@article {pmid42448275,
year = {2026},
author = {Wang, Q and Cui, J and Zhang, X and Zhao, H and Xu, X},
title = {Process-specific inhibition of sediment denitrification by metal oxide nanoparticles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128777},
doi = {10.1016/j.envpol.2026.128777},
pmid = {42448275},
issn = {1873-6424},
abstract = {The continuous accumulation of nanoparticles (NPs) in river sediments poses a potential threat to benthic nitrogen cycling. However, systematic comparisons of their effects on denitrification pathways driven by different electron donors are lacking. This study investigated the impacts of nZVI, nCuO, and nZnO on heterotrophic denitrification (H-DN), iron-based autotrophic denitrification (Fe-AD), and sulfur-based autotrophic denitrification (S-AD) in sediment. An integrated analysis was conducted including denitrification performance, key enzyme activities, extracellular polymeric substance (EPS) responses, microbial community structure, and functional gene abundance. Results revealed process- and particle-specific nanoparticle toxicity. H-DN was sensitive only to nZnO (11.6% reduction in nitrate removal rate). Fe-AD was sensitive to three NPs, with nZnO showing the strongest inhibition (38.7% reduction). In contrast, S-AD exhibited high tolerance. Nitrite reductase (NIR) activity reached 5.1 times that of the control, coupled with lower oxyR abundance, suggesting that sulfide-mediated passivation alleviated oxidative stress. NIR was identified as the common enzymatic target. Microorganisms defended against NP stress by increasing the protein fraction of EPS. nZnO triggered abnormal soluble microbial products (SMP) profiles across all systems, with protein/polysaccharide ratios surging to 45.0-45.3. Metagenomics revealed higher abundances of heavy-metal efflux and oxidative-stress genes in H-DN and Fe-AD under NP stress, imposing an energy trade-off between defense and metabolism; these genes were less abundant in S-AD. Gene abundance-enzyme activity decoupling further cautions that ecological risk assessments based solely on community abundance may underestimate nanoparticle toxicity.},
}

@article {pmid42448379,
year = {2026},
author = {Feng, Y and Lin, G and Jiang, Z and Shi, W and Deng, L and Dong, J},
title = {A Phenotype-Embedded Mapper Framework Links Microbiome-Metabolome Interaction Modules to Colorectal Cancer.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.6c00192},
pmid = {42448379},
issn = {1535-3907},
abstract = {Integrative analysis of the gut microbiome and metabolome can help characterize colorectal cancer (CRC)-associated molecular changes that are difficult to resolve from either omics layer alone. However, microbiome-metabolome data are high-dimensional, heterogeneous, and often contain nonlinear or locally confined associations that may be obscured by global linear models. Here, we propose a phenotype-guided topological framework that extends the Mapper algorithm for local interpretation of paired microbiome and metabolome profiles. Disease-associated variation from each omics block was summarized by partial least-squares regression and used to construct a two-dimensional filter space for Mapper graph construction. We further developed an Extended Spatial Analysis of Functional Enrichment strategy (eSAFE) to evaluate the spatial enrichment of phenotypes, individual features, and feature-pair associations on the resulting graph. Applied to paired fecal metagenomic and metabolomic profiles from a CRC cohort, the framework organized samples into phenotype-aligned neighborhoods and identified localized microbial, metabolic, and cross-omics association patterns linked to CRC. Coenrichment analysis further prioritized disease-associated features and interaction modules that were partly distinct from those obtained by univariate differential analysis or supervised sparse multiblock integration. One disease-localized microbiome-metabolome module showed moderate CRC discrimination in internal cross-validation and was enriched for metabolites involved in butanoate and amino acid-related pathways. These results suggest that phenotype-guided topological analysis can provide a complementary, interpretable view of localized multiomics organization in CRC-associated gut ecosystems.},
}

@article {pmid42448967,
year = {2026},
author = {Sittipo, P and Park, JY and Tiffany, E and Oh, A and Moon, S and Lee, CH and Oh, JS and Kim, TY and Kweon, MN and Choi, J and Song, KH and Lee, DW and Nam, MH and Hong, SJ and Lee, EY and Jeon, SR and Song, HY and Kim, BS and Lee, YK},
title = {Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42448967},
issn = {2092-6413},
support = {2021M3A9I4027993//National Research Foundation of Korea (NRF)/ ; RS-2023-00219563//National Research Foundation of Korea (NRF)/ ; 2021M3A9I4023974//National Research Foundation of Korea (NRF)/ ; },
abstract = {The progression of multiple sclerosis (MS) is potentially influenced by the microbiome. Elucidating host-microbiome interactions in MS may aid in developing microbiome-based applications; however, these interactions remain unclear. Here, we aimed to elucidate how Veillonella ratti MHL0042, isolated from human infant feces, modulates neuroinflammation and disease severity in experimental autoimmune encephalomyelitis, a murine MS model. Whole metagenomic sequencing revealed that V. ratti MHL0042 reshaped disrupted gut microbiota via microbial interactions throughout the intestinal tract. V. ratti MHL0042 administration significantly reduced central nervous system inflammation, notably decreasing CD4[+]IFN-γ[+] T cell populations and activated spinal cord microglia. Mechanistically, V. ratti MHL0042 depleted pldA-containing bacteria, involved in phosphatidylethanolamine metabolism, thus elevating dioleoyl phosphatidylethanolamine (DOPE) levels. Increased DOPE was not only detected in the intestinal tract but also extended systemically and reflected in the central nervous system. Exogenous DOPE administration recapitulated the attenuation of experimental autoimmune encephalomyelitis pathogenesis by suppressing microglial activation. These findings highlight the therapeutic applicability of the microbiome and underscore its potential in human disease treatment.},
}

@article {pmid42449467,
year = {2026},
author = {Gan, L and Yang, Z and Zhang, Y and Wang, S and Meng, F and Liu, Y and Dorji, T},
title = {Beyond diversity: the functional mechanisms of microbial adapations under climate change in alpine deserts.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00928-1},
pmid = {42449467},
issn = {2524-6372},
support = {QYXTZX-AL2022-05//Regional Science and Technology Collaborative Innovation Special Project of Ngari in Tibetan Autonomous Region of China/ ; 2019QZKK0600//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U20A2005//the Joint Key Research Fund under cooperative agreement between the National Natural Science Foundation of China (NSFC) and Tibet Autonomous Region (TAR)/ ; 42122005//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The functional responses of soil microbiomes to concurrent warming and altered precipitation in alpine deserts remain poorly understood, hindering predictions of these fragile ecosystem to climate change. Specifically, the mechanisms by which microbial communities maintain ecosystem function potential despite climate-induced biodiversity changes are unclear.

RESULTS: A three-year field manipulation experiment in an alpine desert grassland on the Qinghai-Xizang Plateau showed that warming and watering acted as distinct ecological drivers. Warming restructured prokaryotic and fungal communities, favored stress-associated taxa, and increasing interkingdom network complexity, indicating tighter microbial associations under climate stress. Although warming reduced microbial richness and diversity, it did not diminish the overall potential for soil nutrient cycling. Instead, functional stability was associated with sustained microbial abundance, network reorganization, and selective changes in nutrient-cycling genes, particularly those involved in nitrogen and phosphorus transformation hosted by specific bacterial phyla. In contrast, watering did not significantly increase mean soil moisture, but altered soil nutrient availability, affecting key microbial groups and their functions, showing an indirect regulation pathway.

CONCLUSIONS: Functional stability in alpine deserts under climate change was maintained not by taxonomic diversity alone, but through abundance-based compensation, community reorganization, and pathway-specific functional shifts. This study provides a mechanistic framework linking climate drivers to microbial community structure and nutrient-cycling potential, offering predictive insights into the responses of cold-arid ecosystems to future climate change.},
}

@article {pmid42449846,
year = {2026},
author = {Sun, Y and Wang, F and Mao, L and Lu, W and Wu, H and Mao, H and Zhang, Y},
title = {Optimization of Metagenomic Library Construction for Influenza A Virus and SARS-CoV-2: Systematic Comparison of rRNA Depletion Strategies and Fragmentation Orders.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/diagnostics16132065},
pmid = {42449846},
issn = {2075-4418},
support = {2024YFC2309905//National Key R&D Program of China/ ; },
abstract = {Background/Objectives: RNA virus metagenomic sequencing is a core technology for emerging infectious disease prevention and control, as well as for rapid pathogen identification. However, two major bottlenecks hinder its clinical application: the low fraction of informative sequencing reads caused by host rRNA contamination, and insufficient viral genome coverage. This study aimed to optimize the experimental parameters of RNA virus metagenomic sequencing, address the above bottlenecks, and establish a standardized workflow. Methods: Forty-five clinically positive samples (20 influenza virus-positive; 25 SARS-CoV-2-positive) were investigated in three parallel comparative experiments: rRNA depletion versus no depletion; probe-mediated RNase H digestion versus rRNA blocking; and two fragmentation timing strategies (fragmentation before versus after reverse transcription). Sequencing was performed on the GeneMind platform, and key performance metrics were systematically analyzed. Results: Following rRNA depletion, the host sequence proportion in the influenza virus and SARS-CoV-2 samples decreased from 39.5 to 90.5% to 3.6 to 32.2%, while the 10× genomic coverage increased from 0 to 99.4% to 98.1 to 100.0%. The proportion of host sequences captured by probe capture depletion (0.3-16.2%) was significantly (p < 0.05) lower than that captured by rRNA blocking module (14.3-92.3%). No significant differences were observed in the 10× genomic coverage (96.5-100.0%) or the fraction of effective viral reads between the two fragmentation strategies (p > 0.05). rRNA depletion is key to improving library quality, with post-capture probe digestion being optimal. Conclusions: The suggested optimization process will enhance sequencing efficiency and support the standardization of clinical RNA virus identification.},
}

@article {pmid42449918,
year = {2026},
author = {Smirne, C and Romano, G and Ravanini, P and Crobu, MG and Palumbo, A and Ferrari, G and Mercandino, A and Grossini, E and Pirisi, M and Piralla, A},
title = {Phylogenetic and Genomic Characterization of Whole Genome Sequences of a Herpes Simplex Virus Type 1 Isolate Identified Genomic Variant Characteristics in a Human Subject with Fulminant Hepatitis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135640},
pmid = {42449918},
issn = {1422-0067},
support = {PE00000007//European Union/ ; },
mesh = {Humans ; Phylogeny ; *Genome, Viral ; *Herpesvirus 1, Human/genetics/isolation & purification/classification ; Whole Genome Sequencing ; Polymorphism, Single Nucleotide ; *Liver Failure, Acute/virology ; Genomics/methods ; *Herpes Simplex/virology/complications ; },
abstract = {Herpes simplex virus 1 (HSV-1) is a rare cause of acute hepatitis, especially in patients with chronic immunosuppression. We performed whole-genome HSV-1 sequencing with a metagenomics approach on peripheral blood samples from an Italian case of fatal acute liver failure with high circulating HSV-1 (1,129,900,000 copies/mL), followed by phylogenetic analysis. After multiple sequence alignment, a final dataset of 182 whole-genome sequences was selected. The sequenced HSV-1 strain belonged to a phylogenetic clade isolated in Florida in 2002 (OQ724868.1). A characterization of single nucleotide polymorphisms and indels was performed to determine their effects on the viral genome: only one variant, classified as an indel, was detected with a high impact effect (c.905_906insGTTTT) in the UL49A gene, which is known to encode a membrane protein regulating virion morphogenesis, replication and assembly. In addition, this study also detected variants in other genes involved in crucial steps of the HSV-1 life cycle, like alpha-regulation (US7), capsid transport (UL36) and viral polymerase function (UL30). In conclusion, the results of this variant analysis confirmed that in HSV-1 hepatitis, some viral regions may be hotspots for adaptive mutations with a substantial impact on viral replication or immune evasion.},
}

Humans
Phylogeny
*Genome, Viral
*Herpesvirus 1, Human/genetics/isolation & purification/classification
Whole Genome Sequencing
Polymorphism, Single Nucleotide
*Liver Failure, Acute/virology
Genomics/methods
*Herpes Simplex/virology/complications

@article {pmid42449941,
year = {2026},
author = {Wojtyś, M and Górska, EB and Osińska, E and Stępień, W and Gozdowski, D and Gworek, B and Cunha, A and Garcia, INS and Kondras, M and Hewelke, E and Fidler-Jarkowska, J and Chmielewski, J and Orzechowski, S},
title = {Integrating Microbiological Indicators and Shotgun Metagenomics for the Assessment of the Rhizosphere Microbiome of Medicinal Plants.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135665},
pmid = {42449941},
issn = {1422-0067},
support = {UID/50006 + LA/P/0094/2020//Foundation for Science and Technology/ ; 8762E-385/SPUB /2018/31.07.2018//Ministry of Science and Higher Education/ ; },
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Soil Microbiology ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10[2] CFU g[-1] DM), Melissa officinalis (67.1 × 10[2] CFU g[-1] DM) and Calendula officinalis (38.8× 10[2] CFU g[-1] DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups.},
}

*Rhizosphere
*Metagenomics/methods
*Microbiota/genetics
*Plants, Medicinal/microbiology
*Soil Microbiology
Bacteria/genetics/classification
Metagenome

@article {pmid42450074,
year = {2026},
author = {Sheng, L and Wang, Y and Lu, P and Han, G and Hao, Z and Hou, S},
title = {The Composition and Differentiation of the Seed-Associated Microbiome in Rapeseed Seeds as Studied Through 218 Rapeseed Transcriptomes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135801},
pmid = {42450074},
issn = {1422-0067},
support = {CARS-12//China Agriculture Research System/ ; },
mesh = {*Seeds/microbiology/genetics ; *Transcriptome ; *Microbiota/genetics ; *Brassica rapa/microbiology/genetics ; Gene Expression Profiling ; Stress, Physiological ; *Brassica napus/microbiology/genetics ; },
abstract = {Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.},
}

*Seeds/microbiology/genetics
*Transcriptome
*Microbiota/genetics
*Brassica rapa/microbiology/genetics
Gene Expression Profiling
Stress, Physiological
*Brassica napus/microbiology/genetics

@article {pmid42450138,
year = {2026},
author = {Getsina, M and Tsyba, N and Chernevskaya, E},
title = {Modern Approaches to Diagnosis and Evaluation of Survival Prognosis in Patients with Pancreatic Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135867},
pmid = {42450138},
issn = {1422-0067},
mesh = {*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism ; Humans ; Prognosis ; *Biomarkers, Tumor/metabolism ; Microbiota ; Metabolomics/methods ; Circulating Tumor DNA/blood ; Early Detection of Cancer ; },
abstract = {Pancreatic cancer is among the most aggressive malignancies, and late diagnosis remains a key challenge. For a systematic review of pancreatic cancer diagnosis and prognosis, Scopus and Web of Science databases were used for the period from 2016 to 2026. The search query included the following keywords and their combinations: pancreatic cancer, diagnosis, early detection, prognosis, biomarkers, metabolomic profiling, CA19-9, microbiome, metagenomic changes, circulating tumor DNA, genomic analysis. Inclusion criteria included only articles published in English. Exclusion criteria included case reports and studies that did not examine pancreatic cancer. Our analysis demonstrates that integrating multi-omics data, particularly combining traditional CA19-9 with circulating tumor DNA (ctDNA) and metabolomic profiles (lipids, amino acids, carbohydrates), significantly improves diagnostic accuracy. Microbiome composition and genomic alterations further refine risk stratification and prognostic assessment. The synergistic use of these biomarkers may facilitate the development of screening, early diagnosis, risk stratification, and treatment optimization. However, the introduction of new diagnostic approaches into clinical practice requires additional verification, standardization and prospective clinical studies.},
}

*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism
Humans
Prognosis
*Biomarkers, Tumor/metabolism
Microbiota
Metabolomics/methods
Circulating Tumor DNA/blood
Early Detection of Cancer

@article {pmid42450507,
year = {2026},
author = {Xu, M and Ma, B and Zhu, K and Tu, W and Li, C and Hao, P and Zhang, M},
title = {Research Progress in Multi-Omics Analysis of Dairy Products: Nutritional Quality, Safety Evaluation, and Health Functions.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/foods15132389},
pmid = {42450507},
issn = {2304-8158},
support = {2023YFF1104704//National Key Research and Development Program of China/ ; 2025SNJF021//Zhejiang Provincial Department of Agriculture and Rural Affairs Project/ ; },
abstract = {This review evaluates multi-omics applications in dairy research across nutrition, safety, and health. Through multi-omics integration, we reveal nutrient differences driven by species, rearing practices, and processing techniques, identify protein patterns and allergen profiles, and construct adulteration detection fingerprints and species-specific peptide markers, thereby improving the timeliness and accuracy of safety assessment. The coupling of metagenomics and metabolomics effectively predicts spoilage-related microbial risks, enabling better risk control. Furthermore, multi-omics approaches systematically elucidate the functional mechanisms of bioactive peptides (e.g., ACE-inhibitory peptides), clarify the prebiotic effects of functional oligosaccharides, and build interaction networks between dairy components and gut microbiota. The introduction of machine learning enables origin and shelf-life prediction, as well as the discovery of novel biomarkers, promoting personalized nutrition and precision fermentation strategies. However, the field is currently constrained by severe reproducibility issues arising from the absence of standardized operating procedures, excessive optimism regarding machine learning models that rarely generalize across laboratories or product matrices, and a persistent disconnect between laboratory-scale biomarker discovery and industrial implementation. Without rigorous cross-platform validation and openly shared multi-omics reference datasets, most published markers remain unfit for regulatory or industrial application. Future efforts should establish standardized workflows and expand the evidence base to drive the dairy industry toward safer, healthier, and more traceable directions.},
}

@article {pmid42450525,
year = {2026},
author = {Oo-Puthinan, S and Limpeanchob, N and Pichitsiri, W and Wangteeraprasert, A and Trisat, K and Chumee, S and Sutheerawattananonda, M},
title = {Safety, Tolerability, and Gut Microbiota Impact of Sericin-Derived Oligopeptides (SDOs) from Yellow Silk Cocoons in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/foods15132405},
pmid = {42450525},
issn = {2304-8158},
support = {CRP6105022920//Agricultural Research Development Agency/ ; CRP6105022920//Ministry of Agriculture and Cooperatives/ ; },
abstract = {Sericin-derived oligopeptides (SDOs) from the Bombyx mori yellow silk cocoons show strong bioactive properties. However, clinical safety data on SDOs produced by specific enzymatic hydrolysis with a particular serine-rich (20.5%) and aspartic acid-rich (16.9%) composition is required to obtain regulatory approval as a novel food ingredient. This Phase 0 randomized, double-blind, placebo-controlled trial evaluated the short-term safety, tolerability, and gut microbiota effects of SDOs supplementation in healthy adults. Forty-two healthy volunteers were randomized (1:1:1) to receive daily doses of placebo, 0.9 g SDOs or 1.8 g SDOs for eight weeks. Primary safety endpoints included vital signs, hematology, and comprehensive clinical chemistry (renal and hepatic functions). Secondary outcomes included lipid profiles, oxidative stress markers (hs-CRP, TAC, SOD, MDA) and gut microbiota composition analyzed by 16S rRNA metagenome sequencing. Forty-one participants (97.6%) completed the study with high compliance (>98%). No serious adverse events were reported. All primary clinical parameters remained within clinically normal ranges, and no significant differences between groups were observed throughout the study (p > 0.05). No adverse effects on fasting blood glucose, lipid profiles or systemic oxidative stress were observed after SDOs supplementation. Importantly, 16S rRNA sequencing analysis showed that SDOs maintained gut microbial homeostasis throughout the 8-week intervention period, with Bacteroidetes and Firmicutes as the predominant phyla in the core community structure. Oral intake of enzymatically generated SDOs up to 1.8 g/day in healthy adults was well-tolerated with only occasional mild and transient gastrointestinal symptoms that did not appear to be dose-dependent. These first preliminary findings suggest a favorable safety profile for this unique peptide preparation, supporting its potential evaluation as a novel food ingredient and providing a reasonable basis for future, larger-scale trials to evaluate its efficacy in metabolic health.},
}

@article {pmid42450613,
year = {2026},
author = {Jiang, Z and Chen, J and Ren, Y and Lin, T and Li, S and Shen, F and Qin, B and Li, L and Li, C and Ying, N and Zheng, H},
title = {Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131066},
pmid = {42450613},
issn = {2079-7737},
support = {2024TD08//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025QT04//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025ZX03//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; SF2407//Lianyungang Key Research and Development Program/ ; },
abstract = {The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome-mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater-seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG-MGE associations. Risk assessment should therefore move beyond ARG abundance toward host-ARG-MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons.},
}

@article {pmid42450643,
year = {2026},
author = {Han, Y and Yuan, Z and Liu, B and Liu, T and Zhang, Q and Zhang, Z and Zhang, F and Yuan, H},
title = {Effects of Dietary Nucleotides on Growth Performance, Antioxidant Capacity, Intestinal Morphology and Gut Microbiota of Swamp Eel (Monopterus albus).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16131936},
pmid = {42450643},
issn = {2076-2615},
support = {2022CFB314//Natural Science Foundation of Hubei Province of China/ ; },
abstract = {This study evaluated how graded dietary nucleotide supplementation (0, 0.25, 0.5, 0.75, 1.0, and 2.0 g/kg) affects growth performance, antioxidant capacity, intestinal morphology, and gut microbiota in swamp eel (Monopterus albus) (initial body weight 10.07 ± 0.92 g). Three hundred sixty fish were randomly assigned to six diets, each in triplicate, for eight weeks. Compared with the control, nucleotide addition significantly increased final body weight, weight gain rate, and specific growth rate, and decreased feed conversion ratio (p < 0.05), with optimal results at 0.75 g/kg (HS3). Survival was 100% in all groups. Supplemented fish showed lower serum and intestinal malondialdehyde levels and higher superoxide dismutase and catalase activities (p < 0.05). Serum total protein, albumin, and triglycerides increased, whereas alanine aminotransferase, aspartate aminotransferase, and γ-glutamyl transpeptidase decreased (p < 0.05), pointing to improved hepatic and lipid metabolism. Intestinal trypsin, lipase, and amylase activities also rose markedly (p < 0.05), peaking in HS3. Histological examination revealed greater mucosal thickness and villus height (p < 0.05); in HS3, these values reached approximately 0.95 mm and 0.87 mm, respectively. Metagenomic analysis showed that 0.75-1.0 g/kg nucleotides increased alpha diversity and restructured the microbial community, enriching Bacteroidetes- and Prevotella-related taxa while reducing Proteobacteria, including Acinetobacter baumannii and Escherichia coli. LEfSe identified dose-specific discriminant taxa, and refined KEGG Level 3 pathway analysis predicted enhanced butyrate and propanoate biosynthesis, starch utilization, and purine/pyrimidine interconversion at moderate doses. Genus-level abundances of Prevotella and Bacteroides correlated inversely with serum oxidative and hepatic stress markers. Quadratic regression estimated the optimal dietary nucleotide level at 764 mg/kg (0.76 g/kg), consistent with the best-performing 0.75 g/kg group. Collectively, 0.75-0.76 g/kg dietary nucleotides optimize growth and intestinal health in M. albus through coordinated improvements in antioxidant status, digestive function, mucosal architecture, and beneficial gut microbiota remodeling.},
}

@article {pmid42450707,
year = {2026},
author = {Dai, Y and Qiao, Y and Xie, N and Zhu, J and Lin, Q and Xu, B and Dai, Y},
title = {Contrasting Roles of Mobile Genetic Elements and Metal Resistance Genes in Shaping the Gut Resistome of Wild Fish from the Qiantang River.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132000},
pmid = {42450707},
issn = {2076-2615},
support = {LHZY24C190001//Zhejiang Provincial Natural Science Foundation/ ; },
abstract = {The dissemination of antibiotic resistance genes (ARGs) in riverine ecosystems poses a pressing public health threat, while the mechanisms governing the assembly of the gut resistome in wild fish remain poorly elucidated. This study aimed to elucidate the distributional patterns of ARGs across multiple environmental compartments and to identify factors associated with their variation, particularly the contributions of mobile genetic elements (MGEs) and metal resistance genes (MRGs) to gut resistome variation. Metagenomic sequencing was conducted on 60 samples, comprising water, sediment, and gut contents from three wild fish species (Megalobrama terminalis, Aristichthys nobilis, and Coilia nasus) with distinct feeding habits, collected from four reaches of the Qiantang River basin. A total of 305 ARG subtypes belonging to 23 classes were identified. ARG composition differed significantly across environmental media and host species (permutational multivariate analysis of variance, PERMANOVA; p < 0.01), with host species identity as the primary structuring factor. Variance partitioning analysis (VPA) revealed that MGEs independently explained the largest fraction of ARG variation in A. nobilis (33.8%, p = 0.006), whereas MRGs dominated in C. nasus (33.3%, p = 0.005); in M. terminalis, MGEs and MRGs together accounted for 47.9% of the variation. Metagenomic assembly recovered 2622 ARG-carrying contigs, of which 28.3% (743) were predicted as plasmid sequences; physical co-localization among ARGs, MGEs, and MRGs was detected on both chromosomes and plasmids. Metagenomic binning validated the physical co-localization of ARG-MGE-MRG modules in genera such as Morganella and Burkholderia at the genome level, while plasmid-borne high-risk ARGs were identified in Aeromonas. Risk ranking further revealed significant enrichment of Rank II potentially high-risk ARGs (e.g., mcr-7.1, blaZ) in fish guts, carried by potential pathogens. These findings suggest that horizontal gene transfer involving MGEs and co-selection related to MRGs are closely associated with the fish gut resistome composition in a manner dependent on host ecology, providing a scientific basis for shifting riverine resistance management from concentration-based control toward the interruption of dissemination pathways.},
}

@article {pmid42450796,
year = {2026},
author = {Wei, Q and Chen, Y and Yang, H and Du, J and Li, H and Song, Z},
title = {Host-Associated and Environmental Microbiota of Hatchery-Reared Sichuan Taimen (Hucho bleekeri): Community Structure and Functional Profiling.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132089},
pmid = {42450796},
issn = {2076-2615},
support = {BL2023/D-88//the Sichuan Zumuzu River Hydropower Development Company, Ltd./ ; NJTCSC25-2//the Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; YSCX2035-011//the Project of Original Innovation 2035/ ; SCCXTD-2026-15//the Sichuan Fresh Water Fish Innovation Team/ ; },
abstract = {The diversity and complexity of symbiotic microbiota in fish may significantly influence the host's physiological, metabolic and immunological functions. In order to understand the microbial assembly in Sichuan taimen (Hucho bleekeri), an endangered fish species in the upper reaches of the Yangtze River, the microbiota of the skin, oral cavity and feces of artificially reared individuals and the microbiota of the rearing water were characterized through metagenomic sequencing. The results demonstrated that Pseudomonadota were shared across the skin, oral cavity, feces and rearing water, suggesting that they may constitute a shared microbial group connecting the aquatic environment and host mucosal surfaces. Based on functional prediction analyses, these taxa were potentially associated with organic matter degradation, nutrient cycling, and microbial and immune homeostasis. Likewise, Actinomycetota and Bacillota were consistently detected across multiple mucosal tissues and were predicted to be associated with nutrient transformation, antimicrobial defense, and the maintenance of mucosal microbial stability. Fusobacteriota were detected solely in feces, suggesting a strong tissue-specific colonization capacity. The alpha diversity of the microbiota did not differ significantly among tissues, and the beta diversity revealed strong clustering of host-associated samples and clear separation from water samples. Functional annotation further revealed that the water microbiota exhibited broader yet more dispersed functional potential, whereas host-associated microbiota showed stronger functional specialization closely aligned with host physiological demands. Collectively, the findings are better presented as baseline information for future comparative and hypothesis-driven studies in Sichuan taimen.},
}

@article {pmid42451140,
year = {2026},
author = {Ibor-Miguel, M and Pérez-Sánchez, D and Marques-Martínez, L and Aura-Tormos, JI and Guinot-Barona, C and Miralles, EG},
title = {Influence of Early Feeding Practices on Oral Microbiota Composition During Infancy and Potential Implications for Early Childhood Caries: A Systematic Review.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132138},
pmid = {42451140},
issn = {2072-6643},
mesh = {Humans ; Infant ; *Dental Caries/microbiology/epidemiology ; *Microbiota ; *Mouth/microbiology ; Breast Feeding ; Child, Preschool ; Infant, Newborn ; Female ; *Feeding Behavior ; Child ; Infant Nutritional Physiological Phenomena ; Milk, Human ; Infant Formula ; },
abstract = {BACKGROUND: Early feeding practices are among the most influential determinants of the infant oral microbiota during the first years of life. Breastfeeding provides bioactive components-immunoglobulins, human milk oligosaccharides (HMOs), and commensal bacteria-that may shape microbial colonisation patterns with long-term implications for oral health. However, the nature, magnitude, and clinical relevance of these effects remain poorly characterised, particularly with regard to early childhood caries (ECC) risk.

OBJECTIVES: The primary objective was to evaluate the association between early feeding practices and oral microbiota composition during infancy. A secondary exploratory objective was to assess whether feeding-associated microbiota differences had been linked to subsequent dental caries outcomes.

METHODS: A systematic review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, and Embase were searched from January 2010 to June 2026. Eligible studies compared at least two feeding groups and measured oral microbiota directly using culture-independent methods (16S rRNA gene sequencing, metagenomics, or quantitative PCR targeting multiple taxa). Study selection, data extraction, and risk of bias assessment using the ROBINS-E tool were performed independently. Qualitative synthesis was conducted given clinical and methodological heterogeneity.

RESULTS: Of 8582 records identified, 12 studies met the inclusion criteria (sample size range: 12-448 participants; age range at microbiota assessment: 2 days-14 years, although eligibility was based on feeding exposure during infancy; six countries). Most included studies reported differences in oral microbiota composition associated with feeding type. During the first months of life, breastfed infants generally showed lower oral microbial diversity and higher abundance of Lactobacillus, the Streptococcus mitis group and Bifidobacterium compared with formula-fed infants, who exhibited greater alpha diversity, higher transmission of maternal oral bacteria, and higher abundance of Prevotella and Actinomyces. Effects were most pronounced in the first three months of life and attenuated by 12 months in most cohorts. Only one study reported subsequent dental caries outcomes after early-life microbiota assessment, finding that Streptococcus cristatus abundance at three months was associated with dental caries at nine years of age, and that longer breastfeeding duration (≥12 months) was associated with a distinct microbiota profile and lower caries rates in this single available longitudinal study. Risk of bias was low in two studies, moderate in six, and high in four. Publication bias could not be formally evaluated.

CONCLUSIONS: Early feeding practices are associated with measurable differences in oral microbiota composition during infancy, particularly during the first months of life. However, evidence linking these microbiota differences to subsequent dental caries outcomes remains extremely limited, with only one included study assessing later caries development. Therefore, the clinical significance of feeding-associated microbiota profiles remains uncertain and should be investigated through well-designed prospective longitudinal studies.},
}

Humans
Infant
*Dental Caries/microbiology/epidemiology
*Microbiota
*Mouth/microbiology
Breast Feeding
Child, Preschool
Infant, Newborn
Female
*Feeding Behavior
Child
Infant Nutritional Physiological Phenomena
Milk, Human
Infant Formula

@article {pmid42451600,
year = {2026},
author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I},
title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132229},
pmid = {42451600},
issn = {1420-3049},
mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; },
abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.},
}

Humans
*Wound Healing/drug effects
*Microbiota
Chronic Disease
*Host Microbial Interactions
Animals
Probiotics/therapeutic use
Skin Microbiome
Biofilms
Translational Research, Biomedical

@article {pmid42451744,
year = {2026},
author = {Yan, S and Li, J and Chen, K and Ren, C and Zhang, S and Chen, Q and Gao, Y and Liu, B},
title = {Metagenomic and Metabolomic Insights into Volatile Flavor Changes and Microbial Community Shifts in Physalis pubescens L. Fermentation by Lactiplantibacillus plantarum.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132377},
pmid = {42451744},
issn = {1420-3049},
support = {CZKYF2025-1-B013//Provincial Research Institutes Scientific Research Operating Funds Project of Heilongjiang Province/ ; },
mesh = {*Fermentation ; *Metagenomics/methods ; *Metabolomics/methods ; *Volatile Organic Compounds/metabolism/analysis ; *Physalis/microbiology/metabolism/chemistry ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Metabolome ; Fruit/microbiology/chemistry ; *Flavoring Agents/metabolism ; Metagenome ; },
abstract = {Physalis pubescens L. is a seasonal fruit with high nutritional value but a short shelf life that limits its processing and utilization. This study integrated metagenomics and metabolomics to investigate the comparative effects of Lactiplantibacillus plantarum fermentation on volatile flavor metabolites and microbial community composition of P. pubescens by comparing initial (0 h) and post-fermentation (24 h) states. After 24 h of fermentation, 1316 volatile compounds were putatively identified by GC-MS, with 592 metabolites significantly changed and 501 upregulated and 91 downregulated. Key flavor compounds that impart citrus, floral, fruity, and rose notes including D-limonene, geraniol, D-carvone, and phenylethyl alcohol were markedly increased. Metagenomic analysis revealed that L. plantarum rapidly dominated the microbial community (relative abundance surged from <0.05% to ~72%) while effectively suppressing potential spoilage bacteria such as Escherichia coli. Functional gene annotation demonstrated significant enrichment of amino acid, carbohydrate, and fatty acid metabolism pathways, with key enzyme genes (L-lactate dehydrogenase, pyruvate oxidase, acetyl-CoA carboxylase) predominantly assigned to L. plantarum, suggesting their potential contribution to the generation of organic acids, ethanol, and esters. Spearman correlation analysis indicated that Lactobacillaceae genera were significantly positively correlated with terpenoids, phenols, alcohols, and aldehydes. This study provides the first metagenomics-metabolomics insight into the microbial and molecular mechanisms associated with flavor formation in LAB-fermented P. pubescens, offering a theoretical foundation for developing stable and controllable fermented fruit products.},
}

*Fermentation
*Metagenomics/methods
*Metabolomics/methods
*Volatile Organic Compounds/metabolism/analysis
*Physalis/microbiology/metabolism/chemistry
*Microbiota
Gas Chromatography-Mass Spectrometry
Metabolome
Fruit/microbiology/chemistry
*Flavoring Agents/metabolism
Metagenome

@article {pmid42452294,
year = {2026},
author = {Huang, J and Zhang, X and Tian, Y and Luo, G and Xie, D and Li, J and Duan, B and Peng, S},
title = {Moss Cover Redirects Soil Organic Carbon from Active Turnover to Mineral-Associated Stabilization in Subalpine Forests.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/plants15132098},
pmid = {42452294},
issn = {2223-7747},
support = {N5132112023000495//Huanglong Nature Reserve/ ; },
abstract = {Understory mosses modify near-surface soil conditions, but how elevation regulates their influence on active and mineral-associated soil organic carbon (SOC) remains unclear. We compared independently selected moss-covered and non-moss-covered soils across a 3200-3500 m elevational gradient and integrated soil physicochemical measurements, microbial biomass (MB), dissolved organic matter (DOM), microbial necromass carbon (MNC), particulate organic carbon (POC), mineral-associated organic carbon (MAOC), metagenomic profiling, and piecewise structural equation modeling. Moss-covered soils consistently contained higher SOC and MAOC, but lower DOM, MB, and generally lower POC, than non-moss-covered soils. MNC showed an elevation-dependent reversal, with higher values under moss cover at 3200 m but lower values under moss cover at 3300-3500 m. Elevation was not a significant uniform driver of MB, DOM, MNC, POC, or MAOC; instead, its influence was mainly reflected in interactions with surface cover and in elevation-related changes in moss-layer structure, diversity, and hydrothermal conditions. Core carbon-fixation and degradation functions remained broadly stable, whereas specific functional modules shifted within moss-covered soils: acetate and acetyl-CoA metabolism genes (ackA and abfD) were relatively abundant at 3300-3400 m, while the polysaccharide-reprocessing gene SGA1 and oxidative-transformation gene katG increased toward higher elevations, and pmoC/amoC rebounded at 3500 m. Structural equation models linked the microbial functional gene system more strongly to POC, whereas MNC was positively associated with MAOC, and the direct POC-to-MAOC pathway was not significant. These findings indicate that moss cover is associated with contrasting SOC allocation patterns and stronger microbial necromass-MAOC coupling, while elevation modulates these relationships indirectly through changes in moss communities, soil microenvironment, and microbial functional potential.},
}

@article {pmid42453369,
year = {2026},
author = {Cui, Y and Li, Q and Liu, Z and Yu, Y},
title = {Induced Sputum Microbial Diversity and Function Changes in Patients with Acute Exacerbations of Chronic Obstructive Pulmonary Disease by Metagenomic Sequencing: A Cross-Sectional Study.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {600218},
pmid = {42453369},
issn = {1178-2005},
mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Female ; Aged ; Cross-Sectional Studies ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Disease Progression ; *Microbiota ; Middle Aged ; *Lung/microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; China ; Phenotype ; Ribotyping ; },
abstract = {PURPOSE: The underlying pathogenesis of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is closely related to airway microbiota dysregulation. Currently, there is a lack of systematic elaboration based on deep metagenomic sequencing regarding the species-level and functional characteristics of the microbiota during AECOPD, as well as its correlation with clinical phenotypes of the host. This study aims to systematically analyze the taxonomic composition and functional profile changes of the microbiota in induced sputum samples from COPD patients during the stable and acute exacerbation periods using metagenomic next-generation sequencing and to explore their correlations with clinical indicators through metagenomic methods.

PATIENTS AND METHODS: A total of 66 patients with COPD were recruited from the Department of Respiratory and Critical Care Medicine at Jiading District Central Hospital in Shanghai, China. Of these, 49 induced sputum samples were obtained from 47 patients (17 in the stable group; 30 in the acute exacerbation group) after the quality control with DNA extraction and deep metagenomic sequencing. The species annotation and functional analysis were conducted using bioinformatics procedures, and microbial α-diversity analysis, LEfSe analysis was performed to identify differentially expressed markers. Spearman correlation analysis was used to evaluate the correlation between microbial/functional characteristics and a series of clinical indicators.

RESULTS: The α-diversity of the sputum microbiota in AECOPD patients was significantly lower at the species level compared to the stable stage (p < 0.01), and the community structure also underwent significant changes. Functional annotation and comparative analysis further identified 9 KEGG pathways (ko00970, ko04112, ko03420, ko03440, ko03060/ko03070, ko03410, ko04930, and ko00680) and 1 eggNOG functional category (M: Cell wall/membrane/envelope biogenesis) that differed significantly between the two groups. Among them, pathways such as methane metabolism were downregulated in the exacerbation period.

CONCLUSION: This study revealed significant dysregulation of the airway microbiome in AECOPD patients at species-level diversity, community structure, and functional metabolism, providing a molecular basis for the discovery of functional biomarkers and therapeutic targets in the microbiome.},
}

Humans
*Sputum/microbiology
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis
Male
Female
Aged
Cross-Sectional Studies
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Disease Progression
*Microbiota
Middle Aged
*Lung/microbiology/physiopathology
High-Throughput Nucleotide Sequencing
China
Phenotype
Ribotyping

@article {pmid42453735,
year = {2026},
author = {Shulga, S and Tigunova, O and Andriiash, H and Yemets, A and Blume, Y},
title = {Harnessing plant microbiomes to enhance crop resilience and restore war-affected soils in Ukraine.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1868751},
pmid = {42453735},
issn = {1664-462X},
abstract = {This review presents the current understanding of the rhizosphere microbiome and its potential application for the regeneration of damaged soils. The aim was to examine the issues of soil degradation associated with military actions and the latest developments in microbiome engineering for their application in the bioremediation of damaged lands. The review analyses recent developments and achievements in the study of the microbiome, its role in soil fertility, and plant protection against stress. Various directions and approaches to microbial profiling and addressing relevant pollution issues using developed bioengineered models and constructs have been examined. It has been shown that the most common explosive organic compounds - TNT, hexogen, and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine - and heavy metals - lead, cadmium, zinc, and antimony - account for the greatest soil contamination. The restoration of soils damaged as a result of military actions is feasible through the engineering of a specific soil microbiome (including genera Bacillus, Pseudomonas, and Arthrobackter, as well as arbuscular mycorrhiza). Military-related stress on soil is exerted by a mixture of organic pollutants and heavy metals, and the use of microbial consortia is a promising approach for mitigating their impact. The main economic advantage of such associations is that a consortium not only degrades toxic contaminants but also contains strains capable of nitrogen fixation and phosphorus mobilisation. The economic feasibility of applying synthetic microbial consortia and microbial engineering in war-affected regions is based on balancing the initial costs of research and development against substantial savings in capital investments compared with conventional land remediation methods.},
}

@article {pmid42454139,
year = {2026},
author = {Wang, Q and Tang, C},
title = {Diagnosis and treatment of severe tuberculosis complicated by ARDS and MODS in a young immunosuppressed host: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1846671},
pmid = {42454139},
issn = {2296-858X},
abstract = {BACKGROUND: Severe tuberculosis (TB) presents with complex clinical manifestations and high mortality. Immunosuppressed hosts are at high risk for TB infection and prone to progress to severe disease.

CASE PRESENTATION: A young female patient was admitted to our Respiratory Intensive Care Unit with fever, cough, and progressive dyspnea. She had a history of nephrotic syndrome and was on long-term corticosteroids and immunosuppressive agents, but without TB screening at baseline. Following admission, she rapidly developed acute respiratory distress syndrome (ARDS), diffuse alveolar hemorrhage, and multiple organ dysfunction syndrome (MODS). While providing broad-spectrum anti-infective therapy, invasive mechanical ventilation, continuous renal replacement therapy, and supportive care to maintain vital signs, we achieved an early definitive diagnosis of disseminated tuberculosis through rapid sputum acid-fast bacilli staining, Mycobacterium tuberculosis nucleic acid testing, and metagenomic next-generation sequencing (mNGS). A multidisciplinary team collaborated to formulate an individualized anti-tuberculosis treatment plan, leading to a favorable clinical outcome.

CONCLUSION: This case highlights the necessity of TB screening in immunosuppressed hosts, early recognition of severe TB, the importance of precise etiological diagnosis, and emphasizing the application of comprehensive treatment strategies in such patients.},
}

@article {pmid42454225,
year = {2026},
author = {Kafaie, S and Naseri, S and Mahoney, DBJ and Gagie, T and Beiko, RG and Maguire, F},
title = {Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag066},
pmid = {42454225},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Drug Resistance, Bacterial/genetics ; *Software ; Humans ; },
abstract = {Antimicrobial resistance (AMR) is a major global challenge to human and animal health. The genomic element (e.g. chromosome, plasmid, and genomic islands) and neighbouring genes associated with an AMR gene play a major role in its function, regulation, evolution, and propensity to undergo lateral gene transfer. Therefore, characterizing these genomic contexts is vital for effective AMR surveillance, risk assessment, and stewardship. Metagenomic sequencing is widely used to identify AMR genes in microbial communities but fragmentary short-read data do not directly provide this critical contextual information. Assembly of these reads provides some contextual information but fails to recover many mobile genetic elements. Here, we introduce Sarand, a method retaining some of the sensitivity of read-based methods while providing the genomic context of assembly by extracting AMR genes and their associated context directly from metagenomic assembly graphs. Sarand uses BLAST-based homology searches with coverage statistics to identify and visualize AMR gene contexts while filtering false chimeric contexts. Using both real and simulated metagenomic data, we show that Sarand outperforms metagenomic assembly and other recently developed graph-based tools in terms of precision and sensitivity for this problem. Sarand enables effective extraction of metagenomic AMR gene contexts to better characterize AMR evolutionary dynamics within complex microbial communities.},
}

*Metagenomics/methods
*Drug Resistance, Bacterial/genetics
*Software
Humans

@article {pmid42454401,
year = {2026},
author = {Pettinga, D and Fonseca-García, C and Krause, G and Ploemacher, H and Wheeler, T and Clendinen, CS and Handakumbura, P and Egbert, R and Coleman-Derr, D},
title = {Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant-microbe interactions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71425},
pmid = {42454401},
issn = {1469-8137},
support = {2019-67019-29306//National Institute of Food and Agriculture/ ; DE-AC05-76RL01830//Pacific Northwest National Laboratory/ ; CRIS 2030-12210-003-000D//Agricultural Research Service/ ; DE-AC05-76RL0183//Biological and Environmental Research/ ; },
abstract = {Plant growth is influenced by the composition of its associated microbiome. The inherent complexity and functional redundancy of natural plant microbiomes present a formidable barrier to understanding the myriad biological interactions therein. Efforts have been made to develop synthetic microbial communities (SynComs) that can provide a rigorous and generalizable framework for the rational design of next-generation microbial products for sustainable agriculture. We test multiple strategies for stable, plant growth promoting SynCom design and evaluate the phenotypic and molecular impacts of a successful plant-SynCom interaction. We designed four distinct, reduced-complexity variants of SynCom Sorghum Root Consortium 1 and assessed their capacities for colonization, stability, and plant growth promotion (PGP). To understand the impact on plant performance of our highest performing SynCom variant, we characterized the host's longitudinal transcriptional response to SynCom inoculation and corroborated the results with metabolomics analysis. The top-performing SynCom stably colonized Sorghum bicolor roots and rhizospheres, elicited PGP, and induced dynamic spatiotemporal gene transcription in S. bicolor roots and shoots defined by modulation of growth-defense trade-off machinery and enhanced flavonoid production. The resultant reduced-complexity SynCom is a highly stable, soil-independent, plant growth promoting, and demonstrates the utility of colonization-based selection criteria, integrated with longitudinal transcriptomic and metabolomic characterization.},
}

@article {pmid42454923,
year = {2026},
author = {Shen, J and Hu, Y and Zou, X and Zhao, X and Li, S and Jiang, Y and Zhu, F},
title = {Impact of corticosteroids on lung antibiotic resistance genes in patients with lower respiratory tract infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208025},
doi = {10.1128/spectrum.02080-25},
pmid = {42454923},
issn = {2165-0497},
abstract = {UNLABELLED: Lower respiratory tract infections (LRTIs) are a major global health concern, complicated by rising antibiotic resistance driven by antibiotic resistance genes (ARGs). Despite its role in the treatment of respiratory diseases, the impact of corticosteroids on ARGs in LRTI patients remains underexplored. Bronchial alveolar lavage (BAL) samples were collected from LRTI patients from two intensive care units (ICUs). Patients were classified into the corticosteroid group (CS group) and the non-corticosteroid group (NCS group) based on corticosteroid use. Next-generation sequencing assessed ARGs and associated microbes, with multivariable logistic regression analyzing the relationship between corticosteroid therapy and ARG accumulation. Ninety-one patients were recruited; the CS group (n = 57) exhibited a distinct ARG profile, marked by higher alpha-diversity and increased prevalence of ARGs than the NCS group (n = 34). The duration of corticosteroid therapy was positively associated with ARG accumulation, with individuals receiving treatment for more than 30 days exhibiting the highest ARG burden. The duration of corticosteroid therapy and the underlying hematological diseases were two independent risk factors for ARG accumulation. Our data provide new evidence that, in patients with LRTIs, extended corticosteroid use is associated with the accumulation of ARGs and modifications in the microbial composition of the lower respiratory tract.

IMPORTANCE: This research provides new evidence that prolonged use of corticosteroid drastically increases antibiotic resistance genes (ARGs) in the lungs of LRTI patients. It reveals a duration-dependent accumulation of ARGs, notably for common broad-spectrum antibiotics. These findings highlight the need to consider ARG burden when evaluating corticosteroid prescribing practices in patients with lower respiratory tract infections.},
}

@article {pmid42454926,
year = {2026},
author = {Davies, J and Ireland-Hughes, J and Stronati, S and Smith, RP and Oastler, C and Nunez-Garcia, J and Anjum, MF and AbuOun, M},
title = {Exploratory analysis of livestock waste treatment impacts on microbial diversity and antimicrobial resistance gene abundance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0147626},
doi = {10.1128/spectrum.01476-26},
pmid = {42454926},
issn = {2165-0497},
abstract = {UNLABELLED: The potential spread of antimicrobial resistance (AMR) through agricultural waste is underexplored and may contribute to the dissemination of AMR genes into the environment. This pilot study used metagenomic sequencing to investigate how anaerobic digestion (AD) and on-farm slurry lagoon treatment affect microbial community composition and relative AMR gene abundance in livestock waste. Samples were collected before and after treatment from three AD sites and two on-farm slurry lagoon sites. Taxonomic profiles and diversity metrics were generated from short-read Illumina sequencing, and AMR gene presence and relative abundance were assessed using APHA SeqFinder, an in-house analysis pipeline. AD treatment led to decreased microbial richness and evenness, and reduced the relative abundance of several high-prevalence taxa, including members of the Enterobacteriaceae. On-farm slurry lagoon treatment had a comparatively minor effect on microbial composition. AD was also associated with significant reductions in the relative abundance of genes conferring resistance to macrolides, aminoglycosides, fusidic acid, and beta-lactams. These findings suggest that AD and on-farm slurry lagoon treatment exert distinct effects on microbial communities and AMR gene profiles. The results provide preliminary evidence that AD may contribute to reducing AMR gene burden in agricultural waste, although further investigation across broader temporal scales and treatment methods is needed.

IMPORTANCE: Antimicrobial resistance is a major global health challenge, and agricultural waste is a key environmental reservoir of resistance genes. This study examined how two livestock waste treatments (anaerobic digestion and on-farm slurry lagoon storage) affect microbial communities and relative antimicrobial resistance gene (ARG) abundance. The findings show that anaerobic digestion reduces both microbial diversity and the relative abundance of several resistance genes, while on-farm slurry lagoon treatment has a limited impact. These results highlight the potential for treatment strategies to reduce the environmental spread of resistance.},
}

@article {pmid42454932,
year = {2026},
author = {Li, J and Xue, S and Hou, L and Zhang, Z and Yuan, K and Chen, X and Kong, C and Wang, L and Gu, B and Liu, X},
title = {Construction and validation of a phenotypic prediction model for bacterial gentamicin resistance using deep learning with gene sequences.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0190625},
doi = {10.1128/spectrum.01906-25},
pmid = {42454932},
issn = {2165-0497},
abstract = {The emergence of bacterial resistance to antibiotics poses a significant threat to human health; thus, there is an urgent need for new strategies in understanding the mechanisms of resistance and further fast prediction of it. Deep learning models offer promising solutions through analyzing genetic sequences in the prediction of bacterial resistance patterns. This study develops and validates a transformer-based deep learning model, DNABERT-2-117M, to predict gentamicin resistance in Klebsiella pneumoniae directly from whole-genome sequences. Our central methodological advance investigates the impact of the DNA tokenization strategy on predictive performance. We prospectively compared a dynamic tokenization approach against conventional fixed-length tokenization. Evaluated through rigorous fivefold cross-validation and on a hold-out test set, the model employing dynamic tokenization achieved superior performance, with a mean F1-score of 0.95 and an area under the curve of 0.97. Our findings establish that optimizing sub-sequence tokenization is crucial for model accuracy, and this dynamic tokenization approach significantly enhances model accuracy for antibiotic resistance prediction from genomic data. This genome-based predictive model represents a scalable and rapid alternative to traditional antibiotic susceptibility testing, offering the potential to accelerate clinical decision-making and improve patient outcomes in managing K. pneumoniae infections.IMPORTANCEThis study addresses a critical gap in diagnostic technologies for hypervirulent, antibiotic-resistant Klebsiella pneumoniae. We introduce a transformer-based deep learning framework that utilizes dynamic tokenization strategies to predict drug resistance directly from genomic sequences. The core significance of our work is the development of a robust genomic prediction model that serves as a foundational component for future diagnostic paradigms. The significance of this work lies in its potential to fundamentally alter clinical timelines. By decoupling resistance prediction from the requirement for phenotypic growth, our approach is a critical step toward next-generation workflows (e.g., clinical metagenomics) that could deliver a complete diagnostic and susceptibility report directly from a patient sample within hours. This represents a scalable, rapid diagnostic platform that promises to accelerate the administration of targeted treatment for high-risk K. pneumoniae infections, with a clear trajectory toward same-day, specimen-to-result diagnostics in the near future.},
}

@article {pmid42454939,
year = {2026},
author = {Sen, P and Oliver, LL and Makarova, KS and Wolf, YI and Pavloudi, C and Shlafstein, M and Saw, JH},
title = {Hawaiian geothermal fumaroles contain diverse and novel viruses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156726},
doi = {10.1128/spectrum.01567-26},
pmid = {42454939},
issn = {2165-0497},
abstract = {UNLABELLED: Viral community structure is known to influence the evolution of microbes in diverse and complex environments. While the diversity of microbes and their viruses have been metagenomically explored in terrestrial hot springs and hydrothermal vent systems, other volcanic features remain remarkably understudied. Fumaroles (steam vents) are geothermal features that heat groundwater with magma, releasing heated water vapor and volcanic gases, such as CO2 and H2S. Fumaroles are physicochemically dynamic compared to terrestrial hot springs-temperatures and gas emissions fluctuate rapidly with volcanic activity. The viral community structures and diversity have never been systematically characterized or explored. We hypothesize that viruses facilitate microbial community adaptation to the harsh and dynamic fumarole environment. Using a sensitive profile-based approach for identification, we identify 383 viral operational taxonomic units (vOTUs) from 46 metagenomes of biofilms hosted near basaltic fumaroles. We estimate two previously undescribed order-level clades of Caudoviricetes (tailed phages), and find evidence of phylogenetic diversification within the fumarole systems. Read-mapping analysis of three sampled geothermal regions shows unexpected diversity and community structure within the geologic system: 99.7% of fumarole vOTUs are shared between distant fumaroles, and 40°C-60°C biofilms have high viral richness and evenness that do not correspond to biofilm microbial composition or diversity. Lastly, we provide the first description of a terrestrial environment dominated by Microviridae, which has only been described in viral communities of deep-ocean hydrothermal vents. Our study offers a unique geological system for the exploration of viral ecology in extreme environments.

IMPORTANCE: Geothermal environments serve as natural laboratories for studying adaptations to extreme conditions that challenge the limits of microbial life and offer insight into early life on Earth. Exploring microbial diversity in these systems reveals how ecological factors shape complex communities in extreme environments. Evidence increasingly shows that viruses influence microbial diversity in terrestrial hot springs and oceanic hydrothermal vents, yet the biogeography of viruses across these systems remains largely unexplored. We present the first metagenomic characterization of viral diversity and ecology in Hawaiian terrestrial volcanic fumaroles. Our results indicate extensive viral dispersal, in contrast to the typically more constrained dispersal observed in hot springs and hydrothermal vent systems. Furthermore, we observe a dominance of ssDNA viruses in fumarole viral communities, a pattern not previously reported in terrestrial systems. Our comprehensive analyses indicate that Hawaiian fumaroles are a valuable system for studying community patterns and the ecological determinants of viral biogeography.},
}

@article {pmid42454945,
year = {2026},
author = {Oworae, KO and Rabacal, W and Hu, A and Wychrij, DA and Rayens, E and Chapman, TI and Bahl, J and Norris, KA},
title = {Evaluating the impact of immunization with the "pan-fungal" vaccine, NXT-2, on the gut mycobiome and microbiome in non-human primates (NHPs).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0104726},
doi = {10.1128/spectrum.01047-26},
pmid = {42454945},
issn = {2165-0497},
abstract = {Fungal infections remain a significant public health concern with high mortality, morbidity, and increasing associated health costs. This burden is projected to rise due to expansion of at-risk populations, limited therapeutics, increasing drug resistance, and the emergence of new fungal pathogens. Even with these challenges, there are currently no approved vaccines. We previously developed a "pan-fungal" vaccine candidate, NXT-2, that confers protection against multiple invasive fungal infections such as pulmonary aspergillosis, pneumocystosis, and invasive candidiasis, as well as non-invasive vulvovaginal candidiasis. NXT-2 is a 90 amino acid consensus peptide designed from a conserved region of the fungal antigen (KEX1). We assessed the effect of NXT-2 immunization on gut microbial diversity, composition, and functional capacity in non-human primates. To do this, we monitored changes in the gut mycobiome and microbiome pre- and post-vaccination using ITS2 and metagenomic sequencing, respectively, in Japanese and rhesus macaque cohorts. NXT-2 elicited a robust antibody response without disrupting the gut microbial communities in both macaque species. The mycobiome exhibited stability with no significant changes in alpha and beta diversity, taxonomic composition, or functional guild distributions. The relative abundance of gut resident Candida and Aspergillus species remained stable and was not significantly altered following vaccination. The microbiome showed stability with preserved alpha and beta diversities, taxonomic composition, and functional capacity. Results from this study show the first cross-kingdom analysis demonstrating that antifungal vaccination can achieve protective immunity without perturbing gut microbial communities. This establishes a framework for microbiome-informed vaccine assessment beyond conventional immunogenicity and adverse effect monitoring.IMPORTANCEFungal infections cause millions of deaths annually, yet no vaccines are approved despite growing drug resistance and limited treatment options. NXT-2 is a pan-fungal vaccine that protects against multiple fungal infections such as pneumocystosis, candidiasis, and aspergillosis. Here, we demonstrate in NHPs that NXT-2 elicits robust protective antibody responses without altering gut bacterial or fungal communities. This is the first study to assess antifungal vaccination across both microbial kingdoms and establish that protective antifungal immunity can be achieved while preserving resident microbiota. This work provides a framework for incorporating microbiome assessment into vaccine development beyond conventional immunogenicity and adverse event monitoring.},
}

@article {pmid42455045,
year = {2026},
author = {Deng, L and Ju, Z and Chen, J and Lin, Y and Zhou, W and Lee, SS and Yung, CCM and Liu, H},
title = {Sulfur-cycling diazotrophs dominate nitrogen fixation in seagrass sediments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0099326},
doi = {10.1128/aem.00993-26},
pmid = {42455045},
issn = {1098-5336},
abstract = {Diazotrophs, the microbes capable of fixing dinitrogen, are essential for providing bioavailable nitrogen that supports marine primary production. Traditionally, nitrogen fixation in seagrass sediments has been linked primarily to heterotrophic sulfate reduction, leaving the roles of other metabolic processes, like sulfur oxidation, largely unexplored. Here, we employed metagenomic and metatranscriptomic approaches to explore the distribution, metabolic capabilities, and activity of diazotrophs in sediments dominated by the seagrass Halophila ovalis in a subtropical bay in Hong Kong. Our results revealed significantly higher nitrogen fixation rates in seagrass-vegetated sediments compared to adjacent bare sediments, with peak rates occurring in subsurface layers, suggesting that seagrass sediments may serve as hotspots for nitrogen fixation. We recovered 305 metagenome-assembled genomes, including those of diazotrophic sulfur-cycling bacteria. Notably, sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Desulfobacterota emerged as the dominant and active members of the diazotroph community in seagrass sediments, expressing specific genes related to both nitrogen and sulfur metabolic pathways. Furthermore, our findings suggest that sulfate-reducing Desulfobacterota likely drive the high nitrogen fixation rates observed in deeper sediment layers, while sulfur-oxidizing Gammaproteobacteria may play a crucial role in surface layers. This study underscores the important roles of both sulfate-reducing and sulfur-oxidizing bacteria in nitrogen fixation within seagrass sediments, revealing a complex interplay between nitrogen fixation and sulfur metabolism.IMPORTANCESeagrass meadows are vital blue carbon ecosystems found in coastal and estuarine regions, playing a crucial role in carbon sequestration and supporting marine diversity. Traditionally, biological nitrogen fixation, an essential process for supplying bioavailable nitrogen to living organisms, has been primarily associated with heterotrophic sulfate reduction in these ecosystems. Our research offers novel insights into the nitrogen-fixing microorganisms present in the sediments dominated by the seagrass Halophila ovalis. We found that both sulfur-oxidizing and sulfate-reducing bacteria contribute to nitrogen fixation processes in seagrass sediments. This study highlights the intricate connections between nitrogen and sulfur metabolic pathways, providing a more comprehensive understanding of nutrient cycling in coastal ecosystems.},
}

@article {pmid42455624,
year = {2026},
author = {Signorelli, T and Walker, M and Robertson, J and Quizon, K and Zhang, Y and Reimer, AR and Eagle, SHC},
title = {Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001738},
pmid = {42455624},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; *DNA, Bacterial/isolation & purification/genetics ; Humans ; Microbiota/genetics ; Feces/microbiology ; Nanopores ; *DNA/isolation & purification ; },
abstract = {Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.},
}

*Metagenomics/methods
*Nanopore Sequencing/methods
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Benchmarking
*DNA, Bacterial/isolation & purification/genetics
Humans
Microbiota/genetics
Feces/microbiology
Nanopores
*DNA/isolation & purification

@article {pmid42456224,
year = {2026},
author = {Zhang, Y and Wang, D and Su, N and Lu, H and Xu, H and Wan, W and Li, Z and Li, W},
title = {Chronic prosthetic joint infection caused by Coxiella burnetii diagnosed by metagenomic next-generation sequencing: A case report and literature review.},
journal = {Journal of infection and public health},
volume = {19},
number = {9},
pages = {103301},
doi = {10.1016/j.jiph.2026.103301},
pmid = {42456224},
issn = {1876-035X},
abstract = {Prosthetic joint infection (PJI) caused by Coxiella burnetii (C. burnetii) remains a rare but clinically significant diagnostic challenge due to its culture-negative characteristics and nonspecific clinical manifestations. Metagenomic next-generation sequencing (mNGS) has emerged as a valuable tool for identifying fastidious pathogens in culture-negative PJI cases. A patient with a history of joint arthroplasty presented with persistent joint pain and swelling. Despite multiple surgical interventions and prolonged empirical antibiotic therapy, routine bacterial cultures remained negative and the infection recurred. mNGS performed on periprosthetic tissue detected C. burnetii in two independent specimens, while all conventional cultures remained negative. Targeted antimicrobial therapy with doxycycline combined with levofloxacin was initiated, resulting in gradual symptom resolution and sustained clinical improvement during follow-up. This case highlights C. burnetii as an underrecognized cause of culture-negative PJI and demonstrates the clinical value of mNGS for early pathogen identification when conventional diagnostics fail. Repeated detection in independent specimens strengthened diagnostic confidence and enabled timely targeted therapy. Our findings support the early incorporation of mNGS into the diagnostic algorithm for suspected culture-negative PJI. In the present case, targeted doxycycline-levofloxacin therapy following mNGS-based pathogen identification was associated with sustained clinical improvement.},
}

@article {pmid42456442,
year = {2026},
author = {Wills, OC and Chua, XY and McEvoy, C and Fitzmaurice, M and El-Assaad, F and El-Omar, E and Probst, Y},
title = {A case-control study of the oral microbiome among Australian female adults with relapsing-remitting multiple sclerosis: A pilot study.},
journal = {Multiple sclerosis and related disorders},
volume = {113},
number = {},
pages = {107383},
doi = {10.1016/j.msard.2026.107383},
pmid = {42456442},
issn = {2211-0356},
abstract = {BACKGROUND: There is growing evidence investigating the role of the gut microbiome in the onset and progression of multiple sclerosis (MS). However, the role of the oral microbiome in MS is poorly understood, despite its importance in immune regulation and systemic health.

METHODS: A cross-sectional, case-control, pilot study comparing the oral microbiome among adults with relapsing-remitting MS to matched controls based on age, sex and body mass index (BMI), was conducted. Participants provided fasting oral swabs where DNA was extracted and shotgun metagenomic sequencing performed. Comparative analyses between cases and controls explored alpha-and beta-diversities including differential abundance testing.

RESULTS: Across 24 oral microbiome samples, 355 species from 12 phylum were detected. Alpha diversity was lower in MS at the species level, however, did not reach statistical significance for either richness or Shannon diversity. Beta diversity demonstrated a significant difference using Bray-Curtis dissimilarity with group status accounting for ∼6.7% of the total variation in microbial community structure. Differential abundance testing highlighted Veillonella parvula as the most enriched species among cases (coef=2.56, stderr=0.74, FDR=0.17), while Porphyromonas pasteri (coef=-3.57, stderr=1.02, FDR=0.17) and s__GGB4936_SGB6889 (coef=-4.29, stderr=1.30, FDR=0.17) were predominant among controls.

CONCLUSION: The oral microbiome of Australian females with RRMS differs in a subtle but detectable manner from those without MS, characterised by a non-significant trend towards reduced microbial diversity and distinct compositional clustering based on Bray-Curtis dissimilarity. Findings support the emerging concept of an oral-immune axis in MS, underscoring the need for longitudinal and functional studies to explore causality.},
}

@article {pmid42456685,
year = {2026},
author = {Steriade, C and Segata, N and Saxena, D},
title = {The role of the gut microbiome in mediating neuroinflammation in immune-based neurological disorders.},
journal = {The Lancet. Neurology},
volume = {25},
number = {8},
pages = {764-780},
doi = {10.1016/S1474-4422(26)00193-6},
pmid = {42456685},
issn = {1474-4465},
abstract = {The gut microbiome can influence brain health by modulating neuroinflammation through various mechanisms, including immune regulation, the production of metabolites that affect neural function, gut and blood-brain barrier integrity, upstream effects via the vagus nerve, upstream migration of gut-resident lymphocytes to the brain, bile acid signalling, and endocrine activity. Changes in gut microbiota have been observed in demyelinating conditions, autoimmune encephalitis, and epilepsy. Gut microbiota composition changes can affect neuroinflammation, disease progression, and treatment outcomes. Advances in microbiome research have improved the potential for clinical translation of findings; but limitations persist, driven by the largely correlational nature of clinical studies and the complexity of microbiome sequencing and interpretation. At present, only the ketogenic diet is routinely recommended by clinicians, whereas other microbiome-based interventions remain investigational. Multiple strategies for manipulating the gut microbiome, including dietary changes, prebiotics, probiotics, postbiotics, and faecal microbiota transplantation, might be used as disease-modifying therapies in the future.},
}

@article {pmid42456986,
year = {2026},
author = {Yang, C and Xu, Y and Nie, Y and Li, Y and Zeng, XC},
title = {Beyond arsenite: Arsenite-oxidizing prokaryotes drive sulfur compound oxidation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135419},
doi = {10.1016/j.biortech.2026.135419},
pmid = {42456986},
issn = {1873-2976},
abstract = {Arsenite oxidation prokaryotes (AsOPs) contribute significantly to the biogeochemical processes governing arsenic cycling. Since AsOPs can oxidize As[III] to As[V], markedly reducing arsenic toxicity and decreasing its migration potential, they have been widely utilized in the restoration of As[III]-affected sites and in the design of bioreactors for treating As[III]-polluted groundwater. However, it is still unclear whether AsOPs possess additional catalytic activities that may interfere with their bioremediation capacity, highlighting a critical knowledge gap that warrants further investigation. Because arsenic often coexists with sulfur, it was hypothesized that AsOPs may also oxidize reduced sulfur compounds. To verify this hypothesis, an AsOP-enriched culture was successfully established. Metagenomic analysis revealed that ∼ 96.1% of the AsOP metagenome-assembled genomes (MAGs) contained at least one pathway for the oxidation of reduced sulfur compounds, including sulfide, thiosulfate, or sulfite. Functional assays using both the AsOP community and three cultivable AsOP strains demonstrated that AsOPs actively catalyzed anaerobic sulfide oxidation coupled with nitrate reduction to ammonium, leading to complete sulfide oxidation to sulfate and a marked decrease in pH from ∼ 7 to ∼ 3. In addition, AsOP also directly degraded arsenopyrite, releasing As[V] and sulfate and causing acidification (pH 2.5). The findings from this study, for the first time, reveal that AsOP possesses not only As[III] oxidation capability but also anaerobic reduced sulfur compound oxidation activity that may lead to environmental acidification, highlighting the need for extreme caution when applying AsOPs in arsenic bioremediation.},
}

@article {pmid42456987,
year = {2026},
author = {Zhu, Y and Guo, J and Sun, H and Zhu, M and Shan, W and Lv, X and Qu, Z and Zhang, S and Liu, Y},
title = {Perfluorobutane sulfonate reshapes microbial metabolism and enhances antibiotic resistance and pathogen dissemination in anammox systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135422},
doi = {10.1016/j.biortech.2026.135422},
pmid = {42456987},
issn = {1873-2976},
abstract = {As the use of short-chain per- and polyfluoroalkyl substances, particularly perfluorobutane sulfonate (PFBS), continues to increase, their accumulation in wastewater treatment plants (WWTPs) and the associated ecological risks have attracted growing attention. Nevertheless, the impacts of PFBS on the anaerobic ammonium oxidation (anammox) process, as well as its role in the dissemination of antibiotic resistance genes (ARGs) and the proliferation of pathogens, remain poorly understood. In this study, metagenomic analysis combined with multidimensional data integration was employed to systematically investigate the effects of PFBS exposure on anammox performance, microbial metabolism, and ARG dynamics. The results revealed that PFBS exposure significantly deteriorated nitrogen removal, leading to a 10.16% reduction in total nitrogen removal efficiency. Carbon metabolism was inhibited, whereas microbial communities adapted by enhancing antioxidant capacity and electron transport activity. The relative abundance of key anammox functional genes (hzs and hdh) decreased by 54.65% and 57.32%, respectively. Molecular docking analysis demonstrated a strong binding affinity between PFBS and hydrazine dehydrogenase (-8 kcal/mol), suggesting potential interactions. Moreover, PFBS exhibited notable interactions with denitrification-related enzymes, suggesting potential perturbations to denitrification pathways. Additionally, PFBS facilitated the enrichment of ARG and mobile genetic elements (MGE), thereby increasing the potential for MGE-mediated ARG dissemination. PFBS enriched potential pathogenic microorganisms and strengthened their associations with ARGs. Collectively, these findings demonstrate that PFBS exposure compromises anammox performance while simultaneously elevating antimicrobial resistance dissemination and pathogen-associated risks, highlighting its ecological implications in WWTPs.},
}

@article {pmid42457325,
year = {2026},
author = {Zhang, YY and Gan, MY and Zhu, YQ and Wu, BB and Zhou, WH},
title = {[Application of metagenomic next-generation sequencing in the pathogen spectrum analysis of suspected infections in neonatal blood and cerebrospinal fluid].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {28},
number = {7},
pages = {824-831},
doi = {10.7499/j.issn.1008-8830.2511025},
pmid = {42457325},
issn = {1008-8830},
abstract = {OBJECTIVES: To evaluate the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in suspected neonatal sepsis and central nervous system infections.

METHODS: This retrospective study included 648 neonates with suspected sepsis or central nervous system infections, with 734 cerebrospinal fluid and 733 blood samples collected. The pathogen spectra detected by mNGS and traditional culture were compared. Using clinical diagnosis as the gold standard, the diagnostic efficacy of the two methods was analyzed.

RESULTS: The positive rates of pathogen detection by mNGS in cerebrospinal fluid and blood samples were 15.3% and 40.0%, respectively, significantly higher than those of traditional culture (1.4% and 10.7%, respectively). mNGS identified 25 and 40 distinct pathogenic species from cerebrospinal fluid and blood, respectively, exceeding the 4 and 24 species detected by culture. Ureaplasma, Mycoplasma, and other fastidious pathogens difficult to culture were detected exclusively by mNGS. Using clinical diagnosis as the reference, mNGS showed sensitivities of 50.4% (cerebrospinal fluid) and 46.7% (blood), compared to 5.8% and 18.0% for culture.

CONCLUSIONS: mNGS significantly improves pathogen detection rates in neonatal infections compared with traditional culture, provides more comprehensive pathogen information, and holds important clinical value for the precise diagnosis and treatment of neonatal infections.},
}

@article {pmid42457685,
year = {2026},
author = {Wei, L and Cui, Z and Mu, Z and Li, Y and Deng, F},
title = {Comparative fecal microbiome and metabolome reveal enhanced lignocellulose-degrading potential in Cervus elaphus yarkandensis.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-01002-3},
pmid = {42457685},
issn = {2396-8370},
support = {ygzbhly2025102//School-level project fund of Chongqing Medical and Pharmaceutical College/ ; QN[2025]100//Guizhou Provincial Basic Research Program (Natural Science) Youth Guidance Project/ ; },
abstract = {Reed is rich in lignocellulose and is therefore challenging for many ruminants to use efficiently. The endangered Tarim red deer subspecies Cervus elaphus yarkandensis (TH) inhabits the Tarim Basin, where reed represents an important forage resource, whereas captive observations suggest that the closely related Cervus elaphus songaricus (TS) may exhibit poorer tolerance to reed-rich diets. Here, we compared fecal microbial composition, metagenomic functional potential, metagenome-assembled genome (MAG)-level carbohydrate-active enzyme (CAZyme) profiles, fecal enzymatic activities, in vitro reed-straw degradation capacity, and fecal and serum metabolomic profiles between TH and TS under the same reed-containing feeding conditions. Compared with TS, TH showed higher fecal microbial diversity and increased abundances of fiber-associated taxa, including Ruminococcaceae, Lachnospiraceae, and Alistipes. Shotgun metagenomics and MAG-level CAZyme analysis indicated that TH-associated microbial communities carried a broader repertoire of functions related to lignocellulose degradation and plant-polysaccharide deconstruction. Consistent with these functional profiles, TH fecal samples exhibited higher cellulase and hemicellulase activities, and TH fecal inocula showed greater reed-straw degradation capacity than TS fecal inocula in vitro. Untargeted metabolomics revealed group-specific fecal and serum metabolites related to carbohydrate fermentation, short-chain fatty-acid-related metabolism, and lipid metabolism, which were associated with TH-enriched fiber-degrading taxa and microbial functional pathways. In an exploratory mouse colonization experiment, TH-derived fecal microbiota was associated with changes in fiber-associated microbial taxa, metabolic pathways, fecal metabolites, body weight, and intestinal morphology in antibiotic-treated mice fed a reed-containing diet. Together, these results indicate that TH harbors fecal microbial and metabolic features associated with enhanced lignocellulose and reed-straw degradation capacity. These findings suggest candidate microbiome-associated pathways relevant to reed-rich forage utilization and may help identify microbial and enzymatic resources for lignocellulose bioconversion.},
}

@article {pmid42457990,
year = {2026},
author = {Danielsson, H and Portlock, T and Hellström, A and Nilsson, A and Sävman, K and Wackernagel, D and Hansen-Pupp, I and Ley, D and Shoaie, S and Uhlén, M and Brusselaers, N and Elfvin, A},
title = {Supplementation with long-chain polyunsaturated fatty acids to extremely preterm infants associates with development of the intestinal microbiota.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42457990},
issn = {1530-0447},
abstract = {BACKGROUND: Supplementation with arachidonic acid (AA) and docosahexaenoic acid (DHA) to extremely preterm infants reduces the risk of severe retinopathy of prematurity (ROP). The main aim of this study was to explore the involvement of AA:DHA supplementation in the developing gut microbiome, and its possible contribution to the ROP-protective effect. Secondly, additional covariates for microbiome maturation were evaluated.

METHODS: Longitudinal gut microbiome profiles and bacterial gene pathways were characterised using shot-gun metagenomics in 75 extremely preterm infants who participated in a randomized clinical trial on AA:DHA supplementation. Serum protein levels quantified using proximity extension assays were merged with the microbiome data.

RESULTS: AA:DHA supplementation was linked to an increase in relative abundance of Citrobacter koseri and associated with changes in proteins and metabolic pathways. Occurrence of severe ROP was associated with microbiome alpha diversity (Shannon and Evenness) and beta diversity (Bray-Curtis). Additionally, study centre and gestational age at birth impacted the microbiome composition.

CONCLUSION: We conclude that AA:DHA supplementation impacts the microbiome. However, the current study could not determine the causality between the supplementation, microbiome and ROP-decrease. Nonetheless, these findings highlight the complex interplay between external interventions, including nutritional supplements, and the gut microbiome development in extremely preterm infants.

IMPACT: Longitudinal gut microbiome profiles, bacterial gene pathways and serum protein expressions were determined using shotgun metagenomics and proximity extension assays in 75 extremely preterm infants included in a multicentre randomized clinical trial investigating enteral fatty acid supplementation. Dynamic shifts in microbiome and pathway composition were seen from birth to 34 weeks gestational age. Arachidonic acid (AA) and docosahexaenoic acid (DHA) supplementation was linked to an increase in relative abundance of Citrobacter koseri and associated with changes in proteins and metabolic pathways. However, the causality between the supplementation, microbiome, and ROP-decrease could not be determined.},
}

@article {pmid42443209,
year = {2026},
author = {Xie, YG and Cao, XR and Qi, YL and Chen, L and Mao, YH and Li, Y and Wang, CJ and Li, ZW and Qu, YN and Li, WJ and Hua, ZS},
title = {Genome-resolved discovery of Candidatus Vitaminotrophota reveals carbon fixation and multi-vitamin biosynthetic potential in hot springs.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01093-6},
pmid = {42443209},
issn = {2055-5008},
support = {32400002//National Natural Science Foundation of China/ ; 32471574//National Natural Science Foundation of China/ ; },
abstract = {Geothermal environments harbor abundant microbial diversity, yet rare lineages remain poorly resolved, limiting understanding of ecosystem function and evolutionary innovation under energy limitation. Here, we describe Candidatus Vitaminotrophota, a previously unrecognized bacterial phylum represented by 35 metagenome-assembled genomes (MAGs) from Tengchong hot spring sediments, China. Phylogenomic analyses support a coherent internal taxonomy comprising one order, two families and four candidate genera. Metabolic reconstruction indicates a predominantly anaerobic, mixotrophic lifestyle, with widespread carbon fixation potential via the Wood-Ljungdahl pathway and a noncanonical CODH/ACS architecture featuring divergent acsA paralogs. Nitrogenase structural genes (nifHDK) occur in two genera, suggesting diazotrophic potential in part of the lineage. All MAGs encode complete or near-complete cobalamin and pantothenate biosynthesis pathways, and most retain conserved thiamine pathway components, alongside transport systems consistent with corrinoid and metal acquisition. Ca. Vitaminotrophota dominated community-level cobalamin biosynthetic potential in several samples, reaching 99.11% and accounting for >50% in nearly half of the samples. Conserved flagellar and chemotaxis gene sets suggest capacity to navigate steep physicochemical gradients. These findings expand the phylogenetic and functional landscape of geothermal bacteria and identify Ca. Vitaminotrophota as a candidate contributor to carbon fixation and vitamin-mediated metabolic interactions in nutrient-limited hot springs.},
}

@article {pmid42443210,
year = {2026},
author = {Wang, YF and Xu, JY and Liu, Y and Ni, B and Zhang, TL and Cui, HL and Qi, FY and Qiao, M and Li, HZ and Gillings, MR and Zhu, YG and Zhu, D},
title = {Divergent mechanisms of active antibiotic resistance gene enrichment in soil driven by pesticide diversity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75445-3},
pmid = {42443210},
issn = {2041-1723},
support = {22193062//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Antimicrobial resistance is an escalating global threat, with soils serving as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs). Pesticide use in agriculture contributes to ARG proliferation, and ~60% of agricultural soils contain multiple pesticide residues. However, how pesticide diversity influences ARG dynamics in active microbial populations (active ARGs) remains unclear. Here, we evaluate the effects of pesticide diversity on active soil ARGs through a long-term field experiment integrating bioorthogonal non-canonical amino acid tagging (BONCAT), fluorescence-activated cell sorting (FACS), and metagenomics. We show that both low and high pesticide diversity significantly increase active ARG abundance relative to untreated control, whereas total ARG levels remain largely unchanged. The underlying mechanisms differ with pesticide diversity. At low diversity, active ARG co-selection via efflux pumps in Acinetobacter baumannii is a prominent mechanism. At high diversity, elevated reactive oxygen species and SOS responses promote horizontal gene transfer of active ARGs, as validated by culture experiments. These findings demonstrate that increasing pesticide diversity accelerates the emergence and dissemination of active ARGs, highlighting the need for integrated pesticide management strategies that consider both application intensity and diversity to mitigate resistance risks under the One Health framework.},
}

@article {pmid42443349,
year = {2026},
author = {Yang, Q and Fu, L and Chen, H and Huang, W and Guo, Y and Liu, L and Fu, Q and Liu, T and Chen, F},
title = {An investigation of the abnormalities in the microbiome‑gut‑brain axis in betel quid chewers.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60616-5},
pmid = {42443349},
issn = {2045-2322},
support = {Qhyb2023-183//the Hainan Provincial Graduate Innovation Research Project/ ; ZDYF2024SHFZ058, ZDYF2023SHFZ096//the Key Science and Technology Project of Hainan Province/ ; 82271977, 82160327//the National Nature Science Foundation of China/ ; YSPTZX202514//the Innovation Platform for Academicians of Hainan Province and Hainan Academician Innovation Platform Scientific Research Project/ ; },
abstract = {Betel quid (BQ) chewing, a prevalent practice affecting over 600 million people globally, is associated with systemic toxicity and neurological alterations. While dysbiosis of the gut microbiota is implicated in neuropsychiatric disorders via the gut-brain axis (GBA), its role in BQ chewers remains unexplored. This exploratory study aimed to investigate whether chronic BQ chewing is associated with gut dysbiosis and alterations in spontaneous brain activity. Fecal samples (n = 30 BQ chewers, n = 19 healthy controls) were subjected to whole metagenome shotgun sequencing (WMGS) to assess microbial composition and function. Amplitude of low-frequency fluctuations (ALFF) values, a resting-state functional magnetic resonance imaging metric reflecting regional spontaneous neural activity, were assessed in a subset of 29 BQ chewers and 21 healthy controls. Group differences in microbiota and ALFF were analyzed using the Wilcoxon rank-sum test and two-sample t-test (adjusted for age, sex, education, smoking and alchohol). Partial Spearman's correlation analysis was performed to link microbial taxa with ALFF alterations. Motivated by the presence of complex polysaccharides and polyphenols in BQ, carbohydrate-active enzyme (CAZyme) profiles were also assessed. Chronic BQ chewers exhibited significant gut microbiome alterations, characterized by reduced microbial diversity, enrichment of pro-inflammatory genera, and depletion of beneficial taxa. Analysis of carbohydrate-active enzymes further revealed altered metabolic potential in BQ chewers. Furthermore, reduced ALFF was observed in the limbic lobe of BQ chewers. At a nominal significance level, Streptococcus abundance correlated positively with limbic ALFF (partial ρ = 0.35, 95% CI [0.07, 0.58], raw p = 0.04), whereas Dorea formicigenerans exhibited a negative correlation (partial ρ = -0.36, 95% CI [- 0.55, - 0.08], raw p = 0.04). Chronic BQ chewing is associated with gut microbial dysbiosis and functional metabolic shifts. Exploratory analyses suggest that these microbial features may correlate with spontaneous neural activity in the limbic lobe, providing preliminary evidence for a potential involvement of the GBA in BQ‑associated neurological sequelae. These findings highlight the need for further investigation into microbiota‑targeted strategies in BQ chewers.},
}

@article {pmid42443738,
year = {2026},
author = {Carasso, S and Gefen, T and Bakria, R and Bar-Yoseph, H and Geva-Zatorsky, N},
title = {Microbiome changes associated with FMT-mediated clearance of antibiotic-resistant Klebsiella pneumoniae in a murine carriage model.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05354-4},
pmid = {42443738},
issn = {1471-2180},
support = {grant 1571/17 and 3165/20//Israeli Science Foundation/ ; grant FL-000969/FL-001245/FL-001381//CIFAR Azrieli Global Scholars/ ; grant CDA00025/2019-C//Human Frontier Science Program Career Development Award/ ; ERC, ExtractABact, 101078712//the European Union/ ; },
abstract = {Carbapenem-resistant Enterobacterales (CRE), including Klebsiella pneumoniae (KP), pose a significant public health threat due to their resistance to last-line antibiotics. Eliminating CRE colonization in asymptomatic carriers is crucial to prevent the spread of resistance, as carriage often serves as a reservoir that enables the transmission of resistant strains to vulnerable populations. Fecal microbiota transplantation (FMT) has emerged as a potential strategy to restore gut microbiome balance and eliminate CRE colonization. However, the mechanisms driving successful decolonization warrant further research. This study investigates the impact of FMT on gut microbiome composition, CRE-KP clearance and host response, in a mouse model of CRE-KP carriage. Mice colonized with CRE-KP, were treated with FMT or left untreated. Shotgun metagenomics of fecal samples were used to monitor changes in microbiome composition and function. FMT resulted in substantial changes in the gut microbiome, with successful clearance correlating with an expansion of commensal bacteria including Bifidobacterium and Lactobacillus species. Notably, a reduction in K. pneumoniae was also observed in some untreated control mice as the microbiome recovered naturally, also associated with Bifidobacterium expansion. Phage profiling revealed distinct viral populations that were associated with successful decolonization. Flow cytometry was employed to quantify bacterial populations bound by immunoglobulins, providing insight into host immune modulation. These findings suggest potential mechanisms for CRE carriage eradication using microbiome targeted therapies. The results emphasize the importance of microbiome resilience in combating antibiotic-resistant infections and suggest that phage-microbiome interactions could play a role in restoring microbial balance.},
}

@article {pmid42443941,
year = {2026},
author = {Markkanen, M and Putkuri, H and Kičiatovas, D and Mustonen, V and Virta, M and Karkman, A},
title = {Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-04200-0},
pmid = {42443941},
issn = {1474-760X},
support = {364234//Research Council of Finland funding for the Multidisciplinary Center of Excellence in Antimicrobial Resistance Research/ ; 364231//Research Council of Finland funding for the Multidisciplinary Center of Excellence in Antimicrobial Resistance Research/ ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) circulating among clinically relevant bacteria pose serious challenges to public health. Given the ancient and environmental bacterial origins of ARGs, a better understanding of the carriers of ARGs beyond the clinically most relevant species is urgently needed for longer-term resistance monitoring and intervention measures. While the risks of emerging ARGs from environmental sources have been recognized, the identification bottlenecks stem from the limitations of shotgun metagenomic sequencing and bioinformatic methods.

RESULTS: We use long-read metagenomic sequencing and bacteria-specific methylation profiles to re-establish the links between established (well-described) or latent (absent in databases) ARGs and their bacterial and genetic contexts in wastewater. We analyze base modification data produced by PacBio SMRT sequencing using an in-house pipeline utilizing position weight matrices and UMAP visualizations, which we validate by a synthetic community with known bacterial composition. Our analysis reveals several previously unreported ARGs and ARG-host linkages in wastewater. For instance, we find that Arcobacter, a key wastewater associated taxon and emerging pathogen, carries a latent beta-lactamase gene with high predicted mobility potential. Of the other understudied beta-lactamases, we describe blaMCA within pdif-modules across highly varying contexts suggesting its recent acquisition events. Additionally, we uncover the wastewater resident taxa mediated carriage of clinically important ARGs.

CONCLUSIONS: By linking ARGs to their wider genetic contexts and hosts, our findings shed light on the previously unrecognized carriers of resistance genes in wastewater. The presented approach provides a valuable methodology for early identification of newly arising ARGs and their hosts.},
}

@article {pmid42444523,
year = {2026},
author = {Santucci, NR and Dike, CR and Hellmann, J and Ollberding, NJ and Duan, Q and Minar, P and Denson, LA and Haslam, DB and Castillo, D and Abu-El-Haija, M},
title = {Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70504},
pmid = {42444523},
issn = {1536-4801},
support = {K23DK135797//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; 23DK118190//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; R03 DK131156/DK/NIDDK NIH HHS/United States ; P30 DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati/ ; NCT04131504//Leona M. and Harry B. Helmsley Charitable Trust for the ENvISION study/ ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP), Crohn's disease (CD), and irritable bowel syndrome (IBS) are associated with gut dysbiosis, but differences and similarities between conditions are unknown. We hypothesized that gut microbial ecology would differ across these disorders.

METHODS: Stool was collected from 120 subjects (AP [n = 30], CD [n = 29], IBS Rome IV [n = 27], and healthy controls [HC, n = 34]). Shotgun metagenomic sequencing was performed on extracted DNA and taxonomic and functional profiles obtained using sylph and HUMAnN3 with default parameters.

RESULTS: Age interquartile range for all participants was 8.1-17.7 years. Shannon diversity was decreased in AP compared to IBS or HC (p < 0.0001) and similar to CD (p = 0.97). CD differed from IBS (p = 0.001) and HC (p < 0.0001) while IBS and HC were similar (p = 0.61). Ordination of the first two principal coordinate analyses axes showed sample clustering by condition (R[2] = 0.12, p < 0.001), and differences between all conditions in pairwise comparisons (p < 0.001). Escherichia coli, Ruminococcus gnavus, Staphylococcus aureus, and Thomasciavelia ramosa remained enriched when all conditions (AP, CD, and IBS) were compared as a single group to HC. Using a random forest machine learning algorithm for species relative abundance, the ability to classify a sample to each condition versus all others was highest for CD (area under the receiver operative characteristic curve, AUC = 0.97), followed by AP (AUC = 0.92), HC (AUC = 0.88), and IBS (AUC = 0.83).

CONCLUSION: Organic disorders (AP and CD) are associated with significant gut dysbiosis than IBS which appears more like HC. Interventions targeting shifts in commensals in AP and CD may be helpful in improving outcomes in both disorders.},
}

@article {pmid42445134,
year = {2026},
author = {Yang, Q and Chen, Y and Chen, L and Wei, S},
title = {Tropheryma whipplei pneumonia: a retrospective case series of nine patients with treatment response.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1883057},
pmid = {42445134},
issn = {2296-858X},
abstract = {BACKGROUND: The detection of Tropheryma whipplei in respiratory specimens has increased with metagenomic next-generation sequencing (mNGS), yet distinguishing colonization from active infection remains challenging. In clinical settings lacking quantitative PCR or pathological confirmation, practical approaches to guide treatment decisions are urgently needed.

METHODS: We retrospectively analyzed nine patients (January 2019-January 2024) with T. whipplei detected by bronchoalveolar lavage fluid (BALF) mNGS. All patients initially received cefoperazone-sulbactam (3.0 g q8h) as empirical therapy for 3-5 days without improvement. Targeted therapy (ceftriaxone or meropenem combined with doxycycline or trimethoprim-sulfamethoxazole) was subsequently initiated. We describe clinical characteristics and treatment outcomes.

RESULTS: Among nine patients (3 male, 6 female; mean age 59 years, range 32-79), six (67%) were immunosuppressed. Primary manifestations included fever (67%), cough with sputum (89%), and dyspnea (78%). Common laboratory findings were anemia (67%), lymphocytopenia (67%), hypoalbuminemia (100%), and elevated inflammatory markers (78%). Chest CT predominantly showed patchy ground-glass opacities. Eight cases (89%) had co-infections. All patients showed no improvement after initial cefoperazone-sulbactam therapy. After targeted therapy was initiated, eight patients (89%) achieved defervescence within 3-5 days, with resolution of pulmonary infiltrates on follow-up CT within 10-14 days. Among these eight responders, one patient (Case 4) underwent repeat BALF mNGS which demonstrated a >99.99% reduction in T. whipplei (from 6,100,499 to 383 reads), reported in the suspected colonizer list rather than the pathogen panel. One non-responder (Case 8) showed a >99% reduction in T. whipplei read count on repeat BALF mNGS after targeted therapy, but ultimately died of polymicrobial sepsis from multidrug-resistant co-pathogens. No relapse occurred during 1-year follow-up.

CONCLUSION: This retrospective case series suggests that rapid improvement after adding targeted anti-T. whipplei therapy is compatible with possible T. whipplei-associated infection in selected mNGS-positive patients, rather than colonization alone. Sequential mNGS showed marked burden reduction in two cases. These observations require prospective validation.},
}

@article {pmid42445282,
year = {2026},
author = {Xue, K and Lei, S and Cheng, X and Xu, W and Lin, Z and Zhou, Y and Mao, X and Ge, X and Zhu, H and Zhu, F},
title = {A two-hit ecological framework linking social context to caries-associated microbiome shifts in children.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2677291},
pmid = {42445282},
issn = {2000-2297},
abstract = {BACKGROUND: Dental caries arises from an ecological imbalance within a complex community. How chronic social context relates to ecological heterogeneity and dysbiosis-associated microbial shifts in school-age children remains unclear.

OBJECTIVE: To investigate the associations of left-behind status and caries burden with the salivary microbiome and to explore a two-hit ecological framework linking social context to caries-associated microbial shifts.

DESIGN: In this cross-sectional study, 127 rural children were classified using a 2 × 2 framework based on left-behind status and caries burden. Saliva samples underwent shotgun metagenomic sequencing. Ecological analyses and covariate-adjusted multivariable models were performed.

RESULTS: Alpha diversity did not differ across groups. Global community centroids were similar, whereas within-group dispersion was higher in left-behind children, suggesting greater ecological heterogeneity. After covariate adjustment, no genus-level associations remained significant, whereas several KEGG level 3 pathways related to translation and carbohydrate utilization were positively associated with dmft. Stratified analyses showed concordant caries-related enrichment of Streptococcus, Veillonella, and carbohydrate-utilization pathways across social strata. Ecological subtyping identified Neisseria- and Veillonella-anchored community types.

CONCLUSION: The findings are consistent with a two-hit ecological framework in which social context is associated with greater ecological heterogeneity and cariogenic pressure is associated with reproducible functional shifts. Given the cross-sectional design, this framework should be considered hypothesis-generating.},
}

@article {pmid42445283,
year = {2026},
author = {Al-Maweri, SA and Ba-Hattab, R and Alomairi, A and Syed, A and Azouni, K and Batta, N and Almeer, F and Assad, R and Al-Mansoori, A and Eltai, NO and Al-Hashimi, N and Al-Hebshi, NN and Almashraqi, AA},
title = {Metagenomic analysis of tongue samples from healthy subjects identifies distinct microbiome orotypes.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687934},
pmid = {42445283},
issn = {2000-2297},
abstract = {BACKGROUND: The tongue dorsum harbors a complex microbiome that remains incompletely characterized.

OBJECTIVE: This study aimed to characterize the tongue microbiome-including its phageome-in a healthy Qatari population.

DESIGN: Shotgun metagenomic sequencing was performed on tongue-coating samples from 92 systemically healthy adults to comprehensively profile the bacteriome, phageome and functional potential of the tongue microbiome.

RESULTS: Taxonomic profiling revealed a predominantly bacterial community (>99%) dominated by Veillonella, Streptococcus, Neisseria, Rothia, Prevotella, Haemophilus and Pauljensenia. Among low-abundance domains, the fungus Saccharomyces and the protist Entamoeba were most prevalent. Dirichlet-multinomial mixture clustering identified three distinct bacterial 'orotypes' (C1-C3) showing significant compositional separation (PERMANOVA, p = 0.001) and alpha diversity differences at both genus and species levels. A major compositional gradient involved enrichment of Neisseria and Haemophilus in C2, their absence in C3 and intermediate representation in C1. Functional profiling revealed a conserved core of housekeeping pathways across orotypes, wherease adaptive functionsdiffered across orotypes, particularly in the Neisseria/Haemophilus-enriched C2 orotype. The phageome was dominated by Uroviricota (class Caudoviricetes).

CONCLUSION: The findings identify distinct tongue microbiome orotypes with conserved core functions, divergent taxonomic and metabolic profiles, and provide new insights into the tongue phageome, establishing a foundation for investigating their roles in health.},
}

@article {pmid42445473,
year = {2026},
author = {Zhuang, J and Yu, Z and Jin, C and Qiu, H and Wu, Y and Feng, Q and Zheng, S and Wang, J},
title = {Detection Blind Spots in Microbial Culture, tNGS, and mNGS: Anaerobic Bacterial Infections in the Lung-A Retrospective Analysis of Two Cases.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {611567},
pmid = {42445473},
issn = {1178-6973},
abstract = {Aspiration pneumonia is often associated with specific obligate anaerobic bacteria, particularly oral commensals, as causative agents; however, these infections are frequently misdiagnosed in clinical settings. This retrospective analysis of two patients presenting with fever and cough demonstrates that, in the setting of inconclusive routine microbiological testing and tNGS results, along with ineffective empirical antimicrobial therapy, comprehensive mNGS analysis of BALF microbiota-combined with the presence of high-risk oral factors (such as dental caries and severe periodontitis)-facilitated the diagnosis of anaerobic pneumonia. In both cases, tNGS was unable to detect anaerobic pathogens due to the limited scope of anaerobic bacterial targets in commercial panels. In contrast, comprehensive mNGS, when correctly interpreted in conjunction with clinical context, can detect anaerobic sequences. The key difference lies in that mNGS offers a broader detection capability, but it requires careful correlation with clinical circumstances to distinguish between true pathogens and colonizing bacteria. Specifically, Case 1 revealed the presence of Bacteroides timidum and Fusobacterium nucleatum. Case 2 identified Prevotella oralis, Streptococcus australis, and Actinomyces caries. The administration of targeted anti-anaerobic therapy (metronidazole, ornidazole) subsequently resulted in significant improvement in clinical symptoms and radiographic findings. These cases underscore the diagnostic value of integrating metagenomic next-generation sequencing (mNGS) with clinical risk factor assessment when conventional diagnostics produce negative results.},
}

@article {pmid42445487,
year = {2026},
author = {Liu, M and Liu, T and Jin, S and Liu, P and Wang, X and Liu, X},
title = {Remodeling of gut bacteriome and virome in acute retinal necrosis: expansion of Enterobacteriaceae-related taxa.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1848524},
pmid = {42445487},
issn = {1664-302X},
abstract = {BACKGROUND: This study was designed to examine the alterations in the gut bacteriome and virome of patients with acute retinal necrosis (ARN), and to explore potential cross-kingdom microbial associations.

METHODS: The gut virome and bacteriome of 10 patients with new-onset ARN and 10 age- and sex-matched healthy individuals (N) were profiled using viral metagenomics and 16S rRNA sequencing, respectively.

RESULTS: The gut bacteriome in ARN patients was significantly altered, with Enterobacteriaceae_A increased at the family level. Genus-level analysis further described higher relative abundances of opportunistic pathogens, such as Escherichia and Klebsiella, alongside lower relative abundances of commensal anaerobes, including Fusicatenibacter and Anaerobutyricum. Exploratory clinical association analysis suggested a positive association between Klebsiella and intraocular pressure, while Fusicatenibacter tended to be further reduced in patients with vasculitis involving the major retinal arteries. Predicted bacterial functional profiling indicated an enrichment in enterobactin biosynthesis and related metabolic pathways. In contrast, differences in the gut eukaryotic virome were limited, and no significant enrichment of fecal Herpesviridae was detected. Virome perturbations predominantly occurred at the bacteriophage level, featuring shifts in predicted bacterial host assignment from commensal bacteria toward opportunistic pathogen-associated taxa and an increased inferred proportion of temperate phages. Exploratory cross-kingdom analysis suggested associations involving Escherichia and three related phage features.

CONCLUSION: Gut dysbiosis in ARN was associated with Enterobacteriaceae-related bacterial remodeling and phage alterations. These findings highlight an ARN-associated bacteriome-phage alteration pattern that warrants validation in larger independent cohorts.},
}

@article {pmid42445491,
year = {2026},
author = {Luo, L and Cheng, K and Chen, B and Li, Y and Ruan, L and Li, Z and Zhu, S and Zhao, L and Zhang, C and Liu, Y and Li, T},
title = {Depletion of Blautia wexlerae and Parabacteroides distasonis in adiposity-related prehypertension.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1873803},
pmid = {42445491},
issn = {1664-302X},
abstract = {BACKGROUND: Prehypertension is more likely to develop into hypertension in individuals with adiposity. We aimed to explore how adiposity influences prehypertension through gut microbiota.

METHODS: Kaplan-Meier and Cox proportional hazard regression models were employed to evaluate the association between prehypertension and adiposity in 649 individuals. Among them, 197 consented to provide fecal samples and were divided, along with 184 additional participants, into healthy controls (HC), individuals with adiposity and normal tension (Ad-NT), and those with prehypertension (Ad-pHT) based on body mass index (BMI) and blood pressure. Shotgun metagenomic sequencing was performed on fecal samples, followed by taxonomic and functional annotations using MetaPhlAn and HUMAnN. Linear discriminant analysis effect size (LEfSe) was used to analyze differences in microbial species and metabolic pathways across groups. Partial Spearman rank correlation analysis was used to assess microbial interactions, and the relationships among metabolic pathways, species, BMI, and blood pressure.

RESULTS: Elevated BMI independently predicted the risk of prehypertension (adjusted HR = 1.072, 95% CI: 1.002-1.147). We observed the depletion of Blautia wexlerae and Parabacteroides distasonis in populations with Ad-pHT. A multiclass logistic regression model distinguished individuals with Ad-pHT from HC and those with adiposity and normal tension (Ad-NT) (AUC = 0.704). Microbiota-microbiota interactions gradually become complex from HC to Ad-NT to Ad-pHT groups. Blautia wexlerae and Parabacteroides distasonis were associated with pathways involved in carbohydrate degradation (PWY-8004), fermentation (ANAEROFRUCAT-PWY), biosynthesis of secondary metabolites (PWY-6270), amino acid (ARGININE-SYN4-PWY), quinol and quinone (PWY-7992), and nucleoside and nucleotide (PWY-6700).

CONCLUSION: Shifts in Blautia wexlerae and Parabacteroides distasonis, as well as their relationships with pathways (energy metabolism and amino acid biosynthesis), were observed in adiposity-related prehypertension. Blautia wexlerae and Parabacteroides distasonis might represent promising candidates for next-generation probiotics targeting weight management and blood pressure reduction, which require validation in clinical studies.},
}

@article {pmid42445502,
year = {2026},
author = {Hou, H and Zhang, X and Chen, S and Kong, Y and Yang, S and Gao, Z and Cui, Z and Lv, Z and Yang, Z and Yuan, Y and Feng, B},
title = {Saline-alkali gradients reshape soil microbial network complexity and niche breadth.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1886660},
pmid = {42445502},
issn = {1664-302X},
abstract = {INTRODUCTION: Saline-alkali soils impose combined osmotic, ionic and alkaline constraints on soil microorganisms, yet how bacterial and fungal ecological strategies vary along saline-alkali gradients remains insufficiently resolved.

METHODS: We analyzed 30 composite soil samples from 10 sites across China using bacterial 16S rRNA and fungal ITS amplicon sequencing, soil physicochemical profiling, co-occurrence network analysis, niche breadth classification and PICRUSt2-based functional prediction.

RESULTS: Higher saline-alkali intensity was associated with reduced nutrient availability, lower microbial network complexity and greater network vulnerability. Bacterial specialists showed stronger diversity and compositional responses than generalists, whereas fungal communities displayed comparatively stable patterns across the sampled gradient. Predicted bacterial functional profiles suggested an increased representation of stress-survival-related pathways under high saline-alkali conditions.

DISCUSSION: These findings identify microbial taxa, network properties and predicted functional features associated with saline-alkali soil degradation and provide candidate targets for future culture-based, metagenomic and experimental validation.},
}

@article {pmid42445733,
year = {2026},
author = {Yang, L and Liu, Y and Li, J and Lv, J and Zhang, Q and Cong, M and Shi, H and Zhang, H},
title = {Bifidobacterium animalis subsp. lactis V9 improves quality of life in advanced gastrointestinal cancer through gut microbiota-metabolite modulation.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag127},
pmid = {42445733},
issn = {2730-6151},
abstract = {Chemotherapy for advanced gastric and esophageal cancer is often limited by severe gastrointestinal and systemic toxicities that profoundly impair patients' quality of life. We conducted a randomized, double-blind, placebo-controlled trial in 104 patients to evaluate whether Bifidobacterium animalis subsp. lactis V9 (V9; 2 × 10[10] CFU/day) mitigates these effects. Participants received V9 or placebo daily for 18 weeks alongside standard chemotherapy. Supplementation with V9 significantly improved EORTC QLQ-C30 scores for overall health status, fatigue, nausea, vomiting, appetite loss, cognitive functioning, role functioning, and insomnia (all P < .01). Integrated metagenomic and metabolomic analyses of stool samples revealed that V9 did not alter overall microbial α- or β-diversity but induced targeted shifts: it enriched beneficial taxa, such as B. pseudocatenulatum, Agathobacter rectalis, and Lachnospira hominis, while depleting pathobionts such as Fusobacterium varium and Enterocloster clostridioformis. These microbial changes correlated with favorable metabolic reprogramming, including increased fecal levels of pyridoxamine, 5'-methylthioadenosine, and palmitoylcarnitine, as well as decreased levels of taurine-conjugated bile acids and several amino acids (P < .05). Critically, these metabolite alterations were significantly associated with clinical improvements. Our findings demonstrate that V9 enhances quality of life during chemotherapy not through global microbiota restructuring, but via precise modulation of functionally relevant bacteria and their metabolic outputs. This supports V9 as a mechanistically grounded, targeted adjuvant therapy to improve resilience and well-being in patients with advanced upper gastrointestinal cancers.},
}

@article {pmid42445734,
year = {2026},
author = {Storck, V and Ponton, DE and Lawruk-Desjardins, C and Ferriz, LM and Leclerc, M and Kraemer, S and Planas, D and Amyot, M and Walsh, D},
title = {Cross-habitat interactions drive methylmercury contamination in a disturbed river ecosystem: novel metagenomic and biogeochemical insights.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag176},
pmid = {42445734},
issn = {2730-6151},
abstract = {Understanding contaminant dynamics in ecosystems requires considering interactions between habitats-an aspect often overlooked in research. Mercury (Hg) studies typically focus on methylmercury (MeHg) production in sediments, often neglecting the role of biofilms such as periphyton. This study analyzes sediments and periphyton in a disturbed river using biogeochemical and metagenomic approaches. We found that microbial communities differed between habitats, but Hg-methylating microbes were taxonomically similar, with higher abundance in sediments. Organic matter (OM), a key Hg vector, likely affects Hg dynamics differently across habitats: MeHg concentrations increased with increasing terrigenous OM in sediments, whereas in periphyton, MeHg increased with greater contributions of aquatic-derived OM. Surprisingly, periphyton showed higher MeHg concentrations than sediments, despite lower hgcA abundance, the gene associated with MeHg production. Our multi-indicator analysis provides a conceptual model suggesting that MeHg is primarily produced in active sediments (indicated by elevated carbon dioxide and methane), diffuses into the water column (supported by carbon dioxide-MeHg correlations), and accumulates in protein-rich periphyton in shallow, low-flow waters where prolonged exposure can enhance MeHg retention. While some MeHg production occurs in periphyton, especially at a wetland site with thick growth, periphyton at a hydroelectric-impacted site showed the highest MeHg levels despite absent hgcA and methylation activity, pointing towards MeHg retention from the water. As a major food source for primary consumers, periphyton likely redistributes accumulated MeHg through the food web. This study highlights the importance of considering MeHg transfer between habitats and the need to examine entire aquatic ecosystems to fully understand MeHg dynamics.},
}

@article {pmid42445853,
year = {2026},
author = {Chen, X and Pan, J and Wang, Y and Wei, Y and Zhang, X and Jiang, H and Zhang, L and Wu, G and Chen, B and Xie, J and Tong, P},
title = {Detection and molecular characterization of bovine enterovirus E2 from dairy calves with respiratory disease in Urumqi, Xinjiang, China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1800707},
pmid = {42445853},
issn = {2235-2988},
mesh = {Animals ; Cattle ; China/epidemiology ; Phylogeny ; *Cattle Diseases/virology/epidemiology ; *Enterovirus, Bovine/genetics/isolation & purification/classification ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Disease Outbreaks/veterinary ; *Enterovirus Infections/veterinary/virology/epidemiology ; Genome, Viral ; Metagenomics ; },
abstract = {INTRODUCTION: Bovine enterovirus (BEV) is a contagious viral agent that can cause respiratory infections and disease outbreaks among calves. This study reports an outbreak that occurred in a population of dairy calves in northern Xinjiang in November 2024.

METHODS: Nasal swab samples were collected from 58 clinically symptomatic calves and analyzed for some bovine respiratory viruses using RT-PCR and viral metagenomic sequencing.

RESULTS: Viral metagenomic analysis annotated only one bovine pathogen, BEV, in respiratory disease samples. RT-PCR further confirmed that BEV was detected in all nasal swab samples from symptomatic dairy calves, while it was not detected in samples from healthy dairy cattle, suggesting that BEV may be the etiological agent of this respiratory disease. One BEV strain, designated XJ-FHT, was successfully isolated and found to be responsible for respiratory illness in calves. Comparative analysis of the whole genome, the encoded polyprotein, and the nucleotide and amino acid sequences of VP1 and P1, along with phylogenetic analysis of VP1 amino acid sequences, classified this isolate as belonging to the E2 subtype.

DISCUSSION: This study provides the first identification of a BEV-associated respiratory disease among calves in Xinjiang, China, in 2024. Molecular characterization and phylogenetic analysis identified the isolated strain as belonging to the E2 subtype. These findings highlight the potential role of BEV in bovine respiratory infections and emphasize the need for continued surveillance and preventive measures.},
}

Animals
Cattle
China/epidemiology
Phylogeny
*Cattle Diseases/virology/epidemiology
*Enterovirus, Bovine/genetics/isolation & purification/classification
*Respiratory Tract Infections/veterinary/virology/epidemiology
Disease Outbreaks/veterinary
*Enterovirus Infections/veterinary/virology/epidemiology
Genome, Viral
Metagenomics

@article {pmid42446199,
year = {2026},
author = {Landa, MM and Mendoza, A and Rossoff, J and Rosenthal, A and Chaudhury, S and Muller, WJ},
title = {Plasma metagenomic sequencing testing for diagnosis of invasive fungal infection in children and young adults.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0069926},
doi = {10.1128/spectrum.00699-26},
pmid = {42446199},
issn = {2165-0497},
abstract = {UNLABELLED: Invasive fungal infection (IFI) is challenging to diagnose, often involving invasive sampling. Plasma cell-free metagenomic next-generation sequencing (mNGS) has shown promise in diagnosing infections, but data are limited on specific clinical scenarios in which this test is most helpful. We conducted a retrospective single-center study of children and young adults with high-risk conditions evaluated for IFI between December 2016 and November 2024. Clinical concern for IFI was indicated by (i) evaluation with both serum β-D-glucan and galactomannan testing, (ii) either or both of CT scans of sinuses and chest, and (iii) antifungal treatment either started or broadened. Episodes in which mNGS testing was sent within 30 days of initiation or broadening of antifungal coverage were evaluated to determine the diagnostic performance of mNGS testing, using EORTC-MSG criteria for proven or probable IFI as the comparator. We identified 227 episodes in 180 high-risk patients consistent with clinical concern for IFI. Of these, 45 episodes met EORTC-MSG criteria for proven/probable IFI. Plasma mNGS testing was sent in 36 episodes and identified the causative organism in 28. Positive and negative percent agreement for diagnosis of proven/probable IFI in this population was 77.8% and 90.4%, respectively. Among proven/probable cases with mNGS testing, Candida and Aspergillus were the most commonly identified fungi. Plasma mNGS testing in pediatric and young adult patients at risk for IFI compares favorably with diagnostic criteria used for IFI diagnosis and may be added to the diagnostic evaluation of patients at high-risk of IFI.

IMPORTANCE: Performance of plasma mNGS testing for diagnosis of invasive fungal infection in high-risk pediatric and young adult patients was comparable to the combination of fungal culture and targeted PCR from invasively acquired samples, suggesting that it might allow earlier diagnosis for some patients.},
}

@article {pmid42446240,
year = {2026},
author = {Tamm, SC and Doster, E and Wolfe, CA and Pinnell, LJ and Crosby, WB and Newcomer, BW and Funk, JL and Richeson, JT and Gow, SP and Valeris-Chacin, R and Woolums, AR and Morley, PS},
title = {Mannheimia haemolytica strain-level diversity in cattle populations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0404925},
doi = {10.1128/spectrum.04049-25},
pmid = {42446240},
issn = {2165-0497},
abstract = {High-resolution genomic characterization is essential for understanding diversity, pathogenicity, and transmission dynamics of bacterial pathogens. Mannheimia haemolytica (Mh) is the most consequential bacterial agent associated with bovine respiratory disease (BRD) in cattle, as a leading cause of morbidity, mortality, and antimicrobial use. Historically, BRD pathogens, including Mh, have been studied using culture or PCR approaches that provided limited ability to characterize fine-scale genomic variation across communities. Here, we evaluated target-enriched (TE) shotgun sequencing, a culture-independent method capable of strain-level resolution within metagenomic data, for detecting and characterizing Mh in comparison with qPCR and 16S rRNA gene sequencing. Nasal swabs (10 individual and 2 composited DNA samples per pen) and environmental samples (three ropes hung on pen rails and three water bowl swabs per pen) were collected from four pens in each of five distinct cattle populations. DNA was extracted for TE sequencing to identify Mh at both species and genomic sequence variant (GSV) levels, and to characterize antimicrobial resistance genes across the bacterial communities. qPCR was performed to quantify Mh genome copies, and 16S rRNA gene sequencing was used to assess the broader respiratory microbiome. TE sequencing identified Mh in 100% of TE-tested samples and classified multiple GSVs in all but 3 of 121 samples. GSV profiles clustered within housing groups and varied across cattle populations, indicating structured strain-level diversity. In contrast, Mannheimia spp. were detected in only 47.7% of samples by 16S rRNA sequencing. These findings demonstrate that TE sequencing enables sensitive, strain-level characterization of Mh in cattle and environmental samples and reveals substantial within-population genomic diversity not captured by conventional approaches.IMPORTANCETarget-enriched shotgun sequencing enabled sensitive, strain-level detection of Mannheimia haemolytica (Mh), revealing multiple co-circulating genomic sequence variants (GSVs) within and among cattle groups. This demonstrates greater genetic variability of Mh populations in beef cattle than has been previously recognized. The clustering of GSVs within housing groups, together with the overlap between respiratory and environmental samples, is consistent with the hypothesis that contagious transmission contributes to Mh ecology. These results highlight the potential utility of composite nasal swab and environmental samples for future studies evaluating relationships between Mh genomic variation and disease risk.},
}

@article {pmid42446350,
year = {2026},
author = {Gregory, JB and Harrison, JW and Uehling, JK and Farrer, RA and Ballou, ER},
title = {Phylogenetically diverse Mucorales-Mycetohabitans endosymbiotic interactions identified from whole-genome sequencing using a targeted metagenomic assembly pipeline.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001746},
pmid = {42446350},
issn = {2057-5858},
mesh = {*Symbiosis/genetics ; Phylogeny ; *Mucorales/genetics/classification/physiology ; Whole Genome Sequencing/methods ; Metagenomics/methods ; Metagenome ; Genome, Fungal ; },
abstract = {Endosymbiotic bacteria of the genus Mycetohabitans are obligate intracellular associates of Mucorales fungi, yet the understanding of their diversity, distribution and evolutionary dynamics is in its infancy. By screening 1,696 public sequencing datasets from Mucorales fungi, we detected Mycetohabitans in 46 fungal accessions spanning 5 host taxa across the fungal genera Rhizopus and Apophysomyces. These included 13 previously unreported associations. Genome reconstruction yielded 38 Mycetohabitans metagenome-assembled genomes (MAGs), of which 34 were of high quality. Incorporating these MAGs into genome-based species delimitation expanded known Mycetohabitans diversity from four to nine species-level clusters, including novel host-associated lineages. Re-examination of fungal host identities revealed frequent misidentification of isolates in fungal collection catalogues and/or misannotation in GenBank, with nearly a quarter of positive datasets requiring correction through internal transcribed spacer and genome-scale verification. Host-symbiont associations were non-random under this revised framework, with significant structure detected by contingency analysis and ParaFit. MAG-focused pangenome analysis revealed an open pangenome and mosaic lineage-associated functional traits, including variation in metabolism, secretion, cell-envelope systems, metal resistance, antimicrobial-resistance-associated functions and mobile elements. The most distinctive lineage comprised two Apophysomyces-associated MAGs, provisionally named M. apophysomyceticola, which showed pronounced genome reduction compared with other sampled Mycetohabitans spp. and loss of multiple central metabolic, nutrient assimilation, cofactor biosynthesis, catabolic, stress-response and defence pathways, consistent with reduced metabolic flexibility and increased host dependence. Together, these results show that Mycetohabitans symbioses are more geographically widespread, taxonomically diverse and functionally differentiated than previously recognized. More broadly, this work demonstrates the value of public sequencing repositories for uncovering hidden fungal-bacterial symbioses, while emphasizing that repository-derived patterns must be interpreted considering host misidentification, uneven sampling and incomplete metadata. Overall, our work establishes a global framework for Mycetohabitans diversity and function, with implications for fungal ecology, evolution and clinical mycology.},
}

*Symbiosis/genetics
Phylogeny
*Mucorales/genetics/classification/physiology
Whole Genome Sequencing/methods
Metagenomics/methods
Metagenome
Genome, Fungal

@article {pmid42446470,
year = {2026},
author = {Almulhim, F and Narayanasamy, S and Wang, C and Mandal, P and Bensaddek, D and Amad, M and Hong, PY},
title = {Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70372},
doi = {10.1111/1462-2920.70372},
pmid = {42446470},
issn = {1462-2920},
support = {BAS/1/1033-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Wastewater/microbiology/chemistry ; Proteomics ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Biofilms ; Metagenomics ; Nitrogen/metabolism ; Denitrification ; },
abstract = {Reclaimed wastewater is increasingly reused for irrigation and other non-potable applications; however, inadequately treated effluent has raised concerns regarding environmental and public health impacts. Water quality in reclaimed distribution systems is shaped by multiple factors, particularly hydraulic stagnation in pipes and storage reservoirs. Stagnation can alter microbial community stability and facilitate persistence of pathogenic taxa. To investigate how prolonged stagnation affects microbial community structure and function, we integrated metagenomics and metaproteomics analyses of biofilms under flow and stagnant conditions over 3, 5 and 7 months. Prolonged stagnation caused pronounced compositional shifts, including strong reductions in nitrogen-removing taxa such as Nitrospira and Nitrosomonas. Correspondingly, key nitrification and denitrification proteins were depleted ≥ twofold under stagnation, indicating impaired nitrogen conversion processes. Stagnation also enriched motility- and transport-related functions and promoted Acidovorax persistence, a genus including phytopathogenic species. In contrast, flow conditions sustained nitrogen-cycling activity, contaminant-degrading enzymes, and quorum-quenching proteins, supporting greater biostability. Overall, our findings show that prolonged stagnation disrupts microbial community balance, suppresses essential nitrogen-cycling and detoxification pathways, and reduces the functional robustness of treated wastewater. Maintaining hydraulic flow within reclaimed water systems is therefore critical for preserving microbial functionality and ensuring safe and reliable reuse in irrigation and other non-potable applications.},
}

*Wastewater/microbiology/chemistry
Proteomics
*Microbiota
*Bacteria/genetics/classification/metabolism/isolation & purification
Biofilms
Metagenomics
Nitrogen/metabolism
Denitrification

@article {pmid42446573,
year = {2026},
author = {Zhang, C and Zhang, YT and Cao, J and Li, X and Yuan, S and Dai, X and Xu, Y},
title = {Hydrovoltaic Energy Harvesting from Sewage Sludge Induces Its Efficient Anaerobic Digestion.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01444},
pmid = {42446573},
issn = {1520-5851},
abstract = {The hydrovoltaic effect originates from leveraging water-material interactions to generate electricity. Sewage sludge inherently possesses an abundant porous structure and water-solid interfaces favorable for hydrovoltaic power generation. Herein, we explored the influence of promoting the hydrovoltaic effect of sludge on its subsequent methanogenesis during anaerobic digestion (AD). It was observed that a maximum open-circuit voltage of 0.62 V was achieved from sludge, and in its subsequent AD, the methane production and proportion of methane in biogas increased by 82% and 24.6%, respectively, indicating that the hydrovoltaic effect of sludge enables the direct recovery of electricity and significantly enhances its subsequent methanogenesis. The stable isotope-labeled AD experiments demonstrate that the hydrovoltaic effect enhanced water participation in CO2-reduction methanogenesis. Statistical analyses of variations in physicochemical properties of sludge, key enzymes closely related to electron/proton transfer, and microbial community in AD reveal that the hydrovoltaic effect induced significant enhancement of water-mediated proton-coupled electron transfer-associated methanogenesis, providing a thermodynamic advantage for methanogenic reactions. It was further verified by metagenomic and metatranscriptomic analyses, which showed that the expression levels of key genes associated with the classical and RuBisCO-mediated CO2 reduction methanogenic pathways were almost all significantly upregulated. This study provides a reference for directly recovering electricity from sludge by utilizing inherent properties while inducing efficient AD.},
}

@article {pmid42446674,
year = {2026},
author = {Jahnavi, S and Devendu, KV and Saha, S and Dey, P and Osborne, WJ},
title = {Marine bacteria and fungi: the hidden treasure of oceans in the biodegradation of microplastics and hydrocarbons integrated with omics technologies.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {42446674},
issn = {1432-0738},
abstract = {Marine microorganisms play a crucial role in maintaining oceanic ecosystem stability by mediating essential biogeochemical cycles, nutrient cycling and natural attenuation of environmental pollutants through diverse metabolic processes. Owing to their remarkable metabolic diversity, marine bacteria, fungi, and archaea possess the ability to utilize complex organic compounds as carbon and energy sources enabling them to transform and degrade a wide range of contaminants in aquatic environments, making them key agents in marine bioremediation. Among these, the most persistent pollutants threatening the marine ecosystem are the Microplastics (MPs) and hydrocarbons, both of which originate largely from anthropogenic activities including plastic waste accumulation, industrial discharge, petroleum extraction and accidental spills. MPs, are plastic particles of size less than or equal to 5 mm, produced due to the fragmentation of larger plastic debris while hydrocarbons consist of complex mixtures of aliphatic and aromatic compounds including polycyclic aromatic hydrocarbons (PAHs) and BTEX compounds. In marine systems, MPs frequently act as carriers for hydrocarbons and other contaminants, facilitating the formation of specialized microbial biofilms known as the plastisphere. Microbial degradation of these pollutants involves sequential processes including surface colonization, enzymatic depolymerization, biofragmentation, assimilation and mineralization. Several studies have reported the potential of marine bacteria and fungi in the degradation of MPs and HCs through the synthesis of key enzymes such as PETase and MHETase for MPs and laccases, peroxidases for HCs. Recent advances in omics technologies including metagenomics, metabolomics, proteomics, and transcriptomics have significantly improved our understanding of microbial community dynamics, degradation pathways, and functional genes involved in pollutant degradation. Therefore, integration of recent technologies alongside conventional methods could enhance the remediation process. In this review, we have collated the collective role of marine microorganisms in the biodegradation of MPs and hydrocarbons, highlighting their key degradation mechanisms, microbial interactions and the contributions of omics based approaches in advancing marine bioremediation research.},
}

@article {pmid42446958,
year = {2026},
author = {Nguyen-Dinh, T and Hutchinson, TF and Ricci, F and Prayitno, H and Jimenez, L and Eate, V and Leung, PM and Lappan, R and Yoon, S and Wong, WW and Cook, PLM and Greening, C},
title = {Flavobacteria consume nitrous oxide produced by partial denitrifiers in coastal sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag186},
pmid = {42446958},
issn = {1751-7370},
abstract = {Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling showed that both clade II nosZ flavobacterial isolates and whole sand communities exhibited a low apparent affinity for N2O under the tested experimental conditions, expanding the currently limited kinetic data available for N2O reducing microorganisms from coastal permeable sediments, including flavobacterial clade II N2O reducers. Collectively, these findings indicate that abundant N2O reducing communities can substantially consume N2O within permeable sediments, thus limiting N2O accumulation despite active N2O production. Together with previous hydrodynamic models predicting low N2O release from permeable sediments, our results highlight the important role of specialized microbial communities in regulating N2O cycling under increasing nutrient pollution.},
}

@article {pmid42447082,
year = {2026},
author = {Rodríguez, JA and Santos-Bay, L and Narechania, A and Carøe, C and Sirén, K and Mak, SST and Broman Nielsen, I and Ramsøe, M and Pontén, TS and Lillevang, S and Andersen, LT and Gilbert, MTP},
title = {The effect of different milk pretreatment methods on microbiome community development during Herrgårds cheese production and ripening.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0350187},
doi = {10.1371/journal.pone.0350187},
pmid = {42447082},
issn = {1932-6203},
mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota/genetics ; Metagenome ; Food Microbiology ; Pasteurization ; Lactococcus lactis/genetics/isolation & purification ; Clostridium tyrobutyricum/genetics/isolation & purification ; },
abstract = {One of the biggest challenges for dairy producers is the substantial variability in final product properties caused by changes in the production environment. In cheese production, this variation is influenced by several factors, particularly the milk base and its pretreatment, which shape the microbiome throughout the process and ultimately affect the cheese's organoleptic characteristics. To examine the impact of three different pretreatments for pasteurised milk- microfiltration, protein fortification, and pasteurisation only (control)- on microbiome dynamics, we generated metagenome sequencing data from 14 cheese production steps across these three production trials at a Danish dairy factory. We constructed three metagenomic co-assemblies, identifying nine high-quality metagenome-assembled genomes. Our analysis revealed that a specific strain of Lactococcus lactis dominates the process, while other minor bacterial species persist at very low abundances (<1%), contributing non-negligibly to product properties. Notably, we detected DNA from Clostridium tyrobutyricum, a known bacterium whose heat-resistant spores may cause dairy spoilage, in pasteurised only and protein-fortified milk trials but was nearly absent in microfiltered milk. To enhance our analyses, we implemented KHILL, a novel k-mer based method, which facilitates metagenomic co-assembly and enables early detection of unwanted microorganisms. Our findings provide industrial dairy producers with a comprehensive view of microbial dynamics during cheese production, offering insights to improve process consistency and product quality.},
}

*Cheese/microbiology
Animals
*Milk/microbiology
*Microbiota/genetics
Metagenome
Food Microbiology
Pasteurization
Lactococcus lactis/genetics/isolation & purification
Clostridium tyrobutyricum/genetics/isolation & purification

@article {pmid42447281,
year = {2026},
author = {Su, Y and Fan, L and Chen, Z and Tang, X and Wang, J and Klümper, U and Shi, G and Han, P},
title = {Nitrification Couples Microbial CO2 Fixation to Warming and Drought Responses in Alpine Grassland Soils.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17815},
pmid = {42447281},
issn = {1520-5851},
abstract = {Microbial CO2 fixation in alpine grassland soils is highly sensitive to warming and drought. Nitrogen inputs from grazing may stimulate autotrophic nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). These nitrifiers assimilate carbon through CO2 fixation, but how their activity is associated with microbial CO2 fixation under warming and drought remains unclear. Here, we investigated microbial CO2 fixation and nitrification under altered temperature and moisture using urea-amended soil microcosms with [13]CO2 labeling, DNA-stable isotope probing (DNA-SIP), metagenomics, and quantitative PCR. Warming increased CO2 fixation rates to 1.48-2.58 times those at 15 °C under moist conditions, whereas drought reduced it by 59-91%. Nitrification rates were positively correlated with CO2 fixation, whereas the CO2 fixation offset only 1.3-12.1% of associated N2O emissions (measured as CO2 equivalents). DNA-SIP and metagenomics indicated that nitrifiers contributed to microbial CO2 fixation, with AOA showing more pronounced [13]C-labeling under combined warming and drought. Co-occurrence network indicated that AOA occupied more highly connected positions than AOB and NOB. This study provides microbial evidence that warming and drought reshape the linkage between nitrification and microbial CO2 fixation in urea-amended alpine grassland soil microcosms, with implications for carbon-nitrogen cycling and greenhouse-gas feedbacks.},
}

@article {pmid42447304,
year = {2026},
author = {Cao, J and Ye, Z and Pan, J},
title = {Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0009026},
doi = {10.1128/jb.00090-26},
pmid = {42447304},
issn = {1098-5530},
abstract = {Antimicrobial resistance (AMR) is a global health crisis shaped by complex ecological and evolutionary processes that often occur in polymicrobial communities. Metagenomics enables culture-independent profiling of microbial DNA directly from clinical or environmental samples, providing an unparalleled view of community composition, resistome content, and the mobile genetic elements that drive horizontal gene transfer (HGT). Yet, a recurring challenge is that metagenomic detection of antibiotic-resistance genes does not automatically translate into a mechanistic understanding of resistance phenotypes, nor does it replace culture-based functional validation. Here, we synthesize how modern metagenomics supports AMR research across three linked questions: (i) what resistance determinants are present and how do they change across time and space, (ii) which hosts and mobile genetic elements carry these determinants, and how gene flow can be inferred, and (iii) what evidence is required to move from "resistance potential" to robust mechanistic claims. We emphasize practical design principles (sampling, controls, and contamination management), analytical choices (database and parameter effects), and recent advances, including long-read sequencing for resolving antibiotic-resistance genes context, and rapid clinical metagenomic sequencing for time-sensitive decision support. We propose an evidence ladder for mechanistic inference that integrates metagenomics with targeted assays and culture-dependent experiments. Beyond synthesizing recent advances, this review provides operational tools for critical appraisal and study design: an evidence ladder for mechanistic inference, a decision-gated workflow that ties metagenomic outputs to allowable claim language, a minimum reporting checklist aligned to evidence strength, and a "pitfall → consequence → fix" guide to reduce over-interpretation. To support a more comprehensive, forward-looking view, we also summarize emerging directions that are rapidly reshaping AMR metagenomics-multi-omics integration, single-cell, and epigenetic linkage strategies, CRISPR-enabled enrichment/depletion, and AI-assisted discovery/mining-and clarify where these advances strengthen (or do not strengthen) mechanistic claims within the same evidence ladder.},
}

@article {pmid42447582,
year = {2026},
author = {Lin, H and Li, X and Wang, X and Yuan, Q and Yang, F and Hu, W and Li, X and Lei, L and Luo, Y},
title = {The antibiotic resistome in oysters across the Chinese coastline: Enrichment, microbial drivers, and implications for health risk.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {142811},
doi = {10.1016/j.jhazmat.2026.142811},
pmid = {42447582},
issn = {1873-3336},
abstract = {Oysters extensively farmed in China represent a critical but under-investigated pathway for human exposure to antibiotic resistance genes (ARGs). This study employed metagenomic analysis of 75 samples from representative Chinese oyster farms to explore ARGs distribution in oysters and their surrounding environments, alongside assessing their health risk. Results exhibited significant spatial heterogeneity and marked ARG enrichment in oyster compared to surrounding seawater along the Chinese coastline, with an enrichment factor 2.60 ± 2.43 folds higher. This enrichment is primarily driven by selective retention of specific microbes, particularly the opportunistic pathogen Vibrio, which emerged as a dominant ARG host. Furthermore, the co-occurrence of mobile genetic elements and diverse ARGs, particularly IS91 and tnpA, suggests a high potential for horizontal gene transfer within oyster bacteriome, potentially exacerbating the dissemination of antibiotic resistance. From a public health perspective, the mean estimated daily intake (EDI) of ARGs via oyster consumption was calculated at 1.7E-1 ± 1.7E-1 copies/16S/g/individual. Given that oyster can be consumed raw and harbor pathogenic Vibrio, this ARG exposure may underscores potential health risk for consumers. Integrating the EDI with a resistome scoring system, the Risk Index (RI) demonstrated site-specific health threats that necessitate differentiated management priorities. Collectively, these results provide critical evidence of how marine aquaculture serves as a reservoir for ARGs and highlight the urgent need for integrated surveillance under the One Health approach to mitigate the transmission of antibiotic resistance from marine environments to the human food chain.},
}

@article {pmid42447623,
year = {2026},
author = {Su, K and Tian, S and Xia, Y and Zhao, X and Huang, J and Hu, S and Ye, J},
title = {Species composition and functional characteristics of the human multi-organ microbiome: A metagenomic study.},
journal = {Journal of forensic and legal medicine},
volume = {122},
number = {},
pages = {103213},
doi = {10.1016/j.jflm.2026.103213},
pmid = {42447623},
issn = {1878-7487},
abstract = {Postmortem microbial communities may provide useful information for forensic microbiology, but species-level and functional profiles across multiple cadaveric anatomical sites remain poorly characterized. Here, shotgun metagenomic sequencing was performed on 144 samples from six anatomical sites, including the oral cavity, nasal cavity, trachea, lung, colon, and anus, collected from 24 human cadavers. A total of 15,301,799,968 raw reads were obtained, and 6565 species were identified, and KEGG pathways were annotated at the L1, L2, and L3 levels. Species-level microbial composition differed significantly among anatomical sites. PERMANOVA with permutations blocked by individual identity showed that anatomical site was the dominant factor explaining microbial community variation (R[2] = 0.3778, p = 0.001, q = 0.001), whereas postmortem interval did not show a significant independent effect within the 1-38-day interval. KEGG functional profiles also differed significantly among anatomical sites at the L2 and L3 levels, and 182 of 214 L3 pathways showed significant site-associated differences after false-discovery-rate correction. Pathway-level mixed-effect models further indicated that anatomical site remained significantly associated with most L3 pathways after accounting for postmortem interval, age, sex, cause of death, and repeated sampling from the same individual. Species-pathway correlation analysis identified significant taxon-function associations, but these were interpreted as correlative rather than direct evidence of species-specific functional contribution. Low-biomass sensitivity analyses indicated that respiratory-site results, especially lung and tracheal findings, should be interpreted cautiously because of high host DNA proportions and low non-host read counts. Inter-site shared occurrence and intra-site co-occurrence analyses further described distributional associations across anatomical sites. This study establishes a multi-site postmortem metagenomic reference framework for characterizing anatomical-site-specific microbial and functional patterns, offering insights into forensic microbiology and postmortem microbial ecology.},
}

@article {pmid42447671,
year = {2026},
author = {Han, Z and Zhang, H and Li, H and Luan, X and Guruge, SK and Hu, C and Yang, M and Zhang, Y},
title = {Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.},
journal = {Water research},
volume = {305},
number = {},
pages = {126471},
doi = {10.1016/j.watres.2026.126471},
pmid = {42447671},
issn = {1879-2448},
abstract = {Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.},
}

@article {pmid42448116,
year = {2026},
author = {Wu, J and He, C and Wu, K and Feng, W and Zhou, Q and Yang, Y and Tyagi, RD},
title = {Black soldier fly bioconversion improves agronomic value but sustains resistome risks in silver-bearing sewage sludge compost.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135402},
doi = {10.1016/j.biortech.2026.135402},
pmid = {42448116},
issn = {1873-2976},
abstract = {Agricultural reuse of sewage sludge can improve crop production but may also introduce metals and antibiotic resistance genes (ARGs) into soil-plant systems. We evaluated sludge-derived composts, with and without black soldier fly (BSF) bioconversion, in a red amaranth pot experiment under exposure to silver nanoparticles (Ag-NPs) and silver sulfide nanoparticles (Ag2S-NPs). During composting, BSF was associated with greater dissolved organic matter humification, reduced extractable Ag and co-existing metal concentrations, while Ag exposure selectively reshaped compost microbiota and the BSF gut resistome. However, BSF bioconversion remained the main driver of microbial community reassembly, whereas Ag exposure mainly promoted host turnover and mobile genetic element enrichment rather than broad ARG amplification. After soil application, compost significantly enhanced red amaranth growth. Total biomass increased from 1.3 g pot[-1] in the unfertilized control to 3.8 g pot[-1] with BSF-derived compost and 5.1-5.2 g pot[-1] with BSF-derived Ag2S-NP composts, accompanied by higher shoot N and P concentrations. However, shoot Ag and selected co-existing metals also increased, indicating an agronomic benefit-risk trade-off. Metagenomic analyses showed that compost application reshaped the rhizosphere resistome mainly through host filtering, with ARG dissemination potential linked to the co-localization of ARGs, metal resistance genes, and mobile genetic elements in a limited number of enriched hosts. Plant growth was driven mainly by fertilization and nutrient status, whereas ARG abundance was associated primarily with metals, metal resistance genes, and gene mobility. These findings support BSF-assisted sludge recycling as a promising but risk-aware strategy for agricultural reuse.},
}

@article {pmid42448240,
year = {2026},
author = {Thompson, KN and Ma, S and Bhosle, A and Nickols, WA and Shen, J and Ghazi, AR and Dang, NH and Zhang, Y and Nzabarushimana, E and Kim, H and Xavier, RJ and Chan, AT and Franzosa, EA and Huttenhower, C and Nguyen, LH},
title = {Harmonized metagenomic signatures of the gut microbiome reveal robust species, functions, and strain links to inflammatory bowel disease.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.06.023},
pmid = {42448240},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Coupled with well-characterized host genetic and environmental risk factors, alterations of gut microbial communities contribute to risk and severity of inflammatory bowel disease (IBD) and its subtypes, Crohn's disease (CD) and ulcerative colitis (UC). In a rapidly advancing field in which diverse multinational cohorts and molecular methods have been created, highly-resolved microbial traits such as protein function and strain genetics can now be investigated through meta-analysis.

METHODS: We integrated 2,371 stool metagenomes from 542 individuals with IBD and their referent counterparts from the United States, Canada, and Europe, utilizing all seven IBD cohorts in the Human Microbiome Bioactives Resource, which we interrogated using taxonomic, functional, and strain profiling.

RESULTS: We systematically identified the mass expansion of pro-inflammatory, oral-predominant taxa in the IBD gut, such as Veillonella and Streptococcus spp. We also accurately discriminate CD from UC, a clinically challenging problem, using highly-resolved microbial strain genetics (AUC=0.69). Further, we observed disease-specific shifts in carbohydrate metabolism, a likely consequence of small bowel dysfunction in CD, but not UC, as well as perturbations in mucin utilization, increased microbial virulence and invasion cassettes, and loss of carnitine degradation pathways in IBD. Finally, we observed novel and significant differences in the gene carriage among both IBD- and non-IBD-associated taxa, suggesting that strain-specific functional variation may contribute to pathogenesis and disease-related bacterial fitness.

CONCLUSION: Microbial clades responsible for IBD-linked dysbiosis are not uniform, and their functionality in IBD and CD/UC subsets are driven by species and strain lineage-specific variants.},
}

@article {pmid42437837,
year = {2026},
author = {Devi, U and Ramadass, B and Pullattayil, AK and Vishnu Bhat, B},
title = {Gut Microbiome in Neonatal Necrotizing Enterocolitis - A Comprehensive Review of Evidence.},
journal = {Indian journal of pediatrics},
volume = {},
number = {},
pages = {},
pmid = {42437837},
issn = {0973-7693},
abstract = {Necrotizing enterocolitis (NEC) is one of the most catastrophic gastrointestinal emergency occurring predominantly in preterm neonates. It contributes to substantial neonatal morbidity and mortality. Disturbances in the intestinal microbiome are crucial to disease pathogenesis. In preterm infants, an immature intestinal barrier, dysregulated immune responses, and environmental exposures altogether predispose to alteration in microbial colonization and intestinal inflammation. This review was done to present the current evidence on gut microbiome alterations associated with NEC in preterm infants. A systematic search of the MEDLINE and EMBASE databases was performed using search strategy related to prematurity, intestinal microbiota, and necrotizing enterocolitis. A total of 42 studies assessing microbial composition, microbial progression, or microbial functional patterns in relation to NEC were included. Across the included studies, NEC was commonly preceded by reduced microbial diversity, delayed maturation of anerobic communities, and expansion of Proteobacteria, particularly Enterobacteriaceae family such as Klebsiella and Escherichia. Longitudinal studies further showed that these microbial changes may become evident days to weeks before clinical disease, suggesting a potential window for early risk identification. Functional analyses also showed alterations in microbial metabolic pathways, including short-chain fatty acids, tricarboxylic acid intermediates, volatile compounds, and viral signatures that may lead to epithelial injury and inflammatory signaling. Clinical and environmental factors including antibiotic exposure, mode of delivery, feeding practices, and NICU microbial ecosystem are important determinants of neonatal gut microbiome development. Thus, the current evidence supports a reproducible pattern of intestinal dysbiosis preceding NEC. Better understanding of microbiome dynamics may aid early risk stratification and support microbiome-targeted preventive strategies in vulnerable preterm populations.},
}

@article {pmid42437892,
year = {2026},
author = {Chen, Y and Lu, S and Zhao, A and Li, M and Gan, X and Wang, Y and Yang, Y and Huang, M and Wang, Q and Niu, T and Zhou, Y},
title = {Blood mNGS: an effective non-invasive diagnostic tool for Pneumocystis jirovecii pneumonia.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05408-7},
pmid = {42437892},
issn = {1471-2180},
support = {2024J0304//the Scientific Research Fund of Yunnan Provincial Department of Education/ ; 202401AY070001-295//the Kunming Medical Joint Special Project of Yunnan Provincial Science and Technology Plan Project/ ; 82370192//National Natural Science Foundation of China/ ; GYYX24003//1.3.5 Project of High Altitude Medicine/ ; 2024NSFSC1746//West China Hospital, Sichuan University, the Natural Science Foundation of Sichuan Province/ ; 2022YFC2406804//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection. Colonization is prevalent but cannot be reliably distinguished from active infection by conventional methods. Metagenomic next-generation sequencing (mNGS) is a promising diagnostic tool, but the value of blood mNGS for diagnosis, microbial community comparison, and outcome-related associations in PJP remains unclear.

METHODS: We analyzed 73 suspected PJP patients with paired BALF and blood mNGS. Using strict diagnostic criteria, patients were classified as: PJP (n = 50) and P. jirovecii colonization (PJC, n = 23). Bioinformatic analyses compared compartment-specific microbiota. BALF-blood concordance and associations between P. jirovecii load and outcomes were evaluated.

RESULTS: BALF showed higher α-diversity than blood (both Shannon and Simpson, P < 0.001), whereas β-diversity showed no compartmental segregation. BALF identified 216 species versus 43 in blood; however, the top-10 species were concordantly ranked (90% concordance). Blood mNGS distinguished PJP from PJC with an AUC of 0.80 (specificity 95.7%, sensitivity 62.0% at RPM > 4.8), outperforming BALF mNGS (AUC 0.76), blood PCR (AUC 0.64) and BALF PCR (AUC 0.73). Gram-negative bacteria accounted for a large proportion of blood taxa (75% of top 20 taxa), while BALF showed additional fungal taxa including Aspergillus fumigatus. LEfSe identified matrix-specific taxa: oral commensals in PJC-BALF. Blood P. jirovecii load correlated positively with LDH (r = 0.34, P = 0.0035), CRP (r = 0.34, P = 0.0031), and BDG (r = 0.26, P = 0.025), and was higher in non-survivors (P < 0.05).

CONCLUSION: Blood mNGS may serve as a non-invasive, highly specific complementary tool for PJP diagnosis and broader microbiological assessment.},
}

@article {pmid42437920,
year = {2026},
author = {Diaz-Canestro, C and Cheung, K and Roche, E and Sarabia, JM and Tse, MA and Xu, A},
title = {Multi-omics signatures of circulating factors associated with cardiorespiratory fitness adaptations in individuals with prediabetes.},
journal = {Cardiovascular diabetology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12933-026-03286-x},
pmid = {42437920},
issn = {1475-2840},
abstract = {BACKGROUND: Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO2peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO2peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO2peak to HIIT in individuals with prediabetes.

METHODS: Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles.

RESULTS: After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO.

CONCLUSIONS: Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.},
}

@article {pmid42437978,
year = {2026},
author = {Xia, J and Meng, L and Fang, Y and Ban, H and Okazaki, Y and Yoshida, T and Endo, H and Nagasaki, K and Ogata, H},
title = {Rapid Diversification of a Natural Heterosigma akashiwo Virus Population during a Host Bloom.},
journal = {Microbes and environments},
volume = {41},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME26018},
pmid = {42437978},
issn = {1347-4405},
mesh = {Japan ; *Genetic Variation ; *Giant Viruses/genetics/classification/isolation & purification ; *Eutrophication ; Phylogeny ; Genome, Viral ; Metagenomics ; Seawater/virology ; Biodiversity ; },
abstract = {Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Knowledge on their population genetic dynamics is mostly derived from a small number of laboratory-based experiments, while patterns in nature are rarely observed. To overcome this limitation, we traced the genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan by integrating cell counting, metabarcoding, and metagenomic and metatranscriptomic sequencing. The results obtained revealed that HaV dominated the giant virus community in most samples, with relative abundance up to 56%. Despite its high abundance, the HaV population exhibited a low level of microdiversity, but had a higher pN/pS ratio than other giant viruses in the study site. Microdiversity increased during the early sampling period, peaked mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, which may be driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Collectively, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variations.},
}

Japan
*Genetic Variation
*Giant Viruses/genetics/classification/isolation & purification
*Eutrophication
Phylogeny
Genome, Viral
Metagenomics
Seawater/virology
Biodiversity

@article {pmid42438180,
year = {2026},
author = {Castells-Ballester, J and Taron, A and Smith, M and Gawron, R and Beaulieu, J and Papa, O and Buss, J and Ong, J and Chen, M},
title = {Development of a Microdroplet-Based Functional Genomic Screening Pipeline by Combination of DNA Nanoflowers and PURExpress Cell-Free Expression.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.6c00061},
pmid = {42438180},
issn = {2161-5063},
abstract = {We present a microfluidic workflow that couples reconstituted in vitro transcription-translation (IVTT) with ultrahigh-throughput droplet screening to directly link genotype and phenotype within complex, heterogeneous DNA pools. The approach employs DNA nanoflowers as clonal, high-copy templates, enabling robust protein expression from single DNA molecules encapsulated in picoliter droplets. When integrated with fluorescence-assisted microdroplet sorting (FADS) and a DNA recovery pipeline that reconstituted selected libraries for subsequent iterative rounds, the platform achieves approximately 400-600-fold enrichment per selection cycle and supports functional discovery and directed evolution entirely independent of host cell expression. As a proof of principle, we demonstrate recovery of the recombinase RecA from an E. coli genomic library screened for single-stranded DNA binders, highlighting the platform's capability to identify DNA-interacting and DNA-modifying enzymes. By eliminating host-derived background activity and toxicity constraints that often complicate lysate- or cell-based metagenomic screens, this method potentially expands access to enzyme classes that have historically been difficult to assay.},
}

@article {pmid42438386,
year = {2026},
author = {Yuan, D and Cui, X and Zhang, S and Wang, Y and Sun, Y and Xiao, M and Zhang, M and Zheng, L},
title = {Nitrifiers Drive Different N2O Production Patterns in Tropical River Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01501},
pmid = {42438386},
issn = {1520-5851},
abstract = {Since the 20th century, global riverine nitrous oxide (N2O) emissions have increased 4-fold; however, the N2O emissions of tropical rivers are still unclear. Here, we employed a series of techniques (closed chamber, biological inhibitor, [15]N-[18]O double tracer, metagenomic sequencing, and reverse transcription qPCR) to analyze in situ N2O flux, potential N2O production rate, and N2O production mechanism of China's tropical rivers. In the 82 sediment samples from the top 10 Hainan rivers, high levels of in situ N2O flux and potential N2O production rate were detected in all samples, indicating that Hainan rivers are significant hotspots of N2O emissions. The higher values were observed in estuary samples (avg: 4.48 ± 0.25 mg m[-2] d[-1], 39.17 ± 3.28 ng N g[-1] d[-1]) compared to nonestuary samples (avg: 1.98 ± 0.16 mg m[-2] d[-1], 21.29 ± 4.68 ng N g[-1] d[-1]). Nitrifier denitrification (ND) dominates the N2O production, and its contribution to estuary samples (avg. 49.31-78.90%) is higher than that for nonestuary samples (avg. 32.27-66.19%). We found that complete ammonia-oxidizing bacteria (comammox) Nitrospira nitrificans and ammonia-oxidizing bacteria (AOB) Nitrosomonas marina cooperate to produce N2O via the ND pathway in estuary samples, and AOB Nitrosomonas europaea produces N2O via the ND pathway in nonestuary samples. Salinity, NH4[+], pH, and total organic matter (TOM) affect N2O production via three key species. Our findings advance the mechanistic understanding of tropical rivers in the tropical N-cycle and global climate change. Ammonium fertilizer management and estuary ecological restoration should be prioritized in tropical river basins.},
}

@article {pmid42438737,
year = {2026},
author = {Faleiros, CA and Gonçalves, OS and Nunes, AT and Pires, CS and Poleti, MD and Fukumasu, H},
title = {Host breed and geography shape the antiviral defense landscape of the bovine rumen microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag162},
pmid = {42438737},
issn = {2730-6151},
abstract = {The rumen microbiome represents a complex, phage-rich ecosystem where microbial survival depends on both metabolic cooperation and antiviral defense. However, global and breed-associated variations in rumen prokaryotic immune systems remain poorly understood. Here, we performed the most comprehensive profile to date of antiviral defense systems (DS) in the rumen, analyzing 6530 microbial genomes and metagenome-assembled genomes (MAGs) from diverse cattle breeds and geographic regions. In this global dataset, we identified >90 000 DS, the most abundant of which were restriction-modification, PDC-S01, deoxyribonucleic acid modification systems (DMS_other), AbiE and SoFic, with variations influenced by both host the lineage and geographic region. A more in-depth analysis was performed using two complementary antiviral annotation frameworks for Nellore cattle (Bos indicus) from Brazil. Data exhibited a remarkably enriched antiviral defense repertoire, with over 15 632 DS encoded across 547 high-quality MAGs. These systems were densely clustered in dominant rumen lineages, such as Prevotella, and positively correlated with prophage abundance, consistent with virus-host coevolution. Notably, we also detected viral contigs encoding both antiviral defense and anti-defense genes, underscoring the arms race between the phages and their microbial hosts. Metatranscriptomic data from North America and Oceania revealed high expression levels of toxin-antitoxin modules, clustered regularly interspaced short palindromic repeats components, and restriction enzymes, suggesting a basal level of antiviral activity. These findings reveal the rumen as an antiviral innovation hotspot, highlighting microbiome resilience with implications for ecology, adaptation, and phage-based interventions.},
}

@article {pmid42439467,
year = {2026},
author = {Luo, Y and Kang, FL and Li, QM and Yang, WC},
title = {Metagenomic Association Uncovers Host Genotype-Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76373},
doi = {10.1002/advs.76373},
pmid = {42439467},
issn = {2198-3844},
support = {YSBR-011//CAS project for Young Scientists in Basic Research/ ; 2023YFD1200600//National Key Research and Development Program of China/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2016QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
abstract = {Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth-promoting function, and systematic approaches to uncover salt-tolerance-enhancing plant growth-promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co-occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter. Correlation analyses identified bacterial taxa positively associated with STI, including documented salt-tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis, enhances soybean salt tolerance and reshapes host ion-transport and oxidative-stress gene expression under salinity, validating our screening strategy. Our culture-independent metagenomic association approach reveals host genotype-structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor-saving means for high-throughput identification of salt-tolerant PGPR.},
}

@article {pmid42439510,
year = {2026},
author = {Hertramph, TL and Dorda, M and Pallenberg, ST and Sauer-Heilborn, A and Ringshausen, FC and Steglich, M and Hansen, G and Tümmler, B and Wiehlmann, L and Rosenboom, I and Dittrich, A-M},
title = {Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0060126},
doi = {10.1128/spectrum.00601-26},
pmid = {42439510},
issn = {2165-0497},
abstract = {Mutation-specific cystic fibrosis (CF) transmembrane conductance regulator (CFTR) modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved clinical outcomes for people with CF (pwCF), yet its impact on the nasal microbial metagenome remains insufficiently understood. This prospective, post-approval study investigated the impact of 15-week ETI therapy on sinonasal microbiota of pwCF aged 12 years and older. Whole-genome shotgun sequencing was performed on total DNA from 24 paired nasal lavage samples, with synthetic spike-in controls enabling absolute abundance normalization. Taxonomic profiling was conducted using the Wochenende pipeline. ETI did not induce major shifts in alpha or beta diversity. Instead, the overall microbial community became further dominated by the skin commensals Staphylococcus epidermidis and Cutibacterium acnes, accompanied by a more than twofold increase in total bacterial load. Classical CF pathogens showed divergent trajectories: Pseudomonas aeruginosa tended to decrease, whereas Staphylococcus aureus exhibited a tendency toward increased abundance. Co-occurrence network analysis revealed a transition from a dense, multicomponent baseline network to a single, fully connected, but less densely integrated network following treatment initiation.IMPORTANCEThe nasal cavity represents the primary entry point of microorganisms into the respiratory tract and a potential reservoir for lower airway infection, the major cause of CF disease progression. Using shotgun metagenomics with spike-in controls, this study provides the first genome-wide characterization of how ETI alters microbial load and pathogen dynamics in CF nasal airways. Treatment with ETI strengthened the dominance of skin commensals in the nares while reducing P. aeruginosa. Given the observed increase in S. aureus, further work is needed to determine whether this represents expansion of a typical nasal colonizer or a clinically relevant rise of a key CF pathogen that could act as a reservoir for future lower airway infection.},
}

@article {pmid42439573,
year = {2026},
author = {van Haren, MHI and Have, Lt and Koopman, PD and Buil, JB and Maat, I and Rahamat-Langendoen, JC and Martens, L and Moorlag, SJCFM and van den Bosch, B and Koenraad, E and Wertheim, HFL and Melchers, WJG and Pas, SD},
title = {Clinical impact of 16S rRNA RC-PCR NGS on infectious disease management.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0002326},
doi = {10.1128/spectrum.00023-26},
pmid = {42439573},
issn = {2165-0497},
abstract = {16S rRNA metagenomics provides a culture-independent method for diagnosing infections with fastidious or uncultivable organisms, guiding targeted therapy, and detecting polymicrobial communities. This study utilizes reverse complement (RC)-PCR next-generation sequencing (NGS) to accurately identify bacterial pathogens from clinical specimens and assess its impact on clinical decision-making, setting it apart from conventional 16S sequencing approaches. A retrospective analysis of an ISO 15189 accredited 16S RC-PCR NGS diagnostic workflow targeting the V1-6 and V9 regions of the 16S rRNA gene was conducted over a 2-year period, including 390 clinical specimens from 316 patients. 16S RC-PCR NGS results were discussed in a multidisciplinary consultation and subsequently reported to the clinic. In total, 1,283 RC-PCR results were analyzed, of which 517 were from clinical specimens, 284 were negative controls, 66 were positive controls, and 416 were from wet lab and bioinformatic pipeline validation. 16S RC-PCR NGS assay detected bacterial taxa in 179/390 (45.9%) of clinical specimens, while 201/390 (51.5%) were negative, and 10/390 (2.6%) yielded uninterpretable results. The specimen types pus, pleural fluid, and heart valves exhibited the highest positivity rate (68% to 70%). Overall, 16S RC-PCR NGS influenced diagnostic decision making in 145/282 (51.4%) clinical cases and guided therapeutic management in 77/282 (27.3%) cases. Results providing definite evidence for either the presence or absence of bacterial infection were considered clinically valuable. Integration of 16S RC-PCR NGS pathogen detection with multidisciplinary consultation markedly improved clinical management, directly impacting diagnosis and treatment of complex clinical cases in a tertiary care setting. The effect was most pronounced in brain abscess patients, where RC-PCR results guided treatment decisions in 9/13 (69.2%) of cases.IMPORTANCETimely and accurate diagnosis is essential for managing serious infections, yet clinicians often face situations where routine laboratory tests do not provide clear answers. This study demonstrates that next-generation sequencing (NGS) of the bacterial 16S rRNA gene can decisively resolve these uncertainties. By revealing whether bacteria are present in clinical specimens, this approach influenced clinical reasoning and supported treatment decisions across a variety of challenging cases. 16S reverse-complement PCR was especially powerful for brain abscesses and infections where the causative microorganism was unclear, providing clarity that directly improved patient care. These findings show that integrating advanced sequencing with expert clinical interpretation can enhance the management of complex infections and support more confident, evidence-based therapy.},
}

@article {pmid42440035,
year = {2026},
author = {Mathiyazhagan, S and Balu, B and Gunaseelan, RJ and Piliyan, R and Perumal, S and Natesan, M},
title = {Discovery of novel bio-resources from the hidden biodiversity of marine mangrove ecosystems.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {10},
pages = {},
pmid = {42440035},
issn = {1573-2983},
mesh = {*Wetlands ; *Biodiversity ; Animals ; Biological Products ; Fungi/metabolism ; Bacteria/metabolism ; Biotechnology ; Invertebrates/metabolism ; },
abstract = {Marine mangrove wetlands are ecologically complex ecosystems that serve as rich reservoirs of biologically active compounds with significant biotechnological potential. This review synthesizes current knowledge on mangrove-associated microorganisms and biota, including bacteria, fungi, algae, and invertebrates, with emphasis on their bioassay activities and derived bioactive metabolites. Various analytical approaches, including chromatographic techniques, LC-MS/NMR analysis, and in silico tools, have been employed to identify and characterize compounds such as enzymes, polysaccharides, biosurfactants, and antimicrobial peptides. These biomolecules exhibit diverse functional applications in medicine, environmental management, and industrial processes, including nitrogen fixation, bioremediation, and hydrocarbon degradation. The review highlights that mangrove-derived bioactive compounds are influenced by both ecological interactions and environmental conditions. Furthermore, recent advances indicate a shift toward genome-guided discovery using multi-omics and metagenomic approaches, enabling the identification of novel biosynthetic pathways, particularly from unculturable microorganisms. This integrated approach enhances the efficiency of bioactive compound discovery and supports scalable production through synthetic biology. Overall, mangrove ecosystems represent promising platforms for sustainable biotechnological innovation, underscoring the need for their conservation and the development of integrated validation strategies.},
}

*Wetlands
*Biodiversity
Animals
Biological Products
Fungi/metabolism
Bacteria/metabolism
Biotechnology
Invertebrates/metabolism

@article {pmid42440756,
year = {2026},
author = {Kraiselburd, I and Susenburger-Lange, R and Balzer, M and Magin, S and Block, K and Consten, L and Dörr, A and Dörr, AK and Gosch, J and Nishad, S and Sachse, S and Thomas, A and Triebs, A and Welling, J and Wilhelm, A and Widera, M and Schmithausen, R and Meyer, F},
title = {Wastewater-based epidemiology for public health - benefits and trade-offs of different molecular methods for the generation of actionable data in a small-town context.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1828355},
doi = {10.3389/fpubh.2026.1828355},
pmid = {42440756},
issn = {2296-2565},
mesh = {*Wastewater/microbiology ; Humans ; Germany/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; *Public Health ; Metagenomics ; },
abstract = {BACKGROUND: Wastewater-based epidemiology (WBE) is a promising complement to traditional surveillance systems, yet its practical utility and performance in real-world public health settings remain insufficiently characterized. This study aims to evaluate the feasibility and added value of WBE for monitoring infectious disease dynamics at the regional level, with a particular focus on jointly identifying, together with public health authorities, actionable and scalable methodological strategies based on cost, applicability, and the relevance and timeliness of the information generated.

METHODS: Composite influent wastewater samples were collected over 6 weeks from a treatment plant serving a defined district in western Germany. Samples were analyzed using quantitative PCR and both targeted and shotgun metagenomic sequencing. WBE findings were compared with routine case-based surveillance data from the corresponding catchment area.

RESULTS: All pathogens reported through routine public health surveillance during the study period were also detected in wastewater. In addition, WBE identified signals from clinically relevant pathogens not captured by case-based surveillance. Sequencing approaches provided further resolution on pathogen diversity and resistance profiles. The combined use of targeted and untargeted methods revealed differences in sensitivity and resolution, with complementary strengths across approaches, and enabled the definition of a practical, tiered approach to support actionable surveillance at the regional level.

CONCLUSION: This study describes the operational integration of WBE into a regional public health workflow, providing timely, population-level data that complements routine surveillance and can reveal pathogen circulation not captured by reported cases. Building on the established advantages of WBE, our results highlight its practical value when jointly implemented with public health authorities, enabling context-specific, actionable insights that enhance situational awareness, guide targeted local responses and support earlier detection of emerging threats.},
}

*Wastewater/microbiology
Humans
Germany/epidemiology
*Wastewater-Based Epidemiological Monitoring
*Public Health
Metagenomics

@article {pmid42441076,
year = {2026},
author = {Mohammadzadeh, P and Pilvaieh, A and Dousti, A and Bahrami, MRS and Ziaee, F},
title = {Multimodal characterisation of spontaneous Merkel cell carcinoma in the endangered Caucasian squirrel (Sciurus anomalus pallescens): integrating spatial transcriptomics, imaging mass cytometry and metagenomic sequencing.},
journal = {Journal of veterinary research},
volume = {70},
number = {2},
pages = {321-334},
doi = {10.2478/jvetres-2026-0034},
pmid = {42441076},
issn = {2450-7393},
abstract = {INTRODUCTION: Merkel cell carcinoma is an aggressive neuroendocrine skin malignancy rarely reported in non-domestic species.

MATERIAL AND METHODS: A cutaneous nodule from an endangered Caucasian squirrel (Sciurus anomalus pallescens) was examined using histopathology, immunohistochemistry, imaging mass cytometry, spatial transcriptomics (10× Visium) and metagenomic sequencing.

RESULTS: Histology revealed a high-grade neuroendocrine carcinoma with frequent mitoses (52 per 2.37 mm[2]) and necrosis. Tumour cells were positive for cytokeratin 20 (paranuclear dot pattern), synaptophysin and chromogranin A, with a high Ki-67 index (68%). Spatial analyses delineated a distinct tumour core and combined invasive front and stromal compartments, revealing upregulation of neuroendocrine (atonal basic helix-loop-helix transcription factor 1 and neurogenic differentiation factor 1) and proliferative (marker of proliferation Ki-67) programmes, and activation of phosphoinositide 3-kinase-AKT serine/threonine kinase 1-mechanistic target of rapamycin and mitogen-activated protein kinase pathways. No evidence of Merkel cell polyomavirus was found. The tumour microenvironment was immune-excluded, with programmed-death ligand 1 expression on ~22% of tumour cells and CD8[+] T cells restricted to the stroma.

CONCLUSION: This study provides a comprehensive methodological framework for high-resolution tumour profiling in conservation pathology and highlights the emergence of neoplasia in threatened wildlife.},
}

@article {pmid42441094,
year = {2026},
author = {Dal, GE and Çelik, B and Sabuncu, A and Yılmaz, M and Kekeç, AI and Dümen, E and İkiz, S and Diker, KS},
title = {Metagenomic analysis of the vaginal microbiota in cows with ovarian cysts.},
journal = {Journal of veterinary research},
volume = {70},
number = {2},
pages = {215-225},
doi = {10.2478/jvetres-2026-0028},
pmid = {42441094},
issn = {2450-7393},
abstract = {INTRODUCTION: This study compared the vaginal microbiota composition of dairy cows with follicular and luteal ovarian cysts using metagenomic analysis.

MATERIAL AND METHODS: Ovarian cysts, which impair reproductive performance through endocrine disruption, were diagnosed by ultrasonography and serum hormone evaluation in Holstein cows 30-60 d postpartum. Forty-five cows were initially included and divided into follicular cyst, luteal cyst and control groups. Vaginal lavage samples were analysed using third-generation sequencing, and taxonomic classification was performed through 16S rRNA gene analysis.

RESULTS: A total of 258 operational taxonomic units (OTUs) were identified, with the highest diversity observed in the control group (mean of 56.8 OTUs) and the lowest in the luteal cyst group (mean of 49.0 OTUs). Proteobacteria was the dominant phylum across all groups (93.4%), followed by Tenericutes (5.9%). Firmicutes, Bacteroidetes and Fusobacteria accounted for less than 1%. At the family level, Burkholderiaceae (62.7%) and Pasteurellaceae (24.0%) were predominant, while of the genera, Ralstonia was the most abundant (62.2%). The luteal group had the highest relative abundance of Burkholderiaceae, whereas Pasteurellaceae was most abundant in the control group.

CONCLUSION: These results indicate that cystic cows exhibit reduced microbial diversity and altered bacterial composition in comparison with healthy animals. The predominance of Proteobacteria and Ralstonia suggests a potential link between endocrine imbalance and changes in the vaginal microenvironment. Hormonal analyses supported the classification of cyst types, with follicular cyst cows showing low progesterone (0.31 ± 0.05 ng/mL) and high oestradiol-17β concentrations (55.57 ± 7.91 pg/mL), whereas luteal cyst cows exhibited higher progesterone (2.89 ± 0.74 ng/mL) and lower oestradiol-17β concentrations (6.19 ± 0.56 pg/mL) (P < 0.001). These results may support future studies evaluating vaginal microbial profiles as complementary indicators of ovarian status in dairy cows.},
}

@article {pmid42442076,
year = {2026},
author = {Ma, L and Zhang, J and He, X and Wang, Z and Zhao, M},
title = {Hemophagocytic lymphohistiocytosis secondary to disseminated histoplasmosis diagnosed by bone marrow smear microscopy and metagenomic next-generation sequencing: A case report and review of literature.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117542},
doi = {10.1016/j.diagmicrobio.2026.117542},
pmid = {42442076},
issn = {1879-0070},
abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Histoplasma capsulatum infection is rare in immunocompetent individuals but is associated with an extremely high mortality rate. Here, we report a case of disseminated histoplasmosis (DHP) in an immunocompetent patient. The pathogen was confirmed by bone marrow smear microscopy and metagenomic next-generation sequencing (mNGS). The patient experienced rapid clinical deterioration and was subsequently diagnosed with HLH secondary to DHP. Following targeted antimicrobial therapy with amphotericin B and immunomodulatory treatment involving etoposide and ruxolitinib, the patient's clinical condition improved. Early clinical manifestations of DHP are often atypical, while conventional diagnostic methods frequently yield negative results in the early stage. This case indicates that bone marrow examination combined with mNGS facilitates early definitive diagnosis. Furthermore, this report rarely describes the sequential morphological changes of Histoplasma capsulatum in bone marrow tissue.},
}

@article {pmid42442081,
year = {2026},
author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Kiwelu, I and Alifrangis, M and Aarestrup, FM and Sonda, T},
title = {Identification of enteric viral pathogens in Tanzanian children under the age of five with diarrhea using nanopore-based metagenomic sequencing.},
journal = {Virology},
volume = {623},
number = {},
pages = {111024},
doi = {10.1016/j.virol.2026.111024},
pmid = {42442081},
issn = {1096-0341},
abstract = {Diarrhea continues to be a significant contributor to illness and death among children, especially in low-income settings. In Tanzania, diarrheal disease remains a public health concern with many minors under five seeking healthcare despite the wide coverage of rotavirus vaccine. The diagnosis of pediatric diarrhea in Tanzania primarily focuses on specific viral diseases, which may overlook the broad-spectrum of viral pathogens. In this study, Oxford Nanopore-based metagenomic sequencing was applied to characterize viral pathogens in 200 stool samples from children under the age of five presented with diarrhea. Samples were collected from April 2023 to April 2024 at health facilities in six regions across mainland Tanzania and Zanzibar. At least one known diarrhea linked virus was detected in 31% of the participants. Although no statistical difference could be observed across different age categories, a slightly higher detection was observed in children aged 6-23 months. Human adenovirus was the most frequently detected 16% (32/200) in this study. Rotavirus was the second most frequently detected virus 9.5% (19/200) despite participant vaccination status. Other enteric viruses detected was astrovirus, norovirus, human bocavirus and Aichi virus were detected in 2.5% (5/200), 2% (4/200), 0.5% (1/200) and 0.5% (1/200) of the study participants respectively. Rotavirus showed negative correlation with temperature and relative humidity while human adenovirus was positively correlated to relative humidity. Metagenomics also revealed the presence of non-enteric viral pathogens, including measles and HAdV-C and HAdV-B, within this cohort. This study identified a range of viral pathogens associated with pediatric diarrhea in this cohort, including agents not typically targeted by routine diagnostic assays by using untargeted metagenomic technique direct to the clinical samples. These findings contribute baseline data that could inform future, larger-scale surveillance efforts in Tanzania.},
}

@article {pmid42442149,
year = {2026},
author = {Hong, M and Ji, L and Gao, J and Zhang, H and Ge, S and Yuan, C},
title = {Granulomatous inflammation in lung and lymph node specimens: A molecularly enhanced pathology-based algorithm for etiologic differential diagnosis.},
journal = {Annals of diagnostic pathology},
volume = {85},
number = {},
pages = {152684},
doi = {10.1016/j.anndiagpath.2026.152684},
pmid = {42442149},
issn = {1532-8198},
abstract = {Granulomatous inflammation is frequently encountered in lung and lymph node specimens and represents a diagnostic challenge because diverse infectious, immune-mediated, exposure-related, and neoplastic conditions may produce overlapping histologic patterns. Necrotizing, non-necrotizing, suppurative, foreign body-type, vasculitic, and malignancy-associated granulomas provide important diagnostic clues but are rarely disease-specific. Conventional pathology-based evaluation, including hematoxylin and eosin assessment, special stains, immunohistochemistry, culture, and serologic or antigen testing, remains the foundation of etiologic diagnosis. However, these methods may be limited by low organism burden, prior antimicrobial therapy, small tissue samples, formalin fixation, and broad etiologic heterogeneity. Molecular methods, including targeted polymerase chain reaction, 16S ribosomal RNA sequencing, internal transcribed spacer sequencing, targeted next-generation sequencing, and metagenomic next-generation sequencing, provide complementary tools for pathogen detection and species-level identification. This review summarizes the major histopathologic patterns and etiologic categories of granulomatous inflammation in lung and lymph node specimens and proposes a molecularly enhanced pathology-based algorithm for diagnostic workup. The goal is not to replace morphology with molecular testing, but to use histopathology to guide molecular assay selection and to interpret molecular findings within the appropriate tissue, microbiologic, radiologic, and clinical context.},
}

@article {pmid42442277,
year = {2026},
author = {Zhang, X and Han, S and Zhao, A and Wei, B and Chang, X and Song, S and Zhao, Y and Zhao, Z and Zhang, X and Chen, J},
title = {Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120488},
doi = {10.1016/j.ecoenv.2026.120488},
pmid = {42442277},
issn = {1090-2414},
abstract = {Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.},
}

@article {pmid42442278,
year = {2026},
author = {Li, X and Chen, Y and Wang, J and Shu, Y and Lv, G},
title = {Phytotoxic effects and rhizosphere microecological responses of peanut to oxytetracycline and microplastic co-exposure.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120498},
doi = {10.1016/j.ecoenv.2026.120498},
pmid = {42442278},
issn = {1090-2414},
abstract = {Microplastics (MPs) and antibiotics represent escalating emerging contaminants in global agricultural soils, posing substantial threats to crop health and ecosystem functionality worldwide. However, a comprehensive understanding of their joint toxicity and the underlying rhizosphere mechanisms under co-contamination remains elusive, leaving a critical knowledge gap. This study conducted a pot experiment using the globally cultivated peanut (Arachis hypogaea) exposed to polystyrene (PS) or polylactic acid (PLA) MPs (0.25 and 2% w/w) and oxytetracycline (OTC, 10 mg·kg[-1]), integrating metagenomic sequencing and untargeted metabolomics to elucidate root-zone microecological responses. High-concentration co-exposures significantly suppressed peanut shoot biomass, and OTC was identified as the primary contributor to reduced leaf catalase activity (CAT) (p < 0.01). Metagenomic profiling revealed that co-exposure significantly reshaped the rhizosphere microbiota (R[2] = 0.939, p = 0.001), enriching Pseudomonadota while inhibiting Actinobacteriota. Untargeted metabolomics detected 3789 metabolites, revealing that co-exposure significantly regulated the accumulation of defensive flavonoids (taxifolin and daidzin) and stress-responsive steroids (ponasterone A). Particularly, the combined exposure of PLA MPs and OTC induced the most severe metabolic disruption in the rhizosphere, generating 374 differential metabolites compared to the PLA-alone treatment. Procrustes analysis confirmed a tight coupling between microbial communities and metabolomes (M[2] = 0.619, p = 0.004). Network analysis further identified key regulatory nodes (Nocardioides and taxifolin) that bridge the associations between the rhizosphere microenvironment and plant growth traits. This study demonstrates that microbial shifts and metabolic adjustments are essential in mediating plant responses to multi-pollutant stress, providing crucial theoretical and mechanistic insights for global agricultural environmental risk assessment under co-contamination scenarios.},
}

@article {pmid42442320,
year = {2026},
author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A},
title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111939},
doi = {10.1016/j.ijfoodmicro.2026.111939},
pmid = {42442320},
issn = {1879-3460},
abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.},
}

@article {pmid42442424,
year = {2026},
author = {Luo, Z and Zhang, K and Wang, L and Zhang, J and Huang, Y and Lu, X and Zhao, F and Cao, S and Li, J},
title = {Astragalus polysaccharides reshape gut resistome of postpartum dairy cows.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135399},
doi = {10.1016/j.biortech.2026.135399},
pmid = {42442424},
issn = {1873-2976},
abstract = {Antibiotic resistance genes (ARGs) in livestock feces represent an important environmental reservoir of antimicrobial resistance. Natural product intervention is a potential strategy for regulating the gut microbiome of livestock; however, its effects on the gut resistome of postpartum dairy cows remain poorly understood. In this study, we investigated the effects of Astragalus polysaccharides (APS) supplementation on the fecal microbiome, ARGs, mobile genetic elements (MGEs), virulence factors (VFs), and ARG-carrying metagenome-assembled genomes (MAGs) in dairy cows during postpartum period. Alpha and beta diversity analyses showed that APS supplementation did not significantly alter the global resistome, mobilome, or virulome structure. The content of several ARGs and VFs, including AAC(6')-Iw, qacEdelta1, ast, PM_RS00425, and sdrF, significantly decreased in the APS group, and several plasmid-associated MGEs genes showed group-specific changes. Co-occurrence network analysis revealed complex associations between ARGs, VFs, and core bacterial taxa, with Paludibacter and Parabacteroides identified as potential microbial reservoirs of resistance- and virulence-associated genes. Furthermore, 101 metagenome-assembled genomes (MAGs) were recovered, 42 of which carried multiple ARGs. Bin.1, assigned to Scatovivens, had the highest ARG count. APS supplementation reduced the overall ARG load, particularly the ARG contribution in bin.1. However, APS utilization potential was not significantly correlated with ARG density or ARG load across MAGs. Thus, this study provides new insights into APS supplementation and nutritional strategies that can mitigate the fecal ARG burden in dairy production.},
}

@article {pmid42442443,
year = {2026},
author = {Umair, M and Jamal, Z and Ali, Q and Hakim, R and Rana, MS and Javed, Y and Bugti, AR and Ayub, A and Sabeen, F and Waheed, Y and Salman, M},
title = {Emergence of Reassortant Crimean-Congo Hemorrhagic fever virus lineages, Pakistan, 2023-2024.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105988},
doi = {10.1016/j.meegid.2026.105988},
pmid = {42442443},
issn = {1567-7257},
abstract = {Crimean-Congo hemorrhagic fever virus (CCHFV) remains endemic in Pakistan, yet whole-genome data are limited. During 2023-2024 national surveillance, 151 suspected cases were screened by qRT-PCR; 23 were confirmed at the NIH, Islamabad. Shotgun metagenomic sequencing of 17 cases (15 Pakistan, 2 Afghanistan) generated high-quality genomes, with 65% classified as Asia-1 genotype, while 35% showed segment reassortment involving Asia-2-derived S and/or M segments. Reassortment involved primarily S and M segments, while L segments remained conserved. Phylogenetic analysis revealed Asia-1 sequences closely related to strains from India, Afghanistan, Iran, and the Middle East, whereas Asia-2 sequences clustered with Indian and Central Asian strains, suggesting cross-border and regional viral exchange. S-segment phylogeography indicated northern Punjab (Rawalpindi, Islamabad, Chakwal, Attock) as a region potential involved in viral connectivity. Region-specific mutations (S: G185S, D186N; M: P90L, T122I, M35L, L443S, I1597V) may reflect localized viral evolution. These findings underscore ongoing viral diversification, reassortment, and regional connectivity, highlighting the need for integrated genomic surveillance to guide public health interventions.},
}

@article {pmid42442450,
year = {2026},
author = {Zhang, Z and Xia, Y and Liu, Y and Tao, L and Ju, F},
title = {Future Climate Scenarios Reduce Antibiotic Resistome-associated Risk but Enrich Specific Soil-borne Pathogens.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125248},
doi = {10.1016/j.envres.2026.125248},
pmid = {42442450},
issn = {1096-0953},
abstract = {Understanding how climate change reshapes the soil resistome, i.e., the collection of antibiotic resistance genes (ARGs), is critical for environmental and public health. Using a representative six-year (2014-2019) metagenomic dataset from a long-term climate manipulation experiment, this study investigated the impacts of future climate scenarios on cropland and grassland soil resistomes. Both simulated climate warming (+0.6°C) and extreme summers (+2.2°C during 2018-2019) significantly altered soil resistome structures, reducing ARG richness by 4.4%-12.5% while increasing the abundance of specific ARG types predominantly carried by gram-positive bacteria by 31.5%-72.8%. Simulated climate and extreme summer also reduced the abundance of high-risk ARGs by 10.0% and 27.2%, respectively, and concomitantly lowered the estimated resistome-associated risk by 18.3% and 36.4%, primarily through selectively filtering their bacterial hosts (e.g., Pseudomonadota). At the same time, future climate scenarios confer a competitive advantage for specific soil-dwelling antibiotic-resistant phytopathogens (e.g., Rhodococcus fascians) and human pathogens (e.g., Mycobacterium spp.), potentially increasing their prevalence and public health relevance in soil ecosystems. These findings highlight the contrasting responses of soil resistomes and pathogen communities under future climate scenarios and underscore the importance of long-term monitoring of soil ARGs and pathogens under the context of on-going global change within a One-Health framework.},
}

@article {pmid42442462,
year = {2026},
author = {Fukada, A and Suda, K and Watayo, H and Motooka, D and Shinoda, T and Tohya, M and Ishiyama, A and Nishimura, Y and Fujiwara, K and Ochi, T and Goto, H and Nikai, K and Ishii, J and Yamamoto, Y and Okazaki, T and Nakamura, S and Kirikae, T and Yamataka, A and Watanabe, S and Miyano, G},
title = {Characteristics and environmental susceptibility of first-pass meconium microbiota in neonates with congenital intestinal atresia.},
journal = {Journal of pediatric surgery},
volume = {},
number = {},
pages = {163290},
doi = {10.1016/j.jpedsurg.2026.163290},
pmid = {42442462},
issn = {1531-5037},
abstract = {PURPOSE: Whether congenital gastrointestinal atresia (atresia) specifically affects the meconium microbiota because of an altered intrauterine intestinal environment remains unclear. Therefore, we aimed to characterize the meconium microbiota of neonates with congenital anomalies, specifically atresia.

METHODS: Meconium samples were collected from healthy term neonates (control), neonates with congenital malformations other than atresia (other anomalies), and those with atresia who were admitted to the growing care unit or obstetrics ward. Alpha-diversity (Shannon index and observed features) and beta-diversity (principal coordinate analysis) were assessed through 16S rRNA gene sequencing. The microbial composition was examined at the phylum and genus levels, and stratified by delivery mode and mother's antibiotic exposure.

RESULTS: The study included 20 controls, 37 neonates with other anomalies, and 11 with atresia, including esophageal, duodenal, small intestinal, and colonic atresia. Alpha-diversity was the lowest in atresia, particularly with cesarean delivery or maternal antibiotic exposure (p<0.05). Beta-diversity analysis demonstrated that the distribution of microbial profiles significantly differed between the control and atresia groups (p<0.05). At the phylum level, atresia had a high proportion of Bacteroidetes, whereas Firmicutes and Proteobacteria were reduced. Several genera that were abundant in the control were markedly reduced in atresia (p<0.001 vs. control; p<0.01, among 3 groups), with higher Pseudomonas but lower Staphylococcus (p<0.05, vs. control and other anomalies) and Escherichia (p<0.05 vs. other anomalies).

CONCLUSION: Congenital gastrointestinal atresia demonstrated unique meconium microbiota profiles compared with those of healthy neonates and other congenital anomalies. This suggests differences in the intraintestinal environment during the fetal period.

LEVEL OF EVIDENCE: Ⅱ.},
}

@article {pmid42442593,
year = {2026},
author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W},
title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121232},
doi = {10.1016/j.cca.2026.121232},
pmid = {42442593},
issn = {1873-3492},
abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.

METHODS: This prospective study enrolled 105 patients aged ≥60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.

RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1β, IL-6, IL-8, TNF-α, IFN-γ), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).

CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.},
}

@article {pmid42443172,
year = {2026},
author = {Mühlberg, L and Ruta, J and Mikirtumov, V and Burton-Smith, R and Murata, K and Kudryashev, M and Okamoto, K and Bogdanow, B and Liu, F},
title = {Integrative structural interactomics reveals protein organization and structure in a giant virus.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42443172},
issn = {2041-1723},
support = {LI 3260/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KU 3222/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC-STG-2020 No. 949184//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Leibniz-Wettbewerb P70/2018//Leibniz-Gemeinschaft (Leibniz Association)/ ; 24ama121005j0003//Japan Agency for Medical Research and Development (AMED)/ ; 2018-03387 and 2023-01857//Vetenskapsrådet (Swedish Research Council)/ ; CTS23:2703//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; },
abstract = {Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrate cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocate 88 viral proteins to different virion sub-compartments and propose topologies of 25 inner membrane proteins. We assign eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.},
}

@article {pmid42130477,
year = {2026},
author = {Molano, LG and Hirsch, P and Keller, A and Dolejska, M and Palkovicova, J},
title = {HERA: a web server for host element reference-based aligner.},
journal = {Nucleic acids research},
volume = {54},
number = {W1},
pages = {W154-W159},
pmid = {42130477},
issn = {1362-4962},
support = {469073465//Deutsche Forschungsgemeinschaft/ ; //European Commission/ ; 205/2025/FVHE//University of Veterinary Sciences in Brno/ ; 24-12527S//Czech Science Foundation/ ; },
mesh = {*Software ; Internet ; *Plasmids/genetics/chemistry ; Genome, Bacterial ; Sequence Alignment ; Genomics/methods ; },
abstract = {Plasmids play a central role in bacterial adaptation and in the dissemination of antimicrobial resistance, driving a growing need for accessible tools that support their comparative analysis without requiring local computational infrastructure. Although several circular genome visualization platforms exist, most are designed for general bacterial genome analysis rather than focused on plasmid comparison. Host element reference-based aligner (HERA) is a web server for intuitive visualization and comparison of plasmids and other circular molecules through BLAST alignment against reference sequences. Built on interactive circular genome visualization, HERA simplifies comparative genomics by providing an accessible interface for exploring sequence similarity, identifying conserved regions, and analyzing genetic elements without the complexity of traditional local tools. HERA includes a plasmid-oriented annotation pipeline covering replicon and mobility typing, antimicrobial resistance detection, mobile element identification, and homology search against the PLSDB plasmid database. HERA also provides an automatic selection of the reference which is the most appropriate from the uploaded sequences. The web server is available without login or any restriction at https://web.ccb.uni-saarland.de/hera/.},
}

*Software
Internet
*Plasmids/genetics/chemistry
Genome, Bacterial
Sequence Alignment
Genomics/methods

@article {pmid42436166,
year = {2026},
author = {Chen, Y and Ma, J and Guo, Z and Chen, J and Wang, X and Xiao, J and Hu, D and Yan, J and Deng, W and Nu, Z and He, H and He, W and Luo, J and Zhang, YP and Li, Y},
title = {A rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis).},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01095-4},
pmid = {42436166},
issn = {2055-5008},
support = {CY22624109//Yunnan Provincial Universities Service Key Industry Technology Project - Doctoral Student Industry-Oriented Scientific Research Innovation Training Project/ ; KC-242410789//Graduate Research and Innovation Project of Yunnan University/ ; 2021YFD1200904//National Key Research and Development Program of China/ ; 32470654//National Natural Science Foundation of China/ ; 202407AA110003//Special funds for central guidance of local scientific and technological development/ ; 202601BC070001//Major Program of Yunnan Fundamental Research Projects/ ; XDYC-QNRC-2023-0371//"Xingdian Talent Support Program" Grant of Yunnan Province/ ; },
abstract = {The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.},
}

@article {pmid42436177,
year = {2026},
author = {Eriksson, D and Righetti, D and Benedetti, F and Gruber, N and Paoli, L and Salazar, G and Sunagawa, S and Vogt, M},
title = {Nitrogen fixation rates increase with diazotroph richness in the global ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61132-2},
pmid = {42436177},
issn = {2045-2322},
abstract = {Marine nitrogen fixation is a key process to support and maintain the ocean's primary production, yet our knowledge of the distribution and diversity of the diazotrophic microbes that are capable of fixing nitrogen is very limited. Here, integrating microscopic and metagenomic data, we determine the biogeography and richness of the main diazotrophic taxa across the global ocean. Analyzing 22,000 records and 15 species, we deduce a latitudinal gradient in diazotroph richness, with higher richness to the tropics driven by temperature and nutrient levels. Cyanobacteria dominate in nutrient-poor gyres, while non-cyanobacterial diazotrophs thrive in nutrient-rich zones. Across the global ocean, diazotroph richness is found to correlate positively with nitrogen fixation rates, suggesting a positive biodiversity-ecosystem function relationship. While this relationship is robust to spatial autocorrelation and confounding environmental drivers, spatial dependence in the global datasets and potential unmeasured covariates may influence local-scale inferences. The findings suggest that positive biodiversity-ecosystem functioning relationships with implications for global biogeochemical cycling exist in marine plankton.},
}

@article {pmid42436183,
year = {2026},
author = {Liu, Z and Wu, H and Howe, S and Zuo, B and Tian, Y and Wang, X and Assress, HA and Shang-Lun Lan, R and Mu, C and Xiao, Y and Huang, Y and Looper, M and Tsai, T and Zhao, J},
title = {Lactiplantibacillus plantarum promotes intestinal goblet cell differentiation via indole-3-lactic acid-AHR signaling in pigs.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01085-6},
pmid = {42436183},
issn = {2055-5008},
support = {Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; USDA-ARS 6026-10700-001-000D//USDA/ ; USDA-ARS 6026-10700-001-000D//Food and Nutrition Service/ ; 2023YFE0124400//National Key Research and Development Program of China/ ; 2025-WPY-00-001//the Guangdong Provincial Special Fund Project for Seed Industry Revitalization/ ; },
abstract = {The swine intestinal microbiota dynamically remodels during development and supports gut homeostasis. However, whether stage-specific microbial shifts, are associated with epithelial development remains poorly understood. Here, longitudinal metagenomic profiling of the swine gut microbiome identified Lactiplantibacillus plantarum as a transiently enriched nursery-stage bacterium positively associated with goblet cell numbers. Dietary supplementation with L. plantarum validated this association, showing increased goblet cell numbers and MUC2 expression in the ileum of nursery piglets. Co-culture with porcine ileum organoids further demonstrated that L. plantarum cell-free supernatant promoted ileal organoid growth and goblet cell differentiation. Integrated untargeted metabolomic analyses of ileal samples and bacterial culture supernatants identified indole-3-lactic acid (ILA) as a potential key microbial metabolite from L. plantarum. Mechanistically, ILA promoted intestinal stem cell proliferation and MUC2 expression, accompanied by increased expression of aryl hydrocarbon receptor (AHR) and its downstream target CYP1A1 in ileal organoids. Consistently, activation of AHR using FICZ increased MUC2 expression, whereas inhibition with CH-223191 suppressed MUC2 expression in ileal organoids. Collectively, these findings uncover a L. plantarum-ILA-AHR signaling axis that promotes intestinal goblet cell differentiation, providing mechanistic insight into microbial metabolite-mediated regulation of epithelial homeostasis during post-weaning period in pigs.},
}