@article {pmid42838001,
year = {2026},
author = {Di Nezio, F and Di Cesare, A and Lunardi, D and Munir, M and Fresno López, Z and Sabatino, R and Coci, M and Fontaneto, D and Giordano, R and Corno, G},
title = {Site-specific bacterial and antimicrobial resistome profiles in seawater and sediments from Mediterranean marine aquaculture sites.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108440},
doi = {10.1016/j.marenvres.2026.108440},
pmid = {42838001},
issn = {1879-0291},
abstract = {Aquaculture significantly contributes to meeting the growing global demand for food, primarily driven by the increase in the world population. Despite its importance, aquaculture has also been shown to impact aquatic ecosystems. From an anthropocentric perspective, it can cause disturbances in the affected ecosystems and contribute to the selection and spread of potential pathogens and antimicrobial resistance. With this focus, this study analysed three sites in the Mediterranean Sea: an active fish farm, a recently dismissed farm, and an unreplicated descriptive reference site. The bacterial community and antimicrobial resistome in water and sediment samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Bacterial community composition differed strongly between water and sediments. Observed bacterial richness was lower at the recently dismissed farm than at the active farm in sediments, whereas no corresponding difference was detected in water. Sediments from both fish-farm sites also harboured several high-risk antimicrobial resistance genes. Overall, the study identified descriptive site- and matrix-specific patterns in bacterial richness, community composition and antimicrobial resistance gene distribution across marine aquaculture sites. These findings establish a valuable basis for future longitudinal studies aimed at resolving the ecological processes and temporal dynamics associated with changes in fish-farm operations.},
}

@article {pmid42838164,
year = {2026},
author = {Salini, A and Piccoli, E and Pirone, L and Filocaso, M and Pedone, E and Riedel, SL and Grimm, T and Grabowski, M and Zaccone, C and Cannella, D and Fusco, S},
title = {A PHA depolymerase from Cellulosimicrobium funkei: Discovery, biochemical characterisation and plastic degradation.},
journal = {International journal of biological macromolecules},
volume = {384},
number = {Pt 1},
pages = {154787},
doi = {10.1016/j.ijbiomac.2026.154787},
pmid = {42838164},
issn = {1879-0003},
abstract = {Polyhydroxyalkanoates are biodegradable microbial polyesters considered promising alternatives to petroleum-based plastics. However, the development of sustainable end-of-life strategies for polyhydroxyalkanoates requires the identification of efficient depolymerising enzymes. Here, an extracellular short-chain-length PHA depolymerase, termed CfPhaZ, was identified through metagenomic mining of polyester-enriched microbiomes. The enzyme was assigned to a Cellulosimicrobium funkei metagenome-assembled genome and expressed in Escherichia coli. CfPhaZ shows the canonical architecture of extracellular PHA depolymerases. Biophysical analyses demonstrated that the enzyme adopts a monomeric α/β-fold structure with a melting temperature of 54 °C. The hydrolytic activity of CfPhaZ toward poly(3-hydroxybutyrate) was validated by zymographic and spot-test assays and quantitatively characterised through direct HPLC-based quantification of 3-hydroxybutyrate release. CfPhaZ displayed optimal activity at pH 6.5 and 40 °C, while maintaining prolonged thermostability under mesophilic conditions. Fluorescence-based adsorption assays demonstrated a strong interaction between the enzyme and the substrate surface. Kinetic analyses were performed using both conventional and inverse Michaelis-Menten approaches, and a surface-area-based kinetic framework was implemented to better describe the heterogeneous nature of polymer hydrolysis. Furthermore, CfPhaZ efficiently degraded industrially relevant bioplastic films, reaching up to 40% conversion into soluble monomers. Overall, this study expands the current knowledge of extracellular PHA depolymerases from Gram-positive bacteria and highlights the potential of CfPhaZ for enzymatic recycling and upcycling of biodegradable plastics.},
}

@article {pmid42838172,
year = {2026},
author = {Cobuccio, L and Moser, K and Jacot, D and Kapel, N and Tsaousis, AD and Galperine, T},
title = {Clinical significance of Dientamoeba fragilis and Blastocystis: Lessons from clinical trials, cohort studies, and faecal microbiota transplantation - a narrative review.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.09.031},
pmid = {42838172},
issn = {1469-0691},
abstract = {BACKGROUND: The adoption of highly sensitive syndromic multiplex PCR panels led to an increase in Blastocystis and Dientamoeba fragilis detection, two of the most commonly identified intestinal protists worldwide. With positivity rates of 15-25% on syndromic gastrointestinal panels, a positive result frequently triggers antimicrobial treatment despite uncertain clinical significance.

OBJECTIVES: To synthesise multi-dimensional evidence on the pathogenicity of Blastocystis and D. fragilis from multiple lines of investigation and to propose a pragmatic clinical decision framework for interpreting positive test results.

SOURCES: A systematic search of PubMed/MEDLINE (inception to January 2026) was conducted using structured queries for Blastocystis and D. fragilis across thematic blocks: epidemiology, molecular diagnosis, pathogenicity mechanisms, clinical trials, faecal microbiota transplantation (FMT), and microbiome associations. No language restriction was applied. Study selection prioritised randomised controlled trials, prospective FMT cohorts, large-scale metagenomic analyses, and systematic reviews. Reference lists of retrieved articles were manually screened.

CONTENT: Current evidence suggests asymptomatic carriage is the biological norm for both organisms, and no specific subtypes, genotypes, or parasite load thresholds have been consistently linked to disease. Three placebo-controlled randomised controlled trials (RCTs) showed no treatment benefit: two conducted in paediatric populations and one an adult pilot study. FMT cohort studies demonstrate safe transmission without adverse events. Metagenomic analyses of nearly 57,000 individuals have identified an association between Blastocystis carriage, greater microbial diversity, and more favourable cardiometabolic profiles, although the direction and causality of these relationships remain unclear.

IMPLICATIONS: In immunocompetent hosts, detection of Blastocystis or D. fragilis does not indicate disease; for Blastocystis in particular, carriage should be regarded as an ecological marker of the intestinal microbiota. A clinical decision algorithm is proposed in which reassurance is the default, treatment is reserved for exceptional circumstances (severe immunosuppression or chronic unexplained symptoms after thorough exclusion of alternative diagnoses), and clinical response, not PCR clearance, serves as the only meaningful endpoint.},
}

@article {pmid42838201,
year = {2026},
author = {Dong, H and Ren, K and Lan, J and Peng, C and Pan, X and Tu, C and Song, C and Zhang, W and Cao, J},
title = {Nitrate accumulation and transformation processes within a karst conduit system: Insights from hydrochemistry, stable isotopes, metagenomics, and tracer tests.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125870},
doi = {10.1016/j.envres.2026.125870},
pmid = {42838201},
issn = {1096-0953},
abstract = {Nitrate (NO3[-]) pollution in karst groundwater threatens drinking water security. However, limited subsurface accessibility makes tracing its migration and transformation within karst conduits challenging. This study integrated hydrochemistry, multiple isotopes, functional genes, and tracer tests to elucidate NO3[-] sources and transformation in the Lanfeng watershed, a representative karst conduit system in southwestern China. Nitrification dominated the watershed nitrogen cycle, with soil organic nitrogen (SON) as the primary NO3[-] source, contributing 69.4% and 74.0% to surface and groundwater, respectively. High dissolved oxygen (DO) and low dissolved organic carbon (DOC) conditions in the conduit favored nitrification. Along the flow path, NO3[-] concentrations increased from 1.56 mg L[-1] (inlet) to 14.23 mg L[-1] (outlet), accompanied by increases in the NO3[-]/Cl[-] molar ratio (0.14→1.55) and nitrification functional gene abundances (24.74→97.28 CPM), supporting nitrification as an important nitrogen transformation process within the conduit. However, lateral recharge or water mixing cannot be completely excluded as contributors to the observed NO3[-] enrichment. A conditional apparent NO3[-] concentration change index, based on spatial concentration differences normalized by tracer-derived peak-time differences, ranged from 0.20 to 0.89 mg L[-1] d[-1]. This study demonstrates that karst conduits are not passive transport pathways, but rather "reactors" with an intrinsic capacity for NO3[-] production. These findings highlight the need to consider endogenous NO3[-] production within subsurface flow paths, alongside external anthropogenic nitrogen inputs, in NO3[-] risk assessment and mitigation, providing broader insights into NO3[-] pollution management in karst aquifers worldwide.},
}

@article {pmid42838349,
year = {2026},
author = {Fan, M and Wang, S and Liao, Y and Li, S},
title = {Genomic potential for complete denitrification by Desulfobacillus in anammox bioreactors.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136020},
doi = {10.1016/j.biortech.2026.136020},
pmid = {42838349},
issn = {1873-2976},
abstract = {Desulfobacillus are frequently observed as abundant flanking denitrifying microorganisms in anammox bioreactors and wastewater treatment systems. Previous studies suggested that Desulfobacillus lacked canonical nitric oxide reductase, restricting them to incomplete denitrification. As a result, they were thought to provide NO to anammox bacteria and act as an N2O sink. In this study, 48 Desulfobacillus genomes from GTDB were analyzed, including 21 from anammox-related bioreactors. Multiple potential nitric oxide reductases (eNOR, nNOR, and sNOR) were identified, and all 21 anammox-associated genomes encode at least one candidate nitric oxide reductase, with 5 also encoding a potential nitric oxide dismutase (NOD). The phylogeny, gene context, conserved active site residues, and 3D structures of these NO-transforming enzymes were further investigated. The findings indicated most Desulfobacillus possess the genomic potential for complete denitrification in anammox bioreactors. Furthermore, a discrepancy between 16S rRNA gene amplicon analysis and metagenomic analysis was observed. A proportion of Desulfobacillus 16S rRNA genes may be misclassified as Denitratisoma by the SILVA database. As Denitratisoma was previously detected in especially high abundance (>20%) in anammox bioreactors, this misclassification even highlights the importance of Desulfobacillus in anammox and other nitrogen removal processes.},
}

@article {pmid42838366,
year = {2026},
author = {Zhang, W and Matuszek, G and Dolnikowski, GG and Lamon-Fava, S and Ausman, LM and Lichtenstein, AH and Matthan, NR},
title = {Differential effects of stearic, palmitic and oleic acid enriched diets on gut microbiome, bile acid and cholesterol metabolism in mildly hypercholesterolemic post-menopausal females: A secondary analysis of a randomized controlled trial.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101561},
doi = {10.1016/j.ajcnut.2026.101561},
pmid = {42838366},
issn = {1938-3207},
abstract = {BACKGROUND: Stearic acid (18:0), a saturated fatty acid (SFA), does not raise plasma LDL cholesterol concentrations compared with palmitic acid (16:0), and has similar effects to oleic acid (18:1), but underlying mechanisms remain unclear.

OBJECTIVES: To determine if the hypocholesterolemic effects of dietary 18:0 and 18:1 relative to 16:0 are mediated by alterations in gut microbiome, bile acid (BA), and cholesterol metabolism.

METHODS: Secondary analysis of a randomized controlled crossover trial in mildly hypercholesterolemic postmenopausal females (n=17) who consumed isocaloric diets enriched in 18:0, 16:0 or 18:1 for 5-weeks each with 2-week washouts. Gut microbiome composition, plasma and fecal BA profiles, cholesterol absorption and synthesis markers, and related gene expression were assessed at the end of each dietary phase. Diet effects and multi-omics associations were evaluated using mixed-effects and multivariate models, accounting for repeated measures.

RESULTS: Fecal microbiome diversity was stable across diets, with modest species-level differences. Both 18:0 and 18:1 diets resulted in lower fasting total primary BAs (-159.1 (-313.0,-5.7), and -200.2 (-353.0,-47.7), mean difference (95% CI), respectively) and higher non-fasting unconjugated PBA concentrations (2.7 (1.1,6.4) and 2.4 (1.1,5.6), geometric mean ratio (95% CI), respectively) compared to the 16:0 diet. The 18:0 diet resulted in lower fecal secondary BAs compared to the 18:1 diet (-15.2 (-27.8, -2.6), mean difference (95% CI)) and higher non-fasting conjugated BAs compared to the 16:0 diet (1.4 (0.8,2.3) geometric mean ratio (95% CI)). FXR and SHP expression were 3-4 fold higher (p<0.01), and cholesterol synthesis:absorption ratio 22-24% lower, after both 18:0 and 18:1 compared to the 16:0 diet (p <0.05). Multi-omics analyses identified moderate-to-strong correlations (r = 0.43 to 0.72) among microbes, BAs, gene expression, cholesterol metabolism markers, and lipid profiles.

CONCLUSIONS: The cholesterol-lowering effects of 18:0 and 18:1 relative to 16:0 involved shared hepatic regulation of BA and cholesterol metabolism, while 18:0 uniquely modulated specific microbial taxa and BAs, suggestive of altered enterohepatic BA recycling.

CLINICAL TRIAL REGISTRY: https://clinicaltrials.gov/study/ NCT02145936.},
}

@article {pmid42838558,
year = {2026},
author = {Dussex, N and Andersson, L and Bergström, U and Johannesson, K and Wallberg, A},
title = {Harnessing macrogenomics to study changing marine ecosystems under global climate change.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2080},
pages = {},
pmid = {42838558},
issn = {1471-2954},
support = {//Swedish Research Council/ ; //FORMAS/ ; },
mesh = {*Climate Change ; *Ecosystem ; *Genomics ; Biodiversity ; Animals ; Oceans and Seas ; Conservation of Natural Resources ; *Aquatic Organisms/genetics ; },
abstract = {Climate change is reshaping marine ecosystems at an accelerating pace. Predicting its impacts on biodiversity and ecosystem functions is therefore crucial to developing effective conservation strategies. Integration of genomic tools, habitat modelling and simulations offers a transformative approach to forecast these impacts. Yet, current frameworks remain limited to single-species analyses. In this review, we discuss future directions in the emerging field of macrogenomics, the analysis of large-scale genomic data across species and time, and show how its integration with environmental data can be applied to understand past and predict future climate-driven ecological shifts across entire marine communities. We demonstrate how applying a macrogenomic framework can provide insights into future responses of marine ecosystems under global climate change by integrating multi-species demographic analyses, metagenomics and signatures of adaptation associated with past climate fluctuations. We also show how macrogenomics combined with predictive approaches can be used to forecast cascading effects of species fluctuations on ecosystem structure and potentially identify ecosystem tipping points. Ultimately, coupling empirical and prediction data offers a powerful approach for ecosystem-based management, improving our ability to predict adaptive responses and extinction risks at relevant scales, and equipping managers and policymakers with actionable insights to prioritize biodiversity conservation strategies.},
}

*Climate Change
*Ecosystem
*Genomics
Biodiversity
Animals
Oceans and Seas
Conservation of Natural Resources
*Aquatic Organisms/genetics

@article {pmid42838722,
year = {2026},
author = {Ware, K and Ollberding, N and Duan, Q and Haslam, D and Phipatanakul, W and Glazman, M and Bernstein, JA},
title = {Ultraviolet irradiation and the home microbiome in childhood asthma: An exploratory environmental analysis.},
journal = {Allergy and asthma proceedings},
volume = {},
number = {},
pages = {},
doi = {10.2500/aap.2026.47.260079},
pmid = {42838722},
issn = {1539-6304},
abstract = {BACKGROUND: Ultraviolet (UV) filtration units installed into central heating, ventilation, and air conditioning systemshave been shown to modify indoor environmental microbiomes (EM), but it remains unclear whether central UV air filtrationsystems as a targeted intervention alters the EM sufficiently to modify asthma outcomes.

OBJECTIVE: The objective was to investigate changes in the microbiome from dust samples collected before and after installation of a central UV filtration system in homes of children with mild-moderate persistent asthma.

METHODS: Enrolled pediatric subjects with asthma were randomized to receive UV filtration or sham devices in their heating,ventilation, and air conditioning units. Dust samples were collected from the furnace filters and each child's bedroominflow air ducts from the first 20 homes randomized at the two largest recruiting sites at the time of device placement and atstudy completion (12 months), along with periodic measurements of asthma outcomes markers by using the Composite Asthma Severity Index. Microbial DNA from each paired dust sample underwent shotgun metagenomic sequencing, and taxonomic profiles were generated with MetaPhlAn 4. Associations between changes in bacterial species abundance and changes in asthma severity were assessed with Microbiome Multivariable Associations with Linear Models in R.

RESULTS: A total of 14 paired dust samples (7 from the UV homes and 7 from the sham homes) from inflow air ducts with sufficient quantity of dust were included for EM analysis. Within the UV filtration homes, false discovery rate adjusted q-values< 0.05 identified associations between worsening asthma severity and reduced relative abundance of common gastrointestinalcommensals, such as Bacteroides and Bifidobacterium, previously linked to a reduced risk of allergic disease and asthma; no associations at this threshold were observed in the sham homes.

CONCLUSION: An exploratory study of UV air filtration units installed in homes of children with asthma identified hypothesis-generating associations between bacterial species changes and asthma severity; because the study was underpowered forbetween-arm comparisons, these findings do not establish that UV air filtration caused the microbiome changes and should not be interpreted as confirmatory of a UV-specific effect.Clinical trial NCT02715375, www.

CLINICALTRIALS: gov.},
}

@article {pmid42838980,
year = {2026},
author = {Human, ZR and Hoover, R and Chan, C and Küsel, K and Wegner, CE},
title = {High diversity but limited expression of biosynthetic gene clusters in a peatland microbial community.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42838980},
issn = {2041-1723},
mesh = {*Multigene Family ; *Soil Microbiology ; Metagenome ; Gene Expression Regulation, Bacterial ; Phylogeny ; *Biosynthetic Pathways/genetics ; *Bacteria/genetics/metabolism/classification ; Genetic Variation ; },
abstract = {The in situ relevance of biosynthetic gene clusters (BGCs) remains poorly understood. We apply meta-omics to characterize BGC diversity and activity along a peatland redox gradient. From seven metagenomes, we recover 9,694 BGCs, spanning diverse taxa, most lacking close relatives in reference databases, indicating extensive novelty. Only 9-27% of this potential is expressed in situ, with Acidobacteriota, despite moderate repertoires, accounting for over half of all BGC transcription. Talented producers with up to 24 clusters are largely silent, and expression is inversely related to BGCs per genome. Acidobacteriota, specialized in complex carbon processing potential express a larger proportion of their BGC repertoires than BGC-rich Pseudomonadota, which had shorter doubling times and lower potential for complex carbon processing. At the genome level, the degree of BGC expression is most strongly coupled to carbohydrate-active enzyme expression, particularly glycoside hydrolases, linking secondary metabolism to active carbon processing in peatland microbes. Thus, although BGCs are widespread, BGC expression in situ is integrated into the carbon-cycling activity of individual taxa rather than a shared physiological state.},
}

*Multigene Family
*Soil Microbiology
Metagenome
Gene Expression Regulation, Bacterial
Phylogeny
*Biosynthetic Pathways/genetics
*Bacteria/genetics/metabolism/classification
Genetic Variation

@article {pmid42839180,
year = {2026},
author = {Tworuszka, M and Gliwa, D and Kurek-Górecka, A and Sędek, Ł},
title = {Rare bacterial infections and metagenomics: current diagnostic and therapeutic challenges-a literature review.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42839180},
issn = {1439-0973},
abstract = {PURPOSE: This review aims to summarize the diagnostic and therapeutic challenges associated with rare bacterial infections, with particular focus on Whipple's disease, melioidosis, Lemierre's syndrome, and nocardiosis. It also evaluates the clinical utility of emerging molecular diagnostic techniques, particularly polymerase chain reaction (PCR) and metagenomic next-generation sequencing (mNGS), in improving pathogen identification. The primary research question concerns how advances in molecular microbiology may enhance the early diagnosis and targeted treatment of these infections.

METHODS: A narrative literature review with a structured search strategy was conducted. PubMed/MEDLINE and Scopus were searched for studies published between January 1998 and April 2026 using MeSH terms and keywords related to rare bacterial infections and molecular diagnostics. Eligible peer-reviewed articles in English or Polish, including original studies, reviews, meta-analyses, and selected case reports, were included. Data extraction and study selection were performed independently by two reviewers.

RESULTS: Rare bacterial infections are frequently associated with delayed diagnosis due to nonspecific clinical manifestations, limited clinician awareness, negative culture results, and restricted access to advanced diagnostic methods. Molecular techniques improve detection sensitivity and identify pathogens not recoverable by routine culture. For metagenomic sequencing this comes at the cost of reduced specificity. In these infections the supporting evidence comes largely from case reports and small single-center series.

CONCLUSION: Rare bacterial infections remain a significant diagnostic and therapeutic challenge. Broader implementation of advanced molecular diagnostic techniques, increased clinical awareness, and standardized diagnostic strategies are needed to reduce diagnostic delay. Whether this in turn reduces morbidity and mortality requires prospective evaluation.},
}

@article {pmid42839250,
year = {2026},
author = {Nipko, MA and Wu, Z and Aanderud, ZT and Robinson, DM},
title = {Substrate-driven phage community structure and phage-host dynamics in anaerobic digesters.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42839250},
issn = {2524-6372},
abstract = {BACKGROUND: Phages shape microbial communities by regulating metabolic pathways, driving biogeochemical processes, and impacting stability and functionality of ecosystems. Phages contributions to natural ecosystems are undeniable; however, their role in built systems especially in anaerobic digesters remain poorly characterized. To discover the functional role of phage communities in anaerobic digesters, we evaluated phage-bacterial and virus-archaeal relationships in metagenomic sequences from fifteen commercial, full-scale anaerobic digesters of chicken, cattle, and pig manure, the three most commonly utilized organic waste streams globally.

RESULTS: Here, we predict the abundance, auxiliary metabolic genes, and microbial-host interactions of phage and archaeal viruses under anaerobic fermentation processes and methanogenesis. We found phages and prokaryote abundances were coupled and both populations were driven by feedstock characteristics (20% phage variance and 25% prokaryotes explained by feedstock), indicating interactions of phage, host, and the environment. Phages encoded auxiliary metabolic genes relevant to and supporting anaerobic digestion including glycoside hydrolase, pyruvate formate lyase, and cobalamin biosynthesis genes.

CONCLUSIONS: Together, our results reveal that phages are not only integral to bacterial and archaeal community structure and function in anaerobic digesters but are also strongly shaped by feedstock type. These findings provide a basis for understanding and potentially manipulating viral-host interactions to enhance digester performance.},
}

@article {pmid42839672,
year = {2026},
author = {Zhu, L and Xiong, X and Zhang, Q and Cai, W and Wang, Y},
title = {Single-Microbe Transcriptomics Reveal Functional Heterogeneity in Sediment Microbiomes.},
journal = {Small methods},
volume = {},
number = {},
pages = {e71082},
doi = {10.1002/smtd.71082},
pmid = {42839672},
issn = {2366-9608},
support = {2024C03005//Pioneer R&D Programs of Zhejiang Province/ ; 2024SSYS0022//Key R&D Program of Zhejiang/ ; },
abstract = {Sediment microbiomes drive global biogeochemical cycling, but their functional heterogeneity and transcriptional activity are hardly resolved at single-cell resolution. We optimized a scalable single-microbe RNA sequencing workflow for environmental muddy sediment samples, achieving high-throughput single cell sequencing across environmental gradients. The method integrates iohexol-based microbial enrichment, optimized enzymatic digestion step, droplet-based single-cell barcoding, and RNA sequencing, then generating a transcriptomic atlas of 55 859 high-quality microbial cells from 8 composite samples covering freshwater, estuarine and nearshore marine habitats. Comparison with metagenomic data showed a high consistency in species composition, supporting the reliability of single-microbe RNA sequencing in community profiling. Taxonomic analysis revealed site-specific microbial communities associated with methane oxidation, sulfur cycling and anaerobic nitrogen metabolism. 15 distinct functional clusters were identified transcriptionally, showing functional heterogeneity within sedimentary microbiome. Co-expression network analysis further resolved coordinated gene modules, with module activities varying across samples. Overall, this work establishes a practical framework for single-microbe transcriptomics in sediment systems and demonstrates the potential of single-cell resolution to uncover functional heterogeneity within complex microbial communities.},
}

@article {pmid42839991,
year = {2026},
author = {Barton, J and Lehmann, C and Richardt, U and Cadar, D and Volkmer, B and Greinert, R and Jacobs, T and Gálvez, RI},
title = {CD160 mediated NK cell activation shapes host defense against acute Trypanosoma cruzi infection in the skin.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1872132},
pmid = {42839991},
issn = {1664-3224},
mesh = {Animals ; *Killer Cells, Natural/immunology/metabolism ; Humans ; *Chagas Disease/immunology/parasitology ; *Trypanosoma cruzi/immunology ; Mice ; *Antigens, CD/immunology/genetics/metabolism ; *Lymphocyte Activation/immunology ; Receptors, Tumor Necrosis Factor, Member 14/metabolism/immunology/genetics ; *Skin/immunology/parasitology ; Fibroblasts/immunology/parasitology/metabolism ; *Receptors, Immunologic/immunology/genetics/metabolism ; Mice, Knockout ; Mice, Inbred C57BL ; GPI-Linked Proteins ; },
abstract = {INTRODUCTION: Trypanosoma cruzi, the causative agent of Chagas disease, enters the host through the skin. While natural killer (NK) cell antimicrobial activity against T. cruzi-infected keratinocytes in the epidermis has previously been shown, NK cell interactions with dermal fibroblasts, a primary target of parasite replication at the skin entry site, remain poorly understood.

METHODS: Bulk RNA-sequencing of mock- and T. cruzi-infected human dermal fibroblasts (HDF) and the BJ fibroblast cell line was performed to identify infection-induced ligand changes. HVEM-CD160 binding and NK cell effector functions were assessed in vitro using fibroblast co-cultures with or without CD160 receptor blockade. In vivo, RAG[-/-] and RAG[-/-]CD160[-/-] mice were infected intradermally with T. cruzi; NK cell degranulation and cytokine production were analyzed by flow cytometry, and parasite burden in skin and muscle was quantified by qPCR.

RESULTS: RNA-sequencing revealed upregulation of herpesvirus entry mediator (HVEM, TNFRSF14) in infected human dermal fibroblasts, confirmed at the protein level. HVEM was functionally engaged by CD160, and CD160 blockade reduced NK cell degranulation and secretion of cytotoxic mediators in fibroblast co-cultures. CD160 deficiency impaired NK cell activation in vivo; NK cell degranulation in the skin showed a trend toward inverse correlation with local parasite burden, and early skin parasite load predicted subsequent dissemination to muscle. HVEM was robustly upregulated in murine skin during acute infection, mirroring the human fibroblast data.

DISCUSSION: These findings establish the HVEM-CD160 axis as a key regulator of NK cell effector function in the skin during acute T. cruzi infection, contributing to local parasite control. This conserved human-mouse regulatory response may offer broader insight into NK cell-mediated defense against pathogens that invade through the skin.},
}

Animals
*Killer Cells, Natural/immunology/metabolism
Humans
*Chagas Disease/immunology/parasitology
*Trypanosoma cruzi/immunology
Mice
*Antigens, CD/immunology/genetics/metabolism
*Lymphocyte Activation/immunology
Receptors, Tumor Necrosis Factor, Member 14/metabolism/immunology/genetics
*Skin/immunology/parasitology
Fibroblasts/immunology/parasitology/metabolism
*Receptors, Immunologic/immunology/genetics/metabolism
Mice, Knockout
Mice, Inbred C57BL
GPI-Linked Proteins

@article {pmid42840056,
year = {2026},
author = {Li, X and He, X and Fu, X and Wu, N and Yang, D and Zhao, J and Ma, X and Chai, S and Ni, W},
title = {Detection of Aspergillus in the lower respiratory tract and its association with mortality in patients with different viral pneumonias: a retrospective multicenter cohort study from China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1906021},
pmid = {42840056},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; China/epidemiology ; Female ; *Aspergillus/isolation & purification/genetics ; *Pneumonia, Viral/mortality/microbiology/complications ; Middle Aged ; Male ; Aged ; SARS-CoV-2 ; COVID-19/mortality/microbiology ; Community-Acquired Pneumonia ; Adult ; Influenza, Human/mortality/microbiology ; },
abstract = {BACKGROUND: The detection of Aspergillus in the lower respiratory tract complicates the clinical course of viral pneumonia and is linked to poor outcomes, but prior evidence is confined to the intensive care unit (ICU) or single-virus settings (e.g., influenza or SARS-CoV-2). Whether its frequency and prognostic significance differ across viral etiologies in hospitalized adults remains unknown.

METHODS: This multicenter retrospective cohort study included adults with community-acquired viral pneumonia at seven tertiary hospitals in China (2017-2025). Patients were categorized into SARS-CoV-2, influenza, or other viral groups. The exposure was lower respiratory tract Aspergillus detection (via using culture, real-time PCR, or metagenomic next-generation sequencing). The primary outcome was in-hospital all-cause mortality.

RESULTS: Among 929 patients, Aspergillus was detected in 175 (18.8%). The detection rates differed significantly across viral etiologies (33.2% in patients with influenza, 14.6% in those with SARS-CoV-2, and 7.4% in those with other viruses; P < 0.001). In the fully adjusted model, Aspergillus detection was independently associated with increased overall mortality (aOR = 2.99; 95% CI 1.60-5.58; P < 0.001), but the association varied markedly by viral etiology. Virus-stratified analyses revealed that in influenza, Aspergillus detection remained independently associated with mortality after multivariable adjustment, and the association was consistently observed across prespecified subgroups, including non-ventilated patients, whereas in SARS-CoV-2, the association was largely confined to ventilated patients.

CONCLUSION: Lower respiratory tract Aspergillus detection differed substantially by viral etiology and was most frequent in patients with influenza pneumonia. It was independently associated with increased mortality across all influenza subgroups, including non-ventilated patients, whereas in SARS-CoV-2 pneumonia this association was largely confined to mechanical ventilation patients. These findings support a virus-stratified approach to fungal surveillance and warrant prospective validation.},
}

Humans
Retrospective Studies
China/epidemiology
Female
*Aspergillus/isolation & purification/genetics
*Pneumonia, Viral/mortality/microbiology/complications
Middle Aged
Male
Aged
SARS-CoV-2
COVID-19/mortality/microbiology
Community-Acquired Pneumonia
Adult
Influenza, Human/mortality/microbiology

@article {pmid42840097,
year = {2026},
author = {Xu, Y and Zhao, X and Gao, S and Xiao, J and Yang, Q and Xu, J and Xie, Y and Xu, Y and Ye, X and Ji, T and Zhang, Y and Yan, D},
title = {High-throughput sequencing reveals the virome characteristics of wastewater in Gansu Province, China from 2024 to 2026.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1966428},
pmid = {42840097},
issn = {1664-302X},
abstract = {Emerging and re-emerging infectious diseases continue to pose a persistent challenge to global public health security. As an unbiased and noninvasive population-level surveillance approach, wastewater-based epidemiology has emerged as an urban-scale monitoring tool for proactively capturing the community disease burden. In this study, metagenomic and targeted next-generation sequencing were employed to preliminarily characterize wastewater viral communities in Gansu Province from 2024 to 2026. Across the three annual sampling groups, the Simpson diversity index calculated from metagenomic taxonomic profiles showed a significant negative correlation with sampling year. Despite viral enrichment, more than 97% of sequencing reads were assigned to bacteria, likely reflecting residual nonviral nucleic acids and limitations in metagenomic classification. The wastewater virome exhibited a complex host-association spectrum, within which bacteriophages and plant-associated viruses displayed relatively stable community structures and high relative abundances. Among human pathogens, astroviruses were consistently detected at high relative abundances across all samples. Human astrovirus 1 accounted for the largest proportion, and a nearly complete genome sequence of the extraintestinal infection-associated astrovirus MLB2 was recovered. Targeted sequencing further revealed a highly structured environmental enterovirus profile dominated by the species Enterovirus betacoxsackie, followed by Enterovirus alphacoxsackie, whereas Enterovirus coxsackiepol was detected at an extremely low abundance and Enterovirus deconjuncti was not detected. In addition to several common viruses associated with hand, foot, and mouth disease, rare viruses, including coxsackievirus A19 and enterovirus B83, were successfully captured. Echovirus 11 was identified as the predominant enterovirus serotype in current wastewater surveillance in Gansu Province. In summary, this study provides a preliminary characterization of the viral community profiles in wastewater samples from Gansu Province, demonstrates the effectiveness of wastewater-based epidemiology for population-level surveillance, and underscores the need to establish a coordinated defense network integrating clinical case surveillance with environmental monitoring.},
}

@article {pmid42840147,
year = {2026},
author = {Jiang, L and Kong, Y and Zhang, G and Wang, P and Fang, M and Liu, Q and Zhang, S and Li, Y},
title = {Large-scale characterization of the bovine virome reveals viral diversity and community patterns in Northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1924807},
pmid = {42840147},
issn = {1664-302X},
abstract = {Cattle play a critical role in global agriculture and food security while serving as hosts for diverse viruses with potential implications for animal and public health. To comprehensively characterize the bovine virome and its community patterns, we conducted a large-scale characterization of the beef cattle-associated virome in Northwest China using viral metagenomic sequencing. A total of 2,353 specimens, including nasal swabs, anal swabs, and serum, were collected from 794 cattle across 28 sites in Shaanxi, Gansu, and Ningxia, with nasal and anal swab specimens used for the metagenomic analyses. High-throughput sequencing identified viruses belonging to 14 phyla, 32 classes, 39 orders, 71 families, and 397 genera, revealing substantial viral diversity. Descriptive comparisons of the pooled libraries revealed differences in virome composition across geographic regions, farming systems, and sampling seasons, with the summer pool showing greater viral richness and contig abundance than the winter pool. Phylogenetic analyses revealed genetic relationships between several viral sequences detected in this study and viral lineages previously reported from humans and other animal hosts, raising hypotheses regarding broader host associations and potential cross-species transmission that require further investigation. Targeted PCR/RT-PCR screening and cell-culture-based virus characterization provided complementary validation of representative metagenomic findings and revealed frequent co-detection of multiple viral targets among the sampled cattle. Collectively, this study provides a large-scale characterization of the beef cattle-associated virome in Northwest China, expands current knowledge of viral diversity associated with beef cattle populations, and establishes a valuable resource for future virome surveillance, studies of viral evolution, and disease prevention.},
}

@article {pmid42840223,
year = {2026},
author = {Lu, J and Yang, Y},
title = {Omics-based biomarkers of immune-related organ toxicities associated with immune checkpoint inhibitors: a scoping review and evidence map.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1945286},
pmid = {42840223},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects ; Multiomics ; Biomarkers ; Genomics/methods ; Metabolomics ; Proteomics ; *Drug-Related Side Effects and Adverse Reactions/diagnosis/etiology ; Animals ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) can cause immune-related adverse events (irAEs) across multiple organs. High-throughput omics approaches may help characterize susceptibility, molecular mechanisms, diagnostic features, and monitoring markers related to irAEs; however, evidence remains dispersed across platforms, clinical applications, and toxicity phenotypes.

OBJECTIVE: To map original human evidence in which high-throughput omics approaches were directly linked to irAE susceptibility, occurrence, severity, diagnosis, longitudinal monitoring, clinical course, recovery, response to irAE-directed treatment, or mechanistic characterization. Methods: This scoping review and evidence map followed a registered protocol and was informed by PRISMA-ScR and JBI guidance. PubMed/MEDLINE, Scopus, Web of Science Core Collection, and Embase were searched from January 1, 2014, with the final database search completed on July 9, 2026. Eligible studies involved ICI-exposed patients or human biospecimens, implemented high-throughput genomics/statistical genetics, transcriptomics, proteomics, metabolomics/lipidomics, microbiome/metagenomics, single-cell or spatial omics, immune-repertoire sequencing, or integrated multi-omics approaches, and directly evaluated an irAE outcome. Genome-wide statistical-genetic studies were retained as a conditional evidence category. Targeted single-marker studies, routine laboratory biomarkers, efficacy-only omics analyses, non-ICI populations, non-original reports, case reports, and preclinical-only omics studies were excluded.

RESULTS: The searches identified 4,669 records. After removal of 1,151 duplicates, 3,518 unique records were screened and 433 reports were sought for retrieval. Thirty-two reports could not be retrieved for full-text assessment. Of 401 reports assessed in full text, 315 were excluded and 86 studies were included. Omics domains were non-mutually exclusive: transcriptomics was used in 50 studies, single-cell/spatial omics in 31, proteomics in 20, microbiome/metagenomics in 20, immune-repertoire sequencing in 16, genomics/statistical genetics in 14, and metabolomics/lipidomics in 6. Forty-seven studies contributed to two or more omics domains in the platform audit; after accounting for overlapping analytical modalities, 35 studies met the predefined criteria for true multi-omics integration involving independent molecular layers. Forty-five studies addressed mixed or general irAEs; among organ-specific studies, myocarditis/cardiovascular toxicity (n=10), pneumonitis/lung toxicity (n=9), and gastrointestinal/colitis toxicity (n=8) were most frequent.

CONCLUSIONS: The high-throughput omics literature directly evaluating irAEs is substantially smaller than the broader biomarker literature and is dominated by transcriptomic and single-cell approaches. Most evidence remains exploratory, with limited independent assessment of predefined models or signatures, incomplete coverage of endocrine, renal, neurologic, hematologic, pancreatic, and musculoskeletal toxicities, and substantial gaps between molecular discovery and clinical implementation. Prospective multicenter cohorts, standardized irAE phenotyping, longitudinal sampling, and independent validation are required to support clinical implementation. Future studies integrating multiple molecular layers with advanced computational approaches may improve biomarker discovery and individualized risk stratification but require transparent development and rigorous validation.

https://osf.io/g79cv, identifier g79cv.},
}

Humans
*Immune Checkpoint Inhibitors/adverse effects
Multiomics
Biomarkers
Genomics/methods
Metabolomics
Proteomics
*Drug-Related Side Effects and Adverse Reactions/diagnosis/etiology
Animals

@article {pmid42840241,
year = {2026},
author = {Zhang, H and Zou, W and Wu, W and Xu, J and Ren, L and Liu, M and Sun, D and Liu, J and Yu, Y and Yu, M and Ding, J},
title = {Metagenomic next-generation sequencing reveals airway microbial dysbiosis and functional alterations in Legionella pneumophila pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1900957},
pmid = {42840241},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Legionella pneumophila/genetics ; *Legionnaires' Disease/microbiology ; Female ; *Dysbiosis/microbiology ; Community-Acquired Pneumonia/microbiology ; Male ; Aged ; Microbiota ; Middle Aged ; Metagenome ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Legionella pneumonia (LP), primarily caused by Legionella pneumophila, is a clinically important subtype of community-acquired pneumonia (CAP) associated with substantial morbidity and mortality. However, the microbial characteristics and functional profiles of LP remain insufficiently understood.

METHODS: In this study, metagenomic next-generation sequencing (mNGS) was used to compare airway microbial communities between patients with LP and those with non-Legionella CAP.

RESULTS: A total of 60 patients were included, comprising 23 patients with LP patients and 37 patients with non-Legionella CAP patients. Airway microbial diversity and composition differed between groups, although the between-group effect size was modest and residual confounding could not be excluded. The LP group showed higher relative abundance of Legionella pneumophila and selected opportunistic species, whereas several oral commensal-associated species were relatively enriched in non-Legionella CAP. In the pooled 60-patient cohort, selected microbial species were associated with inflammatory and clinical severity markers; these associations were not disease-specific and do not imply causality. Inferred functional profiles also differed between groups. Exploratory machine-learning models showed high internal discriminatory performance, with XGBoost yielding the highest mean AUC, but the small cohort and lack of external validation limit conclusions regarding diagnostic utility.

CONCLUSIONS: In this small retrospective cohort, LP was associated with differences in airway microbial composition and inferred functional potential compared with a heterogeneous non-Legionella CAP group. Because the study was observational, the groups differed in important clinical characteristics, and the pooled association analyses were not disease-specific, the findings should be considered exploratory and hypothesis-generating. The reproducibility and diagnostic value of microbiota-derived features require confirmation in larger, prospectively collected, independent cohorts.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Legionella pneumophila/genetics
*Legionnaires' Disease/microbiology
Female
*Dysbiosis/microbiology
Community-Acquired Pneumonia/microbiology
Male
Aged
Microbiota
Middle Aged
Metagenome
*Respiratory System/microbiology

@article {pmid42840894,
year = {2026},
author = {Song, X and Chen, J and Chan, H and Lin, F and Wang, X and Zhu, C and Heidari, MH and Liu, L and Li, C and Liu, Z and Li, Q and Yang, B},
title = {A New Insight into Acne Pathogenesis: Multi-Omics Links a Metabolite to C. acnes Expansion and Lipid Accumulation.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {641284},
pmid = {42840894},
issn = {1178-7015},
abstract = {BACKGROUND: Gut microbiota dysbiosis is implicated in dermatoses, including acne vulgaris. However, gut microbial and metabolomic profiles in acne remain uncharacterized.

METHODS: We performed metagenomic and metabolomic analyses on fecal samples from 29 acne patients and 20 healthy controls. Functional annotations utilized multiple databases. Integrated metagenomic-metabolomic analysis was conducted to identify metabolites, and their effects were subsequently validated in a mouse acne model. Finally, a five-fold cross-validated random forest model evaluated discriminatory capacity of microbial, metabolic, and multi-omics signatures for acne and its subtypes.

RESULTS: Acne patients exhibited reduced gut microbial diversity and decreased abundance of beneficial genera (eg, Blautia, Faecalibacterium) and species (eg, Anaerotardibacter muris, Firmicutes bacterium CAG:321, Clostridium sp. CAG:245, Ruminococcus sp. OM06-36AC). Differentially enriched microbial pathways involved amino acid metabolism. Integrated analysis revealed positive correlations between the key microbes driving the selected pathways and the associated metabolites which promoted the growth of C. acnes. The integrated multi-omics model yielded high diagnostic accuracy (validation AUC=0.921, test AUC=0.915), outperforming single-omic models, showed optimal gender discrimination (test AUC=1.00) and subtype-specific predictive efficacy, with key microbial and metabolite biomarkers identified for acne subtype classification and disease progression regulation.

CONCLUSION: Acne vulgaris demonstrates distinct gut microbiota and metabolite signatures. Our integrated data suggest that gut microbiota may influence acne development via metabolic changes, and some of these metabolites might possess acne‑promoting properties.},
}

@article {pmid42841046,
year = {2026},
author = {Chen, D and Ye, W and Li, X and Zhang, J},
title = {Metagenomic Next-Generation Sequencing in Brucellar Spondylitis with Discordant Serologic Findings in a Non-Endemic Region: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {627757},
pmid = {42841046},
issn = {1178-6973},
abstract = {BACKGROUND: Brucellar spondylitis (BS) is a focal osteoarticular manifestation of brucellosis with nonspecific clinical and imaging features. Diagnosis may be difficult in areas where brucellosis is not traditionally considered endemic, particularly when epidemiologic exposure is not identified and serologic tests yield discordant results. We report a case in which metagenomic next-generation sequencing (mNGS) of vertebral lesion tissue provided additional microbiologic evidence for the diagnosis.

CASE PRESENTATION: A 71-year-old man presented with a 2-month history of fatigue, anorexia, night sweats, and worsening back pain without an identifiable epidemiologic exposure. Imaging showed destructive T8-T9 spondylitis with intervertebral disc involvement, paravertebral soft-tissue swelling, and small abscess formation. CT-guided biopsy demonstrated inflammatory changes, while routine bacterial culture, lesion-based MTBC DNA/RNA testing, and mycobacterial culture were negative. Brucella-specific immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies were positive, whereas the standard tube agglutination test (SAT) titer was <1:25 and the Rose Bengal test (RBT) was negative. mNGS of vertebral lesion tissue detected Brucella spp. DNA. Serial serologic testing subsequently showed SAT titers of 1:200 and 1:400, with later conversion of the RBT to positive, providing further support for brucellar spondylitis. The patient received combination anti-brucellar therapy and underwent posterior thoracic fixation, spinal canal decompression, lesion debridement, and bone graft fusion because of extensive vertebral destruction and concern for spinal instability. At approximately 10 weeks after treatment initiation, while anti-brucellar therapy was ongoing, back pain had markedly improved.

LITERATURE REVIEW: Published studies suggest that mNGS may improve pathogen detection in selected spinal infections when conventional microbiologic testing is unrevealing. Reports of focal brucellosis also show that lesion-derived specimens may provide microbiologic evidence that complements peripheral serologic findings.

CONCLUSION: In this case, mNGS did not identify a previously unsuspected pathogen but added microbiologic evidence from the affected vertebral lesion to an otherwise discordant serologic profile. Tissue-based mNGS may be useful in selected patients with suspected BS when conventional serologic findings are discordant and culture is negative.},
}

@article {pmid42841085,
year = {2026},
author = {Lawson, CE and Howard, JP and Lankiewicz, TS and Brown, JB and Singer, SW and Martín, HG and O'Malley, MA},
title = {Carbohydrate-active enzyme architectures reflect distinct fungal and bacterial strategies for lignocellulose conversion to volatile fatty acids.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag262},
pmid = {42841085},
issn = {2730-6151},
abstract = {Anaerobic fermentation with microbial communities is an emerging platform for converting lignocellulosic biomass to biofuels and bioproducts. The process relies on diverse anaerobic microbes that interact to deconstruct and convert lignocellulosic biomass into a range of products, such as volatile fatty acids (VFAs), through arresting methanogenesis during fermentation. However, defining the distinct functional roles played by various fungi and bacteria during anaerobic biodegradation remains poorly understood. Here, we performed parallel enrichment experiments from cow feces, goat feces, and anaerobic digester sludge, selecting for fungal- or bacterial-dominated communities that convert sorghum biomass into VFAs. Subsequently, we reconstructed metabolic networks across these enrichments using recovered bacterial metagenome-assembled genomes (MAGs), fungal isolate genomes, and genome-centric metatranscriptomics. This enabled direct comparison of the carbohydrate-active enzymes and fermentation pathways expressed by bacterial and fungal communities during lignocellulose conversion to VFAs. Our findings implicate diverse bacteria affiliated with the Bacteroidales and Lachnospiraceae in the direct conversion of lignocellulosic biomass to propionate and butyrate, respectively, whereas Neocallimastix-dominated fungal enrichments converted lignocellulose to lactate, acetate, and formate. Analysis of carbohydrate-active enzymes revealed that bacterial and fungal communities primarily targeted the same dominant lignocellulosic substrates while employing distinct enzyme repertoires and multidomain carbohydrate-active enzyme architectures, highlighting complementary enzymatic strategies for accessing and deconstructing lignocellulosic biomass. We anticipate that these findings will help inform efforts to develop synthetic consortia with tailored functionality for low-cost conversion of lignocellulosic biomass to fuels and bio-based chemicals.},
}

@article {pmid42841094,
year = {2026},
author = {Liu, Q and Su, H and Gong, S and Jin, Y and Fan, Y and Wu, M and Guo, J and Ren, X and Wang, J},
title = {Quorum-sensing microbial dark matter enables core functions in wastewater microbiomes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag264},
pmid = {42841094},
issn = {2730-6151},
abstract = {Quorum-sensing bacteria (QSB) play a crucial role in coordinating microbial activities in activated sludge. However, our knowledge is primarily based on cultivated or taxonomically classified species, neglecting microbial dark matter (MDM), which comprises lineages lacking reference genomes and is prevalent in wastewater communities. Herein, 3569 high- and medium-quality metagenome-assembled genomes were obtained from 69 full-scale wastewater treatment plants. A total of 1289 MDM lineages were identified to possess quorum sensing (QS) capabilities, designated as MDM-QSB. Among them, 127 novel genera were identified. These organisms possess larger genomes enriched in genes for energy metabolism and environmental information processing, allowing a broader ecological niche compared to non-QS MDM (P < .001). They occupy central positions in co-occurrence networks and are predicted as dominant keystones by a deep learning model. Their robust metabolic potential and network keystone position enable coordinated community-level metabolic responses, as evidenced by stronger carbon, nitrogen, phosphorus, and sulfur element cycling functions and higher associations with chemical oxygen demand, total nitrogen, and ammonium nitrogen removal (P < .05). Furthermore, genome-scale metabolic modeling reveals they engage in extensive cross-feeding with nitrifiers, denitrifiers, and polyphosphate-accumulating organisms, supplying metabolites such as protoheme and serine alongside QS signals. Together, these findings identify MDM-QSB as previously overlooked multifunctional hubs of activated sludge microbiomes. Given their crucial roles in community stability and process performance, incorporating these previously overlooked populations into monitoring and control frameworks is expected to improve the resilience and predictability of biological wastewater treatment processes.},
}

@article {pmid42841652,
year = {2026},
author = {Voulgari-Kokota, A and Janson, E and Heikamp de Jong, I and Knol, J and van Elburg, R and van der Aa, NE and Hortensius, LM and Dudink, J and de Theije, CGM and Schipper, L and Kozior, M and van de Lagemaat, M and Groenendaal, F and van Bel, F and Wildt-Grootendorst, A and Drost-Verhoef, S and Hennink, A and Obihara, CC and van Hillegersberg-Schilder, JLAM and Dassel, CM and Oudshoorn, JH and Meijssen, CB and de Boer, IP and Illy, KE and Claessens, N and Viergever, MA and Isgum, I and Shetty, S and Wopereis, H and Benders, M and Belzer, C},
title = {Synbiotic supplementation leads to gut microbiome communities with functional capacity linked to better brain white matter development in preterm infants.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2743949},
doi = {10.1080/19490976.2026.2743949},
pmid = {42841652},
issn = {1949-0984},
mesh = {Humans ; Infant, Newborn ; *Infant, Premature/growth & development ; *White Matter/growth & development ; *Brain/growth & development ; *Gastrointestinal Microbiome ; *Synbiotics/administration & dosage ; Dietary Supplements ; Male ; Bifidobacterium breve ; Glutamine/administration & dosage ; Female ; Oligosaccharides/administration & dosage ; Neurodevelopment ; Magnetic Resonance Imaging ; Infant ; },
abstract = {Preterm birth, a major cause of brain injury, is often linked to dysregulated gut microbiome development. This association underscores microbial metabolic function as a modifiable target to support neurodevelopment. In this secondary analysis of data derived from a randomized controlled trial (Trial Registration: ISRCTN96620855), we tested whether daily nutritional supplementation with Bifidobacterium breve M-16V, short- and long-chain oligosaccharides, and L-glutamine could steer the gut microbiome of very and extremely preterm infants toward communities that support brain maturation. The gut microbiome was profiled with longitudinal shotgun metagenomics at nine time points during the intervention, which started at 48-72 h after birth and continued until 36 weeks postmenstrual age. Additionally, MRI scans were conducted when infants reached term-equivalent age to evaluate brain maturation. Supplementation promoted the early establishment of Bifidobacterium-rich communities in the test group, with enhanced capacity for amino acid biosynthesis and pyruvate fermentation towards acetate and lactate production. Integration of microbiome data with brain developmental markers post hoc showed that the same functions were markedly reduced in infants with delayed white-matter myelination. By integrating microbiome functional capacity profiling and evaluation of brain maturation via MRI, this study demonstrated that early microbial modulation could influence brain development, positioning the preterm gut microbiome as a clinically actionable target.},
}

Humans
Infant, Newborn
*Infant, Premature/growth & development
*White Matter/growth & development
*Brain/growth & development
*Gastrointestinal Microbiome
*Synbiotics/administration & dosage
Dietary Supplements
Male
Bifidobacterium breve
Glutamine/administration & dosage
Female
Oligosaccharides/administration & dosage
Neurodevelopment
Magnetic Resonance Imaging
Infant

@article {pmid42833337,
year = {2026},
author = {Yang, Y and Chen, W and Wang, J and Gao, X and Wang, G and Zou, L and Li, S and Li, G and Yuan, J},
title = {Oxygen availability shapes microbial community composition and function to determine antibiotic resistance genes and expression during composting: A pilot-scale study.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129287},
doi = {10.1016/j.envpol.2026.129287},
pmid = {42833337},
issn = {1873-6424},
abstract = {Temperature was considered the primary factor reducing antibiotic resistance genes (ARGs) during composting, with oxygen availability serving as the fundamental driver of temperature differences. However, how different oxygen levels shaped the composition and function of microbial communities, and subsequently affected ARGs and resistance expression during composting, remained unclear. Here, a pilot-scale long-term thermophilic aerobic and mesophilic facultative composting were constructed with metagenomics and stress (Oxygen/Antibiotic) plate screening to reveal the resistance potential and direct risk. The ratios of aerobic, facultative, and anaerobic bacteria were 1:0.94:0.75 in aerobic composting, and 1:0.96:0.99 in facultative composting. Metabolic functions were significantly enriched in aerobic composting, promoting temperature rise (peak 54 °C). In facultative composting, functions related to horizontal gene transfer and transcription/translation were enriched. Compared with mesophilic facultative composting, aerobic composting significantly reduced ARGs abundance (from 4.80 to 3.59 CPC) and mobility (from 3.66 to 2.27 CPC). ARGs hosts in aerobic composting were widely distributed, predominantly among aerobic microorganisms, while ARGs hosts in facultative composting were more concentrated, mostly among facultative anaerobes. The relative abundance of culturable antibiotic-resistant bacteria (25.00% vs. 15.88%) and active antibiotic-resistant pathogens (44.04% vs. 6.68%) were significantly higher in facultative composting than in aerobic composting. This study revealed the pathway by which oxygen shaped the composition and function of microorganisms with different oxygen requirements, thereby influencing compost antibiotic resistance, providing a theoretical basis for the safe application of manure to agricultural fields.},
}

@article {pmid42833404,
year = {2026},
author = {Wang, Z and Xue, Y and Cao, Y and Zhu, Y and Zhang, G and Zhong, C and Xin, H},
title = {Multi-omics profiling reveals the role of gut microbiota and associated metabolites in postweaning oxidative stress in Holstein dairy calves, particularly in relation to amino acid synthesis and metabolism.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-29112},
pmid = {42833404},
issn = {1525-3198},
abstract = {To investigate the relationship between post-weaning oxidative stress (OS) and gut microbiota in dairy calves, 332 Holstein calves were enrolled and weaned uniformly at 64 d of age. Based on plasma oxidative stress index (OSI) measured at 3 d post-weaning (67 d of age), 10 calves with the highest OSI (post-Hos) and 10 with the lowest OSI (post-Los) were selected for subsequent analyses. Fecal samples collected at the same time point were subjected to 16S rRNA gene sequencing, metagenomic sequencing, and LC-MS untargeted metabolomics analysis. No significant differences in fecal score (FS) were observed between groups on weaning day, although a trend toward incraeased FS was noted in post-Hos calves after weaning (P = 0.075). Microbiota analysis revealed that post-Los calves were enriched in f__Lachnospiraceae, o__Lachnospirales, and f__Barnesiellaceae, whereas post-Hos calves showed enrichment of o__Oscillospirales, f__Oscillospiraceae, and g__Ruminococcaceae_UCG-005, with the latter showing a trend of higher abundance (P = 0.064). Spearman correlation analysis identified multiple genera, particularly Barnesiella and Muribaculum, significantly associated with OSI. Metagenomic functional profiling indicated enhanced pyruvate metabolism and caprolactam degradation pathways in post-Los calves. Metabolomics detected 240 differential metabolites between the 2 groups, significantly enriched in 19 KEGG pathways, notably those related to amino acid metabolism and arginine biosynthesis. Collectively, these findings demonstrate that OS levels in post-weaning calves are associated with distinct alterations in gut microbial composition, functional capacity, and metabolic profiles, with microbiota-involved arginine biosynthesis likely playing a role in this association. This study provides correlational evidence suggesting that modulating amino acid metabolism may represent a potential strategy for alleviating weaning-induced OS.},
}

@article {pmid42833451,
year = {2026},
author = {Luo, Y and Lin, Y and Chen, Z and Lin, J and Owens, G and Chen, Z},
title = {Bioresource amendment promotes early mineralization and nitrification recovery in ammonium-rich rare earth tailings.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136014},
doi = {10.1016/j.biortech.2026.136014},
pmid = {42833451},
issn = {1873-2976},
abstract = {Rare earth tailings soil retains high residual NH4[+]-N after in-situ leaching with ammonium sulfate, creating coupled risks of nitrogen loss and poor revegetation. The substrate and microbial pathways that reopen ammonia oxidation and mediate nitrification restart in this ammonium rich rare earth tailings soil remain unclear. To address this gap, a microcosm incubation over time compared an unamended soil, MgO, and manure, integrating nitrogen transformations, net mineralization, enzymes, qPCR, and shotgun metagenomics. Under OM, extractable NH4[+]-N declined by 88.3 % from its initial value, while oxidized inorganic N accumulated. Three related functional patterns were observed under OM. First, an early apparent net N mineralization pulse occurred under DCD inhibition, peaking at 15.45 mg N kg[-1] d[-1], alongside evidence of peptide cleavage and amino sugar turnover. Second, ammonia oxidation was reactivated, as indicated by enrichment of amoABC and hao and increases of 2.8 to 15-fold in archaeal and bacterial amoA. Third, manure enhanced functional network integration between nitrogen cycling and substrate metabolism genes, with functional coupling associated with inorganic N, CEC, and SOM. These findings suggest a role for biological functional reconstruction in restoring nitrogen cycling in ammonium rich rare earth tailings soil.},
}

@article {pmid42833455,
year = {2026},
author = {Chen, L and He, B and Wu, Y and Wang, G and Yang, F and Ban, S and Yang, L},
title = {Thresholded acidity-oxygen stress activates Acetilactobacillus jinshanensis and drives a shift toward deterministic community assembly during breakpoint fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136011},
doi = {10.1016/j.biortech.2026.136011},
pmid = {42833455},
issn = {1873-2976},
abstract = {Multi-round stacking fermentation links successive production rounds with pit fermentation in Moutai-flavor Baijiu, but quantitative indicators of microbial restructuring remain unclear. This study combined physicochemical monitoring, metagenomics, metatranscriptomics and quantitative polymerase chain reaction across 207 samples from three successive stages. Increasing acidity and lactic acid, starch consumption and late-stage community convergence characterized the stage sequence. Fitted community-displacement relationships showed acidity turning points near 1.0-1.2, whereas no universal oxygen threshold was supported. A composite stress index integrating acidity, acetic acid, lactic acid and inverse oxygen showed a pooled Acetilactobacillus jinshanensis abundance turning point near 0.27. This relationship differed among stages and heaps and did not establish a universal activation threshold. Adding the index did not improve between-team abundance prediction under the evaluated models. Community-level transcripts showed selective redistribution of acid-homeostasis, proton-transport, chaperone, organic-acid-metabolism and redox-related functions. Assembly analyses indicated stronger homogeneous-selection signals, whereas network associations varied by stage without demonstrating a universal hub or experimentally verified ecological role. These observations identify candidate transition windows in the studied stacking system and require process-specific validation before operational application.},
}

@article {pmid42833543,
year = {2026},
author = {An, Z and Yan, C and Cai, J and Ma, WJ and Tian, Y and Zhang, H},
title = {Unveiling the microbial and metabolic mechanisms of a novel anaerobic/micro-aerobic/anoxic (AMA) strategy for nutrient removal and carbon utilization from low C/N high-strength ammonium wastewater.},
journal = {Environmental research},
volume = {309},
number = {Pt 2},
pages = {125851},
doi = {10.1016/j.envres.2026.125851},
pmid = {42833543},
issn = {1096-0953},
abstract = {Achieving cost-effective advanced nitrogen removal with minimal external carbon input remains a key challenge in wastewater treatment plants processing high-strength ammonium wastewater with a low carbon-to-nitrogen (C/N) ratio. In this study, an anaerobic/micro-aerobic/anoxic (AMA) system was established to treat such wastewater at a C/N ratio of 2.5 by integrating simultaneous nitrification, anaerobic ammonium oxidation (anammox), and endogenous denitrification, collectively referred to as SNAED. The system achieved average removal efficiencies of 92.5% for NH4[+]-N, 89.9% for total nitrogen (TN), and 94.8% for COD, treating influent wastewater containing 200.0 mg/L of NH4[+]-N and 200.0 mg/L of TN. The relative abundance of Candidatus Brocadia reached 0.5%, indicating effective in situ enrichment of anammox bacteria (AnAOB). Metagenomic analysis revealed that the elevated abundances of narGHI, norBC, nosZ, and hdh were crucial for enhancing TN removal. Concurrently, the increased number of metagenomic reads (117,130 reads) affiliated with Candidatus Competibacter, a representative denitrifying glycogen-accumulating organism, and annotated to metabolic pathway categories indicates an enhanced functional potential for endogenous denitrification. A stable and functionally diverse microbial community, consisting of ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, AnAOB, denitrifying polyphosphate-accumulating organisms, and denitrifying glycogen-accumulating organism, was established and played a pivotal role in sustaining the SNAED process. These findings demonstrate that AMA system offers a sustainable and efficient strategy for low-energy nitrogen removal.},
}

@article {pmid42833591,
year = {2026},
author = {Galletti, JG and Scholand, KK and Shao, J and Fujisaki, EP and Kumar, P and Demianova, EA and San Juan, EJJ and Schaefer, L and de Paiva, CS},
title = {Mechanisms of CD4[+] T tolerance to a corneal epithelial neoantigen.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {100418},
doi = {10.1016/j.mucimm.2026.100418},
pmid = {42833591},
issn = {1935-3456},
abstract = {Tissue-specific peripheral tolerance mechanisms are essential to prevent autoimmunity. The cornea is immune privileged, and anterior chamber-associated immune deviation (ACAID) governs its inner surface. However, the mechanisms governing corneal epithelial (outer surface) antigens remain unknown. Using an inducible, cornea-restricted neoantigen mouse model, we found that tolerance of corneal epithelial antigens is associated with antigen-specific regulatory T cell (Treg) induction. Although the cornea is both avascular and alymphatic, its epithelial antigens are still efficiently presented by ocular surface-derived antigen-presenting cells to T cells in draining lymph nodes under homeostatic conditions, leading to conventional antigen-specific Treg expansion without ocular pathology. This tolerance was not absolute: systemic immunization redirected antigen-specific responses toward pathogenic effector T cells that disrupted epithelial barrier function. These findings identify Treg induction and anergy as mechanisms linked to corneal epithelial immune homeostasis and demonstrate that inflammatory priming can render a previously tolerated corneal antigen into an autoimmune target, providing mechanistic insight into ocular surface disease pathogenesis.},
}

@article {pmid42833873,
year = {2026},
author = {Haque, M and Lesker, TR and Rolle-Kampczyk, U and Segers, A and De Vos, WM and Molinaro, A and Basavanapura, T and Chen, Y and Backhaus, M and Mohamed, MR and Jiang, L and Salih, Q and Candels, L and Henricsson, M and Bielecka, A and Lang, S and Tacke, F and Hengstler, JG and Schneider, CV and Demir, M and Strowig, T and von Bergen, M and Schneider, KM and Trautwein, C},
title = {Microbiota-host genetic interactions modulate MASLD risk in PNPLA3[I148M] carriers via ceramides and are reversible by targeted microbial interventions.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338178},
pmid = {42833873},
issn = {1468-3288},
abstract = {BACKGROUND: The factors that determine when genetic susceptibility to metabolic dysfunction-associated steatotic liver disease (MASLD) progresses to clinically significant liver injury remain incompletely understood.

OBJECTIVE: We investigated whether disruption of the intestinal host-microbiota interface acts as a contextual modifier that amplifies PNPLA3[I148M] -associated hepatic injury.

DESIGN: We used a dual-hit mouse model combining hepatic Pnpla3[I148M] -expression with Nlrp6-deficiency, a model of impaired intestinal mucosal homeostasis, under western-diet conditions. Multi-omics profiling, including metagenomics, metabolomics and transcriptomics, was integrated with analyses in human cohorts (Lifelines, Charité MASLD, Human Phenotype Project). Microbiota-dependent effects were examined using faecal microbiota transplantation (FMT), antibiotic-mediated depletion and targeted intervention with Akkermansia muciniphila or its membrane protein Amuc_1100.

RESULTS: In mice, the combination of Pnpla3[I148M] expression and impaired intestinal sensing synergistically exacerbated gut-barrier dysfunction and bacterial encroachment, accompanied by increased portal levels of microbiota-associated metabolites, including long-chain ceramides (Cer(d18:1/16:0), Cer(d18:1/18:0)) and bile acids. These changes were associated with hepatic mitochondrial stress and inflammatory responses. Human carriers with advanced MASLD displayed microbial and metabolic signatures consistent with increased gut-derived metabolic signalling. Restoration of eubiotic microbiota via FMT or Amuc_1100 treatment improved intestinal barrier integrity and attenuated hepatic lipid accumulation in experimental models.

CONCLUSION: These findings suggest that gut-derived signals resulting from a disrupted intestinal barrier may act as modifiers of PNPLA3[I148M] -clinical penetrance by amplifying downstream metabolic and inflammatory responses. By identifying these pathways linking environmental context to genetic susceptibility, this study highlights the host-microbiota interface as a potential target for strategies aimed at limiting MASLD progression in genetically at-risk individuals.},
}

@article {pmid42834399,
year = {2026},
author = {Correa, F and Luise, D and Palumbo, F and Scicchitano, D and Rampelli, S and Molino, S and Panciroli, N and Candela, M and Garay-Mayol, B and Ávila-Gálvez, MÁ and González-Sarrías, A and Castagnetti, A and Trevisi, P},
title = {Chestnut-quebracho tannins shape the fecal metabolome of weaned pigs through microbiota-dependent urolithin production.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42834399},
issn = {1674-9782},
support = {n.818290//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Chestnut and quebracho tannins may support gut health in weaned piglets, but their efficacy likely depends on farm environment and microbial capacity to convert tannins into bioactive metabolites. This study evaluated the effects of a blend of chestnut-derived hydrolysable tannins and quebracho-derived condensed tannins on growth performance, diarrhea occurrence, gut metagenome, and fecal metabolome in piglets reared under two commercial farm conditions. A total of 160 weaned piglets (initial body weight 6.53 ± 0.13 kg) were assigned to a 2 × 2 factorial design comprising 2 weaning units (W1 and W2) and 2 dietary treatments (control diet or control diet + 2 g/kg tannin blend; 40 piglets per treatment × farm). The trial lasted 76 d, with weighings at T0 (entry into weaning, median 28 d), T1 (d 35), T2 (d 49), and T3 (d 76). Fecal scores and samples were collected at T1, T2, and T3 for shotgun metagenomics (155 samples per time point) and untargeted metabolomics, and targeted urolithin quantification was performed in tannin-treated piglets at T1 and T2.

RESULTS: Tannin supplementation did not affect overall growth performance throughout the weaning phase, but reduced diarrhea occurrence at T2 in W2 (P = 0.032). Species-level beta diversity was consistently affected by treatment across time points (R[2]= 0.01-0.03; P < 0.01), whereas alpha diversity was mainly farm-driven during the early post-weaning phase. Linear discriminant analysis effect size identified farm-dependent taxonomic markers, including Escherichia coli in control pigs from W1 at T1 and Megasphaera elsdenii, Faecalibacterium prausnitzii, and Lactobacillus amylovorus in tannin-treated pigs at later time points. Untargeted metabolomics revealed treatment-related fecal signatures, with isourolithin A and urolithin B among the most discriminant metabolites in treated pigs, especially in W2. Targeted analysis identified 3 urolithin metabotypes (metabotype B in 50.0% of samples), with higher isourolithin A, urolithin B, and urolithin A in W2 than W1 at T2 (P < 0.01). Network integration identified candidate cooperative microbial consortia associated with urolithin production, including Ellagibacter isourolithinifaciens; these co-abundance associations are correlative and remain to be functionally validated.

CONCLUSIONS: Overall, chestnut-quebracho tannins were associated with a farm-dependent reduction in post-weaning diarrhea and modulated the gut ecosystem through microbiota-dependent polyphenol metabolism.},
}

@article {pmid42834904,
year = {2026},
author = {Chulenbayeva, L and Rakhmankulova, A and Kamzayeva, N and Kozhakhmetov, S and Terzic, M and Bapayeva, G and Aimagambetova, G and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Ukybassova, T and Kushugulova, A},
title = {Cervicovaginal microbiome alterations across HPV infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907605},
pmid = {42834904},
issn = {2235-2988},
mesh = {Humans ; Female ; *Microbiota ; *Papillomavirus Infections/virology/microbiology ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Human Papillomavirus Viruses/classification/genetics ; Cross-Sectional Studies ; Adult ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Dysbiosis ; Papillomaviridae/classification/genetics ; },
abstract = {INTRODUCTION: The cervicovaginal microbiome is a proposed modifier of HPV-associated cervical disease, yet its relationship with viral type heterogeneity, cytological grade, and community state type (CST) remains incompletely understood.

METHODS: This cross-sectional study characterized cervicovaginal microbiome composition and functional potential across HPV infection status, viral type categories (No HPV, HPV High Risk, HPV16, HPV18, HPV Other), cervical cytological grades, and CSTs in 311 non-pregnant women using whole-genome shotgun metagenomic sequencing, integrated diversity analyses, MaAsLin2 differential abundance testing, and HUMAnN 3.0 functional pathway profiling.

RESULTS: HPV-positive samples showed increased bacterial species richness, and a reciprocal Lactobacillus-to-Gardnerella dominance shift compared to HPV-negative samples. HPV Other showed the highest bacterial species richness and distinct taxonomic and predicted functional associations, including higher inferred abundance of siderophore- and lipopolysaccharide-biosynthesis pathways; however, overall species-level community composition did not differ significantly across HPV type groups. CST I and CST II exhibited compositional stability regardless of HPV status, while CST IV showed pronounced Lactobacillus depletion in HPV-positive women. LSIL was associated with lower Fannyhessea vaginae and Alloscardovia omnicolens abundance and higher Phocaeicola vulgatus abundance relative to NILM.

DISCUSSION: These findings indicate that oncogenic potential and dysbiosis severity are not aligned, and that CST type modifies HPV-microbiome interactions.},
}

Humans
Female
*Microbiota
*Papillomavirus Infections/virology/microbiology
*Vagina/microbiology/virology
*Cervix Uteri/microbiology/virology
*Human Papillomavirus Viruses/classification/genetics
Cross-Sectional Studies
Adult
Bacteria/classification/genetics/isolation & purification
Metagenomics
Dysbiosis
Papillomaviridae/classification/genetics

@article {pmid42835196,
year = {2026},
author = {Liang, S and Ma, J and Zhang, H and Li, H and Zou, S and Li, D},
title = {Research on the spillover risk of antibiotic resistance gene from the gut microbiome of wild animal: A case study of the golden snub-nosed monkey.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117624},
pmid = {42835196},
issn = {2589-0042},
abstract = {Wild animals are "reservoirs" of antibiotic resistance genes (ARGs), and the interface of rivers between wild animals and humans is an ideal environment for spreading ARGs. In order to explore the risk of ARGs from wild animals to the human ecosystem through rivers, metagenomic sequencing was used to obtain the microbiome in the gut of golden snub-nosed monkeys (Rhinopithecus roxellana) and in the rivers. We performed collinearity analysis between the high-risk ARGs (Rank I ARGs) from golden snub-nosed monkeys and the metagenome-assembled genomes (MAGs) from river samples to assess the potential of river microorganisms to acquire Rank I ARGs. The number of collinear events between Rank I ARGs and MAGs in the WHD group (rivers within the disturbed monkey habitat) was five times higher than that in the WCK (rivers within the undisturbed monkey habitat) group. This implies a significant spillover risk of ARGs from wild animals to the human ecosystem via river interfaces, a risk that is further intensified by human disturbances. This research complemented the content that evaluated the spillover risk of ARGs from wild animals to humans.},
}

@article {pmid42835245,
year = {2026},
author = {Mujahid, W and Safdar, S and Aftab, A and Tabassum, S and Bakhtiar, SM},
title = {Integrative Metagenomic Analysis Reveals Human Gut Microbiome-Derived Candidate Non-invasive Biomarkers for Type II Diabetes Mellitus.},
journal = {Iranian journal of medical sciences},
volume = {51},
number = {9},
pages = {617-629},
pmid = {42835245},
issn = {1735-3688},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/diagnosis ; Biomarkers/analysis ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics/physiology ; Case-Control Studies ; Bacteroides/genetics ; Dysbiosis/diagnosis ; },
abstract = {BACKGROUND: Type II Diabetes Mellitus (T2DM) is increasingly associated with alterations in the gut microbiome, which influences host metabolism, inflammation, and insulin sensitivity. Metagenomic profiling has emerged as a promising non-invasive strategy for identifying disease-associated microbial signatures. However, distinguishing disease-specific biomarkers from general dysbiosis remains a major challenge. This study aimed to develop an integrative subtractive metagenomic framework to identify candidate disease-specific gut microbial biomarkers.

METHODS: This in silico case-control study used publicly available metagenomics datasets from healthy controls and individuals with T2DM. Assembly-based and read-based taxonomic profiling approaches were integrated. Differential abundance analysis using the Wilcoxon rank-sum test identified key microbial taxa significantly associated with T2DM.

RESULTS: Potential microbial biomarkers were identified as Bacteroides dorei, Bacteroides gracilis, Bacteroides stercoris, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Eggerthella lenta, Escherichia coli, Faecalibacterium prausnitzii, Parabacteroides distasonis, Ruminococcus torques, and Subdoligranulum. These taxa are involved in gut metabolic homeostasis and may serve as candidate non-invasive biomarkers for T2DM.

CONCLUSION: The results of this study advance understanding of microbiome-disease crosstalk and form the basis for further in vitro and in vivo validation and microbiome-targeted therapeutic approaches. Overall, this integrative metagenomic study supports alteration of microbial ecology in T2DM, validating the use of gut microbiome profiling as a diagnostic and therapeutic tool in metabolic disease research.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/diagnosis
Biomarkers/analysis
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics/physiology
Case-Control Studies
Bacteroides/genetics
Dysbiosis/diagnosis

@article {pmid42835332,
year = {2026},
author = {Wang, Z and Guo, M and Huang, Z and Cheng, J and Chen, Y and Lai, L and Xiao, J and Huang, W and Chen, Y},
title = {Metagenomic and metabolomic profiling of laterally spreading tumors identifies a microbiome with putative pro-tumorigenic features in high-grade intraepithelial neoplasia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844759},
pmid = {42835332},
issn = {1664-302X},
abstract = {INTRODUCTION: Laterally spreading tumors (LSTs) are pathologically classified into adenomas, including low-grade intraepithelial neoplasia (LGIN) and high-grade intraepithelial neoplasia (HGIN), and sessile serrated lesions (SSL). HGIN has a higher risk of progressing to colorectal cancer.

METHODS: This study compared the gut microbiome across these three pathological subtypes using fecal shotgun metagenomic sequencing and non-targeted metabolomics in 53 patients.

RESULTS: Overall community structure was similar among groups by Bray-Curtis NMDS and ANOSIM, although HGIN exhibited higher alpha diversity than SSL and enrichment of inflammation-associated and opportunistic taxa (e.g., Desulfovibrio, Bilophila, Helicobacter, Acinetobacter) alongside depletion of selected commensal taxa associated with mucosal homeostasis, including Bifidobacterium-, Lachnospiraceae-, and Ruminococcus-related species. Functionally, the HGIN-associated microbiome showed an expanded resistome and increased mobile genetic element-related potential, particularly in the HGIN versus LGIN comparison, with enrichment of beta-lactamase genes, MCR-family genes, and mobileOG features related to DNA transfer, recombination, transposition, plasmid maintenance, secretion, pilus-associated functions, and phage-linked mobility. In exploratory analyses, untargeted metabolomics suggested a bile- and lipid-rich metabolic pattern in HGIN, with nominal increases (P < 0.05; none significant after FDR correction) in lithocholyltaurine, LysoPE(P-16:0/0:0), tridecanoic acid and cortexolone. GSEA revealed nominal enrichment of unsaturated fatty acid biosynthesis, pyruvate metabolism, and propanoate metabolism. Exploratory species-metabolite correlations linked HGIN-enriched pathobionts with lipid/steroid-, bile-acid-, amino-acid-, and fatty-acid-related metabolites, while HGIN-depleted commensals were associated with amino-acid and organic-acid metabolic features.

DISCUSSION: Together, these findings identify microbial and metabolic features associated with high-grade histopathology within the LST spectrum, including FDR-supported microbial remodeling-pathobiont enrichment and expanded resistome and mobile genetic potential-accompanied by exploratory, nominally significant metabolomic alterations involving bile/lipid- and SCFA-related metabolites.},
}

@article {pmid42835638,
year = {2026},
author = {Nagase, R and Oba, K and Asakura, M and Ogasawara, M and Noda, M and Yamada, Y and Furukawa, A and Kojima, N and Hashino, M and Horiba, K},
title = {Utility of Metagenomic Next-Generation Sequencing in Identifying Anaerobic Pathogens in a Pediatric Brain Abscess Secondary to Sinusitis: A Case Report.},
journal = {Clinical case reports},
volume = {14},
number = {10},
pages = {e73688},
pmid = {42835638},
issn = {2050-0904},
abstract = {In this pediatric brain abscess case, metagenomic next-generation sequencing (mNGS) identified an anaerobic bacterium that remained undetected using conventional culture methods, thus providing clinically relevant information for antimicrobial management. This indicates that mNGS may be a useful adjunct for optimizing treatment strategies.},
}

@article {pmid42836017,
year = {2026},
author = {Agrimbau Vázquez, J and Boggio Marzet, C and Peralta, R and Taussig, R and Lopez, P and Viale, D and Alonso, C and Curtti, T and Perez Gagni, ML and Cassará, ML and Urrutia, L and Bustamante, JP},
title = {Altered gut microbial functional landscape in children with pediatric inflammatory multisystem syndrome following SARS-CoV-2 infection: an exploratory metagenomic study.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1881538},
pmid = {42836017},
issn = {2296-2360},
abstract = {BACKGROUND: Pediatric Inflammatory Multisystem Syndrome (PIMS), also known as MIS-C (Multisystem inflammatory syndrome in children), is a severe post-infectious inflammatory condition associated with SARS-CoV-2 in children. While coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, primarily affects the respiratory system, growing evidence highlights gastrointestinal involvement and the relevance of the gut-lung axis in systemic inflammation. However, the taxonomic and, particularly, the functional landscape of the gut microbiome in children with PIMS remains insufficiently characterized.

METHODS: This exploratory study analyzed fecal samples from pediatric patients diagnosed with PIMS and age-matched clinically healthy controls using shotgun metagenomic sequencing. Taxonomic profiling was performed with MetaPhlAn4, and functional and metabolic pathway analyses were conducted using HUMAnN3. Alpha and beta diversity metrics were assessed, and differential abundance analyses were applied to identify microbial taxa and putative functional pathways associated with PIMS.

RESULTS: 12 pediatric patients diagnosed with PIMS and 11 age-matched clinically healthy controls were included. Alpha diversity indices did not differ significantly between groups, although consistently lower mean values were observed in children with PIMS. In contrast, beta diversity analysis demonstrated a significant separation in microbial community composition between patients with PIMS and controls (PERMANOVA, p = 0.01). Children with PIMS exhibited increased relative abundance of Prevotella copri clade C, Duodenibacillus massiliensis, Phascolarctobacterium succinatutens, and Enterocloster bolteae, alongside a relative reduction of several commensal taxa. Putative functional profiling revealed significant differences in enzyme-coding genes and metabolic pathways, including increased metagenomic abundance of aconitate hydratase and other functions potentially relevant to inflammatory and immunomodulatory processes in the PIMS group.

CONCLUSION: These findings suggest an association between gut microbiota unbalance, potential microbial functional alterations, and PIMS, supporting the need for further investigation of the gut microbiome in post-COVID-19 systemic inflammation in pediatric populations. Given the exploratory nature of this study, these observations require validation in larger, longitudinal cohorts before microbial biomarkers or therapeutic implications can be established.},
}

@article {pmid42836028,
year = {2026},
author = {Emmanuel Shittu, O and Ge, J and Babalola, OO},
title = {Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.},
journal = {International journal of genomics},
volume = {2026},
number = {},
pages = {3098615},
pmid = {42836028},
issn = {2314-4378},
abstract = {The increasing demand for resilient and sustainable food production necessitates a comprehensive understanding of rhizosphere microbial communities and their functional roles in enhancing plant health, nutrient acquisition, stress resilience, and crop productivity, thereby supporting food security and sustainable agriculture. However, soil microbiomes are composed of complex and unculturable communities of beneficial microorganisms that drive critical ecosystem functions, which traditional culture methods cannot capture. This limits the understanding of their roles and impacts on plant health and agricultural sustainability. Metagenomic tools have emerged as transformative approaches for characterizing microbial diversity in soil. Therefore, this review presents an overview of how metagenomic techniques can be harnessed to predict microbial community structures and their associated functional potentials, ultimately contributing to the development of resilient farming strategies. Next-generation sequencing and bioinformatics enable metagenomics to analyze microbial genetic material in soil and rhizospheres. This study provides insights into microbial diversity and profiles of key functional genes linked to nutrient availability and soil functions. We discuss the use of metagenomics tools to predict soil health and microbial functions for sustainable agroecosystems, emphasizing predictive models that help farmers optimize yields and minimize environmental impact. This review explores how metagenomics tools in agriculture can serve as a predictive model to transform our understanding of soil-microbe interactions. This advancement can facilitate the formulation of novel, more resilient, productive, and sustainable agricultural systems.},
}

@article {pmid42836471,
year = {2026},
author = {Husted, C and Alonso, J and Swofford, R and Stengle, AG and Moreira, LR and Neafsey, DE and Johnston, RA and Baitchman, E and Genereux, DP and Daniels, R and Karlsson, EK},
title = {Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus).},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esag080},
pmid = {42836471},
issn = {1465-7333},
abstract = {Genomic tools are increasingly important for conservation and wildlife health surveillance, yet their use is often constrained by limited resources, sample quality, and the need for minimally invasive approaches. Here we show that untargeted low-coverage sequencing applied to scale-clip DNA can jointly address population structure, genotype-phenotype associations, and pathogen surveillance in timber rattlesnakes (Crotalus horridus), a species threatened by habitat fragmentation, human encroachment, and the emerging fungal pathogen Ophidiomyces ophidiicola. We sequenced 107 snakes sampled from eight populations in the Appalachian Mountains of the northeastern United States to a mean depth of 0.94x per individual. Population differentiation is pronounced and only weakly correlated with geographic distance, and inbreeding coefficients in some populations are high enough to suggest fitness consequences. Genome-wide association analysis identifies a locus for black-to-yellow color morph containing ALDH4A1, a member of a gene family implicated in vertebrate pigmentation but distinct from melanin pathway pigmentation genes. Our untargeted sequencing method also captures host-associated microbes: O. ophidiicola loads are higher in snakes with clinical signs of snake fungal disease, though some asymptomatic individuals carry substantial loads, and skin-associated microbial communities are disrupted in snakes with higher fungal burdens. That all of these inferences derive from the same minimally invasive sampling and sequencing workflow highlights the scalability of this approach for biodiversity conservation.},
}

@article {pmid42836481,
year = {2026},
author = {Xie, L and Wang, L and Ma, L and Wang, J and Wu, D and Lin, A and Wang, L and Ye, M and Li, X and Zhang, T and Zhu, D},
title = {Microplastic-driven carbon availability differentiates phage-host interactions in shaping soil resistome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag258},
pmid = {42836481},
issn = {1751-7370},
abstract = {The growing prevalence of microplastics (MPs) in agroecosystem has raised significant concerns regarding their ability in facilitating the dissemination of antibiotic resistance genes (ARGs). Biodegradable and nondegradable MPs exhibited inherently different degradation rates, resulting in divergent carbon bioavailability that might trigger distinct microbial response and ARG profiles. Here, by integrating multi-omics (metagenomics, virome and metatranscriptomics) with experimental validation, we explored how microbial responses to MPs impacted ARG dissemination in a long-term field experiment. We showed that both biodegradable and nondegradable MPs significantly increased ARG abundance and transcriptional activity, differing in the drive mechanisms. Biodegradable MPs triggered bacterial oxidative stress and SOS response, increasing mobile genetic elements abundance and horizontal gene transfer of ARGs. Accordingly, increasing proportion of lysogenic phages and intensified phage-host interactions might promote ARG transduction through lysogenic conversion. In contrast, nondegradable MPs increased recalcitrant carbon, which enriched bacteria harboring genes for complex compound degradation. ARG-carrying bacteria within these taxa gained fitness advantages, facilitating their enrichment and ARG proliferation. Concurrently, phages infecting ARG-carrying bacteria encoded more auxiliary metabolic genes in complex carbohydrate metabolism, thereby enhancing host competitiveness and promoting ARG spread. In vitro validation experiments confirmed that lysogenic phages facilitated transduction of ARGs under biodegradable MPs, while phage-encoded auxiliary metabolic genes conferred growth advantages on ARG-carrying bacteria utilizing recalcitrant carbon source, consistent with conditions induced by nondegradable MPs. Our findings clarify how phages differentially impacted ARG profiles under biodegradable and nondegradable MPs, underscoring the importance of considering phage-mediated processes in assessing the risks of MPs and ARG dissemination.},
}

@article {pmid42836545,
year = {2026},
author = {Toshchakov, SV and Gorlenko, VM and Kalashnikov, AM and Gaisin, VA and Grouzdev, DS and Petrova, KO and Barkhutova, DD and Namsaraev, ZB},
title = {'Candidatus Viridifilum namsaraevi' gen. nov., sp. nov., a new mesophilic filamentous anoxygenic phototrophic bacterium from the mesothermal lake Umkhey (Buryatia).},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag121},
pmid = {42836545},
issn = {1574-6968},
abstract = {The evolution of phototrophy and carbon fixation in the phylum Chloroflexota remains incompletely understood, largely due to the scarcity of cultured mesophilic representatives. Here, we report the isolation and genomic characterization of a novel filamentous anoxygenic phototrophic bacterium from a microbial mat in the mesothermal Lake Umkhey (Southern Siberia). Although the original culture was lost, its genome was recovered via metagenome-assembled genome reconstruction from environmental samples, enabling a detailed phylogenomic and metabolic analysis. The genome of umkhey_bin13 (proposed as 'Candidatus Viridifilum namsaraevi' gen. nov., sp. nov.) encodes a complete 3-hydroxypropionate bicycle for autotrophic CO2 fixation, a type II sulfide:quinone oxidoreductase, but lacks nitrogenase and chemolithotrophic markers. Comparative genomics across 18 Chloroflexota genomes reveals that this new lineage occupies an intermediate phylogenetic position, with distinct gene content for sulfur, nitrogen, and hydrogen metabolism, and highlights a complex evolutionary history within the group. Our findings provide new insights into the evolutionary transitions of photosynthetic and carbon-fixation pathways, and underscore the value of integrating cultivation-independent genomics with classical microbiology. The proposed novel genus and species contribute to a revised framework of Chloroflexota evolution and offer a genomic reference for studying metabolic adaptation in alkaline, sulfide-influenced microbial mats.},
}

@article {pmid42836610,
year = {2026},
author = {Ruth, N and Shakya, M and Lewis, CD and Erickson, CE and Dolinski, A and Jankowski, M and Fair, JM and Owen, JC and Bartlow, AW},
title = {Mallard super-shedders of avian influenza exhibit distinct cloacal microbial abundance profiles.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208926},
doi = {10.1128/spectrum.02089-26},
pmid = {42836610},
issn = {2165-0497},
abstract = {In many infectious disease systems, a small fraction of hosts accounts for a disproportionate share of transmission, but the biological basis of this heterogeneity remains poorly resolved. In avian influenza, mallards show substantial variation in viral shedding, raising the possibility that only a subset of individuals contributes strongly to environmental contamination and onward spread. To examine whether host microbiome structure is associated with this variation, we experimentally infected wild, captive mallards with low-pathogenic avian influenza virus. We characterized cloacal microbiomes across control, low-shedding, and high-shedding birds using shotgun metagenomic sequencing combined with read-based taxonomic profiling and co-assembled metagenome-assembled genome (MAG) reconstruction. Although infected and uninfected birds were highly similar in species presence-absence, abundance-based analyses showed clear differences in shared taxa, particularly in high-shedding birds relative to controls. Differentially abundant taxa were dominated by taxa that belonged to groups that include host-associated opportunists, consistent with compositional imbalance rather than complete community restructuring. The phylum Pseudomonadota, especially the families Enterobacteriaceae and Moraxellaceae, is well represented. Together, these findings suggest that avian influenza infection is associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in species membership and that microbiome structure is associated with heterogeneity in shedding in a key wildlife reservoir.IMPORTANCEA small fraction of infected hosts often accounts for a disproportionate share of pathogen shedding, but the biological factors underlying this variation remain poorly understood. In experimentally infected mallards, a key wildlife reservoir for avian influenza A viruses, we found that high viral shedding was associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in microbial species membership. These results suggest that host-associated microbiome structure may be linked to shedding heterogeneity and could help explain why some individuals contribute more strongly to environmental contamination and onward transmission.},
}

@article {pmid42837015,
year = {2026},
author = {Tanuku, NRS and Pinnaka, AK and Patel, PK and Chavda, H and Garbhapu, NS and Tadi, SR and Rose, A},
title = {Phylogenomic analysis and characterization of a novel metagenome-assembled genome from the Bay of Bengal and description of Candidatus Niobacter visakhapatnamensis gen. nov., sp. nov.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42837015},
issn = {1432-072X},
support = {GAP 3492//Ministry of Earth Sciences/ ; },
mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; *Seawater/microbiology ; *Metagenome ; India ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {A metagenome-assembled genome (NIO.Bin9[T]) belonging to the family Nannocystaceae was generated from a marine sample collected from the Bay of Bengal coastal water, Visakhapatnam, India. Phylogenetic analysis based on the 16 S rRNA gene placed NIO.Bin9[T] within the family Nannocystaceae, showing the sequence similarity (92.4%) to Pseudenhygromyxa salsuginis SYR-2[T]. Genome-wide comparisons revealed average amino acid identity (AAI) values ranging from 52.2% to 53.4% and average nucleotide identity (ANI) values between 75.8% and 75.9%, relative to closely related genera, including Nannocystis, Pseudenhygromyxa, Plesiocystis, and Enhygromyxa. Phylogenomic and 16 S rRNA gene-based analysis consistently supported the placement of NIO.Bin9[T] within the Nannocystaceae but distinct from existing taxa. Comprises complete pathways for carbohydrate degradation, glycolysis, the TCA cycle, nitrogen assimilation, sulfur metabolism, and biosynthesis of vitamins and cofactors. In particular, 29 biosynthetic gene clusters and an expanded CAZyme repertoire indicated robust potential for secondary metabolite production and complex carbohydrate utilization. Distinctive characteristics, such as the Csa3-type CRISPR component, the rifampin-resistance gene (arr), and an enriched suite of flagellar chemotaxis genes, differentiate the lineage from closely related taxa. Genome-relatedness analyses showed that NIO.Bin9[T] was distinct from members of genera of Nanocystaceae, with both AAI and ANI values falling below the established genus threshold (< 65% AAI and < 80-83% for ANI), supporting its designation as a novel genus and species, for which we propose the name "Candidatus Niobacter visakhapatnamensis" gen. nov., sp. nov.},
}

*Phylogeny
RNA, Ribosomal, 16S/genetics
*Genome, Bacterial
*Seawater/microbiology
*Metagenome
India
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid42837295,
year = {2026},
author = {Kiefer, ZE and Anderson, CJ and Rahic-Seggerman, FM and Schmitz-Esser, S and Ross, JW},
title = {Metagenome shotgun sequencing allows insights into the functional potential of the vaginal microbiome associated with pelvic organ prolapse in sows†.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioag222},
pmid = {42837295},
issn = {1529-7268},
abstract = {Pelvic organ prolapse (POP) is a leading cause for sow mortality in the United States. Recent work has evaluated biological factors associated with POP, and differences have been observed within the vaginal microbiota of sows at high risk using 16S rRNA gene amplicon sequencing. Additional functional studies are needed to better understand the relationship of dysbiosis of the vaginal microbiome with POP risk in sows. The current study's objective was to provide information about the functional potential of the sow vaginal microbiome, and to identify candidate genes and organisms that may be associated with POP. For this, metagenome shotgun sequencing was conducted on DNA extracted from 16 vaginal swab samples from late gestation sows. Of the 16 samples, 8 were from sows at high risk and 8 from sows at low risk for POP. Of the 8 samples from sows at high risk for POP four subsequently experienced POP. Subsequent contigs were annotated to generate a gene catalog of the vaginal microbiome of sows. The contigs were binned into metagenome assembled genomes (MAGs), resulting in 10 high-quality MAGs identified as Mannheimia varigena, Corynebacterium maris, Turicibacter bilis, Staphylococcus hyicus, Streptococcus dysgalactiae, Anaerococcus prevotii, Actinobacillus rossii, Prevotellaceae, Methanobrevibacter, and Veillonella caviae. MAGs classified as Streptococcus dysgalactiae and Staphylococcus hyicus contained potential virulence factors that are linked to the weakening of the connective tissue of the reproductive tract. This work provides initial insights into the functional potential of the vaginal microbial communities in late gestation sows in relation to POP and reproductive health.},
}

@article {pmid42837831,
year = {2026},
author = {Meng, G and Xing, L and Song, W and Sui, R and Ma, F and Guo, H},
title = {Cross-layer functional decoupling marks the transition toward structural deterioration in aerobic granular sludge.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127069},
doi = {10.1016/j.watres.2026.127069},
pmid = {42837831},
issn = {1879-2448},
abstract = {Identifying aerobic granular sludge (AGS) that is progressing toward instability before visible structural damage occurs remains a key challenge. Existing studies mostly compare stable and disintegrated granules at discrete endpoints, and conventional omics analyses focus on what changed rather than whether different molecular layers remain coordinated. We hypothesised that the transition toward granule instability is associated with progressive loss of functional coordination across genomic, proteomic, and metabolic layers. Aerobic granules were collected at five size classes (0.5, 1.0, 2.0, 3.5, and 5.0 mm) and analysed by morphology, SEM, reactor performance monitoring, metagenomics, metaproteomics, and metabolomics. Module-level coordination analysis and an inter-module coordination index (IMCI) were applied across the size gradient. At 3.5 mm, granules retained largely intact surface architecture and sustained bulk COD removal above 90%, yet metabolomic IMCI had declined continuously from 0.75 to 0.15 and proteomic IMCI had peaked at 2.0 mm before decreasing, revealing asynchronous coordination loss across molecular layers. A candidate pre-destabilisation window (2.0-3.5 mm) was identified where functional coherence had weakened but pronounced structural deterioration had not yet developed. Based on these findings, we propose hierarchical functional decoupling as a mechanistic framework in which cross-layer coordination loss marks the transition toward structural deterioration, providing an early molecular signature of incipient instability prior to macroscopic failure.},
}

@article {pmid42828930,
year = {2026},
author = {Yang, M and Pan, C and Kang, D and Li, J and Ge, Z and Zhang, L and Peng, Y},
title = {Nitrogen starvation coupled with extended anoxic time induces rapid growth of ammonia oxidizers and enrichment of anammox bacteria in low-ammonium wastewater.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127038},
doi = {10.1016/j.watres.2026.127038},
pmid = {42828930},
issn = {1879-2448},
abstract = {Partial nitrification-anammox (PNA) is an energy-efficient autotrophic nitrogen removal process, yet its application to low-ammonium wastewater remains challenging due to the difficulty in selectively suppressing nitrite-oxidizing bacteria (NOB) while maintaining ammonia-oxidizing bacteria (AOB) and anaerobic ammonium oxidation (anammox) bacteria. Here, we developed a chemical-free strategy based on sequential nitrogen starvation and extended anoxic operation to successfully establish one-stage PNA. Long-term reactor operation and cyclic nitrogen conversion performance demonstrated that repeated nitrogen starvation shifted the system from complete nitrification toward partial nitrification, while subsequent extension of the anoxic period promoted anammox activity and finally reached PNA performance. Batch activity tests revealed differential kinetic responses between nitrifiers, with faster AOB activity recovery rates, whereas repeated nitrogen starvation caused greater activity declines in NOB. Community-level microbial composition and functional gene analyses revealed a clear transition from a Nitrospira-dominated community toward an Nitrosomonas-Candidatus Brocadia consortium, accompanied by rapid increase of amoA gene abundance following starvation and enrichment of anammox populations. Genome-resolved metagenomics further revealed distinct succession trajectories among nitrifier populations, with some Nitrospira lineages persisting throughout the operation. Comparative genomic analyses incorporating global wastewater-treatment-plant metagenomes demonstrated that Nitrosomonas possessed greater genomic potential for reactive oxygen species (ROS) defense and redox maintenance than Nitrospira, suggesting a potential mechanism underlying their differential resilience to metabolic stress induced by the imbalance between nitrogen availability and oxygen supply. Nitrogen starvation also selectively reduced non-denitrifying heterotrophic organisms and enhanced the genomic potential for denitrification. Overall, this study demonstrates that a combined nitrogen starvation and oxygen availability strategy can effectively drive PNA establishment in low-strength ammonium wastewater, and provides new insights into stress-induced recovery and ecological selection of nitrifying communities.},
}

@article {pmid42829110,
year = {2026},
author = {Badr, T and Hatem, K},
title = {The regulatory landscape for clinical metagenomics-based diagnostics in Europe: a critical review.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107738},
doi = {10.1016/j.mimet.2026.107738},
pmid = {42829110},
issn = {1872-8359},
abstract = {Metagenomic next-generation sequencing (mNGS) enables broad, untargeted pathogen detection and is increasingly used in the diagnosis of central nervous system infections, infections in immunocompromised or post-transplant patients, ICU patients, and sepsis. This growing clinical role makes the regulatory landscape surrounding mNGS an urgent subject for evaluation, particularly given the phased implementation of the European In Vitro Diagnostic Regulation (IVDR). The transition from the In Vitro Diagnostic Directive (IVDD) to the IVDR marks a shift toward a harmonized, risk-based framework for in vitro diagnostics in the European Economic Area (EEA), but several aspects remain unclear for complex laboratory-developed tests (LDTs) such as clinical mNGS - including the practical implementation of the health institution exemption under Article 5(5), the classification of broad mNGS assays within the current risk tiers, and the scope of required analytical and clinical validation. Notably, validation strategies for mNGS may need to focus on the overall analytical method and intended use rather than on individual target pathogens. Further priorities include harmonized quality requirements, broader availability of external quality assessment (EQA), and clearer frameworks for transferring validated protocols between institutions. This review critically evaluates the current European regulatory framework for clinical mNGS-based LDTs and identifies areas requiring further clarification. Continued collaboration between healthcare institutions, regulators, scientific societies, and industry will be essential to keep requirements proportionate while supporting safe, reliable, and clinically useful implementation of mNGS in routine diagnostics.},
}

@article {pmid42829135,
year = {2026},
author = {Zhan, Y and Li, P and Chen, N and Hu, W and Feng, C},
title = {Enhanced Fe[0]-based autotrophic Cr(VI) biorduction with eggshell as an alternative inorganic carbon source: bioavailability mechanisms and microbial response.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125848},
doi = {10.1016/j.envres.2026.125848},
pmid = {42829135},
issn = {1096-0953},
abstract = {Zerovalent iron-based autotrophic bioreduction of Cr(VI) [FAR-Cr(VI)] is a promising remediation strategy for Cr(VI) contamination in groundwater, but its performance depends on inorganic carbon (IC) delivery and microbial colonization. This study investigated waste derived eggshell as a multifunctional IC source and biostimulatory substrate for enhancing FAR-Cr(VI). Bioreactors were operated with NaHCO3 (LC), CaCO3 (SC), and eggshell (ES) as IC supplements during three consecutive 48 h cycles. The ES biosystem achieved complete Cr(VI) removal (100%) in all cycles, whereas the LC and SC biosystems reached final removal efficiencies of 88.9 ± 0.9% and 93.7 ± 0.6%, respectively. The pseudo-first-order rate constant in the ES biosystem (0.147 h[-1]) was 3.3- and 2.6-fold higher than those in the LC (0.045 h[-1]) and SC (0.057 h[-1]) biosystems. ES promoted denser biofilm formation and significantly increased electron transfer system activity, cell viability and counts. XPS analysis showed higher relative Fe(III) and Cr(III) signals in ES precipitates, indicating more efficient Fe[0] oxidation and Cr(VI) reduction. Metagenomic analysis revealed higher abundances of Fe oxidation genes (feoA and fetA) and Wood-Ljungdahl pathway genes in the ES biosystem, suggesting an ATP-efficient carbon fixation strategy. Component-based experiments showed that calcined eggshell still improved the rate constant by 28.3% over SC, demembraned eggshell by 46.3-78.3%, and the inner membrane provided an additional 39.9-70.5% enhancement beyond demembraned eggshell. These findings indicate that eggshell enhances FAR-Cr(VI) through coupled carrier effects, and native organic, and trace element biostimulation, supporting a "waste-treating-waste" strategy for Cr(VI) contaminated groundwater remediation.},
}

@article {pmid42829285,
year = {2026},
author = {Liu, Y and Liu, Y and Dai, C and Gu, M and Luo, J and Cao, H},
title = {A Kidney Transplant Patient Suffering From Multiple Colonic Ulcers and Hepatic Abscess: A Case Report and Literature Review.},
journal = {Transplantation proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.transproceed.2026.08.003},
pmid = {42829285},
issn = {1873-2623},
abstract = {We present a rare case of colonic mucormycosis with hepatic dissemination after kidney transplantation. Early diagnosis was achieved through rapid metagenomic next-generation sequencing (mNGS) of blood and liver abscess samples, enabling timely intervention. The patient achieved complete clinical recovery with preserved allograft function. Gastrointestinal mucormycosis is extremely rare, reported cases frequently require colectomy (83.3%) and carry a mortality rate approaching 50%. This case highlights key management principles for intestinal mucormycosis in transplant recipients: rapid pathogen identification via mNGS, prompt initiation of dual antifungal therapy against Mucorales, and urgent surgical debridement of necrotic tissue.},
}

@article {pmid42829421,
year = {2026},
author = {Murugan, SB and Thomas, AA and Kene, RD and Rajan, A and Kelgaonkar, A and Rajesh, V and Somanath, A and Mahendradas, P and Deivasenathipathi, G and Majumder, PD},
title = {Current landscape of drug induced retinal vasculitis.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {16},
number = {1},
pages = {},
pmid = {42829421},
issn = {1869-5760},
abstract = {Drug-induced retinal vasculitis (DIRV), a complex diagnostic entity, masquerades as infectious or primary autoimmune diseases. Delineating them is a daunting task. This update aims to consolidate clinical evidence focussing on characteristic "vascular signatures" using advanced multimodal imaging tools. Type III (immune complex-mediated) and Type IV (T-cell-mediated) hypersensitivity pathways were involved in diverse range of drugs causing DRIV. The critical therapeutic strategies are highlighted to prevent permanent ischemic damage. Advances in the recent metagenomic markers are added to aid the clinician from a practical standpoint to aid in preventive and personalised ophthalmic care.},
}

@article {pmid42830273,
year = {2026},
author = {Wang, R and Yang, R and Hu, D and Xin, T and Yang, Z and Guan, Y and Niu, Y},
title = {A 5:2 Intermittent Fasting Regimen Ameliorates High-Fat Diet-Induced MASLD-Associated Skeletal Muscle Impairment in Mice.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {5},
pages = {e70398},
doi = {10.1002/jcsm.70398},
pmid = {42830273},
issn = {2190-6009},
support = {2024ZD0531800//Non-communicable Chronic Diseases National Science and Technology Major Project/ ; 82473614//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; Intermittent Fasting ; *Muscle, Skeletal/pathology/metabolism/physiopathology ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Liver/pathology/metabolism ; *Fasting ; *Non-alcoholic Fatty Liver Disease/etiology ; *Fatty Liver/etiology ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent chronic liver disorder worldwide. Its pathogenesis is closely linked to high-fat diets (HFDs) and is frequently accompanied by decreased skeletal muscle quality. Although intermittent fasting (IF) has been shown to effectively alleviate hepatic steatosis and inflammation, its impact on skeletal muscle quality remains unclear.

METHODS: Eight-week-old male C57BL/6J mice were randomly divided into two groups and fed a normal chow (NC) or 45% HFD for 14 weeks to induce MASLD. Subsequently, the MASLD model mice were subjected to a 5:2 intermittent fasting (IF5:2) regimen for 12 cycles (2 days of fasting per week, with ad libitum HFD feeding on the remaining 5 days). Grip strength, liver weight and quadriceps muscle mass were measured at sacrifice. Serum samples were collected for biochemical analysis and lipopolysaccharide (LPS) measurement. Liver, skeletal muscle and intestinal tissues were harvested for histopathological examination. Faecal samples were analysed by metagenomic sequencing. The mRNA expression of bile acid receptors and inflammatory genes was detected by qRT-PCR. Targeted free fatty acid profiling was performed in liver and skeletal muscle tissues.

RESULTS: Compared with the continuous HFD group, the IF5:2 group showed no significant difference in cumulative energy intake but exhibited significantly reduced body weight, as well as alleviated hepatic steatosis and inflammation. IF5:2 significantly increased grip strength and skeletal muscle cross-sectional area and markedly downregulated mRNA expression of inflammation-related genes in muscle tissue. Regarding intestinal barrier function, the IF5:2 group displayed significantly higher mRNA expression of intestinal tight junction-related genes, a thicker colonic wall and lower serum LPS levels compared with the HFD group. Metagenomic analysis suggested that IF5:2 effectively remodelled HFD-induced gut microbiota dysbiosis and significantly enriched beneficial bacteria including Limosilactobacillus reuteri and Faecalibaculum rodentium, accompanied by significant upregulation of microbial secondary bile acid biosynthesis pathways. mRNA expression levels of bile acid receptors and their downstream regulatory genes in the intestine, liver and skeletal muscle were significantly elevated in the IF5:2 group. IF5:2 treatment significantly reduced free fatty acid levels in the liver and skeletal muscle, which were negatively correlated with the gene expression of bile acid-related receptors in these two tissues.

CONCLUSIONS: Cyclic IF5:2 effectively ameliorates HFD-induced MASLD and protects against skeletal muscle impairment. It represents a promising dietary intervention with dual beneficial effects on alleviating hepatic steatosis and maintaining skeletal muscle quality.},
}

Animals
Mice
Intermittent Fasting
*Muscle, Skeletal/pathology/metabolism/physiopathology
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
Disease Models, Animal
Liver/pathology/metabolism
*Fasting
*Non-alcoholic Fatty Liver Disease/etiology
*Fatty Liver/etiology

@article {pmid42830277,
year = {2026},
author = {Feng, T and Shang, J and Ma, Y and Li, J and Qin, Y and Zhang, J and Cheng, S and Zhang, G and Xie, H},
title = {Metagenomic analysis of rhizosphere soil microbiota in wild and cultivated Notopterygium incisum, an umbelliferae medicinal herb.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42830277},
issn = {1471-2180},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics/methods ; *Apiaceae/microbiology/growth & development ; *Plants, Medicinal/microbiology/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.},
}

*Rhizosphere
*Soil Microbiology
*Metagenomics/methods
*Apiaceae/microbiology/growth & development
*Plants, Medicinal/microbiology/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification

@article {pmid42830300,
year = {2026},
author = {Nguyen, TT and Steen, IH and Stokke, R},
title = {Diverse biosynthetic pathways in Arctic hydrothermal biofilms.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42830300},
issn = {2041-1723},
support = {315427//Norges Forskningsråd (Research Council of Norway)/ ; },
mesh = {*Biofilms ; *Biosynthetic Pathways/genetics ; Arctic Regions ; *Archaea/genetics/metabolism ; *Hydrothermal Vents/microbiology ; *Bacteria/genetics/metabolism ; Metagenome ; Multigene Family ; Metagenomics ; Microbiota/genetics ; Peptide Synthases/genetics/metabolism ; Protein Processing, Post-Translational ; },
abstract = {Biosynthetic gene clusters (BGCs) which encode diverse secondary metabolites are ubiquitous across microbiomes and support critical ecological functions. They also serve as attractive targets for new drug discovery. Here we combined genome-resolved metagenomics with long-read Nanopore RNA sequencing, yielding 1016 bacterial and 124 archaeal medium-to-high quality MAGs from previously unchartered microbial communities in Arctic hydrothermal vent biofilms. We identified 2965 BGCs from 870 metagenome-assembled genomes (MAGs) comprising a distinctive and rich diversity of BGCs, with ribosomally synthesized and post-translationally modified peptides (RiPPs) predominating across all samples. RiPPs and non-ribosomal peptide synthetases (NRPs), also known to encode metabolites with antimicrobial potential, are represented among the most expressed transcripts. Terpenes, though less expressed, contribute to microbial signaling and defense. Notably, we identify hydrogen cyanide (HCN) synthesis pathways in archaeal genomes, challenging the view that cyanogenesis is restricted to bacteria and eukaryotes. Our findings demonstrate that microbial adaptation to extreme environments favors RiPP-based biosynthesis and that HCN may play a role in archaeal ecological interactions. Moreover, microbial communities in Arctic hydrothermal vent biofilms provide a rich reservoir of unique bioactive compounds, with implications for drug discovery.},
}

*Biofilms
*Biosynthetic Pathways/genetics
Arctic Regions
*Archaea/genetics/metabolism
*Hydrothermal Vents/microbiology
*Bacteria/genetics/metabolism
Metagenome
Multigene Family
Metagenomics
Microbiota/genetics
Peptide Synthases/genetics/metabolism
Protein Processing, Post-Translational

@article {pmid42830672,
year = {2026},
author = {Carew, M and Chung, J and Hehir, G and Hoffmann, A and Coleman, R},
title = {Simplifying Macroinvertebrate Biodiversity Assessment: A Standardised Metabarcoding Method for Invertebrate Samples With High Volumes of Debris.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70213},
doi = {10.1111/1755-0998.70213},
pmid = {42830672},
issn = {1755-0998},
support = {LP200100381//Australian Research Council/ ; },
mesh = {Animals ; *Invertebrates/classification/genetics ; *DNA Barcoding, Taxonomic/methods/standards ; *Biodiversity ; Australia ; Fresh Water ; *Metagenomics/methods/standards ; },
abstract = {DNA metabarcoding of freshwater macroinvertebrate samples can provide rapid and accurate identification of species diversity. Processing samples where macroinvertebrates are not separated from net contents can substantially reduce time and cost. We devised and tested a standardised method for processing combined kick/sweep samples using DNA metabarcoding to provide accurate estimates of macroinvertebrate species diversity. Kick and sweep samples were collected from 10 sites across Greater Melbourne known to vary in catchment land use, macroinvertebrate abundance and diversity as well as the type and volume of sampling debris. A sieving, blending and DNA extraction protocol was developed to reduce large debris, rocks and sand in samples, and to concentrate macroinvertebrates for metabarcoding. Variable percentages of the dry weight of samples from each site were used as a source of DNA for metabarcoding. We found that the macroinvertebrate species diversity recovered was mostly consistent when processing different percentages (20%-40%) of dry weight, but a minimum dry weight would be recommended for samples with low total dry weight. We present a method with a laboratory and bioinformatic workflow that enables the cost-effective and reliable processing of large volume samples, like those encountered in freshwater bioassessment. This metabarcoding approach has potential to be applied to any invertebrate biodiversity analysis where invertebrates are not separated from sampling debris, regardless of volume and composition, and used on samples varying in species abundance, diversity and density.},
}

Animals
*Invertebrates/classification/genetics
*DNA Barcoding, Taxonomic/methods/standards
*Biodiversity
Australia
Fresh Water
*Metagenomics/methods/standards

@article {pmid42831335,
year = {2026},
author = {Atayan, AA and Belov, YV and Kuznetsov, MR and Sinyavin, GV and Chernookov, AI and Belykh, EN and Yumasheva, VA and Parfenov, IM},
title = {[Current knowledge of pathophysiology of ischemia-induced intestinal wall damage: comprehensive analysis of pathogenesis and perspectives].},
journal = {Khirurgiia},
volume = {},
number = {10},
pages = {71-79},
doi = {10.17116/hirurgia202610171},
pmid = {42831335},
issn = {0023-1207},
mesh = {Humans ; *Reperfusion Injury/physiopathology/etiology/metabolism/diagnosis ; Intestinal Barrier Function ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation/methods ; *Intestines/blood supply/physiopathology ; *Intestinal Mucosa/metabolism/physiopathology/pathology ; *Ischemia/physiopathology ; Oxidative Stress ; },
abstract = {Intestinal ischemia is still one of the most complex pathological processes and characterized by high mortality and difficulties in early diagnosis. The article presents modern data on pathophysiological mechanisms of ischemia-induced intestinal wall damage. Etiological factors, molecular basis of ischemia-reperfusion injury, role of intestinal microbiota and innovative approaches to diagnosis and therapy are considered. Particular attention is paid to the paradoxical role of reperfusion. Indeed, the last one causes almost 70% of structural damages through activation of NADPH oxidase (NOX-4) and mitochondrial dysfunction. Metagenomic studies revealed a critical decrease in microbiota diversity (Shannon index 1.5-2.0) and butyrate deficiency. This directly correlates with violation of intestinal barrier function. In addition, the authors discuss clinical implications of new data, including probiotics and fecal microbiota transplantation. The article highlights the need for interdisciplinary approach involving microbiologists, clinicians and bioinformaticians to develop personalized strategies to reduce mortality and improve treatment outcomes.},
}

Humans
*Reperfusion Injury/physiopathology/etiology/metabolism/diagnosis
Intestinal Barrier Function
*Gastrointestinal Microbiome/physiology
Fecal Microbiota Transplantation/methods
*Intestines/blood supply/physiopathology
*Intestinal Mucosa/metabolism/physiopathology/pathology
*Ischemia/physiopathology
Oxidative Stress

@article {pmid42831354,
year = {2026},
author = {Mainguy, J and Lemane, T and Bazin, A and Arnoux, J and Gautreau, G and Médigue, C and Calteau, A and Vallenet, D},
title = {PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag948},
pmid = {42831354},
issn = {1362-4962},
support = {//French Alternative Energies and Atomic Energy Commission/ ; 101082304//Horizon Europe Program/ ; //Priority Antibiotic Resistance Research Program (PPR Antibiotic Resistance)/ ; //General Secretariat for Investment (SGPI)/ ; ANR-25-CE45-7210//Agence Nationale pour la Recherche/ ; ANR-21-ESRE-0048//Agence Nationale pour la Recherche under France 2030/ ; //ABRomics/ ; },
abstract = {PanGBank (https://pangbank.genoscope.cns.fr) is a comprehensive open-access database providing precomputed prokaryotic pangenomes at a broad taxonomic scale. Built upon PPanGGOLiN partitioned pangenome graphs, PanGBank addresses the growing need for large-scale comparative genomics through a standardized, regularly updated, and fully accessible resource. The initial release comprises two complementary collections covering >4600 prokaryotic species from the Genome Taxonomy Database (GTDB), encompassing over 393 000 genomes: GTDB_all, maximizing taxonomic and environmental diversity through the inclusion of metagenome-assembled genomes and single-cell amplified genomes, and GTDB_refseq, focusing on high-quality, annotation-rich genomes. Each species-level pangenome integrates graph-based statistical partitions into persistent, shell, and cloud gene families, together with regions of genomic plasticity (panRGP) and co-localized functional modules (panModule). PanGBank offers multiple access modes, including a REST API, a command-line interface, and an interactive web interface. By combining large-scale pangenome resources with advanced graph-based analyses, PanGBank provides a scalable framework for exploring microbial diversity, genome evolution, functional variation, and the dissemination of adaptive traits across prokaryotic populations, as illustrated by a use case on Acinetobacter baumannii pangenome investigating the distribution and evolution of antimicrobial resistance determinants.},
}

@article {pmid42831379,
year = {2026},
author = {Huang, S and Tang, Y and Wang, Z and Li, D},
title = {Biofilm-associated microbial risks in a mega water diversion project: distribution of putative pathogen-associated taxa and concrete biocorrosion potential in the Middle Route canal of the South-to-North water diversion project.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2026.2742367},
pmid = {42831379},
issn = {1029-2454},
abstract = {The ecological assembly of putative pathogen-associated taxa and the biogeochemical potential related to concrete biocorrosion have rarely been examined within an integrated framework in large freshwater diversion systems. We conducted quarterly biofilm sampling at eight stations along the Middle Route canal of the South-to-North Water Diversion Project, and combined 16S rRNA gene amplicon sequencing with shotgun metagenomics to characterize longitudinal and seasonal microbial patterns. Taxonomy-based screening identified 279 putative pathogen-associated ASVs with a mean relative abundance of 3.40%, primarily affiliated with Bacillus and Brevundimonas. Their relative abundance was lowest in the middle reaches, where higher flow velocity and dissolved oxygen may reduce biofilm-associated retention. Total nitrogen accounted for the largest individual contribution among the measured environmental variables (6.13%), whereas normalized stochasticity ratios indicated that stochastic processes predominated in overall community assembly. Metagenomic analysis further revealed spatially structured nitrogen- and sulfur-cycling potential, including biocorrosion-associated taxa such as Thiobacillus and Desulfovibrio, with several related functional pathways showing comparatively higher abundances in upstream biofilms. These findings establish an integrated ecological framework in which stochastic assembly, nutrient-associated selection, and hydrodynamic modulation jointly shape biofilm-associated microbial risks. The study provides critical insights for safeguarding both water-quality monitoring and century-scale infrastructure performance in mega water diversion systems.},
}

@article {pmid42831621,
year = {2026},
author = {Espinoza, JL and Phillips, AJ and Dupont, CL},
title = {Leviathan: fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0097026},
doi = {10.1128/msystems.00970-26},
pmid = {42831621},
issn = {2379-5077},
abstract = {Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing resource requirements, while translated searches in protein space lose classification resolution from ambiguous mapping events. Leviathan's utility is demonstrated through two case studies: a marine plastisphere metagenomics data set analyzing metabolic shifts between early and mature biofilm communities, and a dental caries metatranscriptomics data set where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.IMPORTANCEUnderstanding what microbes can do, not just which ones are present, is central to translating microbiome research into actionable insight. Existing functional profiling tools either rely on fixed reference databases or require complex multi-step pipelines when applied to custom genome collections, and none natively compute per-(pan)genome pathway abundance and graph-based pathway completeness in a single workflow. This limits the ability for researchers to directly compare functional profiles to tangential analyses on their specific genome catalogs. Leviathan addresses this gap with integrated taxonomic and functional profiling against user-defined (pan)genome-resolved references using pseudo-alignment, achieving competitive classification accuracy, with lower resource requirements compared to current methods. Native pangenome support enables routine quantification of metabolic potential and transcriptional activity at both genome and pangenome resolution, revealing functional variation across related strains that single-genome or community-level analyses obscure.},
}

@article {pmid42831635,
year = {2026},
author = {Pfaff, F and Meier, D and Seeholzer, A and Wunderlich, A and Einsiedl, F and Lueders, T},
title = {Impacts of temperature on hydrogenotrophic denitrifying aquifer microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0120626},
doi = {10.1128/aem.01206-26},
pmid = {42831635},
issn = {1098-5336},
abstract = {Groundwater is a globally relevant drinking water resource, yet nitrate pollution from agriculture increasingly threatens its quality, especially in shallow, oxygen-rich aquifers where natural attenuation is limited. This study examined whether gaseous hydrogen can stimulate autochthonous chemolithoautotrophic denitrification in nitrate-polluted, gravel aquifer sediments, and whether this process remains effective across temperatures relevant for laboratory and field conditions. We hypothesized that both microbial community composition and the kinetics of nitrate reduction will change under distinct temperature regimes. Microcosm incubations of sediments from a nitrate-polluted aquifer successfully enriched native hydrogenotrophic denitrifiers. Denitrification activity was quantified at 12°C, 15°C, 20°C, and 25°C, with maximum rates ranging from ~1 to ~1.8 µmol g[-1] sediment day[-1], and average rates generally following the expected kinetic temperature responses. Higher temperatures supported greater microbial biomass and community diversity, including a broader range of denitrifiers. Nevertheless, a single population, a novel strain of Acidovorax defluvii, dominated the community across all temperatures. Unlike the heterotrophic type strain, it possessed a conserved, likely transferable gene cluster for hydrogen oxidation, hydrogen sensing, and CO2 fixation, as revealed by metagenomics. Although complete denitrifiers with hydrogen-oxidation capacity dominated at all temperatures, nitrite accumulated transiently below 15°C. The presence of aerobic respiration genes in all enriched denitrifiers indicates their ability to switch to oxygen as an electron acceptor if available. Our study demonstrates a notable presence of an autochthonous hydrogenotrophic denitrification potential in the studied aquifer and its effective stimulation by hydrogen injection alone. Furthermore, it identifies mass transfer constraints and redox control as targets for future process optimization.IMPORTANCENitrate contamination of groundwater remains a widespread challenge in agricultural regions, and effective in situ remediation strategies are urgently needed. Hydrogen-stimulated chemolithoautotrophic denitrification represents a promising, low-carbon approach, yet its robustness under environmentally relevant temperature conditions has remained unclear. Our findings show that indigenous aquifer microorganisms can rapidly and consistently perform hydrogenotrophic denitrification across a broad temperature range (12-25°C), driven by a dominant Acidovorax species with a specialized hydrogen-oxidizing gene cluster. Identification of a conserved, potentially transferable gene cluster conferring chemolithoautotrophic lifestyle is not only biotechnologically interesting but also contributes to debate about genomic and ecological definitions of microbial species. This demonstrates that hydrogen injection can reliably activate existing microbial potential without requiring bioaugmentation and that temperature-driven shifts in community composition do not compromise nitrate removal. These insights advance the development of hydrogen-based bioremediation strategies for nitrate-impacted aquifers.},
}

@article {pmid42832260,
year = {2026},
author = {Song, X and Jia, S and Chen, L and Cao, C and Chen, Z and Hang, L and Jiang, H and Chen, Z},
title = {Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001847},
pmid = {42832260},
issn = {2057-5858},
mesh = {Antarctic Regions ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; Phylogeny ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Oceans and Seas ; Metagenomics ; Biodiversity ; },
abstract = {Antarctic deep-sea ecosystems harboured unique and metabolically versatile micro-organisms that sustained key biogeochemical processes under extreme polar conditions. However, the genomic diversity and ecological functions of these sedimentary or deep-sea microbial communities remained largely unexplored. Here, we constructed a comprehensive deep-sea microbial dataset of the Antarctic Ocean (dsMDAO) by integrating three newly sequenced Prydz Bay sediment metagenomes with 22 publicly available datasets (9 seawater and 13 sediment samples), spanning water depths of ~300-3500 m. Genome binning yielded 186 metagenome-assembled genomes spanning 19 phyla, including 175 bacteria and 11 archaea, a substantial proportion of which represent previously uncharacterized species. Meanwhile, reads mapping with the available standard Kraken2 database (k2_standard) enabled the expansion of species richness of the dsMDAO database. Furthermore, functional annotation revealed diverse metabolic and ecological potentials, including carbon, nitrogen and sulphur cycling, as well as secondary metabolite biosynthesis, virulence-associated defence and cold-adaptation mechanisms. Sediment microbiomes exhibited higher phylogenetic and functional diversity, enriched in Thaumarchaeota and Chloroflexi, whereas seawater communities were dominated by Proteobacteria with more competitive biosynthetic and interaction potentials. Co-occurrence analyses further indicated complex and competitive networks in seawater versus modular and cooperative assemblages in sediments, reflecting distinct ecological strategies. Collectively, dsMDAO provides the first genome-resolved dataset of Antarctic deep-sea microbiota, revealing the hidden taxonomic and functional diversity that underpins ecosystem resilience in polar oceans. This resource lays a foundation for future ecological, evolutionary and biotechnological exploration of Antarctic microbial dark matter.},
}

Antarctic Regions
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Archaea/genetics/classification/isolation & purification
Metagenome
Phylogeny
*Microbiota/genetics
Geologic Sediments/microbiology
Oceans and Seas
Metagenomics
Biodiversity

@article {pmid42832270,
year = {2026},
author = {Almatrafi, R and Alqurainy, N and Hakami, M and Ajina, R and Alrabiah, S and Arafah, AM and Alotibi, RS and Aldriwesh, MG},
title = {Gut microbiome and healthy ageing: a systematic review of literature.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {10},
pages = {},
doi = {10.1099/mic.0.001779},
pmid = {42832270},
issn = {1465-2080},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Healthy Aging/physiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Aged ; Aging ; Centenarians ; Aged, 80 and over ; Longevity ; },
abstract = {The gut microbiome undergoes compositional and functional changes with ageing. However, microbial signatures specifically associated with healthy ageing, independent of age-related diseases, remain poorly defined. This systematic review aimed to identify compositional and functional features of the gut microbiome associated with healthy ageing. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic search was conducted using PubMed, Web of Science and ScienceDirect for studies published up to January 2026. The search strategy focused on gut microbiome, ageing and healthy terms. Risk of bias was assessed using the Newcastle-Ottawa Scale. Gut microbiome composition was reviewed across five predefined age groups, while the functional pathways were reviewed for older adults and centenarians. The included studies represented several regions, including recognized longevity hotspots, although geographic representation remained limited. Most studies used 16S rRNA gene sequencing (n=24; 58.5%), followed by shotgun metagenomics (n=13; 31.7%), both (n=3; 7.4%) or metaproteomics (n=1; 2.4%). Enrichment of specific taxa such as Akkermansia, Alistipes and Parabacteroides was consistently reported in centenarians, alongside distinct patterns in older adults and long-lived individuals. Functional profiling suggested differences in pathways related to amino acid catabolism, vitamin biosynthesis and pathways potentially linked to immune modulation, inflammatory processes and gut barrier support. This review provides the first structured synthesis of gut microbiome signatures associated with healthy ageing across the lifespan, highlighting consistent functional traits and the need for a wider geographic representation in future research. It supports standardized, multi-omics framework to identify robust biomarkers and potential microbiome-based interventions for promoting healthy ageing.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Healthy Aging/physiology
*Bacteria/classification/genetics/isolation & purification
Metagenomics
RNA, Ribosomal, 16S/genetics
Aged
Aging
Centenarians
Aged, 80 and over
Longevity

@article {pmid42832495,
year = {2026},
author = {Qian, Y and Song, Q and Xie, X and Deng, L},
title = {Codon-aware multi-scale feature fusion for metagenomic sequence classification.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359090},
doi = {10.1371/journal.pone.0359090},
pmid = {42832495},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Codon/genetics ; Algorithms ; Plasmids/genetics/classification ; Humans ; Chromosomes/genetics ; *Metagenome ; },
abstract = {Microorganisms exert profound influences on both natural ecosystems and human society. As the cornerstone of microbial research, metagenomics relies on the precise analysis of large-scale, multi-source genomic data. However, discriminating among diverse sequence types remains a formidable challenge. To address this, we present CamFi (Codon-aware Multi-scale Feature Fusion), a unified framework integrating overlapping nucleotide-triplet representations with multi-scale dilated convolutions for classifying prokaryotic chromosomes, eukaryotic chromosomes, plasmids, and viruses. Benchmark evaluations demonstrate strong mean F1 scores of 97.70% for eukaryotic chromosomes and 94.13% for plasmids. On the CAMI II marine dataset, CamFi achieved a weighted F1 of 82.65%, ranking second among six methods based on reported aggregate metrics. In a balanced four-class benchmark, CamFi attained a macro-F1 of 93.77%, compared with DeepMicroClass (90.03%) and the XGBoost stage of 4CAC (64.66%). These results establish CamFi as a competitive approach for unified metagenomic contig classification under the evaluated conditions.},
}

*Metagenomics/methods
*Codon/genetics
Algorithms
Plasmids/genetics/classification
Humans
Chromosomes/genetics
*Metagenome

@article {pmid42832513,
year = {2026},
author = {Yuan, X and Arany, Á and Formanek, A and Moreau, Y and Lähdesmäki, H and Vatanen, T},
title = {LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2741488},
doi = {10.1080/19490976.2026.2741488},
pmid = {42832513},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Models, Statistical ; Metagenome ; Normal Distribution ; },
abstract = {Longitudinal microbiome data are key to understanding the dynamics of microbial communities and their relationships with the host and environment. However, analysis of such data is challenging due to high dimensionality, compositionality, irregular sampling and temporal dependencies on external covariates. Existing analytical approaches typically address only subsets of these challenges, limiting their ability to yield biologically interpretable insights. We introduce LGTM, a probabilistic modeling framework that combines flexible non-linear longitudinal modeling with interpretable topic-based representations of the microbiome. LGTM simultaneously identifies microbial co-abundance patterns ("topics") and models how their proportions change over time and in relation to host and environmental covariates. Using multiple longitudinal human gut microbiome datasets, we demonstrate that LGTM identifies diverse microbial topics whose major patterns are reproducible across runs, while achieving competitive performance in imputation and forecasting tasks. A key strength of the framework is its interpretability: LGTM yields microbial topics with biologically interpretable taxonomic compositions and directly quantifies associations between covariates and microbial dynamics. LGTM is available at https://github.com/yuanx749/lgtm.},
}

Humans
*Gastrointestinal Microbiome
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Models, Statistical
Metagenome
Normal Distribution

@article {pmid42832582,
year = {2026},
author = {Garamszegi, LZ and Nagy, G and Klein, Á and Szentiványi, T and Vásárhelyi, Z and Markó, G and Zsebők, S and Soltész, Z},
title = {The effect of ULV-based mosquito control on target and non-target organisms in Hungary: An experimental field study.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {10},
pages = {e0014140},
doi = {10.1371/journal.pntd.0014140},
pmid = {42832582},
issn = {1935-2735},
abstract = {Ultra-low volume (ULV) insecticide spraying with deltamethrin as the active ingredient is widely used in mosquito control programs, yet its effectiveness against target mosquitoes and its ecological side effects remain poorly quantified under field conditions in Central Europe. Here, we experimentally evaluated the short-term impact of ground ULV spraying (using deltamethrin + Chrysanthemum cinerariaefolium extract) on both mosquito populations and non-target flying insects in Hungary using a paired before-after-control-impact (BACI) design. Mosquitoes were sampled with BG Sentinel traps, while non-target insects were collected using malaise traps. ULV treatment resulted in a significant reduction in mosquito abundance at treated sites, with an average decline of approximately 47%. Native and invasive mosquito species, including Aedes albopictus and Aedes koreicus, showed similar proportional decreases. However, treatment effectiveness varied substantially among sites and was influenced by initial mosquito abundance and wind conditions. In parallel, malaise trap samples revealed a marked decline in non-target flying insects, with reductions exceeding 40% across multiple taxonomic groups, particularly among small and medium-sized insects, and also when considering pollinator taxa together. Our results indicate that while ULV spraying can temporarily reduce mosquito abundance, it also imposes considerable short-term impacts on non-target insect communities, highlighting trade-offs between vector control and insect conservation within mosquito management programs.},
}

@article {pmid42832605,
year = {2026},
author = {Dong, H and Yang, A and Shan, W and Zhao, C and Li, X and Rui, B and Zhao, J and Wumaier, M and Peng, H and Ma, Y},
title = {First record of Phlebotomus sergenti (Diptera: Psychodidae) in China and its potential epidemiological implications.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {10},
pages = {e0014726},
doi = {10.1371/journal.pntd.0014726},
pmid = {42832605},
issn = {1935-2735},
abstract = {BACKGROUND: Leishmaniasis is a severe parasitic disease transmitted by sand fly bites. Phlebotomus sergenti is a principal vector of Leishmania tropica, causing anthroponotic cutaneous leishmaniasis (ACL) across the Mediterranean, North Africa, South Asia, and West Asia. The Xinjiang Uygur Autonomous Region, located in northwestern China, is a well-recognized endemic focus of visceral leishmaniasis (VL), with sporadic cutaneous leishmaniasis cases also documented in the region. Nevertheless, Ph. sergenti has never been reported in China prior to this study.

Field investigations were carried out in Artux City (July 2023) and Akto County (August-September 2024), Kizilsu Kirghiz Autonomous Prefecture, Xinjiang Uygur Autonomous Region. Sand flies were collected using light traps in livestock pens and residential areas. A total of 2,013 sand fly specimens were collected and 319 of them were identified through morphological examination of the pharynx, spermathecae, and genitalia, combined with molecular analysis of mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cyt b) genes. Among the identified specimens, 145 specimens were identified as Ph. sergenti (36 from Artux City, 109 from Akto County), representing the first record of this species in China. Phylogenetic analysis based on COI and Cyt b sequences showed that Chinese Ph. sergenti populations clustered with those from neighboring countries (e.g., Afghanistan), with no significant genetic differentiation between the two sampling localities. Metagenomic screening of pooled samples revealed the presence of Wolbachia endosymbionts but no detection of Leishmania spp., Trypanosoma spp. or Bartonella spp. in the collected Ph. sergenti specimens.

CONCLUSIONS/SIGNIFICANCE: This study represents the first confirmed record of Ph. sergenti in China, filling a critical gap in the distribution map of this medically important sand fly species. The occurrence of Ph. sergenti at the China-Kyrgyzstan border region suggests potential transboundary dispersal of this vector and underscores the need for enhanced surveillance and cross-border collaborative efforts to monitor the spread of leishmaniasis and other vector-borne diseases in Central Asia.},
}

@article {pmid42832823,
year = {2026},
author = {Saito, H and Makino, R and Yonezawa, H and Fujio, S and Higa, N and Yamahata, H and Adachi, T and Yoshimura, A and Sakiyama, Y and Takashima, H and Hanaya, R},
title = {Intraventricular black fungal hyphal masses caused by Cladophialophora bantiana: illustrative case.},
journal = {Journal of neurosurgery. Case lessons},
volume = {12},
number = {14},
pages = {},
doi = {10.3171/CASE26730},
pmid = {42832823},
issn = {2694-1902},
abstract = {BACKGROUND: CNS fungal infections are rare, life-threatening conditions primarily affecting immunocompromised hosts. While they typically present as brain abscesses, intraventricular proliferation of fungal hyphae is exceedingly rare, and its neuroendoscopic findings have seldom been reported.

OBSERVATIONS: A man in his 80s with a history of malignancies presented with a 1-month history of headache. Brain MRI showed contrast-enhancing lesions along the genu of corpus callosum and lateral ventricles, as well as a nonenhancing lesion protruding into the ventricles. Although these findings were atypical, an endoscopic biopsy was performed because the lesions showed a tendency to enlarge, raising suspicion of a malignant tumor. Neuroendoscopic examination revealed a black-pigmented intraventricular fungal mass, which was partially resected. Shotgun metagenomic analysis identified the pathogen as Cladophialophora bantiana.

LESSONS: C. bantiana exhibits marked neurotropism and is known to cause CNS fungal infections even in immunocompetent individuals. Although intraventricular extension of phaeohyphomycosis is extremely rare and preoperative differential diagnosis remains challenging, a nonenhancing lesion protruding into the ventricles was considered to reflect the presence of fungal hyphae in this case. https://thejns.org/doi/10.3171/CASE26730.},
}

@article {pmid42832944,
year = {2026},
author = {Li, X and Zhang, Z and He, M and Jin, Y and Li, D and Chen, B and Chen, X and Yang, H and Ni, Y and Lu, T and Qian, H},
title = {Risk assessment of antibiotic-resistant bacteria in global lakes and their hotspots.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143801},
doi = {10.1016/j.jhazmat.2026.143801},
pmid = {42832944},
issn = {1873-3336},
abstract = {Freshwater lakes are crucial hotspots that have fueled the global antimicrobial resistance crisis. However, the distribution patterns and health risks of antibiotic-resistant bacteria (ARB) in lakes remain largely unexplored at the global scale. In this study, we comprehensively examined 1268 metagenomic samples from lakes globally and identified 12,866 ARBs spanning 28 phyla. Furthermore, based on the co-carriage of resistance genes, mobile genetic elements, and virulence factors, we developed a three-tiered risk framework. This framework distinguishes a critical-risk group comprising six species (belonging to Enterobacteriaceae, Aeromonadaceae, and Pseudomonadaceae) that are phylogenetically closely related to known pathogens, exhibiting the highest resistance, mobility, and pathogenic potential. Geographically, these critical-risk ARBs are primarily concentrated in low-latitude lakes (Amazon Basin, Central Africa, South/Southeast Asia, and Central America). Using machine learning, we identified temperature and wind speed as the primary driving factors. From a One Health perspective, our results inform a clear action plan and pinpoint low-latitude lakes as the priority targets for surveillance. This highlights the urgent need to include ARB risk stratification in security frameworks for global aquatic ecology.},
}

@article {pmid42833075,
year = {2026},
author = {Wang, X and Wang, J and Rehman, A and Ming, H},
title = {Response mechanisms of marine microbial communities during sulfamethoxazole co-metabolic degradation.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108421},
doi = {10.1016/j.marenvres.2026.108421},
pmid = {42833075},
issn = {1879-0291},
abstract = {Antibiotics, as typical emerging contaminants posing significant ecological risks, are frequently detected in global coastal environments. Their biotransformation in marine environments depends on the stress responses of functional microbial communities, while the underlying response mechanisms remain unclear. Through integrated metagenomic and metabolomic approaches, this study systematically investigated the structural and functional responses of marine microbial communities during the co-metabolic degradation of sulfamethoxazole (SMX), a representative antibiotic. A marine microbial consortium was employed for SMX co-metabolism with alginate, prototypical marine natural organic matter, as the co-substrate. Results revealed that under SMX stress, the microbial community underwent a marked shift in OTU composition, alongside significant increases in richness and diversity. The dominant functional taxon Vibrionaceae exhibited a significant decrease in relative abundance from 97.0% to 82.7%, while Paracoccaceae with SMX degradation potential and other low-abundance (<0.01%) functional taxa were significantly enriched, collectively sustaining stable alginate metabolism and facilitating SMX co-metabolism. Co-occurrence network analysis revealed enhanced interspecies associations. Moreover, the functional profile of the microbial community was profoundly reshaped. Specifically, the microbial community activated adaptive responses, enhancing TCS activation, EPS and endospore production, flagellar motility and chemotaxis, antioxidant capacity and DNA repair, and antibiotic resistance, to mitigate the toxicity of SMX and its intermediates. Concurrently, metabolic strategies were altered via regulation of key pathways (e.g., carbohydrate metabolism and amino acid metabolism), which increased by 7.8% and 17.5% in relative abundance compared to the control, boosting energy supply and SMX-degrading enzyme synthesis to enable SMX co-metabolism. This study provides new insights into the response mechanisms of marine microbial communities to SMX stress and the ecological risk assessment of antibiotics in coastal waters.},
}

@article {pmid42833218,
year = {2026},
author = {Bushnell, B and Schulz, F and Villada, JC},
title = {RandomReadsMG: Rapid, realistic metagenome simulation at terabase scale for benchmarking and experimental design.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101384},
doi = {10.1016/j.xgen.2026.101384},
pmid = {42833218},
issn = {2666-979X},
abstract = {Realistic synthetic metagenomes are essential for benchmarking bioinformatics tools, guiding experimental design, and generating labeled data for artificial intelligence and machine learning. We present RandomReadsMG, an open-source metagenomic read simulator distributed with BBTools. It generates communities containing hundreds to 50,000 genomes in a single command and supports user-defined abundance profiles, configurable within-genome coverage variation, retained read provenance, sequencing errors, and library artifacts. Presets are provided for Illumina, Oxford Nanopore Technologies (ONT), and PacBio sequencing. In benchmarks, RandomReadsMG produced terabase-scale datasets in under 6 h while maintaining bounded memory use. Simulations based on empirical drinking water profiles preserved genome-level depth after remapping. Controlled pathogen spike-ins further showed how simulation can estimate thresholds for read detection and metagenome-assembled genome (MAG) recovery. RandomReadsMG provides a fast, reproducible framework for metagenomics benchmarking, biosurveillance study design, and large-scale synthetic data generation.},
}

@article {pmid42833252,
year = {2026},
author = {van Vorstenbosch, R and Esenkova, EE and Jonkers, DMAE and Elizalde Vilalta, M and de Graaf, MCG and Keszthelyi, D and Pachen, D and van Schooten, FJJ and Mujagic, Z and Smolinska, A},
title = {Investigating the presence of microbiota-based phenotypes in Irritable Bowel Syndrome.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/aeb043},
pmid = {42833252},
issn = {1752-7163},
abstract = {Irritable Bowel Syndrome (IBS) is heterogenous disorder of gut-brain interaction, with a key role for the dysregulated host-gut microbiota interplay. IBS subtyping is based only on symptoms of bowel habits, reflecting limited insight into underlying biological mechanisms. Aims: This study aimed to define microbiota-based IBS phenotypes and to compare these to traditional stool-based subtyping. Methods: The study utilised data from the Maastricht IBS cohort. Gut microbiota composition was analysed using shotgun metagenomic sequencing. Faecal volatile organic compounds (VOCs) were measured by gas chromatography mass spectrometry. Dietary intake and gastrointestinal and mental health symptoms were assessed using a food frequency questionnaire, the Dutch Healthy Diet-15 index, the Gastrointestinal Symptom Rating Scale, and Hospital Anxiety and Depression scores, respectively. Machine-learning approaches were applied to identify microbiota-based phenotypical clusters, which were compared with established Rome III subtypes, and associated with faecal VOCs, gastrointestinal symptom severity, diet and mental health. Results: 178 IBS patients and 134 healthy controls were included. Gut microbiota composition distinguished IBS patients from healthy controls with an AUCROC 0·8. This discriminatory profile was not associated with Rome III subtypes, while statistically significant associations were found with faecal VOCs profiles (i.e. R=0·67, p=4·46e-4) and symptom severity scores of abdominal pain (p=0·05), reflux (p=0·03), and diarrhoea (p=0·01) and depression (p<0·001). Dietary associations varied across clusters. Conclusion: These results suggest that gut microbiota profiling might provide a basis to define relevant IBS endotypes. Further exploration and validation efforts into this direction are needed using longitudinal studies to refine IBS patient stratification ultimately. .},
}

@article {pmid42828686,
year = {2026},
author = {Kazarina, A and Vaškevica, A and Senkāne, DE and Zayakin, P and Hušča, S and Vīksne, K and Pirsko, V and Sokolovska, L and Sergejeva, N and Nakurte, I and Pastare, L and Ruhl, S},
title = {Salivary microbiome responses to chlorhexidine and Coriandrum sativum essential oil mouthwashes in patients with periodontitis in a randomized 2-week clinical trial.},
journal = {Clinical oral investigations},
volume = {30},
number = {10},
pages = {},
pmid = {42828686},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology ; *Saliva/microbiology ; *Chlorhexidine/pharmacology ; *Microbiota/drug effects ; *Oils, Volatile/pharmacology ; Female ; Male ; *Periodontitis/drug therapy/microbiology ; *Coriandrum/chemistry ; Adult ; Middle Aged ; Porphyromonas gingivalis/drug effects ; },
abstract = {OBJECTIVES: To compare the short-term salivary microbiome effects of a Coriandrum sativum essential oil (CSEO) mouthwash, chlorhexidine (CHX) as a benchmark comparator, and water in patients with periodontitis.

MATERIALS AND METHODS: In this randomized three-arm trial, participants with periodontitis rinsed twice daily for 14 days with water, CSEO, or 0.12% CHX. Preclinical anti-Porphyromonas gingivalis and fibroblast cytotoxicity assays informed CSEO concentration selection. Shotgun metagenomic sequencing was performed on 54 saliva libraries, two per participant, from 27 participants sampled at baseline and week 2 (H2O n = 9, CSEO n = 8, CHX n = 10). Alpha diversity, within-subject Bray-Curtis change, and differential abundance were analysed longitudinally.

RESULTS: Both active agents inhibited P. gingivalis in vitro, with CHX showing greater potency. In the clinical trial, no statistically detectable difference between CSEO and water was observed for the primary species-level Bray-Curtis outcome (q = 0.413), alpha diversity (all q ≥ 0.259), or differential abundance. CHX showed greater species-level Bray-Curtis change than water (q = 0.020), lower species-level Simpson diversity (q = 0.014), and broad taxonomic restructuring.

CONCLUSIONS: Under the tested formulation and exposure conditions, CSEO did not produce a statistically detectable group-level salivary microbiome shift relative to water. CHX provided a benchmark for broad ecological perturbation. The CSEO null finding does not exclude modest or heterogeneous effects in a larger cohort.

CLINICAL RELEVANCE: No clinical benefit can be inferred from the absence of a detectable CSEO-associated microbiome shift. Larger studies integrating clinical, inflammatory, and direct functional outcomes are needed.

TRIAL REGISTRATION: ISRCTN79156900, retrospectively registered on 11 May 2026.},
}

Humans
*Mouthwashes/pharmacology
*Saliva/microbiology
*Chlorhexidine/pharmacology
*Microbiota/drug effects
*Oils, Volatile/pharmacology
Female
Male
*Periodontitis/drug therapy/microbiology
*Coriandrum/chemistry
Adult
Middle Aged
Porphyromonas gingivalis/drug effects

@article {pmid42828800,
year = {2026},
author = {Zhao, Z and Zhang, X and Shen, T},
title = {From relative dominance to overproliferation: clarifying microbial and sensory inference in mechanized Hongqu fermentation.},
journal = {International journal of food microbiology},
volume = {463},
number = {},
pages = {112091},
doi = {10.1016/j.ijfoodmicro.2026.112091},
pmid = {42828800},
issn = {1879-3460},
}

@article {pmid42826539,
year = {2026},
author = {Pu, S and Ye, Q and Gao, Z and Zhang, Y and Zhang, S and Zhang, J and Wu, Y},
title = {Williamsia profundi sp. nov., a novel deep-sea Actinomycetota isolate with versatile metabolic potential and specialized ecological adaptability.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126775},
doi = {10.1016/j.syapm.2026.126775},
pmid = {42826539},
issn = {1618-0984},
abstract = {The deep-sea biosphere hosts distinctive microbial communities with specialized adaptive traits, yet the mechanisms underpinning their physiological survival remain largely obscure. In this study a novel Gram-stain-positive, aerobic bacterium, designated strain SKLECPSW1[T], was isolated from the Eastern Indian Ocean at a depth of 5318 m. The strain grows optimally at 32 °C and has a DNA G + C content of 70.0 mol%. Its major fatty acids are C16:0, C18:1 ω9c, and 10-methyl-C18:0. Genome analysis revealed a versatile metabolic repertoire, including complete central carbon metabolic pathways, dissimilatory nitrate reduction to ammonium (DNRA), anaplerotic CO2 fixation, and multiple genes associated with environmental stress responses. Furthermore, CAZyme profiling and 12 putative biosynthetic regions suggested potential for complex carbohydrate processing and secondary-metabolite biosynthesis. Comparative 16S rRNA gene sequence analysis showed that strain SKLECPSW1[T] shared the highest sequence similarity with Williamsia aurantiaca B375[T] (98.3%). Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values with related Williamsia species ranged from 71.15% to 83.35% and 18.8% to 26.6%, respectively, supporting its novel status. Metagenomic analysis of 25 deep-ocean datasets showed broad high-identity genome-wide recruitment in 2 samples, with breadths of 45.60% and 34.64% at ≥95% nucleotide identity, remaining 42.76% and 34.09% at ≥97.5%. Complementary marker-gene analyses further supported the occurrence of low-abundance environmental populations related to W. profundi in these two samples. Collectively, strain SKLECPSW1[T] represents a novel species, for which the name Williamsia profundi sp. nov. is proposed. The type strain is SKLECPSW1[T] (= MCCC 1K09832[T] = JCM 37991[T]).},
}

@article {pmid42826548,
year = {2026},
author = {Huang, P and Zhang, M and Li, Q and Xu, H and Shou, H},
title = {Altered gut microbiota composition and function potential in polycystic ovary syndrome: a multicohort metagenome-assembled genomes study.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {327},
number = {},
pages = {115453},
doi = {10.1016/j.ejogrb.2026.115453},
pmid = {42826548},
issn = {1872-7654},
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) has been associated with gut microbial dysbiosis, but cross-cohort reproducibility and genome-resolved alterations remain insufficiently characterized.

METHODS: We integrated fecal shotgun metagenomic data from three independent PCOS cohorts comprising 169 participants. Taxonomic and functional profiles were generated using MetaPhlAn4 and HUMAnN, while de novo assembly and binning were used to reconstruct species-level genome bins (SGBs). Linear mixed models accounted for cohort heterogeneity. Phylogenetic, co-occurrence network, KEGG-based functional, and prevalence-bias analyses were performed. PCOS classification was evaluated across genus, species, and SGB layers using leakage-safe nested cross-validation and leave-one-cohort-out testing.

RESULTS: PCOS was associated with reduced species richness, contraction of the core microbiota, altered community structure, and lower microbial network connectivity in the two larger cohorts. Eleven species showed differential abundance, including enrichment of Phocaeicola vulgatus and Bacteroides uniformis in PCOS. Genome-resolved analysis recovered 540 dereplicated SGBs, including 32 putative novel species. SGB prevalence bias was phylogenetically structured and remained associated with distinct KEGG Orthology profiles after adjustment for genome length and completeness. PCOS-biased SGBs were enriched in phosphotransferase-system and carbohydrate-utilization functions, whereas Healthy-biased SGBs were enriched in carbon and amino-acid metabolic pathways. Species-level XGBoost achieved the highest internal discrimination (AUC 0.757), but leave-one-cohort-out performance declined substantially, indicating limited cross-cohort generalizability.

CONCLUSIONS: PCOS is associated with multi-resolution gut microbiome alterations, with several community-level features showing cross-cohort reproducibility. These findings extend from community structure to genome-resolved functional programs, refine candidate microbial biomarkers, and highlight the need for external validation before clinical translation.},
}

@article {pmid42826561,
year = {2026},
author = {Zhang, Y and Wu, H and Zhang, X and Wu, Y and Hysen, L and Liu, Y and Zhang, H and Yang, J and Fu, L and Xiao, M and Lu, L and Zhang, Z and Zhang, J and Zhu, D},
title = {Protected area management contexts are associated with variation in Tibetan macaque gut microbiota and antibiotic resistomes.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120878},
doi = {10.1016/j.ecoenv.2026.120878},
pmid = {42826561},
issn = {1090-2414},
abstract = {Protected areas (PAs) are central to global biodiversity conservation and differ in their management contexts and associated patterns of human activity, yet differences in wildlife gut microbiota and antibiotic resistomes across PAs remain poorly understood. This study employed metagenomic analyses to compare the gut microbiota and resistomes of Tibetan macaques (Macaca thibetana) across three PAs in China with differing management contexts: Emeishan Scenic Area (EMS), where ecotourism is prominent; the Tangjiahe sector of Giant Panda National Park (TJH), where ecotourism is permitted but regulated; and Mabian Dafengding National Nature Reserve (MB), where tourist access is prohibited but livelihood-related resource use persists. Results showed that the MB population was characterized by higher gut microbial diversity and antibiotic resistance gene (ARG) abundance, with broader repertoires of potential pathogen taxa and high-risk ARGs. In contrast, potential pathogen signals in EMS and TJH were dominated by a single taxon, while EMS also showed a high-abundance signal of high-risk ARGs dominated by erm(B). Study area, gut microbiota and mobile genetic element (MGE) profiles were independently associated with gut ARG composition. This study provides a new perspective for global wildlife conservation and supports incorporating microbiota and resistome surveillance into protected-area management.},
}

@article {pmid42826574,
year = {2026},
author = {Wu, C and Zhang, H and Chen, L},
title = {Evaluation of protein sequence retrieval via protein language model embeddings and FAISS.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 1},
pages = {109411},
doi = {10.1016/j.compbiolchem.2026.109411},
pmid = {42826574},
issn = {1476-928X},
abstract = {Protein sequence similarity search underpins function annotation, evolutionary analysis, and metagenomic mining, yet conventional alignment-based methods face two persistent difficulties. First, their computational cost grows linearly with database size, making them impractical for billion-scale repositories. Second, their sensitivity declines below 30% sequence identity (the "twilight zone"), limiting remote homolog detection. Protein language models (PLMs) produce evolutionarily informative embeddings through self-supervised learning; however, the systematic integration of PLM embeddings with vector search into online retrieval services, together with experimental characterisation across model variants and index types, has received limited attention. We present ProtFaiss, combining ESM2 embeddings with FAISS approximate nearest neighbour search. On SCOPe40, we evaluate classification accuracy, ranking quality, remote homology sensitivity, retrieval speed, and storage footprint. Ablations spanning index type, model capacity, database scale, pooling strategy, and layer selection characterise the design space. ProtFaiss vector search completes in ∼0.02ms per query - roughly 3×10[5]-fold faster than a BLASTp database scan - and, including ESM2 encoding, the end-to-end latency is ∼30ms, approximately 200-fold faster than BLASTp. ProtFaiss achieves remote homology sensitivity of 7.7% (BLASTp: 6.7%), concentrated in the 15%-25% identity range. A notable finding is that intermediate Transformer layers substantially outperform the final layer: ESM2-650M layer 22 achieves Recall@10 of 0.780, compared with 0.431 for the final layer, suggesting later layers trade global semantic signal for local structural detail. A learned attention-pooling analysis and a preliminary Flat-index evaluation on multi-domain Swiss-Prot proteins further qualify this interpretation: learned pooling partially recovers final-layer performance, whereas intermediate layers remain advantageous in both evaluations. These results support the feasibility of PLM-based retrieval for large-scale protein search; however, generalisability is constrained by the single-domain benchmark.},
}

@article {pmid42826797,
year = {2026},
author = {Cao, B and Yi, Y and Xie, B and Liu, H},
title = {High-sensitivity heavy metal toxicity detection by Acinetobacter baylyi C8: Association with EPS protein deficiency.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135994},
doi = {10.1016/j.biortech.2026.135994},
pmid = {42826797},
issn = {1873-2976},
abstract = {Heavy metal contamination remains a persistent threat to water quality and ecological safety. Although electroactive microorganism (EAM)-based sensing technologies have shown promise for toxicity monitoring, their practical application is constrained by limited sensitivity. Here, we developed a strategy to improve monitoring performance by identifying and exploiting heavy metal-sensitive EAMs from mixed microbial communities. We successfully identified and isolated Acinetobacter baylyi C8 as a highly sensitive strain by integrating metagenomic analysis of mixed EAM communities under metal stress with electrochemical plate-based isolation. In bioelectrochemical sensing systems, C8 showed current-inhibition responses to eight representative heavy metals that were approximately one order of magnitude higher than those of mixed EAMs. For Cd[2+] and Pb[2+], good linear responses were obtained, with detection limits of 0.0157 and 0.0205 mg/L, respectively. C8 also responded consistently to binary and ternary heavy metal mixtures, while common coexisting ions caused little interference with Cd[2+] and Pb[2+] responses. Stable performance was maintained in drinking water, river water, and lake water, with deviations below 5 %. Further analyses showed that the high sensitivity of C8 was associated with low protein content in extracellular polymeric substances (EPS), greater intracellular metal accumulation, and stronger oxidative, metabolic, and electron-transfer disturbances. Overall, this study provides a practical route for identifying heavy metal-sensitive EAMs from mixed communities and highlights their potential for improving bioelectrochemical monitoring of heavy metal toxicity in water environments.},
}

@article {pmid42827076,
year = {2026},
author = {Stensvold, CR},
title = {From patients to populations: biological interpretation in molecular parasitology.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.09.010},
pmid = {42827076},
issn = {1471-5007},
abstract = {Molecular diagnostics have transformed clinical parasitology and molecular epidemiology. As analytical detection continues to improve, biological interpretation must develop alongside it. I would propose integrating complementary evidence and using clinically characterized reference datasets to calibrate biological inference from high-throughput molecular studies, providing a shared interpretative framework from patients to populations.},
}

@article {pmid42827198,
year = {2026},
author = {Tawk, C and El Mouali, Y and Huang, KD and Valkiers, S and Heidrich, V and Gronow, A and Osbelt, L and Rapp, J and Link, H and Segata, N and Typas, A and Strowig, T},
title = {Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42827198},
issn = {2058-5276},
support = {390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1343/15-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1343/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Healthy human gut microbiota is dominated by Bacteroidaceae in industrialized populations and by Prevotellaceae in those with traditional lifestyles, but diet alone is insufficient to explain this dominance of different Bacteroidota. Here we screened 94 dietary components in synthetic gut communities and find that these two bacterial families compete for overlapping nutritional niches. Segatella copri, a key member of Prevotellaceae-rich communities, outcompeted Bacteroidaceae when preferred polysaccharides such as arabinan were available, but this advantage depended on community composition, particularly the presence of Enterobacteriaceae. Metatranscriptomics and targeted metabolomics further revealed that Enterobacteriaceae synergized with dietary components to promote Segatella dominance in human and mouse gut communities. These interactions were validated by using multiple E. coli and Segatella isolates. Analyses of global metagenomes also showed a positive correlation between Segatella-rich non-industrialized microbiomes and Enterobacteriaceae abundance. Our results establish an ecosystem-level dynamic interplay between dietary components and key gut commensals that favour the dominance of Prevotellaceae.},
}

@article {pmid42827448,
year = {2026},
author = {Imokhai, PO and Metellus, R and Karsten, M and Alhoda, M and Gandhi, S and Ogbuefi, C and Carranza, S and Zhang, J and Lee, D and Brooks, A},
title = {An interdisciplinary scoping review of the emerging impact of periocular skincare products on the ocular surface microbiome and tear film stability.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1898798},
pmid = {42827448},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/drug effects ; *Tears/drug effects/chemistry ; *Cosmetics/adverse effects ; *Eye/microbiology/drug effects ; Personal Care Products ; Bacteria/classification/drug effects ; Meibomian Gland Dysfunction ; Meibomian Glands/drug effects ; },
abstract = {BACKGROUND: The healthy ocular surface microbiome consists of Actinobacteria, Proteobacteria, and Firmicutes phyla, with Corynebacterium, Propionibacterium, and Staphylococcus as dominant genera. This microbial environment is essential for maintaining immune homeostasis and barrier integrity.

OBJECTIVE: To synthesize existing evidence on how periocular skincare and cosmetic products affect the ocular surface microbiome, tear film stability, and downstream ocular surface disease.

METHODS: A systematic literature search was conducted across PubMed, Cochrane Library, Embase, Web of Science, and Scopus using Boolean MeSH term strategies. Studies from 2010 to present evaluating microbial composition of the ocular surface and the effects of exogenous exposures (cosmetics, contact lenses, medications) were included.

RESULTS: Preservatives (benzalkonium chloride, parabens), surfactants, retinoids, and essential oils (tea tree oil/terpinene-4-ol) disrupt the ocular surface through non-selective microbial depletion, epithelial cytotoxicity, and lipid emulsification. These mechanisms contribute to meibomian gland dysfunction (MGD), blepharitis, and evaporative dry eye - all associated with characteristic dysbiotic microbiome shifts. Advanced sequencing technologies, including 16S rRNA gene sequencing and shotgun metagenomics, reveal taxon-level changes and functional alterations linked to inflammation and tear film instability.

CONCLUSIONS: Periocular product ingredients represent an underappreciated source of ocular surface dysbiosis. Regulatory gaps under current FDA and MoCRA frameworks limit ingredient-level safety evaluation. Future longitudinal studies using functional metagenomics, metabolomics, and standardized microbiome-specific testing pipelines are urgently needed.},
}

Humans
*Microbiota/drug effects
*Tears/drug effects/chemistry
*Cosmetics/adverse effects
*Eye/microbiology/drug effects
Personal Care Products
Bacteria/classification/drug effects
Meibomian Gland Dysfunction
Meibomian Glands/drug effects

@article {pmid42827647,
year = {2026},
author = {Huang, Z and Liang, J and Pan, Y and Lao, J},
title = {Cryptococcosis in a seemingly immunocompetent patient presenting with knee and lower limb soft tissue infection complicated by meningitis: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1847042},
doi = {10.3389/fmed.2026.1847042},
pmid = {42827647},
issn = {2296-858X},
abstract = {Cryptococcus neoformans typically causes pulmonary or central nervous system (CNS) infections. However, osteoarticular manifestations, particularly as the initial presentation, are rare, especially in immunocompetent hosts. We report the case of a 65-year-old apparently immunocompetent woman admitted for generalized pain following a fall. Ten days post-admission, she developed fever and rapidly progressing soft tissue swelling in the right lower limb and knee. Despite the absence of overt immunodeficiency, the infection disseminated, leading to meningitis. Diagnosis was confirmed via fungal culture of lower limb secretions and metagenomic next-generation sequencing (mNGS) of knee joint tissue. Despite aggressive antifungal therapy, the patient's condition deteriorated, resulting in a fatal outcome. This case underscores the diagnostic challenge of cryptococcal osteoarticular infections in immunocompetent individuals. It highlights the utility of mNGS in diagnosing culture-negative infections and serves as a reminder that cryptococcosis should be considered in the differential diagnosis of fever of unknown origin with musculoskeletal involvement, even in the absence of traditional risk factors.},
}

@article {pmid42827663,
year = {2026},
author = {Li, P and Yang, X and Chen, Y and Wang, L and Cui, Q and Wu, Z and Cao, F},
title = {When metagenomic next-generation sequencing detects Nocardia: from clinical interpretation to immune-based clinical management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1911562},
doi = {10.3389/fcimb.2026.1911562},
pmid = {42827663},
issn = {2235-2988},
mesh = {Humans ; *Nocardia Infections/diagnosis/microbiology/immunology/drug therapy ; *Nocardia/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Female ; Male ; Middle Aged ; Aged ; Immunocompromised Host ; Risk Factors ; Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) increasingly detects Nocardia, but interpreting positive results remains challenging. We aimed to identify host factors and read thresholds that distinguish nocardiosis (ND) from colonization/contamination, and to characterize clinical features linked to immune status.

METHODS: A retrospective analysis from 74 patients at Qilu Hospital of Shandong University from April 2022 to October 2025 was conducted. We assessed mNGS for distinguishing Nocardia infection from colonization or contamination, identified risk factors for nocardiosis, and compared patients' clinical features, imaging findings, and antimicrobial adjustments.

RESULTS: A total of 56 patients with ND and 18 non-ND patients were included. Multivariate logistic regression identified farming exposure, bronchiectasis, and immunocompromised status were significantly associated with ND. An estimated read per million (RPM) thresholds of 56 could distinguish Nocardia infection from colonization/contamination (AUC 0.774; 95% CI, 0.654 - 0.895), with a higher sensitivity than traditional tests (P < 0.001). In ND group, immunosuppressed patients (ISPs) (42.9%) had more pulmonary interstitial fibrosis (29.17% vs. 6.25%, P = 0.03), lymphadenopathy (62.50% vs. 40.63%, P = 0.046) and fungal co-infections (54.17% vs. 18.75%, P = 0.006), while bronchial wall thickening was more common in immunocompetent patients (ICPs) (31.25% vs. 4.17%, P = 0.019). Nocardia was the sole pathogen in 42.9% of true infection cases, and mNGS led to a change in anti-Nocardia management in 87.5% of patients.

CONCLUSION: Our study indicated mNGS is a useful tool for distinguishing Nocardia infection from colonization/contamination, and immune-based phenotyping may guide individualized management strategies for patients with nocardiosis.},
}

Humans
*Nocardia Infections/diagnosis/microbiology/immunology/drug therapy
*Nocardia/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Female
Male
Middle Aged
Aged
Immunocompromised Host
Risk Factors
Adult

@article {pmid42827939,
year = {2026},
author = {Yang, H and Lei, X},
title = {Diagnostic Challenges in mNGS for Pulmonary Mucormycosis Presenting with Imaging Features Resembling Those of Lung Cancer.},
journal = {International medical case reports journal},
volume = {19},
number = {},
pages = {616885},
doi = {10.2147/IMCRJ.S616885},
pmid = {42827939},
issn = {1179-142X},
mesh = {Humans ; *Mucormycosis/drug therapy/diagnosis/diagnostic imaging ; Female ; Antifungal Agents/therapeutic use ; Aged ; *Lung Diseases, Fungal/drug therapy/diagnosis/diagnostic imaging/microbiology ; *Lung Neoplasms/diagnosis/diagnostic imaging ; Amphotericin B/therapeutic use ; Diagnosis, Differential ; *Bronchoalveolar Lavage Fluid/microbiology ; *Rhizopus oryzae/isolation & purification/genetics ; Triazoles/therapeutic use ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Pulmonary mucormycosis is a rare fungal infection with an increasing incidence in clinical reports. Its non-specific presentation often mimics lung cancer, posing significant diagnostic challenges. This report aims to improve clinician recognition of this condition.

CASE PRESENTATION: A 67-year-old woman with diabetes presented with cough and sputum production. Imaging revealed a right hilar mass with bronchial obstruction, mediastinal lymphadenopathy, and cystic cavities (Figure 1A). While initial suspicion favored lung cancer, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) detected Rhizopus oryzae (26,879 sequences), prompting revision of the diagnosis. Antifungal therapy with amphotericin B and posaconazole resulted in clinical improvement. Follow-up imaging at 67 days showed resolution of mucormycosis (Figure 1B).

CONCLUSION: This case highlights the diagnostic challenge of pulmonary mucormycosis masquerading as malignancy. mNGS serves as a valuable tool for early pathogen identification, though its role in therapeutic monitoring requires further investigation.},
}

Humans
*Mucormycosis/drug therapy/diagnosis/diagnostic imaging
Female
Antifungal Agents/therapeutic use
Aged
*Lung Diseases, Fungal/drug therapy/diagnosis/diagnostic imaging/microbiology
*Lung Neoplasms/diagnosis/diagnostic imaging
Amphotericin B/therapeutic use
Diagnosis, Differential
*Bronchoalveolar Lavage Fluid/microbiology
*Rhizopus oryzae/isolation & purification/genetics
Triazoles/therapeutic use
High-Throughput Nucleotide Sequencing
Tomography, X-Ray Computed

@article {pmid42827961,
year = {2026},
author = {Hughes, AE and Castillo-Sevilla, AM and Berlemont, R},
title = {Phylogeny constrains and environment modulates glycoside hydrolase architecture.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100658},
doi = {10.1016/j.crmicr.2026.100658},
pmid = {42827961},
issn = {2666-5174},
abstract = {Glycoside hydrolases (GHs) are central to microbial carbohydrate degradation and frequently occur as multidomain proteins containing accessory domains involved in substrate binding, localization, and retention. However, the extent to which GH multidomain architectures are shaped by phylogeny versus environmental adaptation remains poorly understood. Here, we analyzed 158,829 GH-containing proteins from 17,108 high-quality metagenome-assembled genomes (MAGs) in the GEM catalog, focusing on major GH families involved in polysaccharide and oligosaccharide degradation. We developed domain-domain adjacency networks (DANs) to quantify multidomain organization and compared network weighted architectural similarity across bacterial genera and environments. GH architectures were highly conserved within genera, with bootstrapped DANs displaying stable network properties and distinct lineage-specific architectural similarities, indicating strong phylogenetic constraints on domain organization. Accessory domains associated with substrate targeting and enzyme retention represented approximately 61% of non-catalytic partner domains, highlighting their importance in GH evolution. Although phylogeny was the dominant determinant of multidomain architecture, environmental effects were detected in cosmopolitan genera. Environmental variation had a limited and lineage-dependent influence on GH abundance but more consistently affected the prevalence of multidomain GHs, particularly within GH3, GH13, and GH18 families. These results support a hierarchical model in which phylogeny establishes a conserved framework of GH organization, while environmental pressures fine-tune multidomain architectures. Our study demonstrates that protein domain architecture represents an important and previously underappreciated dimension of microbial functional adaptation and provides a scalable network-based framework for linking enzyme organization to ecological function.},
}

@article {pmid42828099,
year = {2026},
author = {De Smedt, M and Cuypers, WL and Hudda, NU and Delputte, P},
title = {Sequencing the wastewater virome: Current strategies and bioinformatic pitfalls.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117596},
doi = {10.1016/j.isci.2026.117596},
pmid = {42828099},
issn = {2589-0042},
abstract = {Wastewater-based surveillance (WBS) is a powerful tool for monitoring viral pathogens at the population level, complementing clinical surveillance through anonymous and unbiased insights into viral circulation. Wastewater sequencing allows to move beyond detection toward detailed characterization of circulating pathogens. This review outlines the two main sequencing strategies used in WBS: targeted and untargeted approaches. Targeted methods, including amplicon- and probe-based sequencing, provide sensitive detection and recovery of known viruses but are limited in identifying novel pathogens. Untargeted shotgun metagenomic sequencing offers a broader, unbiased view of the wastewater virome, although its performance is challenged by low human viral abundance, complex background signals, and genome assembly challenges. We also discuss key challenges complicating bioinformatic analysis, including limited human viral sequences, co-circulating viral lineages, viral dark matter, reference database limitations, large data volumes, and methodological biases, as well as emerging computational approaches aimed at improving wastewater sequencing analysis and interpretation.},
}

@article {pmid42828306,
year = {2026},
author = {Wayah, SB and Arakawa, K and Philip, K},
title = {From predicted bacteriocins to ecological function.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100662},
doi = {10.1016/j.crmicr.2026.100662},
pmid = {42828306},
issn = {2666-5174},
abstract = {Genome and metagenome mining have uncovered large repertoires of predicted bacteriocin loci, but ecological interpretation has lagged behind discovery. This review uses bacteriocins as a focused model for a broader problem in antimicrobial gene prediction: sequence identifies encoded potential, but it does not establish expression, product deployment, target engagement, or community-level consequence. We distinguish four forms of bacteriocin "silence": transcriptional silence, where loci are not detectably expressed under tested conditions; conditional silence, where expression or activity emerges only under specific environmental or social cues; phenotypic silence, where expression or product formation does not yield detectable activity in routine assays; and ecological silence, where activity is observed but its consequences for coexistence, exclusion, colonization, or community assembly remain unresolved. We also clarify how this framework extends previous reviews of bacteriocin diversity and microbiome-shaping roles by providing an inference-centered taxonomy that separates encoded potential from demonstrated ecological function. Finally, we propose a function-first roadmap for bacteriocin research, including condition-resolved transcriptomics and proteomics, promoter and cue-dissection experiments, expanded target panels, spatially structured assays, defined consortia and microcosms, producer/non-producer comparisons, and explicit tests of resistance, immunity, and fitness consequences. Treating predicted bacteriocin loci as hypotheses rather than conclusions will improve how the field moves from gene catalogs to causal ecological understanding.},
}

@article {pmid42828409,
year = {2026},
author = {Song, Y and Xing, Y and Liu, Y and Zhang, X},
title = {Forensic applications of the skin microbiome: a structured narrative review of donor association, contact inference, and crime-scene reconstruction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1947173},
doi = {10.3389/fmicb.2026.1947173},
pmid = {42828409},
issn = {1664-302X},
abstract = {BACKGROUND: Skin-associated microbial communities are individualized, anatomically structured, temporally dynamic, and readily transferred to contacted surfaces. These properties have generated interest in the skin microbiome as complementary forensic evidence when conventional human DNA or fingerprint evidence is limited.

METHODS: We conducted a structured narrative review guided by the Scale for the Assessment of Narrative Review Articles (SANRA). PubMed/MEDLINE was searched from database inception through 2 August 2026, and reference lists of eligible studies and recent reviews were examined. Peer-reviewed studies were evaluated for relevance to skin microbial individuality, temporal stability, touch transfer, donor or source inference, postmortem interval estimation, analytical standardization, and legal or ethical interpretation. Evidence was synthesized according to study realism, analytical resolution, validation design, and proximity to forensic casework.

RESULTS: The biological basis for forensic use is supported by reproducible inter-individual and body-site variation, including persistent strain- and gene-level features. Controlled studies show that skin-associated communities can be recovered from touched objects and clothing and can support donor differentiation, particularly when targeted markers, microbial single-nucleotide polymorphisms, or metagenomic features are used. Nevertheless, performance estimates are strongly affected by cohort size, body site, substrate, time since deposition, environmental background, contamination, and machine-learning design. Evidence for body-site and biological-trace source inference is promising, whereas postmortem interval estimation, chronological contact reconstruction, and spatial trajectory inference remain exploratory.

CONCLUSION: Skin microbiome profiling should currently be regarded as a source of investigative intelligence and potentially complementary evidence rather than a replacement for human DNA profiling. Translation into practice requires harmonized protocols, realistic multicenter validation, open and representative reference datasets, explicit error-rate reporting, likelihood-based interpretation, and proportionate ethical and legal safeguards.},
}

@article {pmid42322606,
year = {2026},
author = {Sinha, A and Qian, A and Boutin, T and Maurice, CF},
title = {Prophage induction contributes to alterations in the gut phageome during intestinal inflammation.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {117491},
doi = {10.1016/j.celrep.2026.117491},
pmid = {42322606},
issn = {2211-1247},
mesh = {*Prophages/classification/metabolism ; *Gastrointestinal Microbiome ; Virome ; Dextran Sulfate ; Animals ; Mice ; Colitis/chemically induced/immunology/microbiology/virology ; T-Lymphocytes ; Mice, Inbred C57BL ; Datasets as Topic ; Metagenome ; Biodiversity ; *Inflammatory Bowel Diseases/metabolism/microbiology/pathology/virology ; Germ-Free Life ; *Bacteria/growth & development/metabolism/virology ; },
abstract = {Bacteriophages (phages) are abundant members of the gut microbiota and regulators of bacterial communities. During homeostasis, gut phage communities are longitudinally stable and lysogenic replication is dominant. In chronic gut inflammatory disorders, such as inflammatory bowel diseases (IBDs), there are alterations in phage diversity, which may result from changes in phage replication cycles. Here, we use a combination of in vitro, simplified community, and whole-community bioinformatics approaches to investigate whether prophage induction contributes to these alterations. We identify several compounds associated with gut inflammation that induce prophages from commensal gut bacterial isolates. Analyzing data from two mouse models of colitis, we observe that shifts in the composition of temperate phages occur over the course of inflammation, supporting a switch from lysogenic to lytic replication. Collectively, our observations support the idea that prophage induction contributes to alterations in the phageome associated with intestinal inflammation.},
}

*Prophages/classification/metabolism
*Gastrointestinal Microbiome
Virome
Dextran Sulfate
Animals
Mice
Colitis/chemically induced/immunology/microbiology/virology
T-Lymphocytes
Mice, Inbred C57BL
Datasets as Topic
Metagenome
Biodiversity
*Inflammatory Bowel Diseases/metabolism/microbiology/pathology/virology
Germ-Free Life
*Bacteria/growth & development/metabolism/virology

@article {pmid42822631,
year = {2026},
author = {Fu, Q and Ma, X and Sun, B and Liu, X and Wang, D},
title = {Dimethyl Phthalate Disrupts Sulfur Cycling and Triggers Toxic H2S Pollution in Sludge Anaerobic System.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125821},
doi = {10.1016/j.envres.2026.125821},
pmid = {42822631},
issn = {1096-0953},
abstract = {Dimethyl phthalate (DMP), a crucial plastic additive widely employed, has been detected in sewers, sediments, and sewage sludge at elevated levels, particularly in regions where active sulfur cycling occurs. However, the effect of DMP on anaerobic sulfur conversion, especially toxic H2S production, has not been documented. This study aimed to explore the fate of DMP in anaerobic system and its influence on sulfur conversion through both batch and long-term tests using sludge as substrate. Experimental results showed that sludge can effectively adsorb DMP, which conformed to the Freundlich model and pseudo-second-order adsorption kinetic model, with the equilibrium adsorption capacity of DMP in sludge system being 1.024 mg/g. ∼ 85% of DMP was biodegraded in anaerobic system, with monomethyl phthalate (MMP) and phthalic acid (PAA) as its main degradations. Additionaly, DMP presence at 20-200 mg/kg TSS significantly increased H2S gas production by 35.1%-71.7%. Although PAA and MMP can slightly promote H2S production, DMP was the main contributor. Multidimensional analyses showed that DMP spontaneously binds to the EPS of sludge and increases the secretion of EPS, as well as altering its physical and chemical properties (i.e., increasing its direct electron transfer capacity), thereby promoting the bioprocesses of organic sulfur hydrolysis and sulfur containing amino acids degradation. Metagenomic profiling confirmed this metabolic shift, showing an increase in the abundance of hydrolytic bacteria such as Ferruginibacter, as well as an increase in the abundance of organic sulfur metabolic genes such as pepD and aspB, which accelerated sulfide production from organic sulfur hydrolysis. These findings uncover a novel toxicity mechanism where DMP actively trigger hazardous gas emissions, highlighting unrecognized ecological risks in sulfur rich environmental compartments.},
}

@article {pmid42822808,
year = {2026},
author = {Burgess, AL and Bacela-Spychalska, K and Grabner, D and Lipinskaya, T and Johns, T and Bateman, KS and Ross, SH and Stentiford, GD and Bojko, J},
title = {Origins of the Nimaviridae: an ancient virus from the hepatopancreas of an invasive crustacean.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108756},
doi = {10.1016/j.jip.2026.108756},
pmid = {42822808},
issn = {1096-0805},
abstract = {The only recognised member of the Nimaviridae is white spot syndrome virus (WSSV), which causes billions in annual losses in the shrimp industry; this virus belongs to the Whispovirus genus. Many manuscripts are published each year that highlight the importance of understanding and controlling this virus, as well as attempting to figure out its origin. The evolutionary history of this economically important pathogen has been particularly difficult to unravel. Recently, several endogenous and exogenous nimaviruses have been discovered from decapod crustaceans, allowing insight into their genetic diversity, evolution, and virulence. We characterise an exogenous nimavirus infecting the hepatopancreas of the invasive amphipod, Dikerogammarus haemobaphes, putatively named 'Dikerogammarus haemobaphes amphinimavirus' (DhAV). Histopathology and fluorescence in situ hybridisation (FISH) are used to demonstrate that the virus primarily infects the nuclei of hepatopancreatic epithelia, similarly to their viral relatives, nudiviruses. Metagenomic tools were used to complete the circular 231,466 bp viral genome, which encodes a predicted 103 ORFs. Phylogenetic analysis suggests that this virus is an early diverging member of the Nimaviridae. The characterisation of DhAV opens doors to further evolutionary study, offering the potential to explore the genomic events that precede the emergence of one of aquacultures most deadly pathogens.},
}

@article {pmid42822929,
year = {2026},
author = {Nayak, SK and Bhattacharyya, P and Pradhan, C and Padhy, SR and Parida, SP and Das, A and Moharana, A and Rath, M and Nayak, A},
title = {Soil functional microbial pathways related to GHGs emissions of coastal degraded mangroves-rice ecologies in Sundarban, India: A soil metagenomic approach.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {344-357},
doi = {10.1016/j.jes.2025.12.050},
pmid = {42822929},
issn = {1001-0742},
mesh = {India ; *Wetlands ; *Soil Microbiology ; *Greenhouse Gases/analysis ; Oryza ; Methane/analysis ; Metagenomics ; *Environmental Monitoring ; Soil/chemistry ; },
abstract = {Mangroves and their adjacent rice ecologies play a critical role in regulating greenhouse gas (GHGs) emissions, particularly in tropical coastal wetlands. This study assessed the impact of mangrove degradation on methane (CH4) and nitrous oxide (N2O) emissions by comparing two distinct ecosystems; degraded mangroves, and adjacent rice system in the Sundarban, India. Annual CH4 and N2O emissions were quantified and linked to soil microbial energy metabolism pathways; methanogenesis, methanotrophy, sulphur (S), and nitrogen (N) metabolism by using whole-genome metagenomic analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs was used for functional microbial pathway analysis. Acetoclastic pathway was found to be the dominant CH4 production pathway in rice, where relatively low soil salinity favored CO2 to CH4 conversion. Methane oxidation was higher in degraded mangroves, driven by the serine and xylulose monophosphate pathways, reflecting microbial adaptation to saline and alkaline conditions. The assimilatory pathway (AMP) dominated S metabolism, with adenosine phosphosulfate kinase more abundant in degraded mangroves and adenosine triphosphate sulfurylase in rice ecology. Denitrification was the primary N pathway in degraded mangroves and adjacent rice systems, while dissimilatory nitrate reduction to ammonium (DNRA) prevailed in rice. A higher abundance of enzymes involved in acetate to methane production pathway was observed in rice systems, indicating greater CH4 production potential, whereas a higher abundance of phosphoserine aminotransferase in serine pathways in degraded mangroves suggested relatively higher potential for CH4 oxidation. These results demonstrate that targeted microbial management in mangrove-rice ecologies could serve as a promising strategy for climate change mitigation in coastal ecology.},
}

India
*Wetlands
*Soil Microbiology
*Greenhouse Gases/analysis
Oryza
Methane/analysis
Metagenomics
*Environmental Monitoring
Soil/chemistry

@article {pmid42822935,
year = {2026},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Feng, B and Zhang, B and Zhang, S and Fu, J},
title = {Sulfate addition enhanced antibiotic resistance in lake sediments by enriching resistant bacteria and promoting the potential of horizontal gene transfer.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {405-416},
doi = {10.1016/j.jes.2026.04.061},
pmid = {42822935},
issn = {1001-0742},
mesh = {*Lakes/microbiology/chemistry ; *Sulfates/analysis ; *Geologic Sediments/microbiology/chemistry ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Lake sediments represent a typical reservoir of antibiotic resistance genes (ARGs), an emerging contaminant. As a key nutrient for sediment microorganisms, elevated sulfate levels can profoundly influence sulfur cycling and related microbial processes. However, the impact of sulfate loads on the profiles of ARGs in lake sediments remains poorly understood. This study utilized a microcosm experiment to examine how sulfate addition at various concentrations (200, 400, and 600 mg/kg dry weight) affects the sediment resistome, via metagenomic analysis. Sulfate addition significantly increased sediment sulfides and the relative abundance of sulfate-reducing genes (SRGs). Notably, the high sulfate treatment (600 mg/kg) resulted in a significant rise in the relative abundance of ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), indicating an increased potential for resistance dissemination under high sulfate loading. The relative abundance of horizontal transfer related genes, including those mediating cell membrane permeability and type IV secretion system, was enhanced by sulfate addition, potentially promoting ARG dissemination. Linear regression identified strong positive relationships between the abundance of ARGs and abundances of both MGEs and VFGs. Sulfate addition enriched specific antibiotic-resistant bacteria (ARBs) carrying SRGs that were identified via network analysis. The genera Burkholderia, JACDDX01, and Hylemonella showed marked enrichment, with increases of 16.7 %, 13.2 %, and 94.6 %, respectively. Overall, the rise in ARG abundance under sulfate addition shows close links to specific ARBs and enhanced horizontal transfer. These findings have implications for understanding sulfate-driven changes in sediment resistome and assessing environmental risk in sulfate-enriched lake ecosystems.},
}

*Lakes/microbiology/chemistry
*Sulfates/analysis
*Geologic Sediments/microbiology/chemistry
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid42822967,
year = {2026},
author = {Xu, H and Hei, S and Yang, G and Fu, W and Zhang, X and Liang, P and Pan, B and Huang, X},
title = {Sustained anaerobic valorization of refractory wastewater into bioenergy via abiotic-biotic hybrid systems: Unraveling synergistic hydrolysis and optimized interspecies electron transfer.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {762-775},
doi = {10.1016/j.jes.2026.02.030},
pmid = {42822967},
issn = {1001-0742},
mesh = {*Waste Disposal, Fluid/methods ; *Wastewater/chemistry ; Anaerobiosis ; Bioreactors ; Hydrolysis ; Electron Transport ; },
abstract = {Anaerobic digestion (AD) of refractory industrial wastewater remains challenging due to structural recalcitrance and thermodynamic limitations. While abiotic-biotic hybrid systems incorporating electroactive materials (EMs) offer promise, their long-term efficacy and mechanisms at a system level, particularly with real industrial waste streams, are underexplored. This study demonstrates the sustained, system-level enhancement of anaerobic valorization using magnetite (Mag)- or pyrogenic carbon (PC)-amended reactors during 140-day continuous operation treating real membrane-making wastewater laden with N,N-dimethylformamide (DMF). EMs-augmented systems achieved superior COD removal of 75.5 % or 67.0 % and methane production of 255 or 228 mL/(g VSS·day), respectively, at an organic loading rate of 10.0 g COD/(L·day), representing an 88.5 % or 68.6 % increase in methanogenesis over the control. The enhancement stemmed from EMs synergistically boosting enzymatic hydrolysis to deconstruct refractory amide bonds and conjugated structures, and redirecting interspecies electron transfer (IET) pathways with greater efficiency and conductivity. Mag excelled under shock loads due to conductive Fe(III/II) lattice, whereas PC performed better under moderate loads leveraging pseudocapacitive functionalities. Microbial evolution revealed EM-specific colonization of hydrolytic/acidogenic consortia and IET-active methanogens. Metagenomic reconstruction indicated EMs enhanced cleavage of recalcitrant bonds, redirected DMF biodegradation toward (di)methylamine dehydrogenases-catalyzed hydrolysis pathway, and stimulated CO2-reducing/acetoclastic methanogenesis. Furthermore, EMs appeared to reconstruct intra-extracellular IET channels via membrane-spanning redox-active complexes, reinforcing energy conservation and stress resilience while channeling electrons from fermentation to methanogenesis. These findings establish a sustainable strategy for valorizing recalcitrant wastewater into bioenergy, offering insights into microbial electron flux redirection in abiotic-biotic systems.},
}

*Waste Disposal, Fluid/methods
*Wastewater/chemistry
Anaerobiosis
Bioreactors
Hydrolysis
Electron Transport

@article {pmid42822992,
year = {2026},
author = {Wickström, R and Sheikh, ZB and Hirsch, LJ},
title = {Recognizing NORSE and FIRES - clinical course, diagnosis and evaluation.},
journal = {Seminars in pediatric neurology},
volume = {59},
number = {},
pages = {101294},
doi = {10.1016/j.spen.2026.101294},
pmid = {42822992},
issn = {1558-0776},
mesh = {Humans ; *Status Epilepticus/diagnosis/etiology/physiopathology ; },
abstract = {New-onset refractory status epilepticus (NORSE) is a rare but severe neurological condition affecting both children and adults without prior epilepsy and without an identifiable acute cause at presentation. A substantial proportion of patients progress to super-refractory status epilepticus, which is associated with high morbidity and mortality. Despite its clinical severity, diagnostic strategies remain heterogeneous and are largely based on expert consensus due to limited high-quality evidence. This article summarizes current concepts in the definition, clinical recognition, and diagnostic evaluation of NORSE and its subtype febrile infection-related epilepsy syndrome (FIRES). Early identification is critical, as the clinical course, often characterized by a prodromal phase followed by rapidly escalating, treatment-refractory seizures, may provide important diagnostic clues. A structured diagnostic approach is essential and should include early, broad investigation for infectious, autoimmune, paraneoplastic, metabolic, and genetic etiologies, combined with continuous reassessment as new clinical information emerges. Key diagnostic tools include comprehensive blood and cerebrospinal fluid analyses, continuous EEG monitoring, and early neuroimaging, supplemented by advanced techniques such as cytokine panels, metagenomic sequencing and genetic testing when indicated. However, in more than half of cases, no etiology is identified, and patients are classified as having cryptogenic NORSE. Given the potential for treatable causes and the impact of early targeted therapy, timely and systematic evaluation is essential. We here provide an overview of current diagnostic strategies and propose a practical framework to support clinicians managing this complex condition.},
}

Humans
*Status Epilepticus/diagnosis/etiology/physiopathology

@article {pmid42823503,
year = {2026},
author = {Bayer, T and Meinert, H and Wei, R and Bornscheuer, UT},
title = {Advances in amidases and urethanases as depolymerization biocatalysts.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {42823503},
issn = {1552-4469},
support = {953214//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Stable chemical bonds as well as noncovalent interactions define the properties of industrial chemicals and materials, including polyesters such as polyethylene terephthalate (PET), polyamides (nylons) and polyurethanes. The resistance of plastics to hydrolysis contributes to the global issues of waste accumulation and environmental pollution. Recently identified metagenomic enzymes act on highly stable ester, amide and carbamate bonds in small molecules as well as pretreated polymeric materials. However, depolymerization activities, particularly for nylons and polyurethanes, remain too low to facilitate the efficient treatment of plastic waste. This Perspective highlights the natural diversity of different hydrolase superfamilies suitable for deconstructing synthetic polymers and examines their catalytic features. We also discuss strategies for discovering biocatalysts and tailoring their properties by protein engineering-both assisted by bioinformatics and (ultra)high-throughput screening tools. The combination of these approaches and thorough process analyses will be required to advance hydrolase-based depolymerization of plastics beyond the current recycling schemes for PET.},
}

@article {pmid42824003,
year = {2026},
author = {Qi, G and Wu, Z and Chen, J and Zhang, D and Wang, Q},
title = {Gut microbiota characteristics of gastric cancer patients across distinct pathological stages and their associations with tumor and paratumor mucosal microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1897107},
pmid = {42824003},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; China ; Aged ; Feces/microbiology ; Metagenomics ; Neoplasm Staging ; Dysbiosis ; },
abstract = {Gastric cancer (GC) is closely associated with microbial dysbiosis; however, the spatial-temporal characteristics of the gut, paracancerous, and intratumoral microbiomes, as well as their interrelationships during tumor progression, remain insufficiently defined. This study aimed to characterize these microbiomes in 85 GC patients from Northwest China using shotgun metagenomic sequencing and functional annotation. Clinical samples included feces, tumor tissues, and paratumor mucosal tissues (≥5 cm from the tumor margin), enabling comprehensive profiling of microbial composition at the phylum, genus, and species levels, as well as functional pathway analysis. The results showed that the microbial community was dominated by Firmicutes and Bacteroidetes (combined relative abundance >75%), maintaining structural stability across tumor stages II-IV (Stage I n=2 is only descriptively reported and excluded from formal statistical testing), thereby supporting the "core microbiota resilience" hypothesis. PERMANOVA revealed that tumor stage had a statistically significant yet modest effect on community structure (R[2] = 0.039, P = 0.032). MaAsLin2 identified stage-associated differential genera: Roseburia and Megamonas decreased with advancing stage, whereas Lactobacillus and Enterobacter were enriched in advanced stages (III/IV). Functional pathway analysis revealed stage-specific metabolic remodeling: Stage II was enriched in DNA repair, glycolysis, aromatic amino acid, and nucleotide biosynthesis pathways; Stage IV showed enrichment in protein deamination/demethylation, pyruvate fermentation, and coenzyme metabolism pathways. Correlation analysis further revealed a characteristic pattern of "pathogen enrichment and beneficial bacteria depletion." Fusobacterium nucleatum and Helicobacter pylori exhibited strong positive correlations with GC, whereas short-chain fatty acid-producing bacteria such as Roseburia and Faecalibacterium prausnitzii showed significant negative correlations, particularly in paracancerous tissues. We established multi-layered taxonomic correlation profiles based on intra-cohort microbial shifts, in which Bacteroides stercoris and Bifidobacterium pseudocatenulatum exhibited the most pronounced stage-related abundance changes in the fecal microbiota across tumor stages. Overall, this study systematically delineates the structural stability, stage-specific functional remodeling, and interrelated dynamics of gut, paracancerous, and intratumoral microbiomes in gastric cancer. These findings provide descriptive baseline data of cross-compartment microbiome variation within gastric cancer patients across tumor stages, which only deliver preliminary correlative clues of GC-related microbial shifts and require further multi-cohort verification with non-cancer control populations.},
}

Humans
*Stomach Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome
Female
Male
*Bacteria/classification/genetics/isolation & purification
Middle Aged
China
Aged
Feces/microbiology
Metagenomics
Neoplasm Staging
Dysbiosis

@article {pmid42824150,
year = {2026},
author = {Rabbani, SA and El-Tanani, M and Matalka, II and Sharma, S and Saini, M and Kumar, R},
title = {From surveillance to intelligence: a scoping review of machine learning for antimicrobial resistance surveillance intelligence across One Health.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1922265},
pmid = {42824150},
issn = {2296-2565},
mesh = {*Machine Learning ; Humans ; *One Health ; *Drug Resistance, Bacterial ; *Population Surveillance/methods ; Predictive Learning Models ; Animals ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a leading global health threat requiring coordinated surveillance across human, animal, environmental, and genomic systems. Machine learning is increasingly applied to AMR data, yet its contribution to actionable surveillance intelligence, rather than prediction alone, remains poorly defined.

OBJECTIVE: To map how machine-learning approaches generate AMR surveillance intelligence, to characterise their validation and implementation maturity, and to propose a framework distinguishing technical prediction from actionable surveillance intelligence.

METHODS: We conducted a scoping review following JBI methodology and PRISMA-ScR reporting. PubMed/MEDLINE, Scopus, and Web of Science were searched from January 2015 to May 2026 for studies applying machine learning or related methods to AMR surveillance intelligence. Two reviewers independently screened and charted records. Of 1,985 records, 66 met eligibility and formed the working evidence base; 41 studies (40 core empirical and one supporting preprint) were appraised against TRIPOD+AI- and PROBAST-aligned reporting, validation, and implementation-readiness domains.

RESULTS: Machine learning was applied across five clusters: clinical and electronic-health-record risk prediction and decision support; genomic and whole-genome-sequencing prediction; MALDI-TOF-based rapid resistance prediction; wastewater and metagenomic surveillance; and environmental, animal, food-chain, and One Health early warning. Prediction and risk stratification predominated, but validation maturity was limited: most studies were retrospective or internally validated, with few using external, cross-country, temporal, prospective, or drift-focused evaluation. On appraisal, discrimination was reported in 31 of 41 studies (76%) and explainability in 26 (63%); by contrast, external or temporal validation was present in only 15 (37%), calibration in 5 (12%), prospective evaluation in 1 (2%), and operational deployment with measured clinical or public-health impact in a single study (2%).

CONCLUSION: Machine learning can support AMR surveillance intelligence across clinical, genomic, diagnostic, environmental, and One Health settings, but the evidence demonstrates technical feasibility far more convincingly than operational readiness. Realising this transition will require external and prospective validation, calibration and drift monitoring, transparent and equitable reporting, workflow integration, and explicit linkage of model outputs to clinical and public-health action. We propose a One Health AMR Surveillance Intelligence Framework to organise this shift from data generation toward actionable, adaptive surveillance intelligence.},
}

*Machine Learning
Humans
*One Health
*Drug Resistance, Bacterial
*Population Surveillance/methods
Predictive Learning Models
Animals

@article {pmid42824179,
year = {2026},
author = {Manoharan, RK and Han, KI and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and Chaudhary, J and Shin, HD},
title = {Gut health and microbiome modulation by the heat-killed postbiotic beLP1[®] in adults with excess weight: a randomized, placebo-controlled trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1919277},
pmid = {42824179},
issn = {2296-861X},
abstract = {BACKGROUND: Overweight is linked to gut microbiota dysbiosis and gastrointestinal (GI) symptoms that impair quality of life.

METHODS: This 84-day randomized, double-blind, placebo-controlled study evaluated the gut-health effects of heat-killed Lactiplantibacillus plantarum (beLP1[®]) in otherwise healthy adults (aged 18-45 years) within the BMI range of 25-35 kg/m[2] and a ≥3-month history of mild-to-moderate GI discomfort, confirmed by Gastrointestinal Symptom Rating Scale (GSRS). In this trail 140 adults were allocated in a 1:1 ratio to receive either daily beLP1[®] (>30 billion cells) (n = 70) or placebo (n = 70). A total of 103 participants completed the study without protocol deviations and were included in the primary per-protocol (PP) analysis (beLP1[®]: n = 49; Placebo: n = 54). This predefined analysis directly compares the beLP1[®] and placebo arms using analysis of covariance (ANCOVA), supplemented by two independent-sample Student's t-tests. The primary endpoint was change in gastrointestinal symptoms via the GSRS, secondary endpoints included the Perceived Stress Scale (PSS), the Digestion-associated Quality of Life Questionnaire (DQLQ), Tumor Necrosis Factor-alpha (TNF-α), lipid parameters, Dual-Energy X-ray Absorptiometry (DEXA), and gut microbiome diversity by metagenomic Next-Generation Sequencing (NGS).

RESULTS: Compared to placebo, beLP1[®] significantly reduced total Gastrointestinal Symptom Rating Scale (GSRS) scores at Day 42 (p = 0.0215) and Day 84 (p = 0.0394), with prominent improvements in abdominal pain (p = 0.0205) and dyspeptic syndrome (p = 0.0303) domains. Significant reductions in perceived stress (p = 0.0004) and improvements in digestion-associated quality of life (p = 0.0008) were concurrently achieved. Metagenomic analysis revealed a favorable modulation of the gut microbiota, characterized by an enrichment of several short-chain fatty acid-producing bacteria and a significant reduction in multiple opportunistic pathogens. No significant changes occurred in serum TNF-α, lipid profiles, or DEXA body composition metrics.

CONCLUSION: Overall, beLP1[®] safely and progressively alleviates GI symptoms, reduces stress, and optimizes microbiome composition in adults with excess weight. ClinicalTrials.gov: NCT05820737.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT05820737?cond=NCT05820, identifier NCT05820737.},
}

@article {pmid42824567,
year = {2026},
author = {Wu, B and Wei, W and Zhang, K and Zhang, S},
title = {Pancreatic microbiota composition and diversity in pancreatitis-associated infection: a systematic review with focus on infected pancreatic necrosis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1916175},
pmid = {42824567},
issn = {1664-302X},
abstract = {UNLABELLED: Pancreatitis-associated intra-abdominal infection (PA-IAI), particularly infected pancreatic necrosis (IPN), is a serious complication of severe acute pancreatitis and contributes substantially to late morbidity and mortality. Sequencing-based technologies have expanded the detection of microorganisms in pancreatic infection; however, the characteristics of pancreatic microbiota and their clinical relevance have not been systematically summarized. A systematic literature search was conducted in seven electronic databases to identify studies evaluating pancreatic microbiota in patients with pancreatitis-associated infection. Studies reporting microbial composition or diversity using sequencing-based approaches were included. Study characteristics, microbial findings, diversity patterns, clinical outcomes, and methodological details were systematically extracted and synthesized. Six studies involving 235 participants were included; 188 participants contributed pancreatic or peripancreatic microbiota data. Most available evidence was derived from patients with IPN. Sequencing-based approaches generally detected a broader range of microbial taxa than conventional culture, with enteric-associated microorganisms frequently detected, while phylum-level dominance varied among studies. Reported diversity patterns varied between studies and could not be directly compared because of methodological heterogeneity. Although IPN was associated with worse clinical outcomes, current evidence did not demonstrate that specific microbial taxa or microbiota characteristics independently predicted mortality, organ failure, or treatment response. Current evidence indicates that pancreatic microbiota in pancreatitis-associated infection, particularly IPN, are characterized by frequent detection of enteric-associated microorganisms and substantial methodological heterogeneity. Sequencing-based approaches may provide additional microbiological information beyond conventional culture and may influence clinical management; however, whether sequencing-guided management changes improve antimicrobial stewardship or patient-centered outcomes remains uncertain. Future prospective studies using standardized microbiome workflows are required to determine the clinical significance of pancreatic microbial characteristics.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295285, identifier: CRD420261295285.},
}

@article {pmid42824881,
year = {2026},
author = {Esberg, A and Jönsson, D and Persson, P and Eriksson, L and Haworth, S and Johansson, I},
title = {Cross-platform, multi-cohort identification of a caries microbial signature.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2737699},
pmid = {42824881},
issn = {2000-2297},
abstract = {OBJECTIVE: To identify a robust salivary microbial signature associated with caries using a cross-platform, multi-cohort design.

DESIGN: Full-length 16S rRNA gene sequencing (ONT) and shotgun metagenomics (MET) were performed in a derivation cohort with matched data (n = 463). Associations between the oral microbiome and caries were evaluated using confounder-adjusted linear models with nested cross-validation. Identified species were incorporated into microbial risk scores and tested in two independent ONT-based cohorts (n = 3,457 and n = 215).

RESULTS: ONT and MET shared community structure despite differences in sequencing depth and detection sensitivity. Inter-individual ecological distances were moderately correlated (Spearman ρ = 0.48), with significant Procrustes alignment (r = 0.60), and mean relative abundances of shared species were strongly correlated (ρ = 0.75), but agreement at the individual species level was more variable. Ten species were consistently associated with caries across platforms and analytical approaches. Risk scores based on these species were strongly associated with caries burden in the derivation cohort (R[2] = 0.46 for MET; R[2] = 0.42 for ONT) and replicated in independent cohorts (mean R[2] = 0.27 and 0.10). Detection- and abundance-based scores performed similarly and combining them provided minimal additional predictive value. Detection-based scores showed a slightly greater incremental contribution to model fit. Leave-one-out analyses confirmed that associations were not strongly driven by individual species.

CONCLUSIONS: Key ecological features of the oral microbiome are reproducible across sequencing platforms. The microbial signature of caries can be summarised using a detection-based risk score which may have potential uses in caries risk assessment.},
}