB, and mdtB, predominantly associated with multidrug resistance (relative abundance: 71.42%). The contamination of dental unit waterlines is a concern that cannot be overlooked.},
}

China
*Water Microbiology
Cross-Sectional Studies
*Dental Equipment/microbiology
Humans
*Drug Resistance, Bacterial/genetics
*Bacteria/isolation & purification/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics

@article {pmid42411404,
year = {2026},
author = {Bouras, G and Grigson, SR and Durr, L and Papudeshi, B and Mallawaarachchi, V and Vreugde, S and Edwards, RA},
title = {Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.},
journal = {Current protocols},
volume = {6},
number = {7},
pages = {e70405},
doi = {10.1002/cpz1.70405},
pmid = {42411404},
issn = {2691-1299},
support = {//Australian Research Council/ ; },
mesh = {*Genome, Viral ; *Metagenomics/methods ; *Computational Biology/methods ; *Viruses/genetics ; *Metagenome ; Molecular Sequence Annotation/methods ; *Software ; Bacteriophages/genetics ; Viral Proteins/genetics ; },
abstract = {Viral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential of prokaryotic viral metagenomes is extremely challenging. Pharokka, Phold, and Phynteny are complementary open-source prokaryotic viral genome annotation tools that utilize a variety of bioinformatics approaches to maximally annotate viral metagenomes. This article describes a protocol for installing and running these tools on a viral metagenomic dataset, followed by visualization of annotations using our client-side Phold Plot web assembly application. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Prokaryotic viral metagenome annotation with Pharokka Basic Protocol 2: Enhanced prokaryotic viral metagenome protein annotation using protein structures with Phold Basic Protocol 3: Further prokaryotic viral metagenome protein annotation using genome synteny and protein language models with Phynteny Basic Protocol 4: Visualization of prokaryotic viral metagenome annotations with Phold Plot web assembly application.},
}

*Genome, Viral
*Metagenomics/methods
*Computational Biology/methods
*Viruses/genetics
*Metagenome
Molecular Sequence Annotation/methods
*Software
Bacteriophages/genetics
Viral Proteins/genetics

@article {pmid42412829,
year = {2026},
author = {Wang, S and Du, Y},
title = {VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {Supplement_1},
pages = {},
doi = {10.1093/bioinformatics/btag271},
pmid = {42412829},
issn = {1367-4811},
support = {//University of Texas Systems STARs Program/ ; },
mesh = {*Genome, Viral ; *Metagenomics/methods ; Animals ; Humans ; *Software ; Metagenome ; Algorithms ; },
abstract = {MOTIVATION: Metagenomic Hi-C provides in situ proximity signals that can improve genome binning and enable virus-host-association analysis. However, viral genome recovery remains difficult because virus-virus Hi-C contact matrices are extremely sparse. Viral genomes are small, often low-abundance, and frequently assemble into short contigs, leaving many true within-genome links unobserved and causing viral bins to fragment.

RESULTS: We present VirBinn, a graph-diffusion framework for viral binning from metagenomic Hi-C. VirBinn enhances virus-virus connectivity through two complementary mechanisms: random-walk-with-restart enhancement on the sparse virus-virus contact graph and host-guided diffusion that propagates viral seeds through the host network to infer indirect virus-virus associations. The enhanced views are integrated and clustered using Leiden community detection to produce viral metagenome-assembled genomes (vMAGs). On dataset-specific simulation benchmarks with ground truth, VirBinn consistently recovers more high-quality vMAGs than Hi-C-based and shotgun-based baselines and substantially increases the number of near-complete genomes. On four real metagenomic Hi-C datasets spanning human gut, pig gut, sheep gut (long-read assembly), and wastewater, VirBinn yields more high-completeness vMAGs under CheckV and produces bins with strong within-cluster contact support. Finally, host linkage analysis using reconstructed host MAGs reveals habitat-specific host-association patterns and plausible host taxonomic profiles.

VirBinn is available at https://github.com/dyxstat/VirBinn. The scripts to reproduce the results and figures in this article are available at https://github.com/dyxstat/Reproduce_VirBinn.},
}

*Genome, Viral
*Metagenomics/methods
Animals
Humans
*Software
Metagenome
Algorithms

@article {pmid42412840,
year = {2026},
author = {Zhang, A and Boucher, C and Noyes, N and Yu, YW},
title = {RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {Supplement_1},
pages = {},
doi = {10.1093/bioinformatics/btag303},
pmid = {42412840},
issn = {1367-4811},
support = {R35GM160134/NH/NIH HHS/United States ; R01AI173928/NH/NIH HHS/United States ; R01AI141810/NH/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Thermodynamics ; *Nucleic Acid Hybridization/methods ; *Sequence Analysis, DNA/methods ; *Software ; Computer Simulation ; },
abstract = {MOTIVATION: Simulators that generate synthetic datasets help address the lack of ground truth for developing and benchmarking computational tools. Many read simulators assume uniform sampling across reference genomes; however, for newer capture-based sequencing technologies (e.g. TELSeq), this assumption is intentionally broken to oversample regions of interest. Along with systematic biases arising from probe multiplicity, sequence composition, and species abundances inherent to capture-based sequencing, this mismatch between modeling assumptions and the characteristics of real data necessitates the design of a new capture-based sequencing-specific simulator.

RESULTS: We present RAmpSim, a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing models of platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. RAmpSim generally outperforms a uniform baseline with respect to position-based earth mover's distance when compared against the empirical coverage distribution. Classification analysis also shows high recall in recovering empirical high-coverage regions while outperforming a uniform baseline.

AVAILABILITY: Code, example scripts, and data sources are available at https://github.com/az002/RAmpSim.git.},
}

*Metagenomics/methods
Thermodynamics
*Nucleic Acid Hybridization/methods
*Sequence Analysis, DNA/methods
*Software
Computer Simulation

@article {pmid42413135,
year = {2026},
author = {Hernández-Velázquez, R and Bokulich, NA},
title = {Unlocking the biotechnological potential of traditional fermented food microbiomes.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103550},
doi = {10.1016/j.copbio.2026.103550},
pmid = {42413135},
issn = {1879-0429},
abstract = {Fermented foods are a globally important source of dietary microbes, cultural heritage, and functional diversity, yet current microbiome research captures only a narrow fraction of this richness. Public sequencing datasets are heavily skewed toward a limited set of regions and fermentation types, leaving vast areas of geographic, substrate, and process diversity underrepresented. This imbalance constrains the discovery of novel microbial species, enzymes, and biosynthetic capacities, and risks accelerating homogenization through standardized starter cultures. We argue that coordinated, ethically grounded global efforts integrating metagenomics, multi-omics, standardized metadata, and biobanking are urgently needed to document, preserve, and responsibly leverage fermented food microbial diversity for sustainable food systems and innovation.},
}

@article {pmid42413264,
year = {2026},
author = {Hu, N and Feng, Q and Li, C and Liu, Y and Zhu, B and Guo, T and Tong, L and Shi, J and Sanford, RA and Li, S and He, Y and Hu, Y and Jiang, Z and Jiang, Y and Zhao, L and Wang, M and Xu, M and Li, Y and Dong, Y and Shi, L},
title = {Fe(II)-driven abiotic-biotic relay alleviates denitrification bottleneck via chemical nitrite reduction and intracellular carbon.},
journal = {Water research},
volume = {304},
number = {},
pages = {126366},
doi = {10.1016/j.watres.2026.126366},
pmid = {42413264},
issn = {1879-2448},
abstract = {The coexistence of iron and nitrate (NO3[-]) in natural and engineered environments invites complex abiotic and biotic interactions, yet how such abiotic-biotic synergies operate under fluctuating carbon availability and how light modulates them remain poorly resolved. Using a nitrate-reducing, nitrite-accumulating enrichment culture derived from lake sediment, we uncovered a synergistic abiotic-biotic relay that overcame the kinetic bottleneck of denitrification. During initial heterotrophic denitrification of 2 mM NO3[-], 85.10-89.72% of the substrate was accumulated as NO2[-]. In contrast, ferrous iron (Fe(II)) amendment triggered subsequent iron-dependent nitrate reduction (IDNR) and significantly reduced NO2[-] accumulation. Abiotic controls confirmed that Fe(II) chemically reduced the accumulated NO2[-] to the downstream products. In parallel, metagenomic and metatranscriptomic analyses of the bioactive samples demonstrated that these gaseous intermediates (e.g., NO, N2O) were enzymatically reduced to N2 based on upregulated denitrification-associated genes. More importantly, when exogenous acetate was depleted, the community sustained IDNR not through strict autotrophy but via heterotrophic metabolism using intracellular poly-3-hydroxybutyrate (PHB) and microbial necromass as the carbon/energy sources. This metabolic plasticity drove a functional succession from organotrophic denitrifiers (e.g., Pseudomonas) toward PHB- and necromass-utilizing microbial consortia mainly composed of Pseudomonas, Alicycliphilus and some phototrophic populations. Supporting evidence showed that illumination further accelerated the relay via light-driven reactive oxygen species, and secondary iron minerals (e.g., bernalite, lepidocrocite, and goethite) formed as fingerprints of the Fe(II) oxidation. Collectively, this work deciphers a dual-mechanism model, abiotic nitrite reduction followed with endogenous carbon-fueled denitrification, that governed efficient nitrate reduction under carbon-limited conditions. Leveraging such abiotic-biotic relays offers promising strategies for sustainable nitrogen removal in both natural and engineered systems.},
}

@article {pmid42413404,
year = {2026},
author = {Cao, Z and Gong, H and Qin, H and Wei, T and He, X and Yang, K and Li, X and Wang, Y and Jia, Y and Lan, X and He, W and Jing, X and Long, R and Li, B and Mi, J},
title = {Gut dysbiosis and Escherichia coli-associated enrichment of antibiotic resistance genes in diarrheal yak calves.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142862},
doi = {10.1016/j.jhazmat.2026.142862},
pmid = {42413404},
issn = {1873-3336},
abstract = {Yak grazing systems are fundamental to pastoralist livelihoods on the Qinghai-Tibet Plateau (QTP), and their safe and sustainable development is essential for regional socioeconomic stability. Diarrhea is a multifactorial disease that severely impairs calf growth and may lead to mortality. In this study, we integrated second- and third-generation metagenomic sequencing with untargeted metabolomics to elucidate the underlying mechanisms and associated biosafety risks in yak calves with diarrhea. The results revealed significant gut microbiota dysbiosis in affected calves, characterized by reduced α-diversity and disrupted metabolism of arachidonic acid (AA) and its derivatives. Analysis of 1799 high-quality metagenome-assembled genomes (MAGs; ≥50% completeness and ≤5% contamination) showed a markedly increased relative abundance of Escherichia coli (16.4%) in diarrheal feces, far exceeding that observed in healthy controls. Eight assembled E. coli strains served as major reservoirs of antibiotic resistance genes (ARGs), contributing to high fecal abundances of resistance genes associated with MLS antibiotics (22.1%), bacitracin (21.7%), and β-lactams (19.9%), along with abundant mobile genetic elements (MGEs), including tnpA (21.1%) and IS91 (13.0%). Viral profiling identified E. coli as a key host for bacteriophages belonging to the families Chimeraviridae, Straboviridae, and Suoliviridae. These phages carried ARGs and MGEs that matched those detected in E. coli, potentially facilitating the dissemination of resistance through horizontal gene transfer. StrainPhlAn analysis further demonstrated that multidrug-resistant E. coli strains are widespread even among healthy calves, indicating the presence of a hidden resistome with potential for inter-individual transmission. These findings provide important theoretical guidance for managing yak calf diarrhea and offer valuable references for improving livestock production safety and mitigating antimicrobial resistance on the QTP.},
}

@article {pmid42413405,
year = {2026},
author = {Zhang, K and Fang, Y and Zhang, L and Zhao, W and Zhang, X and Ye, L},
title = {Dissolved oxygen regulation enhances organic micropollutant removal in wastewater treatment bioreactors.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142887},
doi = {10.1016/j.jhazmat.2026.142887},
pmid = {42413405},
issn = {1873-3336},
abstract = {Organic micropollutants (OMPs) are ubiquitously detected in wastewater and pose potential risks to aquatic ecosystems and human health, making their effective removal a critical objective of wastewater treatment processes. Dissolved oxygen (DO) is a central operational parameter that governs microbial metabolism in biological wastewater treatment processes; however, its long-term role in controlling OMP removal remains insufficiently understood. Here, three bioreactors were operated for 166 days under staged DO conditions ranging from 0.8 to 4.5 mg/L to systematically evaluate the effects of DO on the removal of eight representative OMPs and associated microbial responses. Operating at a low DO level maintained stable removal of conventional pollutants while significantly enhancing the biodegradation of several OMPs, including dimetridazole, ofloxacin, trimethoprim, and sulfamethazine. Despite only minor changes in overall community composition, intermediate and rare taxa exhibited pronounced sensitivity to DO variation, suggesting their potential involvement in OMP biodegradation under low-oxygen conditions. Enzyme activity measurements combined with metagenomic and transcriptomic analyses further revealed that low DO promoted higher activity, abundance, and expression of redox-related co-metabolic enzymes, particularly peroxidases and cytochrome P450 enzymes. These results demonstrate that DO regulates OMP removal primarily by reshaping microbial functional potential and redox metabolism. Overall, this study provides both mechanistic understanding and practical guidance for applying DO regulation to achieve enhanced micropollutant removal in wastewater treatment systems.},
}

@article {pmid42413431,
year = {2026},
author = {Mitra, S and Ahmed, MF and Yusuf, MA},
title = {Hidden pathways of antimicrobial resistance: A review of environmental metagenomics and exposure risks in low-resource settings.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130366},
doi = {10.1016/j.jenvman.2026.130366},
pmid = {42413431},
issn = {1095-8630},
abstract = {Antimicrobial resistance (AMR) is increasingly recognised as a One Health challenge in which environmental reservoirs play an important role in the persistence and dissemination of resistance genes. Despite growing recognition that environmental antimicrobial resistance is a critical component of the One Health challenge, the pathways through which antimicrobial resistance genes (ARGs) move between environmental systems and human populations remain incompletely characterised, particularly in low- and middle-income countries where environmental exposures are greatest and surveillance capacity is limited. This review synthesises current knowledge on environmental resistomes across soil, water, sediment and groundwater systems, with a focus on metagenomic and quantitative analytical approaches that have transformed environmental AMR surveillance. Unlike traditional culture-based methods, metagenomics enables comprehensive, culture-independent profiling of microbial communities and their associated resistomes, allowing detection of both known and previously uncharacterised resistance genes, as well as insights into their genetic context and mobility. This has significantly advanced our ability to characterise environmental reservoirs and infer potential transmission pathways at ecosystem scale. Using Bangladesh as an illustrative example of environmental exposure dynamics in rapidly urbanising low- and middle-income settings, we examine how contaminated urban waterways, wastewater discharge, agricultural practices, and seasonal hydrological processes-including monsoon-driven flooding-create interconnected transmission pathways linking environmental, animal, and human microbiomes. We also consider how co-selection pressures from heavy metals and other environmental contaminants contribute to the persistence and amplification of antimicrobial resistance beyond antibiotic-driven selection alone. These dynamics are further intensified by dense surface water networks, strong hydrological connectivity, and limited wastewater treatment infrastructure, which together create high-intensity human-environment interfaces and facilitate large-scale redistribution of antimicrobial resistance genes across environmental compartments. Taken together, these features make Bangladesh an analytically distinctive and tractable model system for understanding environmental AMR dynamics, with relevance to comparable deltaic and monsoon-influenced regions in South and Southeast Asia. Key methodological challenges-including the gap between ARG detection and clinical risk interpretation, biases in resistance gene databases, sampling limitations, and the lack of harmonised environmental surveillance frameworks-are examined alongside emerging tools such as long-read sequencing, functional metagenomics and artificial intelligence-assisted bioinformatic analysis. Finally, we propose an integrated One Health framework linking environmental metagenomics, global surveillance systems and policy interventions to support harmonised, data-driven monitoring and mitigation of environmental AMR across interconnected ecosystems.},
}

@article {pmid42413842,
year = {2026},
author = {Hu, Y and Shi, S and Liu, Y and Chen, H and Cui, K and Wei, L},
title = {Structure and Function of the Coleoptericin Gene in the Ladybird Beetle Serangium japonicum during Seasonal Development.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105675},
doi = {10.1016/j.dci.2026.105675},
pmid = {42413842},
issn = {1879-0089},
abstract = {[OBJECTIVE]: This study was conducted to explain the relationship between structure and function of coleoptericin in Serangium japonicum, and importance of the differential expression patterns of it between in winter and summer, and to provide a theoretical foundation for the rational application of S. japonicum as a natural enemy in pest control. [METHOD]: The full length cDNA was obtained using rapid amplification of cDNA ends (RACE) technology. Bioinformatics software was employed to predict the structure and physicochemical properties of the coleoptericin protein based on its cDNA sequence. The prokaryotic expression protein were tested activity of anti against three experimental strains of microorganisms through using the pore diffusion method. Additionally, metagenome was sequenced and analyzed to find the proteins' effect on microorganism in S.japonicum. [RESULT]: The full-length cDNA sequence of coleoptericin was found to be 606 base pairs (bp) in length. Its open reading frame (ORF) spanned from nucleotide 48 to 495, totaling 447 bp, and encoded a polypeptide of 149 amino acids. Homology analysis revealed that the deduced amino acid sequence shared the highest similarity (55.1%) with the antimicrobial peptide from Tribolium castaneum. The protein had molecular weight of 17.03 kD and theoretical i-soelectric point of 9.19. Hydrophilicity analysis indicated a grand average of hydropathicity (GRAVY) score of -0.85, suggesting a hydrophilic nature. Furthermore, the protein was predicted to contain one transmembrane domain and a signal peptide. Agar well diffusion assays demonstrated that the prokaryotically expressed coleoptericin exhibited antimicrobial activity against Escherichia coli. Results from Metagenome showed that the abundance of Penicillium was significantly lower in winter compared to summer. [CONCLUSION]: The coleoptericin protein from S.japonicum had a sequence of over 100 amino acid residues and an α-helical secondary structure. For S. japonicum, our results supported that coleoptericin protein could protect the beetle from pathogenic bacteria in winter. Some results from relative reports suggested that coleoptericin protein also could be an antifreeze energy source except for immune function.},
}

@article {pmid42413995,
year = {2026},
author = {Halford, C and Toriro, R and Rowlands, E and Le Viet, T and Schaap, S and O'Shea, MK and Fletcher, T and Beeching, NJ and Woolley, S and Lukaszewski, R and Gilmour, M and Weller, SA},
title = {Detection of Cryptosporidium hominis by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya.},
journal = {BMJ military health},
volume = {},
number = {},
pages = {},
doi = {10.1136/military-2026-003248},
pmid = {42413995},
issn = {2633-3775},
abstract = {INTRODUCTION: Traveller's diarrhoea is a common complaint among deployed military personnel. Maintaining sample integrity prior to diagnostic testing is a key challenge in resource-limited environments. We report the comparison of three long-term ambient temperature stool sample stabilisation matrices for the detection of Cryptosporidium hominis from samples collected during an outbreak among British military personnel stationed in Kenya.

METHODS: A retrospective cohort of stool samples, each stabilised for more than 12 months at ambient temperatures using Flinders Technical Associate (FTA) cards, OMNIgene GUT tubes and DNA Shield faecal collection tubes, were analysed by Nanopore-based clinical metagenomic (CMgs) DNA sequencing and quantitative real-time PCR (qPCR) in the UK. The results were compared with BioFire FilmArray Gastrointestinal Panel testing carried out at the point of sampling in Kenya.

RESULTS: Cryptosporidium DNA was detected in 13/24 (54.2%) OMNIgene GUT samples by CMg following long-term storage, compared with 9/24 (37.5%) of DNA Shield samples. Samples stored on FTA cards did not identify Cryptosporidium DNA by CMg in any sample. OMNIgene GUT samples also had the highest rate of detection of C. hominis DNA by qPCR, with 23/24 samples testing positive, compared with 21/24 and 17/20 of DNA Shield and FTA samples, respectively.

CONCLUSIONS: Samples stored in OMNIgene GUT tubes retained detectable levels of Cryptosporidium DNA in a higher proportion of samples following long-term storage. This study demonstrates the importance of selecting the optimal sample collection and stabilisation matrix for CMg and qPCR based diagnostic testing in austere environments.},
}

@article {pmid42414020,
year = {2026},
author = {Clister, D and Chandra, QM and Tan, MW and Gunawan, MC and Bibi, A and Ahmed, A and Bastian, M and Meesakul, P and Cao, S and Kim, B and Nurkolis, F and Syahputra, RA},
title = {Microbiome-Based Precision Interventions in Type 2 Diabetes Mellitus: Mechanisms, Modulators, and Translational Opportunities.},
journal = {The Journal of nutrition},
volume = {156},
number = {7},
pages = {101596},
doi = {10.1016/j.tjnut.2026.101596},
pmid = {42414020},
issn = {1541-6100},
abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disease driven by insulin resistance, chronic low-grade inflammation, and impaired glucose regulation. Although pharmacological options have advanced, sustained glycemic control remains elusive due to heterogeneity in disease progression and therapeutic response. Precision medicine offers a framework to individualize interventions, with the gut microbiota emerging as a central determinant of host metabolic and immune regulation. Dysbiosis has been implicated in T2DM through altered microbial metabolites-including short-chain fatty acids, bile acids, branched-chain amino acids, and indole derivatives-that shape insulin sensitivity, inflammatory pathways, and glucose homeostasis. This review critically examined microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and personalized nutrition, alongside advances in metagenomics and machine learning for biomarker discovery. By integrating mechanistic and translational insights, we highlight opportunities and challenges in implementing microbiome-based precision interventions, underscoring their potential to transform T2DM management.},
}

@article {pmid42402588,
year = {2026},
author = {Jin, Y and Cui, J and Liu, R and Ma, H and Xu, X and Wu, S and Gan, F and Lu, ZJ and Xu, ZZ},
title = {Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02454-1},
pmid = {42402588},
issn = {2049-2618},
abstract = {BACKGROUND: Bacterial transcription termination is a critical yet underexplored layer of gene regulation in microbial ecosystems. Existing computational tools, however, primarily focus on predicting transcript 3' ends generated by Rho-independent terminators (RITs) in a few model species, leaving gaps in understanding those generated by Rho-dependent terminators (RDTs) and their diversity across Bacteria.

RESULTS: We developed BATTER (Bacteria Transcript Three Prime End Recognizer), a deep learning-based framework for predicting bacterial transcript 3' termini. BATTER leverages the observation that conserved stem-loop structures are frequently associated with 3' ends of primary transcripts terminated by both RIT and RDT mechanisms across diverse bacterial clades. Compared with existing approaches, BATTER demonstrated superior performance and scalability, enabling a comprehensive analysis of 42,905 representative bacterial genomes. This large-scale application revealed that stem-loop structures exhibit clade-specific properties with greater variations between species than between gene families. Notably, BATTER uncovered that certain Cyanobacteria lineages, despite lacking rho homologs, harbor Rho utilization (RUT)-like sequences near 3' ends, and preliminary experimental validation in E. coli supports their partial functionality in transcription termination. Additionally, BATTER systematically identified pervasive premature termination events in antimicrobial resistance (AMR) genes.

CONCLUSIONS: BATTER enables large-scale comparative genomic analyses of transcription termination, providing a powerful framework to investigate termination-associated transcriptional regulation in microbial communities. The BATTER tool is available at https://github.com/xu-research-lab/BATTER. Video Abstract.},
}

@article {pmid42402612,
year = {2026},
author = {Cao, L and Zhang, G and Zhang, G and Zhang, F and Li, W and Song, Q and He, J and Zhao, J and Zhang, Z},
title = {Cichorium intybus L. polysaccharide improves growth performance and colonic barrier function in weaned piglets via the microbiota-HDCA-TGR5-Akt-NF-κB signaling axis: validation by FMT and in vitro models.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42402612},
issn = {1674-9782},
support = {32302766//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Weaning stress predisposes piglets to intestinal barrier disruption and gut dysbiosis, which contribute to post-weaning diarrhea and poor feed efficiency. Chicory (Cichorium intybus L.) polysaccharide (CLP) is a fructan-rich prebiotic candidate; however, how CLP reshapes the microbiota-metabolite network to protect the colon remains unclear.

METHODS: In Exp. 1, 96 weaned piglets [Duroc × (Landrace × Yorkshire), 28 days old, 8.03 ± 0.2 kg] were fed a basal diet (CON group) or a 0.5% CLP supplemented diet (CLP group). In Exp. 2, fecal microbiota from piglets were transplanted into dextran sulfate sodium (DSS)-induced mice to confirm the causal role of the CLP-remodeled microbiota. Metagenomic and untargeted metabolomic analyses were employed to identify key microbial species and functional metabolites. In Exp. 3, Caco-2 cells were treated with varying concentrations of hyodeoxycholic acid (HDCA) for 24 h to functionally validate the regulatory effects on TGR5 and FXR expression levels.

RESULTS: The results showed that dietary CLP significantly decreased the feed to gain ratio, diarrhea rate and histology index (P < 0.05), but increased goblet cell numbers (P < 0.05). Metagenomic sequencing revealed that CLP significantly increased microbial α-diversity and remodeled the community structure, specifically enriching beneficial microbes, such as Blautia sp., Eubacterium sp., and Ruminococcus sp. To test microbiota causality, fecal microbiota from CON or CLP piglets was transplanted into antibiotic treated mice followed by DSS challenge. The CLP modified microbiota alleviates DSS induced colitis, upregulated Occludin and ZO-1 expression, and reduced colonic IL-1β and TNF-α levels. Mechanistically, the CLP remodeled microbiota promoted the accumulation of HDCA, which functioned as a signaling ligand to activate the colonic TGR5 receptor. This activation subsequently suppressed the phosphorylation of Akt (P < 0.05), leading to the inhibition of the NF-κB signaling pathway through the reduced phosphorylation of IκBα and the p65 subunit (P < 0.05), thereby effectively abrogating the inflammatory response.

CONCLUSION: Dietary CLP supplementation mitigates weaning induced intestinal injury and inflammation by remodeling the colonic microbiota, specifically enriching HDCA-producing species. The subsequent activation of the HDCA-TGR5-Akt signaling axis inhibits the NF-κB pathway, thereby improving host immune responses and intestinal barrier function.},
}

@article {pmid42402715,
year = {2026},
author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD},
title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70698},
pmid = {42402715},
issn = {1365-3040},
support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; },
abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.},
}

@article {pmid42402854,
year = {2026},
author = {Cai, Y and Yan, H and Qin, J and Qiang, Y and Lin, GQ and Wang, H and He, QL and Zhao, Q},
title = {Heterologous Expression of an Abandoned Termite Mound Fungus Gene Cluster Reveals a Protective Aldehyde-Alcohol Cycle and a Candidate Termiticidal Metabolite.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.6c00101},
pmid = {42402854},
issn = {2161-5063},
abstract = {The medicinal fungus Wulingshen, comprising multiple Xylaria species, inhabits deserted termite mounds as sclerotia. To explore the molecular basis of its niche adaptation, we employed a synthetic biology-driven approach. Metagenomic and transcriptomic mining of wild specimens identified a conserved biosynthetic gene cluster. Its heterologous reconstruction in the fungal host Aspergillus oryzae enabled the characterization of a family of α-pyrone metabolites and, crucially, the elucidation of a spatially separated aldehyde-alcohol cycle. In this self-protection system, an extracellular oxidase (WlsA) converts an alcohol precursor to a reactive aldehyde, while an intracellular reductase (WlsE) catalyzes the reverse reaction. The aldehyde product exhibits potent toxicity against termites in vitro, suggesting a potential role in ecological interactions. This work establishes a functional genomics platform that decodes cryptic ecological metabolism by integrating multiomics with heterologous pathway expression, providing a generalizable strategy for discovering and mechanistically understanding niche-specific natural products.},
}

@article {pmid42402985,
year = {2026},
author = {Asato, Y and Kubo, T and Hashimoto, M and Wakatsuki, T and Sakamoto, H and Tanigawa, T and Kitamura, S and Kadokawa, H},
title = {Bifidobacterium longum BB536 supplementation is associated with increased circulating choline plasmalogen concentrations in non-pregnant, non-lactating dairy cows.},
journal = {Reproduction, fertility, and development},
volume = {38},
number = {10},
pages = {},
doi = {10.1071/RD26107},
pmid = {42402985},
issn = {1448-5990},
mesh = {Animals ; Female ; Cattle ; *Plasmalogens/blood ; Pregnancy ; *Probiotics/administration & dosage ; Dietary Supplements ; Lactation ; *Bifidobacterium ; Animal Feed ; },
abstract = {CONTEXT: Plasmalogens are ether phospholipids implicated in neuroendocrine regulation, including reproductive function. Recent studies have suggested that circulating plasmalogen concentrations are associated with reproductive performance in dairy cows; however, practical strategies to increase these concentrations remain limited.

AIMS: We hypothesised that supplementation with Bifidobacterium longum increases circulating choline plasmalogen concentrations and that this response depends on physiological state.

METHODS: Commercial probiotic products were screened using liquid chromatography-mass spectrometry and metagenomics to identify candidates containing plasmalogen-producing bacteria. A product containing the characterised strain B. longum BB536 and products containing other B. longum strains were selected for in vivo evaluation. Selected products were administered to Holstein cattle, and circulating choline plasmalogen concentrations were measured using an enzyme-based fluorometric assay.

KEY RESULTS: In long-term non-pregnant, non-lactating dairy cows, supplementation with B. longum BB536 significantly increased circulating choline plasmalogen concentrations, with a detectable rise approximately 1 week after the start of treatment and peak concentrations during Days 8-14 (P < 0.05). In contrast, no consistent increase was observed in pregnant, lactating dairy cows. Cross-sectional analysis across pregnancy stages showed significant variation in circulating choline plasmalogen concentrations, with lower concentrations during mid- to late gestation. No adverse effects were observed in ruminal pH, blood lactate concentrations, or bodyweight.

CONCLUSION: These findings suggest that supplementation with B. longum BB536 increases circulating choline plasmalogen concentrations in a state-dependent manner.

IMPLICATIONS: This study has provided new insight into the regulation of plasmalogens in cattle and suggests a potential nutritional approach for modulating reproductive function.},
}

Animals
Female
Cattle
*Plasmalogens/blood
Pregnancy
*Probiotics/administration & dosage
Dietary Supplements
Lactation
*Bifidobacterium
Animal Feed

@article {pmid42403142,
year = {2026},
author = {Zheng, Y and Ruan, P and Chen, H},
title = {Severe <em>Pneumocystis Jirovecii </em>Pneumonia in a Non-HIV Infant: The Diagnostic Value of Metagenomic Next-<br /> Generation Sequencing.},
journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP},
volume = {36},
number = {7},
pages = {961-962},
doi = {10.29271/jcpsp.2026.07.961},
pmid = {42403142},
issn = {1681-7168},
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; *Pneumocystis carinii/genetics/isolation & purification ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Infant ; },
abstract = {Null.},
}

Humans
*Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology
*Pneumocystis carinii/genetics/isolation & purification
*Metagenomics/methods
High-Throughput Nucleotide Sequencing
Infant

@article {pmid42403487,
year = {2026},
author = {Calvanese, CM and Valentino, V and Sequino, G and De Vivo, A and Buzzanca, D and Prencipe, S and Demarinis, C and Perri, G and Pontonio, E and Ferrocino, I and Ercolini, D and De Filippis, F},
title = {Lactobacilli, best allies of mental health: a probiogenomic approach to identify potential psychobiotic strains.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101490},
pmid = {42403487},
issn = {2665-9271},
abstract = {Targeted dietary strategies and supplements represent a promising approach for the treatment of cognitive problems. Multi-omic approaches may facilitate and accelerate the discovery of new psychobiotic strains and their applications. In this work, we applied metagenomics and comparative genomics to guide the isolation and screening of novel psychobiotic strains from fermented foods. Metagenomes of 1185 fermented food were screened, revealing the occurrence of genes coding for the biosynthesis of neuroactive molecules, supporting the isolation of 73 novel Lactic Acid Bacteria (LAB) strains. Comparative genomic analysis highlighted species-specific patterns, identifying Levilactobacillus brevis, Lactiplantibacillus plantarum, Limosilactobacillus fermentum as potential psychobiotics. In vitro functional screening for the production of neuroactive metabolites confirmed four strains, Lactiplantibacillus plantarum TUCC00000144, Limosilactobacillus fermentum TUCC00000777, Levilactobacillus brevis TO10, Lentilactobacillus diolivorans B92, as the most promising candidates for the development of dietary supplements or innovative fermented food products aimed at supporting mental health.},
}

@article {pmid42403498,
year = {2026},
author = {Leprohon, H and Tannir, B and Jolicoeur, G and Domingo, MC and Dufresne, PJ and Morency-Potvin, P and Benoit, P and Grandjean Lapierre, S},
title = {Impact of direct from clinical sample sequencing assays for infectious diseases diagnostics: A single-centre retrospective cohort study.},
journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada},
volume = {11},
number = {2},
pages = {141-154},
pmid = {42403498},
issn = {2371-0888},
abstract = {BACKGROUND: The analytical performance of bacterial targeted sequencing (BTS), fungal targeted/panfungal sequencing (FTS), and metagenomic next-generation sequencing (mNGS) assays has been previously evaluated and their clinical use is increasing. Limited evidence is available on their true clinical impact on infectious disease diagnosis and treatment.

METHODS: We conducted a 3-year retrospective cohort study including all patients for whom broad-range sequencing assays were performed directly from clinical samples for the detection of bacterial and fungal pathogens. The operational characteristics, diagnostic and therapeutic impacts of the assays were assessed by reviewing patient clinical files and laboratory information system charts.

RESULTS: A total of 279 samples from 185 patients were included. The positivity rates for BTS, FTS, and mNGS were respectively 20.5% (47/229), 20% (9/45), and 20% (1/5). Of these 279 samples, 40 (14.3%) had an impact on patient management. The test results helped to establish a diagnosis in 26 (9.3%) cases and led to treatment modifications in 14 (5%). FTS achieved higher impact rates (26.7%) than both BTS (12.2%) and mNGS (0%). Short turnaround times increase impact rates, and the most impactful tests were those performed on bone and intervertebral disc samples, or in patients with negative culture results due to prior antibiotic administration.

CONCLUSIONS: In this study, the overall diagnostic impact of BTS and FTS was high. Both the diagnostic and treatment impact of those assays can be increased if prescribed in well-selected clinical syndromes and performed on well-selected clinical samples.},
}

@article {pmid42404619,
year = {2026},
author = {Ramani, RR and Baskaran, S and Arun, KV and Alamelu, S and Arumugamnainar, D},
title = {Salivary metagenomic profiling of Neisseria , Dialister , and Filifactor species in periodontal health and disease using next-generation sequencing.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {4},
pages = {101482},
pmid = {42404619},
issn = {2212-4268},
abstract = {BACKGROUND: Periodontal diseases represent a complex dysbiosis-driven inflammatory condition, where the transition from health to gingivitis and periodontitis is accompanied by distinct microbial shifts. Emerging evidence highlights the significance of less-studied genera such as Neisseria, Dialister, and Filifactor in shaping periodontal outcomes. This study aimed to investigate the salivary distribution of Neisseria, Dialister, and Filifactor species across periodontal health, gingivitis, periodontitis, and gingival recession using next-generation sequencing (NGS).

METHODS: Whole saliva samples were collected from 40 participants (10 per group) classified according to the American Academy of Periodontology criteria. Microbial DNA was extracted and subjected to 16S rRNA sequencing (V3-V4 region, Illumina MiSeq). Species-level classification was performed using the Human Oral Microbiome Database. Frequency distributions were compared across groups using Fisher's exact test, with significance set at p < 0.05.

RESULTS: Distinct patterns were observed. Several commensal Neisseria species, including N. subflava (p = 0.001), N. elongata(p = 0.015), and N. polysaccharea (p = 0.001), showed significantly reduced prevalence in periodontitis compared with health and gingivitis. In contrast, Dialister pneumosintes exhibited a sharp increase in all diseased groups (p = 0.002). Filifactor alocis was markedly enriched in gingivitis, recession, and periodontitis (p = 0.011), suggesting its strong association with disease states.

CONCLUSION: The findings demonstrate a characteristic microbial shift in saliva: health-associated Neisseria species decline with disease progression, while anaerobic taxa such as D. pneumosintes and F. alocis expand. These results align with the polymicrobial synergy and dysbiosis model and underscore the potential of these species as salivary biomarkers for early detection and monitoring of periodontal disease.},
}

@article {pmid42404879,
year = {2026},
author = {Dai, P and Feng, J and Cao, J and Fan, D},
title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828633},
pmid = {42404879},
issn = {1664-3224},
mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.

METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.

RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-κB, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).

CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.},
}

Humans
Multiomics
*Pancreatitis/metabolism/microbiology/immunology
Metabolomics
Gene Expression Profiling
*Host Microbial Interactions/immunology
Biomarkers
Metabolic Reprogramming
*Gastrointestinal Microbiome/immunology
Acute Disease
Female
Transcriptome
Male
Metabolome

@article {pmid42405192,
year = {2026},
author = {Scott, CJR and Caccia, S},
title = {metaLoc: protein localisation prediction workflow.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag169},
pmid = {42405192},
issn = {2635-0041},
abstract = {SUMMARY: metaLoc combines existing tools for signal peptide, localisation, and transmembrane helices prediction from protein sequences into a workflow for rapid evaluation of protein datasets. By accepting both protein and nucleotide sequences, the workflow is especially suitable for in silico screening of the growing volumes of sequencing data. With a single command, metaLoc provides a simple, accessible, and user-friendly tool for the bioinformatic investigation of proteomic or metagenomic datasets.

metaLoc is freely available on the GitHub platform (https://github.com/scottc-bio/metaLoc). The metaLoc workflow is implemented in Nextflow with a modular design utilizing isolated Conda environments for reproducibility. An archived version of this release is permanently available at Zenodo (https://doi.org/10.5281/zenodo.18936772).},
}

@article {pmid42405317,
year = {2026},
author = {Wang, Y and Cai, Y and Peng, Z and Hou, F and Jia, Z},
title = {Molecular insights into atmospheric methane-oxidizing USCγ from desert grassland soil based on metagenome-assembled genome analysis.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag151},
pmid = {42405317},
issn = {2730-6151},
abstract = {Upland Soil Cluster Gamma (USCγ) is a key high-affinity aerobic methanotroph driving atmospheric methane oxidation in grassland soils; however, it has never been obtained in pure culture, and its metabolic processes remain largely unknown. Here, we reconstructed a USCγ metagenome-assembled genome (MAG) containing the complete pmoA gene from desert grassland soil in northwestern China, designated USC_AKS. At the site, USCγ accounted for 9.83% of the microbial community in the 10-20 cm layer. BLASTn of its 16S rRNA gene against the NCBI database (excluding uncultured/environmental sequences) showed 93.03% similarity to the non-methanotroph Thioalkalivibrio sulfidiphilus HL-EbGr7 (order Chromatiales). The closest match among named species was an uncultured bacterium (JN672117) at 97.86% similarity. Its pmoA shares 96.18% similarity with the original USCγ-defining sequence. Phylogenomic analysis placed USC_AKS and seven other USCγ MAGs into a monophyletic group of three subclades, distantly related to culturable Type I methanotrophs. Their genomic average nucleotide identity values are all below 95%, confirming eight distinct species. Like other USCγ MAGs, USC_AKS encodes a complete pmoCAB operon, an XoxF-type methanol dehydrogenase, and enzymes for formaldehyde oxidation to CO2. However, it lacks key ribulose monophosphate (RuMP) cycle genes encoding 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexulose isomerase (phi). The serine cycle also appears incomplete, as these MAGs lack hpr, the gene encoding hydroxypyruvate reductase. Moreover, none encode Rubisco, ruling out the Calvin-Benson-Bassham CO2-fixation pathway. Consequently, the metabolic characteristics of USCγ-particularly its carbon assimilation pathway-remain enigmatic, and obtaining pure cultures or enriched consortia is likely the only route to resolving this mystery.},
}

@article {pmid42405318,
year = {2026},
author = {Modolon, F and Capo, E and Wardle, DA},
title = {Long-term ecosystem development and retrogression drive microbial specialization for complex organic matter degradation.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag157},
pmid = {42405318},
issn = {2730-6151},
abstract = {Long-term ecosystem development includes a build-up phase followed by a decline (retrogressive) phase characterized by reduced plant productivity and belowground process rates due to reduced nutrient availability. In boreal forests, retrogression is accompanied by soil organic matter (SOM) accumulation, especially in the prolonged absence of fire. However, the role of bacterial communities in SOM dynamics during ecosystem retrogression has been little explored. Using a 5000-year post-fire boreal forest chronosequence, we investigated how long-term succession and retrogression shapes soil bacterial community structure and functional specialization. While the Actinomycetota phylum dominated communities across all chronosequence stages, a significant family-level shift within this phylum occurred in the later (retrogressive) phase, characterized by a transition from Mycobacteriaceae to Streptosporangiaceae. The recovery of metagenome-assembled genomes (MAGs) revealed distinct life-history trade-offs between these families. Streptosporangiaceae MAGs were significantly enriched in genes for degrading phenolics, cellulose, and lignin, and exhibited potential for chitin, lipid and peptide degradation. This positions them as potential decomposers of the primary constituents of stored soil carbon, including plant-derived complex carbohydrates and fungal necromass, during retrogression when fungal activity declines. In contrast, Mycobacteriaceae MAGs are likely to prioritize inorganic phosphate (P i) uptake-by pstS gene enrichment, reflecting adaptation to P availability changes during ecosystem development. Collectively, our results demonstrate that long-term ecosystem retrogression drives shifts in the bacterial communities and functions within the Actinomycetota. These shifts may indicate possible divergent strategies, i.e. recalcitrant carbon turnover versus nutrient scavenging, which could explain shifts in the microbial community as the ecosystem transitions toward retrogressive, nutrient-limited states.},
}

@article {pmid42405543,
year = {2026},
author = {Anggraini, D and Yovi, I and Elliyanti, A and Safari, D and Syah, NA and Jati, AP and Sarassari, R and Simatupang, ETM},
title = {Metagenomic Analysis of Thoracic Empyema Etiology Through Next-Generation Sequencing Enhances Conventional Culture Techniques.},
journal = {Infection & chemotherapy},
volume = {58},
number = {2},
pages = {214-223},
doi = {10.3947/ic.2025.0159},
pmid = {42405543},
issn = {2093-2340},
abstract = {BACKGROUND: This study aimed to analyze the microbiome of thoracic empyema using metagenomic methods and compare the results with conventional culture methods to increase diagnostic accuracy and enhance antibiotic therapy.

MATERIALS AND METHODS: This study involved 30 patients with thoracic empyema from hospitals in Riau Province, Indonesia. Pleural fluid samples were collected for culture analysis and identification using the Vitek 2 compact system and metagenomic analysis. Patient clinical data were also collected.

RESULTS: Culture methods showed a 40.0% positive rate, with Gram-negative bacteria (Klebsiella pneumoniae and Pseudomonas aeruginosa) predominating. Metagenomics showed a 56.7% positive rate, identifying a more diverse microbiome, including fungi (29.4% abundance), other Gram-negative bacteria (26.5%), and anaerobic bacteria (22.5%). Comparison of the two methods showed 36.7% complete agreement and 23.3% partial agreement, with 40% disagreement, with a Kappa coefficient of 0.416 and P-value of 0.016 (P<0.050).

CONCLUSION: Metagenomic NGS offers significant advantages in detecting the microbiome of thoracic empyema, particularly fungi and anaerobic bacteria, which are often missed by conventional culture methods. This has the potential to improve diagnostic accuracy and optimize antibiotic therapy. Further research with larger sample sizes is needed.},
}

@article {pmid42405768,
year = {2026},
author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH},
title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0038626},
doi = {10.1128/msphere.00386-26},
pmid = {42405768},
issn = {2379-5042},
abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.},
}

@article {pmid42406122,
year = {2026},
author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B},
title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02817-z},
pmid = {42406122},
issn = {1432-184X},
support = {REIG-FPS-2025/038//UCSI University/ ; },
abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.},
}

@article {pmid42407310,
year = {2026},
author = {Jiang, ZQ and Xing, RK and Peng, D and Ren, YH and Wei, TY and Guo, WB and Shen, ZM and Wang, CN and Zhang, FL and Yuan, T},
title = {Compartment-specific host association and mobility shape ARG risk in aquaculture systems.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142895},
doi = {10.1016/j.jhazmat.2026.142895},
pmid = {42407310},
issn = {1873-3336},
abstract = {Antimicrobial resistance in aquaculture threatens environmental and public health, but the risk of ARGs cannot be inferred from abundance alone; host context and mobility potential are essential. Here, we investigated how ecological compartments shape ARG host background, mobility, and risk in aquaculture systems. We analyzed 437 metagenomes from water and sediment in freshwater and marine aquaculture across China using resistome profiling, host assignment, genetic localization, ARG-MGE co-occurrence, a four-tier risk framework, and machine learning. We detected 1413 nonredundant ARG subtypes (28 classes). Water had higher ARG diversity, stronger associations with opportunistic pathogens, and stronger mobility-related signals than sediment. High-risk ARGs were concentrated in water: Rank I ARGs were exclusive to water, and water-specific Rank II ARGs accounted for 7.2% (freshwater) and 6.9% (marine) of total ARG diversity, versus 4.2% (freshwater sediment) and 2.9% (marine sediment). The LightGBM model identified salinity, temperature, and pH as key mobility predictors. Together, these results show that ARG risk in aquaculture is jointly shaped by the ecological compartment, host association, and mobility potential, with water acting as the principal high-risk interface. This risk-oriented analytical framework provides a transferable basis for prioritizing surveillance and intervention in aquaculture environments.},
}

@article {pmid42407426,
year = {2026},
author = {Dong, F and Hou, A and Hu, X and Wei, L and Sun, F and Xiao, X and Su, X},
title = {Process-dependent niches of rpf-harboring microorganisms regulate nitrogen and carbon functional networks in full-scale activated sludge.},
journal = {Environmental research},
volume = {306},
number = {Pt 2},
pages = {125198},
doi = {10.1016/j.envres.2026.125198},
pmid = {42407426},
issn = {1096-0953},
abstract = {Resuscitating viable but non-culturable (VBNC) microorganisms offers a strategy to unlock hidden metabolic capabilities, enhancing pollutant degradation and system stability in wastewater bioreactors. However, the ecological mechanisms underlying VBNC resuscitation in activated sludge, particularly the role of resuscitation-promoting factor (Rpf) gene-harboring microbial consortia, remain elusive. Here, metagenomic profiling of full-scale anaerobic/anoxic/oxic (A[2]/O) and oxidation ditch processes demonstrates the widespread distribution of rpf-harboring microorganisms in wastewater treatment plants (WWTPs). A[2]/O systems enriched for taxa associated with denitrification and ammonification, while oxidation ditches showed higher abundance of microorganisms involved in nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The two processes configuration harbored distinct sets of rpf-carrying taxa, with Chloroflexota dominating in A[2]/O systems and Nitrospira and Kouleothrix in oxidation ditches. Network analysis further reveals that rpf-harboring taxa may act as ecological connectors between dormant and metabolically active populations, thereby enhancing community cohesion and resilience under fluctuating operational conditions. These findings uncover process-dependent resuscitation ecology shaping activated sludge communities and nutrient transformation pathways, providing a mechanistic foundation for engineering Rpf-mediated microbial interactions to improve biological wastewater treatment.},
}

@article {pmid42409195,
year = {2026},
author = {Yan, M and Yang, C and Huang, J and Qi, P and Tang, L and Lu, H},
title = {Reactor performance and microbial responses of sulfate-reducing bacteria sludge under stepwise polyvinyl chloride microplastic exposure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135334},
doi = {10.1016/j.biortech.2026.135334},
pmid = {42409195},
issn = {1873-2976},
abstract = {Plastic pollution, particularly microplastic contamination, poses potential risks to biological wastewater treatment processes. However, the response of sulfate-reducing bacteria (SRB) sludge systems to polyvinyl chloride (PVC) microplastics remains poorly understood. In this study, a laboratory-scale sulfate-reducing up-flow sludge bed (SRUSB) reactor was operated under stepwise PVC microplastic exposure at 0, 20, 100, and 500 particles/L. COD removal and sulfate reduction showed limited changes at 20 and 100 particles/L, whereas 500 particles/L caused transient inhibition followed by gradual recovery within the same reactor. PVC exposure increased intracellular reactive oxygen species (ROS) levels and lactate dehydrogenase (LDH) release, while live/dead staining indicated no marked increase in cell mortality across the operational stages. Stepwise PVC exposure was also accompanied by enrichment of protein-rich loosely bound extracellular polymeric substances (LB-EPS) and accumulation of PVC-derived additives, including BPA and ATBC. Microbial community analysis showed that the relative abundance of SRB-related genera increased from 8.7% to 24.9%, mainly involving increased abundances of Desulfobacter, Desulfococcus, and Desulforhabdus. Metagenomic annotation further revealed genes associated with EPS precursor supply, polysaccharide assembly/export, protein secretion, antioxidant response, aromatic metabolism, ester-bond hydrolysis, and dissimilatory sulfate reduction. Overall, this study provides a longitudinal characterization of reactor performance and associated physiological, chemical, microbial, and community-level genetic responses of SRB sludge under stepwise PVC microplastic exposure, offering useful insights for evaluating sulfate-reducing saline wastewater treatment systems facing microplastic contamination.},
}

@article {pmid42409199,
year = {2026},
author = {Agostini, F and Baruzzo, V and Fernandez, FR and Satta, A and Raga, R and Penzo, D and Modesti, M and Valerin, MC and Campanaro, S and Treu, L and Zampieri, G},
title = {Discovering hidden candidate plastic-degrading enzymes: Combined multi-omics and machine learning strategy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135332},
doi = {10.1016/j.biortech.2026.135332},
pmid = {42409199},
issn = {1873-2976},
abstract = {Plastic pollution poses a major threat to the stability of natural ecosystems as well as human health. Microbial enzymes have long been considered a potential resource for targeted biodegradation but, except for a few successful cases, the discovery of efficient enzymes has proved challenging. Aiming to accelerate the process, we propose an approach combining metagenomics, metatranscriptomics and semi-supervised learning that selects promising plastic-degrading candidate enzymes from the proteome of relevant microorganisms. Tested on a dataset of over 10,000 microbial proteins, ranking models consistently prioritize known plastic-degrading enzymes, achieving an area under the cumulative distribution function curve above 0.96, with leave-one-family-out cross-validation indicating that performance is largely retained across protein families. As a case study, this work focuses on mixed microbial cultures exposed for extended periods to polyethylene, polyethylene terephthalate, and polyurethane substrates. The prevalent species after selective enrichment were functionally characterized, finding Rhodococcus aetherivorans as the most relevant species in two of the five cultures under investigation. Among the top-ranked proteins, several have high structural similarity with known enzymes despite not being identified by sequence similarity search. Moreover, according to metatranscriptomics results, several of these enzymes were found to be expressed at the same level or above that of annotated enzymes, suggesting that they may have functional relevance. Overall, this work highlights the potential of integrating multi-omics with data-driven methods for enzyme discovery and for accelerating the development of biotechnological solutions to plastic pollution.},
}

@article {pmid42409336,
year = {2026},
author = {Wu, J and Lin, M and Fan, Y},
title = {An Unusual Cause of Chronic Hematochezia.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.06.025},
pmid = {42409336},
issn = {1528-0012},
}

@article {pmid42409355,
year = {2026},
author = {Nguyen, HT and Bez, C and Tran, MQ and Tran, LT and Pham, VT and Bertani, I and Venturi, V and Dinh, HT},
title = {Rhizospheric Fungal Communities and Their Role in Biocontrol of Fusarium in Robusta Coffee (Coffea canephora) in Vietnam.},
journal = {The plant pathology journal},
volume = {},
number = {},
pages = {},
doi = {10.5423/PPJ.OA.12.2025.0186},
pmid = {42409355},
issn = {1598-2254},
abstract = {Rhizospheric microbial communities are critical to the health and productivity of coffee plantations. This study investigated the microbiome of robusta coffee (Coffea canephora) across three major cultivation areas in Vietnam (Dak-Nong, Dak-Lak, and Gia-Lai) to assess its role in Fusarium suppression. Using ITS ampliconbased metagenomics and culture-dependent approaches, we analyzed fungal community structure in relation to location, plant age, and health status. Metagenomic analysis revealed no significant differences in bacterial communities between healthy and diseased rhizospheres, whereas fungal communities showed clear distinctions, particularly in young plants (<2 years). These differences diminished in mature plants (≥2 years) but continued to vary with age (2-10 years). Healthy rhizospheres were enriched with beneficial fungi, while diseased soils contained more phytopathogenic genera. Fusarium was prevalent in all regions, with higher abundance in diseased soils, whereas Trichoderma, a known biocontrol agent, was more abundant in healthy soils but declined with plant age. Of 343 fungal isolates, 46 strains exhibited strong antagonistic activity against Fusarium, representing 10 genera, including Aspergillus, Penicillium, Gongronella, and Talaromyces. Although Trichoderma isolates were less frequent, they showed promising biocontrol potential. These findings underscore the role of rhizospheric fungi in managing Fusarium wilt and identify candidate biocontrol agents for sustainable robusta coffee cultivation.},
}

@article {pmid42409501,
year = {2026},
author = {Huang, C and Zhao, Y and Gu, M and Li, Z and Li, X and Huang, Y and Zhang, C and Zhang, D},
title = {Metagenomic-metabolomic integration elucidates stage-specific dynamics of microbial communities and metabolites driving pork spoilage in commercial supply chains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119678},
doi = {10.1016/j.foodres.2026.119678},
pmid = {42409501},
issn = {1873-7145},
abstract = {Microbial-metabolic axis drives meat quality deterioration and shelf-life changes along commercial supply chains. This study tracked pork quality and freshness from postmortem processing to retail sale by integrating untargeted metabolomic and metagenomic analyses. Over the first 1700 min postmortem, pork showed a decline in pH and increases in L*, a* and b* values, cooking loss, shear force, total volatile basic nitrogen and total viable counts. At the point of sale, the meat remained in rigor mortis and retained acceptable freshness. Metabolic profiles remained dynamic after warehousing and were further modified by ambient exposure during transport and retail sale. Results revealed that differential metabolites were predominantly enriched in purine metabolism, nucleotide metabolism, lysosome pathway, as well as alanine, aspartate and glutamate metabolism. Likewise, several genera potentially associated with spoilage or contamination-associated bacteria were influenced by commercial condition along the supply chain, with increased abundance of Acinetobacter, Bacillus, Listeria, Psychrobacter, Salmonella andEnterobacter during transport and retail sale, while Listeria, Salmonella andEnterobacter may originate from environmental or processing-associated sources. These findings identify stage-specific metabolic and microbial signatures shaped by commercial handling, such as temperature, relative humidity and provide insights for improving pork quality and safety management during the early postmortem period.},
}

@article {pmid42409516,
year = {2026},
author = {Moon, SH and Yang, X and Kim, J and Leighton, E and Jun, SR and DiCaprio, E and Gale, C and Chen, S and Li, X and Huang, E},
title = {Comprehensive analyses of carbapenem-resistant and ESBL-producing bacteria in fresh vegetables and their resistome in the United States.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119552},
doi = {10.1016/j.foodres.2026.119552},
pmid = {42409516},
issn = {1873-7145},
abstract = {Carbapenem-resistant and extended-spectrum beta-lactamase (ESBL)-producing bacteria, once largely confined to healthcare settings, are increasingly detected in community environments. Food and the environment may act as important reservoirs for clinically relevant antibiotic-resistant bacteria. A large-scale surveillance study was conducted from 2022 to 2023 to assess antibiotic resistance in retail fresh vegetables across three U.S. regions: the Midsouth, Midwest, and West Coast. A total of 1218 samples representing five vegetable categories (carrots, lettuce, spinach, sprouts/microgreens, and salads) were analyzed for carbapenem-resistant bacteria and ESBL-producing Enterobacterales. Culture-based methods included selective isolation on CHROMagar, antibiotic susceptibility testing, phenotypic evaluation of ESBL and carbapenem resistance, and carbapenemase detection and typing. Whole-genome sequencing of phenotypically resistant isolates was used to identify beta-lactamase genes. Overall, 62 carbapenem-resistant isolates (5.09%) and 70 ESBL-producing Enterobacterales isolates (5.74%) were recovered. Carbapenemase-producing Enterobacterales included 30 Enterobacter strains and one Kluyvera strain, with carbapenem-resistant Enterobacter most frequently isolated from sprouts and microgreens. ESBL-producing strains included 39 Serratia, 20 Enterobacter, 6 Klebsiella, 3 Raoultella, and 2 Rahnella isolates. Comparative genomic analyses showed close similarity between vegetable isolates and human clinical strains. Notably, the carbapenemase gene blaIMI-6 identified in Enterobacter asburiae from microgreens was transferable to Escherichia coli by conjugation. Shotgun metagenomics of 40 samples further confirmed diverse resistance genes. These findings highlight vegetables as potential reservoirs of clinically important antibiotic resistance and emphasize the need for ongoing surveillance in both vegetable products and their production environments.},
}

@article {pmid42409884,
year = {2026},
author = {Studer Silva Gutierrez, FAO and Morandi, SC and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Influence of smoking on the human ocular surface microbiome and tear proteome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60743-z},
pmid = {42409884},
issn = {2045-2322},
abstract = {The ocular surface hosts microbes of low abundance and their genomes, collectively called the ocular surface microbiome (OSM). The OSM is involved in maintaining health and protecting the eye from infection. Although disruption of this microbial balance has been linked to various eye diseases, the effect of smoking, a known risk factor for ocular conditions, on the OSM remains unclear. We analysed ocular samples from smokers (n = 17) and non-smokers (n = 24) using metagenomic sequencing and proteomics approaches to assess both microbial composition and functions, as well as the host protein profiles. Microbial DNA was examined for bacterial, fungal, and viral taxa, with contaminants removed using microDecon. Statistical analyses showed no significant differences in microbial diversity or tear proteins between groups, apart from one bacterial gene. No bacterial, fungal, or viral species were uniquely associated with smoking status. While no clear smoking-related effects were observed in microbial communities or tear proteome composition, the overall stability of tear proteins may reflect intrinsic resilience dynamics that maintain low microbial abundance on the ocular surface.},
}

@article {pmid42401772,
year = {2026},
author = {Afonso, AC and Lema, JM and Trueba-Santiso, A},
title = {Metaproteomics for Water Biotechnology: Considerations and Study Cases.},
journal = {Advances in experimental medicine and biology},
volume = {1510},
number = {},
pages = {21-44},
pmid = {42401772},
issn = {0065-2598},
mesh = {*Proteomics/methods ; *Biotechnology/methods ; Multiomics ; *Water Purification/methods ; Water Microbiology ; Wastewater/microbiology ; Biofilms ; },
abstract = {This chapter summarizes the current knowledge on the practical, methodological, and interpretative aspects of applying metaproteomics in water biotechnology. We outline the full metaproteomic workflow-from sampling and protein extraction to LC-MS/MS acquisition, database construction, quantitative analysis, and bioinformatic interpretation-and emphasize critical considerations specific to complex matrices such as EPS-rich biofilms, granular sludge, and low-biomass drinking water. Case studies illustrate how metaproteomics can clarify mechanisms of micropollutant degradation, nitrogen-transforming pathways, biofilm functional architecture, and microbial resilience under operational stress. Recent advances in data-independent acquisition, metagenome-informed databases, and integrative multi-omics are shown to substantially improve depth, reproducibility, and functional resolution. Finally, we discuss emerging applications in wastewater-based epidemiology, where metaproteomics complement nucleic-acid-based surveillance by enabling the detection of large biomolecule biomarkers of population health and industrial activity. Although metaproteomics is already being applied across a wide range of water cycle contexts and is producing promising, robust results, several challenges, including limitations in analytical chemistry, database completeness, and bioinformatics workflows, continue to hinder its broader implementation. Continued technical research and innovation are therefore essential to fully unlock its potential in water biotechnology.},
}

*Proteomics/methods
*Biotechnology/methods
Multiomics
*Water Purification/methods
Water Microbiology
Wastewater/microbiology
Biofilms

@article {pmid42401776,
year = {2026},
author = {Zapata-Peñasco, I and Herrera-Díaz, J},
title = {Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.},
journal = {Advances in experimental medicine and biology},
volume = {1510},
number = {},
pages = {121-145},
pmid = {42401776},
issn = {0065-2598},
mesh = {*Proteomics/methods ; *Petroleum/microbiology ; Corrosion ; *Oil and Gas Industry ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacterial Proteins/metabolism ; Sewage/microbiology ; *Bacteria/metabolism/genetics ; },
abstract = {Petroleum-associated environments are among the most chemically complex and biologically extreme systems encountered in the field of industrial biotechnology. Here, microbial activity plays a pivotal role in hydrocarbon biodegradation, reservoir souring, and microbiologically influenced corrosion (MIC). In these systems, proteins constitute the functional interface between microbial metabolism and physicochemical processes affecting infrastructure integrity and environmental impact. This chapter presents an integrated proteomics-based workflow for the characterization of microbial communities inhabiting oil pipeline sludges, with particular emphasis on sample preparation strategies tailored to hydrocarbon-rich, metal-laden, and saline matrices. Optimized phenol-based extraction, electrochemical in vitro corrosion assays, two-dimensional gel electrophoresis, and high-resolution mass spectrometry are combined with metagenomic information to enable robust identification and functional interpretation of proteins involved in redox metabolism, biofilm formation, extracellular electron transfer, sulfur and nitrogen cycling, and stress adaptation. The approach is illustrated through a biocorrosion case study of marine pipeline sludge, revealing key enzymatic systems, including oxidoreductases, hydrolases, cytochromes, ABC transporters, and biofilm-associated structural proteins that mediate metal dissolution and microbial energy conservation. By integrating proteomics with electrochemical measurements and systems-level analysis, this chapter highlights how tailored sample preparation and functional protein profiling can overcome the limitations of culture-dependent methods, providing mechanistic insight into complex petroleum microbiomes. These advances establish proteomics as a critical tool for monitoring, predicting, and ultimately mitigating biocorrosion, as well as for guiding the development of biotechnology-based strategies in the oil and gas industry.},
}

*Proteomics/methods
*Petroleum/microbiology
Corrosion
*Oil and Gas Industry
Biodegradation, Environmental
Biofilms/growth & development
*Bacterial Proteins/metabolism
Sewage/microbiology
*Bacteria/metabolism/genetics

@article {pmid42401984,
year = {2026},
author = {Pangga, GM and Richmond, A and Hughes, C and Psifidi, A and Xia, D and Blake, D and Ijaz, UZ and Gundogdu, O},
title = {Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00596-z},
pmid = {42401984},
issn = {2524-4671},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {BACKGROUND: The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.

RESULTS: We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.

CONCLUSION: Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.},
}

@article {pmid42402030,
year = {2026},
author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W},
title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084825},
doi = {10.1128/msphere.00848-25},
pmid = {42402030},
issn = {2379-5042},
abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.},
}

@article {pmid42402034,
year = {2026},
author = {Wu, Y and Wang, Y and Qin, R and Liu, L and Wang, L and Liu, Y and Wang, W and Diao, Q},
title = {Dietary supplementation with fermented compound Chinese herbal medicine reshapes the gastrointestinal microbiota and enhances growth in suckling lambs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0388925},
doi = {10.1128/spectrum.03889-25},
pmid = {42402034},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth performance, antioxidant capacity, immune function, and gastrointestinal microbiota in suckling lambs. FCHM consisted of 10 herbs fermented with Candida utilis and Bacillus subtilis. Sixty twin Hu lambs (15 days) were randomly fed a basal diet (CON) or the diet supplemented with 0.6% FCHM (Treat) for 45 days. The results indicated that the Treat group exhibited a significant increase in average daily gain (ADG) (P < 0.05). Serum analyses revealed elevated levels of growth hormone (GH), insulin-like growth factor-1 (IGF-1), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glucose (GLU), whereas malondialdehyde (MDA) and pro-inflammatory cytokines (IL-6 and TNF-α) were reduced (P < 0.05). In the duodenal mucosa, SOD and GSH-Px activities and T-AOC levels were significantly elevated, while MDA content was notably decreased (P < 0.05). Ruminal fermentation profiles showed increased concentrations of propionate and total volatile fatty acids (TVFA) in the Treat group (P < 0.05). Microbiome analysis revealed that FCHM supplementation selectively modulated the ruminal microbial community, enriching beneficial genera such as Prevotellaceae_UCG-003 and Butyrivibrio, while reducing the abundance of potentially harmful genera like Streptococcus, despite no significant changes in the overall community diversity. Metagenomic sequencing further demonstrated the enrichment of KEGG enzymes and carbohydrate-active enzyme genes involved in carbohydrate metabolism and propionate biosynthesis. Correlation network analyses revealed significant associations among specific microbial taxa, serum antioxidant, immune biomarkers, and growth performance. In conclusion, dietary FCHM supplementation improves growth performance in suckling lambs by optimizing ruminal fermentation patterns, selectively regulating gastrointestinal microbiota, and enhancing systemic antioxidant capacity. These findings support the potential of FCHM as a functional feed additive in lamb production systems.

IMPORTANCE: Enhancing growth performance and ensuring gastrointestinal health during the suckling period are critical for lamb productivity and welfare. In the context of the antibiotic-free mandate in animal feed, we evaluated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth, antioxidant status, immune parameters, and gastrointestinal microbiota in lambs. Our findings demonstrate that FCHM improves average daily gain, enhances systemic and mucosal antioxidant capacity, and modulates ruminal and hindgut microbiota by enriching beneficial taxa and suppressing potentially harmful bacteria. These effects are linked to upregulated microbial functions in carbohydrate metabolism and propionate biosynthesis. This study provides a microbial-based mechanism for FCHM as a natural feed additive to promote lamb growth and gastrointestinal resilience, offering a sustainable strategy to support early-life development in ruminant production systems.},
}

@article {pmid42402279,
year = {2026},
author = {Jiang, C and Wang, Z and Xie, B and Huang, H and Zhan, M and Kim, Y and El-Kady, AA and Su, Y},
title = {Fructose-Induced bioenergetic surplus Unlocks fatty acid biosynthesis pathway dominance over reverse β-Oxidation: Mechanistic insights into High-Caproate production from food waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135298},
doi = {10.1016/j.biortech.2026.135298},
pmid = {42402279},
issn = {1873-2976},
abstract = {Chain elongation (CE) is an effective strategy for converting organic wastes into value-added medium-chain fatty acids (MCFAs), wherein electron donors (EDs) dictate process efficiency. However, beyond substrate toxicity and limited reducing power, conventional EDs such as ethanol and lactate impose a chronic bioenergetic constraint: their minimal net ATP yield thermodynamically restricts CE strictly to the energy-neutral reverse β-oxidation (RBO) pathway. To overcome this bioenergetic bottleneck, this study investigated fructose as a high-energy-yielding multidimensional ED to drive n-caproate production from food waste in a mixed-culture system. Herein, the results demonstrated a dose-dependent enhancement of n-caproate, peaking at 12.38 g/L with a remarkable selectivity of 63.0 % (50 g/L fructose dosage). Mechanistically, fructose fermentation established an in-situ synergistic multi-ED microenvironment (fructose, ethanol, and lactate) that buffered toxicity and sustained robust reducing power. More critically, intensive glycolytic flux induced a hyper-energetic intracellular state characterized by abundant ATP and elevated NADH/NAD[+] ratio. Meanwhile, the activities of key enzymes (e.g., phosphofructokinase and butyrate kinase) were significantly stimulated, redirecting carbon flow toward butyrate and n-caproate. This favorable energetic and metabolic environment further selectively enriched Limosilactobacillus spp., which glycolyzed fructose into essential carbon intermediates for CE. Finally, metagenomic profiling revealed that the fructose-induced ATP surplus profoundly enriched genes associated with the ATP-dependent fatty acid biosynthesis (FAB), while suppressing RBO-related genes. This uncovers a paradigm shift from the RBO-dominated route to a FAB-driven mechanism. These findings unravel how a targeted carbohydrate structurally rewires the thermodynamic hierarchy of CE pathways, providing novel mechanistic blueprints for upgrading complex organic wastes into high-value biochemicals.},
}

@article {pmid42402284,
year = {2026},
author = {Dar, RA and Tsui, TH and Du, Z and Zhang, L and Smoliński, A and Xiang, G and Liu, R},
title = {Integrated metagenomic and metaproteomic insights into current-carrying-coil magnetic field enhanced synergistic methanogenic system and antibiotic resistance gene reduction in cow manure anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135326},
doi = {10.1016/j.biortech.2026.135326},
pmid = {42402284},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a sustainable strategy for valorizing cow manure (CM). However, the high ammonia (NH3) concentration and low biodegradability of CM limit hydrolysis and methane production. This study investigated the application of a current-carrying-coil-based magnetic field (CCC-MF) to AD of CM. The CCC-MF digesters showed higher soluble chemical oxygen demand and attained 16.59 % higher ammonium nitrogen reduction, contributing to a 37.50 % higher average methane yield than the control. Further, CCC-MF digesters showed higher enzyme activities (alkaline protease + 30 %, acetate kinase + 22 % and hydrazine dehydrogenase + 26 %) and increased microbial metabolic indices (dehydrogenase activity + 17 % and electron transport system activity + 10 %) than the control. Metagenomics analysis revealed that abundances of the bacterial genera Mesotoga, Aminobacterium, Xiashengella, unclassified Candidatus Cloacimonadota, Advenella, Pseudomonas, and Comamonas increased, whereas the acetoclastic methanogen Methanothrix decreased by 2.58 %, accompanied by 2.07- and 1.64-fold increases in hydrogenotrophic methanogens Methanospirillum and Methanobacterium, respectively, in CCC-MF digesters. The abundance of nitrogen dissimilation and assimilation genes NirK, NorB, NarB, NapA, nmo, and GLT1 were enhanced by 1.14, 1.04, 2.30, 1.32, 1.17, and 1.29-fold in CCC-MF digesters compared to the control. Moreover, metaproteomics revealed higher up-regulated differentially expressed proteins in NH3 reduction-related amino acid metabolism pathways in CCC-MF digester compared to control. Additionally, reduced abundances of bacitracin, polymyxin, sulfonamide, and multidrug antibiotic resistance (MAR) gene types were observed in the CCC-MF digesters. The findings suggest that applying CCC-MF may be associated with higher methane production and ammonium reduction, potentially linked to a more favorable synergistic methanogenic system and nitrogen transformation pathways.},
}

@article {pmid42402338,
year = {2026},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandón, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Gut Microbiome Diversity and Function Linked to Cytotoxic and Natural Killer Cell Immune Responses after N-803 Treatment in People with HIV.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciag369},
pmid = {42402338},
issn = {1537-6591},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this exploratory longitudinal metagenomic study, we analyzed fecal microbiomes from 10 ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were nominally enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii showed a nominal increase after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8+ and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA+ cells. MaAsLin2 analyses further identified potentially important associations between short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These findings in a limited Phase 1B clinical study suggest that gut microbiome diversity prior to immunotherapy may influence host response. These results provide a basis for further investigation into microbiome-based strategies to improve efforts to cure HIV.},
}

@article {pmid42399687,
year = {2026},
author = {Wang, X and Wang, H and Wang, X and Liao, H and Yang, J and Jin, H and Hoffnagle, E and Jeon, MK and Cui, Y and Li, X and Liu, X and Chen, X and Liao, L and Dong, Y and Jiang, L and Xiu, Z and Yang, Y},
title = {Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10434-2},
pmid = {42399687},
issn = {2399-3642},
abstract = {Microbial iron cycling regulates nutrient availability and redox balance in global ecosystems, yet its pathways remain underexplored in ice-free Antarctic terrestrial ecosystems. This study reports the enrichment of a psychrotolerant microbial consortium from penguin-impacted soils on Beaufort Island, Antarctica, capable of reducing Fe(III) to Fe(II) at 4 °C via an anaerobic (likely fermentative) iron-reducing pathway. The consortium was dominated by Clostridium sensu stricto 13 and completely reduced 230 mg L[-1] Fe(III) citrate within three months and drove the biogenic formation of magnetite (Fe3O4). Metagenomic binning yielded four high-quality Clostridium genomes harboring multiple hydrogenases and cold-shock proteins (csp), revealing genomic strategies for energy conservation and psychrotolerance. Hydrogen production was strongly suppressed in the presence of Fe(III) citrate, indicating an intimate coupling of fermentation-derived electron flow to Fe(III) reduction. Our findings reveal a previously unrecognized low-temperature iron reduction mechanism and highlight the ecological significance of anaerobic (likely fermentative) iron reducers in ornithogenic soils-microhabitats enriched in organic matter and metals by penguin guano. This work expands the known diversity of Fe(III)-reducing microorganisms, demonstrates their role in magnetite biomineralization under extreme conditions, and provides insights into microbial modulation of iron speciation in Antarctic ornithogenic soils.},
}

@article {pmid42399871,
year = {2026},
author = {Du, W and Pan, F and Lan, P and Xie, L and Zheng, C and Wu, H},
title = {Metagenomic next-generation sequencing-guided management of descending mediastinitis and empyema caused by Segatella baroniae: a case report.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04465-y},
pmid = {42399871},
issn = {1471-2466},
abstract = {BACKGROUND: Deep neck infections can rapidly progress to descending mediastinitis and empyema, both of which are associated with high morbidity and mortality. Early diagnosis and timely intervention are essential but can be challenging, particularly in infections caused by rare anaerobic pathogens.

CASE PRESENTATION: We report a case of a 63-year-old man presenting with fever and neck pain. Computed tomography revealed extensive cervical emphysema and pneumomediastinum with a large right-sided empyema. The patient developed respiratory failure requiring endotracheal intubation. Endoscopic examination identified a retropharyngeal fistula, and thoracoscopic exploration confirmed communication between the mediastinum and pleural cavity. Combined cervical, mediastinal, and thoracic drainage was performed. Metagenomic next-generation sequencing identified Segatella baroniae as the predominant pathogen, guiding targeted antimicrobial therapy. The patient showed gradual clinical and radiological improvement and was discharged in good condition.

CONCLUSION: This case highlights the importance of early recognition and aggressive surgical management in deep neck infections complicated by descending mediastinitis. Metagenomic next-generation sequencing may facilitate rapid pathogen identification and guide targeted therapy in complex anaerobic infections.},
}

@article {pmid42399943,
year = {2026},
author = {Fu, Y and Song, X and Wang, H and Sun, J and Chen, J and Liu, T and Qi, K and Shi, Y and Li, F and Huang, X and Yang, H and Zhang, W},
title = {Viral metagenomic analysis of the blood virome in patients with multiple autoimmune diseases.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42399943},
issn = {1743-422X},
support = {No.SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; F202322//Jiangsu Province Maternal and Child Health Research Project/ ; JC-2023-004//Clinical Research Project of the Jiangsu University Affiliated People's Hospital/ ; No. 82341106 and 82550118//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Virome ; *Autoimmune Diseases/virology/blood ; *Metagenomics ; Female ; *Viruses/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Lupus Erythematosus, Systemic/virology ; },
abstract = {Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98 million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.},
}

Humans
*Virome
*Autoimmune Diseases/virology/blood
*Metagenomics
Female
*Viruses/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Lupus Erythematosus, Systemic/virology

@article {pmid42400043,
year = {2026},
author = {Wang, Y and Xue, X and Usyk, M and Sharma, A and Anastos, K and Post, WS and Hodis, HN and Wang, Z and Witt, MD and Rinaldo, CR and Brown, TT and Palella, FJ and Gange, S and Kuniholm, MH and Sha, BE and Caron, P and Gerszten, RE and Clish, CB and Guillemette, C and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB and Peters, BA},
title = {Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01709-8},
pmid = {42400043},
issn = {1756-994X},
support = {R01HL095129/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; R01HL148094/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; K01HL137557/HL/NHLBI NIH HHS/United States ; K01HL160146/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Sex hormones and HIV infection both influence cardiovascular health. However, the association between sex hormones and subclinical atherosclerosis is not fully understood, especially in the context of HIV.

METHODS: Among 321 men (65% with HIV) from the MACS/WIHS Combined Cohort Study, we measured 14 serum sex hormones and sex hormone-binding globulin (SHBG), assessed carotid artery plaque (IMT > 1.5 mm) using high-resolution B-mode ultrasound, and performed metagenomic sequencing on stool samples. In 312 men, we measured 986 plasma metabolites via liquid chromatography-tandem mass spectrometry and 2883 plasma proteins using the Olink Explore 3072 platform. In stratified analyses of men with (MWH) and without HIV (MWOH) and adjusting for covariates and multiple testing, we (1) examined associations of sex hormones with plaque; (2) characterized multi-omics profiles related to sex hormones; and (3) generated sex hormone-related omics scores via linear combination of related species, metabolites, and proteins, respectively, to explore whether these sex hormone-related multi-omics profiles were associated with plaque.

RESULTS: Median age of participants was 62 years (interquartile range: 58-68), and 31.5% had carotid artery plaque. Sex hormones were differentially associated with plaque in MWH and MWOH. In MWH, an inverse association was observed between SHBG and plaque (OR = 0.60 per 1-SD increase, 95% CI: 0.41, 0.90). Furthermore, higher SHBG levels were associated with overall gut microbial composition, lower abundance of species from genera Prevotella, Fibrobacter and Coprococcus, higher levels of certain metabolites (primarily lipid and carnitine metabolites) and proteins enriched in the cell-cell adhesion pathway. Some SHBG-related species (e.g., Mediterranea massiliensis), metabolites (e.g., phosphatidylcholine-based lipids) and proteins (e.g., enriched in immune response pathway) were also associated with plaque in MWH. All three SHBG-related omics scores were inter-correlated and inversely associated with plaque in MWH. In MWOH, estrone-sulfate was positively associated with plaque (OR = 3.80, 95% CI: 1.41, 10.22) but not with any species, metabolites or proteins.

CONCLUSIONS: Higher SHBG, and related microbial species, circulating metabolites, and proteins, were inversely associated with carotid artery plaque. These findings suggested that SHBG may play a protective role in subclinical atherosclerosis in MWH.},
}

@article {pmid42400260,
year = {2026},
author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S},
title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2695485},
doi = {10.1080/19490976.2026.2695485},
pmid = {42400260},
issn = {1949-0984},
mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.},
}

Animals
Caenorhabditis elegans/microbiology/metabolism
Humans
*Dopamine/metabolism
*Gastrointestinal Microbiome
*Vitamin B 6/metabolism/biosynthesis
*Parkinson Disease/microbiology/metabolism/genetics
Mice
Pyridoxal Phosphate/metabolism
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism
Phenotype
Escherichia coli/genetics/metabolism
alpha-Synuclein/metabolism
Bacteria/genetics/metabolism/classification/isolation & purification
Male
Mice, Inbred C57BL
Feces/microbiology
Disease Models, Animal

@article {pmid42400618,
year = {2026},
author = {Yu, J and Jiang, C and Sakai, Y and Mino, S and Sawabe, T},
title = {The Sea Cucumber Holobiont and Probiotics: Recent Progress on Apostichopus japonicus.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42400618},
issn = {1432-0991},
support = {JP19K22262//MEXT Kaken/ ; },
mesh = {Animals ; *Symbiosis ; *Probiotics ; *Stichopus/microbiology/physiology/genetics ; *Sea Cucumbers/microbiology/physiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {After the first definition of the term "Holobiont" by Margulis in the introduction of symbiosis as "Association throughout a significant portion of the life history" in 1991 [1], the understanding of holobiont has become an important goal in modern biology today [2]. Recent advances in microbial collection, genome/metagenome/transcriptome sequencings, and bioassays for host-microbes interactions push us towards a fuller understanding of holobiont in various aspects of life on Earth. Historically, holobiont and related hologenome concepts have been tested and expanded through research on marine organisms such as coral, fish, sea cucumber, sponge, and squid. In particular, the sea cucumber Apostichopus japonicus is a physiologically and ecologically unique marine invertebrate in which the holobiont can be studied with its significant capability of organ regeneration, presence of microbes in coelomic fluid, their mysterious nutrition connected to slow growth, and improvements in seed production for the bio-conservation of endangered and essential fisheries resources. The animals are also important in evolutionary terms on a branch of the Deuterostomia clade sharing ancestry with humans, so we can also compare to and learn from knowledge on the human-microbes interactions. In this review, recent progress in the sea cucumber A. japonicus holobiont studies, and the discovery of probiotics candidates among its pioneer microbiomes are described. By understanding this recent progress, we expect to stimulate new and further perspectives on basic biology, bio-conservation, and sustainable aquaculture of sea cucumber.},
}

Animals
*Symbiosis
*Probiotics
*Stichopus/microbiology/physiology/genetics
*Sea Cucumbers/microbiology/physiology
Bacteria/genetics/classification/isolation & purification

@article {pmid42400712,
year = {2026},
author = {Song, Y and Mao, C and Liu, P and Yang, G and Kang, L and Li, Z and Zhou, W and Liu, X and Yao, S and Yang, Y},
title = {Microbial community structure and function and their linkages with methane production in sediments of thermokarst lakes on the Tibetan Plateau.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42400712},
issn = {1869-1889},
abstract = {Thermokarst lakes represent a critical source of atmospheric methane (CH4), owing to large amounts of microbially generated CH4 in sediments. However, the structure and function of lake sediment microbiota, as well as their roles in mediating CH4 production, remain poorly understood across broad geographic scales. Here, we combined high-throughput sequencing, a 224-d anaerobic incubation, and stable isotopic analyses to investigate sediment microbiota and CH4 production across 30 thermokarst lakes along a 1,100 km permafrost transect on the Tibetan Plateau. Our results revealed that lake characteristics (i.e., lake depth and salinity-alkalinity) shaped sediment microbial composition and function. Deeper lakes exhibited enriched methanogenic taxa and pathways. In contrast, shallower lakes with higher salinity-alkalinity were dominated by microbial consortia that suppress net CH4 production via methanotrophs consuming CH4 and sulfate reducers competing with acetoclastic and hydrogenotrophic methanogens. Accordingly, cumulative CH4 production decreased by one order of magnitude from deeper lakes (2.5 log10CH4-C µg/g) to shallow and alkaline lakes (1.3 log10CH4-C µg/g) or salinity-alkalinity lakes (1.1 log10CH4-C µg/g). This variation was modulated by both key microbial consortia and sediment organic carbon and nitrogen supply. Overall, these results disentangled how lake characteristics restructured microbial dynamics to alter sediment CH4 production, and identified critical microbial consortia that could predict spatial variations in sediment CH4 production across thermokarst lakes.},
}

@article {pmid42401057,
year = {2026},
author = {Zheng, Y and Wang, C and Niu, X and Han, C and Zhang, Z and Yang, H and Zhang, S and Ye, X and Li, L and Lv, J and Ma, Z and Liu, H and Ma, Y and Su, X},
title = {Coupled geochemical profiling and metagenomics reveal controls on phosphine preservation and emission in a eutrophic Estuary.},
journal = {Water research},
volume = {304},
number = {},
pages = {126393},
doi = {10.1016/j.watres.2026.126393},
pmid = {42401057},
issn = {1879-2448},
abstract = {Matrix-bound phosphine (MBP) represents a critical yet poorly constrained component of aquatic phosphorus cycling, and the controls governing its preservation and emission in eutrophic estuarine systems remain incompletely resolved. The spatial controls on MBP preservation and atmospheric phosphine emission across the Pearl River Estuary (PRE) were investigated by integrating sediment phosphorus fractionation, sub-millimeter diffusive gradients in thin films (DGT) profiling, and metagenomic sequencing. Sedimentary MBP was detected at all sites and varied markedly along the estuarine gradient, ranging from 2.38 to 36.85 ng kg[-1] ww, with significant positive correlations with Org-P and TP (p < 0.05). The PRE acted as a net atmospheric source of PH3 during summer, with air-water interface (AWI) fluxes ranging from -5.35 ± 0.63 to 28.90 ± 4.67 ng m[-2] h[-1] and highest emissions concentrated at inner-estuarine nearshore sites. DGT-derived labile P-Fe-S coupling patterns and systematic shifts in microbial metabolic functional potential (e.g., dsrA, mcrA, and ptxD genes) were broadly consistent with the spatial distribution of MBP, suggesting that microscale redox conditions and microbial community function may collectively contribute to reduced-P preservation. The accumulation of Org-P and OM in nearshore depositional zones, driven by terrestrial inputs and local hydrological conditions, may progressively shift sedimentary phosphorus cycling toward pathways that favor reduced-P preservation and sustained atmospheric PH3 emissions. Collectively, these findings offer new insights into the spatial controls on MBP preservation and atmospheric PH3 emission in eutrophic estuarine systems, which are essential to understanding the complex biogeochemical processes that regulate nutrient cycling in these fragile ecosystems.},
}

@article {pmid42401342,
year = {2026},
author = {Zeng, Y and Zhang, L and Zou, Y and Liu, L and Chen, B},
title = {Enhancing catalytic efficiency of a deep-sea alkaline lipase through integrated engineering of lid-associated dynamics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135300},
doi = {10.1016/j.biortech.2026.135300},
pmid = {42401342},
issn = {1873-2976},
abstract = {A deep-sea alkaline lipase, MyLip2, fromMoritella yayanosiiwas identified from a metagenomic library of 1,048,576 genes. The wild-type enzyme preferred medium- to long-chain p-nitrophenyl esters, with optimal activity at pH 10.5 and 40 °C, but its specific activity was only 2.93 U/mg toward p-nitrophenyl palmitate. To improve performance, we used a structure- and sequence-guided strategy targeting noncatalytic residues around the catalytic center and lid region. Combinatorial engineering produced triple A271F/V250L/L231P and quadruple A271F/V250L/L231P/T300K (4 M), with comparable specific activities of 743.4 and 745.4 U/mg; 4 M was chosen for its high activity and improved thermal tolerance. This variant showed ∼ 196-fold higher catalytic efficiency (kcat/Km) toward p-nitrophenyl palmitate, with increasedVmax and kcat. Molecular docking, kinetics, and simulations indicated that the substitutions support a more open and catalytically accessible lid conformation, facilitating substrate access and turnover. Comparison with reported lipases indicated that MyLip2 and 4 M combine alkaline preference, medium- to long-chain activity, and improved performance. This work provides a high-performance deep-sea alkaline lipase and suggests that catalytic efficiency can be improved by tuning noncatalytic residues that influence the catalytic-center microenvironment and lid dynamics, without mutating the catalytic triad or redesigning the lid.},
}

@article {pmid42401346,
year = {2026},
author = {Ping, Q and Chen, X and Jin, Y and Chen, Y and Zheng, M and Wang, L and Li, Y},
title = {Deciphering the structural and stoichiometric regulation of anaerobic digestion: A cross-scale perspective from molecular thermodynamics to methanogenic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135314},
doi = {10.1016/j.biortech.2026.135314},
pmid = {42401346},
issn = {1873-2976},
abstract = {Proteins and polysaccharides are the predominant organic fractions of waste activated sludge (WAS). However, the regulation mechanisms of their distinct molecular structures and compositional ratios on the efficiency of anaerobic digestion (AD) remain unclear. This study comprehensively investigates their impacts on AD performance, focusing on molecular thermodynamics and functional gene regulation involved in electron transfer, energy conversion, and methanogenic pathways. The results demonstrate that molecular structure is a key factor determining substrate bioavailability. The protein with a mainly β-structure (xylanase) and randomly coiled polysaccharide (pullulan) exhibited superior hydrolysis, acidification, and methanogenic efficiency due to increased enzyme binding affinity. Conversely, α-helical protein and triple-helix polysaccharide displayed restricted enzymatic accessibility. Further studies revealed the combination of xylanase and pullulan at the optimal C/N ratio (35) effectively balanced nutrition, thereby achieving the highest cumulative methane yield. Metagenomic and metatranscriptomic analyses revealed that the optimal structures and C/N stoichiometry not only enriched GH13 enzymes, but also shifted the metabolic pathway from acetoclastic to hydrogenotrophic methanogenesis. Moreover, it enhanced interspecies electron transfer and energy conversion efficiency by promoting NADH dehydrogenases, formate dehydrogenase and heterodisulfide reductase, thereby establishing a highly efficient and stable metabolic network in AD system. These findings provide novel insights into the microbial and biochemical regulation driven by substrate structure and stoichiometry from cross-scale perspective, thereby offering a theoretical basis and regulatory strategy for the efficient resource recovery of waste activated sludge.},
}

@article {pmid42401622,
year = {2026},
author = {Real, MVF and Vitousek, MN and Sheehan, MJ and Moeller, AH},
title = {The mouse gut microbiota responds to predator odor and predicts host behavior.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01028-1},
pmid = {42401622},
issn = {2055-5008},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; },
abstract = {Chronic stressors can alter the mammalian gut microbiota in ways that mediate host stress responses, but the impacts of acute stressors on these interactions are less well understood. Here, we show that brief exposure of wild-derived mice to predator odor altered gut-microbiota composition, which in turn predicted host behavior. We investigated the individual and combined effects of 15-minute exposures to synthetic fox fecal odor and 30 days of chronic social isolation, an established chronic stressor. Using ethological assays, visceral adipose tissue transcriptomics, and genome-resolved metagenomics, we found that predator-odor exposure significantly affected mouse behavior, gene expression, and gut microbiota. Predator odor-responsive bacteria were associated with the expression of genes involved in anti-microbial defense, and host behavioral responses were predicted by random forest models trained on gut-microbiota profiles. These findings indicate interactions between the gut microbiota and wild-mouse responses to the threat of predation, an ecologically relevant acute stressor.},
}