@article {pmid42848445,
year = {2026},
author = {Cromb, S and Mayboca-Padilla, D and Bedi, R and Narvaez-Bravo, C},
title = {Evaluating packaged ice safety using culture-based and metagenomic methods.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {10},
pages = {},
pmid = {42848445},
issn = {1465-2080},
mesh = {*Metagenomics/methods ; *Ice/analysis ; *Bacteria/isolation & purification/genetics/classification/drug effects ; *Food Microbiology ; Food Safety ; Drug Resistance, Bacterial/genetics ; Pseudomonas/isolation & purification/genetics ; },
abstract = {Ice can serve as a vector for microbial contamination, presenting potential risks to public health. This study aimed to evaluate the microbial quality and safety of commercially available ice in Manitoba as well as to characterize the microbiome of ice cubes and assess the presence of antimicrobial resistance (AMR) genes. Samples from five different brands, four non-International Packaged Ice Association (IPIA)-accredited and one IPIA-accredited brand, were collected from retail stores between May and August 2024. Ice samples were tested using membrane filtration for total plate count, Escherichia coli, coliforms, Pseudomonas, yeasts, moulds and Enterococcus and screened for Listeria monocytogenes and Salmonella. Separate filtration samples were collected for metagenomic analysis. Membrane filtration results showed that 12.8% of samples from non-IPIA-accredited brands failed to meet IPIA standards for total coliforms, whereas 100% of samples from the IPIA-accredited brand complied. All samples tested negative for foodborne pathogens when conventional culture-based methods were used. However, metagenomic sequencing revealed the presence of pathogen-associated DNA. A diverse resistome was identified across all brands, including the IPIA-accredited sample, with genes conferring resistance to β-lactams, aminoglycosides and biocides. Recovered Pseudomonas isolates were identified as Pseudomonas lactis, a psychrotrophic species capable of growth at refrigeration temperatures. Biofilm assays demonstrated that recovered P. lactis formed biofilms at both 4 and 10 °C, with significantly greater biofilm formation observed at 4 °C. Our findings demonstrate consistent compliance among the IPIA-accredited brand, while variability and failures occurred among non-accredited producers. The detection of cold-adapted, biofilm-forming bacteria such as Pseudomonas spp., which can reduce sanitizer efficacy and protect co-existing micro-organisms, including potential pathogens harbouring AMR genes, highlights the need for targeted environmental monitoring using key indicator organisms such as Pseudomonas spp. Broader adoption of IPIA standards could strengthen microbial control practices and enhance consumer protection within the Canadian packaged ice industry.},
}

*Metagenomics/methods
*Ice/analysis
*Bacteria/isolation & purification/genetics/classification/drug effects
*Food Microbiology
Food Safety
Drug Resistance, Bacterial/genetics
Pseudomonas/isolation & purification/genetics

@article {pmid42849072,
year = {2026},
author = {Li, ZT and Yu, ST and Gao, TY and Zhao, HP},
title = {Reductive dechlorination resilience to oxygen intrusion: dehalogenase-dependent differential recovery and community-mediated redox homeostasis.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143849},
doi = {10.1016/j.jhazmat.2026.143849},
pmid = {42849072},
issn = {1873-3336},
abstract = {Oxygen intrusion in chlorinated solvent-contaminated aquifers frequently compromises organohalide-respiring bacteria (OHRB)-driven in-situ bioremediation. This study examined the dechlorination dynamics of a tetrachloroethene (PCE)-respiring consortium for 72 days after exposure to 0-4 mg/L dissolved oxygen (DO). Although DO fell below 0.2 mg/L within 36 h, recovery differed among dechlorination steps. At an initial DO of 4 mg/L, PCE-to-dichloroethene (DCE) dechlorination was retained at up to 3.8 μmol Cl[-]·L[-1]·d[-1], whereas vinyl chloride (VC) detoxification ceased above 2 mg/L. By day 72, the 4 mg/L treatment contained 39.6% DCE and 9.4% VC, with less than 1% of the supplied PCE dechlorinated to ethene. Integrated metagenomic and metatranscriptomic analyses attributed this differential resilience to functional redundancy among diverse PceA-carrying OHRB (Dehalobacter, Dehalococcoides, and other taxa) for upstream steps, versus the confinement of vcrA to a single oxygen-sensitive Dehalococcoides population, whose depletion coincided with delayed VC-to-ethene recovery. Facultative aerobes, particularly Pseudomonas, rapidly depleted O2 through aerobic respiration. These findings identify the terminal VC-to-ethene step as the most vulnerable link in PCE attenuation. Oxygen intrusion therefore shifts attenuation end products from ethene towards the more mobile DCE and VC, prolonging contaminant persistence at oxygen-disturbed sites.},
}

@article {pmid42849098,
year = {2026},
author = {Wen, Y and Huang, X and Zhang, L and Zhang, S and Li, M and Zou, K},
title = {Seasonal dynamics of plastic-degradation-associated microbiomes in an anthropogenically impacted Pearl River Estuary: A genome-resolved metagenomic study.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120421},
doi = {10.1016/j.marpolbul.2026.120421},
pmid = {42849098},
issn = {1879-3363},
abstract = {Estuarine sediments are important sinks for plastic debris and potential reservoirs of microbial functions involved in plastic transformation. Here, metagenomic sequencing and genome-resolved analyses were used to characterize the seasonal distribution and environmental associations of microbial taxa and genes potentially associated with plastic degradation in the Pearl River Estuary. The screened taxa differed between wet and dry seasons, with Priestia and Staphylococcus showing higher relative abundances in the dry season, whereas Vibrio, Photobacterium, Methylobacterium, and Ralstonia were more abundant in the wet season. Microbial community dynamics were associated with variation in organic matter, pH, temperature, and nitrogen variables, with the leading environmental predictors differing between microbial communities and seasons. Genome-resolved analysis recovered 150 non-redundant medium- to high-quality metagenome-assembled genomes (MAGs), of which 42 carried putative plastic-degradation-associated gene homologs identified through comparison with PlasticDB. Approximately 60% of these 42 MAGs belonged to Pseudomonadota, and three Burkholderiaceae MAGs harbored multiple candidate homologs. KEGG annotations further identified genes related to alkane oxidation, fatty acid degradation, ester hydrolysis, and aromatic-compound metabolism, providing a broader metabolic context for these genomes. Together, these findings characterize seasonal variation in the screened microbial communities and identify candidate microbial hosts and genes for investigating plastic transformation in estuarine sediments.},
}

@article {pmid42849177,
year = {2026},
author = {Tang, S and Yang, Y and Wang, Y and Gong, S and Li, N and He, Z and Ni, J and Wang, J and Liu, Y and Chan, JWY and Chu, WCW and Mok, VCT and Chen, Z and Huang, B and Wing, YK},
title = {Deciphering the heterogeneity of prodromal α-synucleinopathy: linking brain biotyping and gut dysbiosis in isolated REM sleep behaviour disorder.},
journal = {EBioMedicine},
volume = {133},
number = {},
pages = {106503},
doi = {10.1016/j.ebiom.2026.106503},
pmid = {42849177},
issn = {2352-3964},
abstract = {BACKGROUND: Isolated/idiopathic REM sleep behaviour disorder (iRBD) is a specific prodrome of α-synucleinopathies. We previously identified two distinct clinical-neuroimaging biotypes in iRBD: Biotype 1, marked by widespread cortical-subcortical-cerebellar atrophy with motor and cognitive deficits, and Biotype 2, with preserved brain structure and neurocognition. Converging evidence implicates the gut-brain axis in early α-synucleinopathy, yet its role in these divergent iRBD phenotypes remains unexplored.

METHODS: We analysed faecal microbiota using shotgun metagenomic sequencing and structural neuroimaging data from 167 participants (42 Biotype 1, 50 Biotype 2, 75 controls). Microbial features and brain structure were compared across groups. Gut-brain associations were assessed using sparse partial least squares regression to link microbiome features with neuroanatomical patterns.

FINDINGS: Overall microbial composition did not significantly differ between Biotype 1 and Biotype 2, and both biotypes showed depletion of short-chain fatty acid-producing bacteria. Relative to the shared dysbiotic background, Biotype 1 displayed more pronounced taxon- and pathway-level alterations, including enrichment of Collinsella aerofaciens, Cloacibacillus evryensis, and Mogibacterium sp. BX12, which were associated with Biotype 1-specific brain atrophy. Biotype 2 showed milder dysbiosis with fewer differentially abundant species. These patterns were consistent in sensitivity analyses and fully adjusted models.

INTERPRETATION: Beyond a shared depletion of short-chain fatty acid-producing bacteria, iRBD biotypes exhibit differences in taxonomic and functional profiles, with these differences being more pronounced in Biotype 1. These findings support a role for the gut-brain axis in early α-synucleinopathy and its phenotypic heterogeneity.

FUNDING: This study was funded by the Health and Medical Research Fund of the Food and Health Bureau (Ref No.: 05162876 and 10210686) and Research Grants Council (RGC-CRF Ref No.: C4044-21G) of Hong Kong.},
}

@article {pmid42849199,
year = {2026},
author = {Shi, X and Sun, J and Zhou, S and Zhang, T and Zeng, Q and Liu, W and Sun, B and Zhu, W and Zeng, M},
title = {Microbial community differentiation and machine learning-driven optimization of nitrogen removal in multi-configured anammox systems.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131096},
doi = {10.1016/j.jenvman.2026.131096},
pmid = {42849199},
issn = {1095-8630},
abstract = {Integrated fixed-film activated sludge (IFAS) reactors are widely adopted for anammox wastewater treatment, but few studies have systematically compared microbial community structure, interactions and functions among suspended sludge, pure biofilm and the two phases of IFAS. A total of 472 16S rRNA gene sequencing samples collected from 2017 to 2023 were analyzed through bioinformatic tools, diversity assessment, co-occurrence network construction and machine learning modeling. The biofilm of IFAS exhibited significantly higher alpha diversity as well as a more complex and stable microbial network with a modularity value of 0.712. Among five algorithms, LightGBM achieved the highest mean accuracy of 0.931 ± 0.034, weighted F1 score of 0.931 ± 0.035, and weighted AUC of 0.989 ± 0.009 across ten repeated stratified splits and was therefore selected for downstream SHAP analysis. SHAP analysis identified Candidatus Brocadia and Candidatus Kuenenia as primary distinguishing microbial genera. Laboratory validation identified Candidatus Anammoxoglobus, A4b, and Candidatus Brocadia as top SHAP features, with Candidatus Kuenenia enriched in biofilm (P = 0.0281), reproducing the phase differentiation observed in public datasets. Complementary shotgun metagenomic sequencing further characterized genetic potential associated with differentiation between the two phases. Fifty days of continuous operation monitoring showed stable reactor performance, suggesting possible involvement of niche complementarity in nitrogen removal. Under the tested conditions, the IFAS process showed distinct suspended-sludge and biofilm community profiles. This study provides microbial evidence and machine learning screening methods to distinguish suspended and biofilm sludge phases in lab IFAS reactors, and characterizes genetic potential associated with niche separation under the tested laboratory conditions.},
}

@article {pmid42849238,
year = {2026},
author = {Zhaxi, D and Zhang, Y and Qing, Y and Zhang, Y and Yang, D and Yu, C and Yang, C and Li, Z},
title = {Puerarin improved meat quality via the gut-muscle axis mediated by liver metabolites in chicken.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107917},
doi = {10.1016/j.psj.2026.107917},
pmid = {42849238},
issn = {1525-3171},
abstract = {Improving the meat quality of chicken is a premier objective driven by surging global consumer demand. As a natural isoflavone derivative, Puerarin (PUE) possesses extensive metabolic and regulatory potential, but its exact mechanism in reshaping avian meat quality traits remains poorly understood. This study investigated the effects of PUE supplementation (0.08%) on Daheng chickens over a 70-day rearing period using metagenomics and untargeted LC-MS metabolomics. The results demonstrated that PUE significantly reduced post-mortem drip loss and cooking loss, and enhanced the 45-min post-mortem redness (a*) of leg muscle, while muscle fiber diameter and intramuscular fat (IMF) content remained statistically unaltered. Metagenomic and cecal metabolomic analyses revealed that PUE enriched key microbial consortia, notably Methanobrevibacter, Candidatus_Pelethomonas, Catenibacillus, and Candidatus_Scybalocola, which positively synchronized with the accumulation of enteric antioxidants such as Equol, Puerarin, 6''-O-Malonyldaidzin, and Liquiritin. Liver metabolomics, Mantel tests and mediation analysis identified Candidatus_Scybalocola as a key genus, proving that the gut-driven signals were channeled through adenosine monophosphate (AMP), Fahfa (9:0/18:3), 6''-O-Malonylglycitin, and 5-Hydroxy-3,6,7,8,3',4'-Hexamethoxyflavone. Intramuscularly, these upstream metabolic realignments culminated in the deposition of Spermidine, endogenous Lipoxin B4, and phytogenic flavonoids (Gossypetin 8-Glucuronide 3-Glucoside and Tricin 7-Diglucuronoside). These localized molecular hubs established a powerful barrier that mitigated post-mortem oxidative leakage and stabilized myofibrillar protein frameworks against thermal shrinkage. The overall optimization of water-holding traits highlights PUE as an effective nutritional intervention to enhance broiler meat quality through gut-muscle axis.},
}

@article {pmid42849293,
year = {2026},
author = {Zhou, X and Cui, G and Dong, H and Wen, S and Li, Y and Han, M and Wang, G},
title = {Genotype-dependent phosphorus acquisition responses of two soybean genotypes under combined low phosphorus and salt stress: evidence from root traits, exudates and rhizosphere microbiome.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111810},
doi = {10.1016/j.plaphy.2026.111810},
pmid = {42849293},
issn = {1873-2690},
abstract = {Soil salinization and phosphorus (P) deficiency often co-occur in coastal saline-alkali soils, severely limiting crop productivity. Although root exudates are known to mediate rhizosphere microbiome assembly, the coordinated associations among root exudates, rhizosphere microbes, and P acquisition under combined salinity stress and phosphate deficiency remain unclear. In this study, we used two salt-tolerant soybean genotypes differing in P efficiency (A74, P-efficient; A6, P-inefficient) as materials. In a controlled pot experiment, four treatments were established: control (CK), low P (LP), salt (S), and combined stress (LPS). By integrating root phenotypes, P acquisition traits, root exudate metabolomics, and rhizosphere metagenomics, the genotype-dependent rhizosphere responses were investigated. Results showed that, compared to A6, A74 maintained a more extensive root-soil interface and superior P nutritional status under LP and LPS, exhibiting more robust P acquisition responses. Metabolomics and metagenomics identified 16 candidate metabolites and 12 candidate microbial taxa, respectively. Effect-size and correlation analyses prioritized naringenin and Sinorhizobium as candidate components associated with genotype-dependent P acquisition responses. KO annotation identified Sinorhizobium-associated genes with potential roles in phosphonate and phosphinate metabolism and benzoate degradation (e.g., phnJ, pcaC, and mhpD). In summary, these results support a genotype-dependent rhizosphere response pattern involving naringenin and Sinorhizobium, in which coordinated changes in root traits, exudate profiles, and microbial functional potential were associated with the stronger P acquisition response of A74 under combined stress. These findings identify candidate relationships for future functional validation under saline conditions.},
}

@article {pmid42849679,
year = {2026},
author = {De Lise, F and Sacco, O and Shaikh-Ibrahim, A and Di Fenza, M and Strazzulli, A and Moracci, M and Terrapon, N and Curci, N and Cobucci-Ponzano, B},
title = {Seeding subfamilies in glycoside hydrolase family 116: New insights into the function and inhibitor sensitivity of subfamily 2.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {154792},
doi = {10.1016/j.ijbiomac.2026.154792},
pmid = {42849679},
issn = {1879-0003},
abstract = {Among glycoside hydrolase (GH) families and characterized enzymes reported in CAZy, GHs from Archaea remain largely underrepresented. Recent 'omics' studies have uncovered numerous uncharacterized GH sequences from extremophilic Archaea, providing unprecedented opportunities to study their diversity, structure, function, and properties. The GH family 116 (GH116) was originally built around a characterized archaeal member, revealing homologous sequences in Eukaryota and Bacteria. Although previous studies proposed or attempted GH116 subdivision into distinct subfamilies associated with different substrate specificity and inhibitor sensitivity, such a classification has never been formally established, mainly because few GH116 enzymes have been biochemically characterized. As a result, its functional landscape remains poorly understood. Here, we formally establish GH116 subfamilies, starting from the discovery of nine novel archaeal GH116 sequences identified from metagenomics samples collected from two mud/water pools in the extreme environment of Pisciarelli solfatara. These sequences were assigned to subfamilies 2 and 3, mainly hyperthermophilic archaeal enzymes. By combining phylogenetic analyses, structural modeling, and biochemical studies, we identified subfamily-specific structural domains that may serve as structural markers and suggest that these subfamilies represent functionally specialized groups. Focusing on subfamily 2, previously with only one characterized member, we biochemically characterized two novel enzymes. Our results expand GH116 functional diversity, reporting for the first time β-galactosidase activity within this family and showing β-xylosidase activity in subfamily 2, previously observed only in subfamily 3. We also examined active-site inhibition profiles and, through active-site mapping and mutational analysis, elucidated the molecular basis of inhibitor sensitivity in one enzyme of this subgroup.},
}

@article {pmid42850249,
year = {2026},
author = {Chen, S and Bahadur, A and Zhu, J and Liu, E and Gu, Y and Liang, H and Zhang, W and Li, S and Li, A and Wei, P and Liu, Q and Wu, T and Yang, P and Zou, Y and Han, M and Malard, LA},
title = {Hydrothermal regimes regulate microbiome patterns across vertical profile and their responses to alpine permafrost degradation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42850249},
issn = {2041-1723},
support = {U23A2062//National Natural Science Foundation of China (National Science Foundation of China)/ ; U24A20586//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Permafrost/microbiology ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification ; Soil Microbiology ; Tibet ; Metagenome ; Nitrogen/metabolism ; },
abstract = {Deciphering microbiomes across vertical profiles is critical for understanding biogeochemical cycling and potential biosafety hazards associated with permafrost degradation under climate warming. However, knowledge about microbiome patterns over key profile layers in response to degradation remains limited in the Qinghai-Tibet Plateau. Using metagenomic data obtained from 150 samples of six 15 m-depth alpine permafrost cores along a degradation gradient, we analyzed microbial community structure and functional potential across different main-layers, including the active, frozen fringe, and frozen layers. We found the recovered microbial and functional diversity decreased with profile depth, and declined only in the active layer as permafrost degraded. Interestingly, Pithoviridae, Caulimoviridae, and virulence factors related to adhesion, biofilm formation, and immune regulation were enriched in the frozen fringe layer, along with increasing relative abundance of Lavidaviridae under the degradation. Along the degradation gradient, carbohydrate-active enzymes diversity decreased in the active layer, while the ratio of nitrite reductase genes to nitrous oxide reductase genes increased in the active and the frozen fringe layers. Hydrothermal regimes emerged as the primary controls shaping microbiome distributions across the vertical profile and along the degradation gradient. Notably, hydrothermal and microbiome attributes jointly regulated carbon/nitrogen loss during the degradation. Taken together, these findings offer crucial insights into microbiome patterns, carbon/nitrogen loss and biosecurity concerning permafrost degradation under global warming.},
}

*Permafrost/microbiology
*Microbiota/genetics/physiology
Bacteria/genetics/classification
Soil Microbiology
Tibet
Metagenome
Nitrogen/metabolism

@article {pmid42850563,
year = {2026},
author = {Viana-Cardenas, E and Jiang, M and Rodriguez-Nava, G and Tariq, W and Conforti, S and Paredes, JL and Pincus, N and Miranti, E and Wick, JM and Whitaker, E and Sampson, MM and Zulli, A and Marra, AR and AlSweed, AM and Boehm, AB and Salinas, JL},
title = {Hospital wastewater-based antimicrobial resistance epidemiology: a scoping review.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/ice.2026.10558},
pmid = {42850563},
issn = {1559-6834},
abstract = {INTRODUCTION: Wastewater-based epidemiology (WBE) offers pooled biological samples of defined populations, complementing clinical surveillance for infectious diseases. Hospitals are hotspots for antimicrobial resistance (AMR). We performed a scoping review assessing hospital wastewater for AMR monitoring.

METHODS: We searched Medline, Embase, Biosis, Web of Science, and biorxiv.org from inception to May 5, 2026, for studies using hospital wastewater to monitor AMR. The primary outcome was AMR detection and concordance with traditional surveillance. Concordance was reported by resistance class, and reported as strain- or gene-level, as discordant, or as not assessed. Secondary outcomes included sampling methods, and laboratory techniques.

RESULTS: Of 4,695 screened studies, 36 from 22 countries met inclusion criteria (high-income 53%, upper-middle-income 42%, and lower-middle-income 5%). Traditional surveillance used mostly routine diagnostics (58%); only 39% of studies aligned temporally with wastewater sampling. Extended-Spectrum Beta-Lactamase-producing organisms showed strain-level concordance in 2/6 studies, and gene-level concordance in 4/6; carbapenem resistance showed strain-level concordance in 2/9 and gene-level concordance in 4/9. Concordance was present for vancomycin-resistant enterococci (2/3), while inconsistent for Methicillin-resistant Staphylococcus aureus (0/2) and Candida auris (1/2). One study quantified correlation statistically, finding strong association (Spearman's rho = .88). Wastewater sampling methods included grab sampling (39%), composite sampling (36%), and was unreported (25%). Most studies combined culture-based (89%) and molecular methods (PCR 75%, WGS 42%, metagenomics 17%), mostly targeting Gram-negatives (83%).

CONCLUSION: Hospital WBE showed variable concordance with traditional surveillance, but methodological heterogeneity and limited temporal alignment constrain comparisons. Standardized frameworks and patient-level studies, particularly from low- and middle-income countries, are needed.},
}

@article {pmid42850800,
year = {2026},
author = {Sharkey, T and Eisner, M and Common, J and Rajan, N},
title = {Towards Personalised Therapeutics for Epidermal Differentiation Disorders: Integrating Host Genetics, Immuno-Endotypes and the Skin Microbiome.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljag447},
pmid = {42850800},
issn = {1365-2133},
abstract = {Epidermal differentiation disorders (EDDs), are a rare, heterogeneous grouping of monogenic disorders. EDDs, comprising the previously termed congenital ichthyosis, are characterised by epidermal barrier dysfunction, cutaneous inflammation, and associated morbidity. Immunomodulatory therapies, particularly repurposed biologics, are an emerging approach for management. However, clinical implementation has been impeded by a variable and unpredictable response rate, reflecting the genetic and immunological heterogeneity of EDD as well as raising questions over other contributory pathogenic mechanisms. Patient genotyping and immune profiling have revealed a shared immune polarisation across EDD subtypes, predominantly Th17, with some subtypes demonstrating a mixed immuno-endotype with contribution from Th2 or lL-36 mediated signalling. This improved immunological understanding has informed the repurposing of established biologics targeting IL-4R, IL-17, IL-12/23, alongside emerging interest in JAK inhibitors. Metagenomic microbiome profiling has revealed a homeostatic disruption across EDD subtypes with depleted commensal organisms, including Cutibacterium acnes and Malassezia species, and enrichment of pathobiont Staphylococcus and Corynebacterium species. Patients may be further stratified into dysbiotic groupings, with pathogenic variant and phenotypic severity influencing microbial composition. Ecological dysbiosis may contribute to immune polarisation through an "outside-inside-outside" model of host-microbe interactions, potentially underlying the variable response rates to repurposed biologics. In this review, we propose a "host genome and microbiome" framework for personalised EDD clinical management, integrating the EDD genotype and immuno-endotype ("Host genome"), and cutaneous microbiome as candidate simultaneous stratifiable elements. Genomic diagnosis, spurred by recent EDD reclassification, provides mechanistic context. Immuno-endotyping may enable a rational biologic selection but requires prospective validation. Microbiome profiling may guide emerging therapeutics or serve as a biomarker. We propose that a route to therapeutic restoration in EDD may require simultaneous targeting of the host-microbe axis. Delineation of the complex interplay between host genetics, immuno-endotypes, epidermal barrier dysfunction, and skin microbiome is a key priority for future research to bring this approach to the clinic.},
}

@article {pmid42851315,
year = {2026},
author = {Niu, B and Wang, R and Tian, H and Li, X and Yu, Y and Ren, J and Zhang, L},
title = {Clinical contribution of mNGS in the diagnosis and management of imported falciparum malaria in a malaria-free region: a five-case series from northern China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1978670},
pmid = {42851315},
issn = {2235-2988},
mesh = {Humans ; China/epidemiology ; *Malaria, Falciparum/diagnosis/drug therapy/parasitology ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Plasmodium falciparum/genetics/isolation & purification ; *Communicable Diseases, Imported/diagnosis/parasitology/drug therapy ; Adult ; *Metagenomics/methods ; Travel ; Antimalarials/therapeutic use ; Middle Aged ; Young Adult ; },
abstract = {BACKGROUND: Although malaria transmission has been eliminated in China, imported Plasmodium falciparum malaria remains a diagnostic challenge, particularly in non-endemic regions where clinical experience is limited. The nonspecific manifestations and potential for rapid progression to severe disease may result in delayed diagnosis and inappropriate management. Metagenomic next-generation sequencing (mNGS) has emerged as a complementary diagnostic approach for complex infectious diseases; however, its role in imported malaria management remains insufficiently characterized.

METHODS: We retrospectively reviewed five patients with imported P. falciparum malaria in whom mNGS contributed to diagnosis or clinical management in a malaria-free region of northern China. Demographic characteristics, epidemiological exposure, clinical manifestations, laboratory findings, mNGS results, treatment strategies, and outcomes were analyzed. Clinical scenarios in which mNGS provided additional diagnostic information were summarized.

RESULTS: All patients had travel or residence histories in malaria-endemic regions in Africa. mNGS detected P. falciparum sequences in all patients, while peripheral blood smear examination demonstrated malaria parasites, with sequencing reads ranging from 121 to 212,513. Clinical presentations ranged from uncomplicated febrile illness to severe malaria with multiorgan involvement, including impaired consciousness, severe anemia, thrombocytopenia, and acute kidney injury requiring continuous renal replacement therapy. In four patients, mNGS was incorporated into early etiological evaluation, whereas in one patient it was used for reassessment of recurrent fever and suspected concomitant infection. In this patient, mNGS provided additional evidence supporting malaria-related evaluation without identifying clinically significant alternative pathogens.

CONCLUSION: Imported P. falciparum malaria remains challenging to diagnose and manage in malaria-free regions. This case series highlights that mNGS may provide complementary information beyond pathogen detection, particularly in patients with complex presentations or uncertain clinical trajectories. Integration of mNGS with conventional parasitological methods and clinical assessment may facilitate the management of imported malaria in non-endemic settings.},
}

Humans
China/epidemiology
*Malaria, Falciparum/diagnosis/drug therapy/parasitology
Male
Female
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Plasmodium falciparum/genetics/isolation & purification
*Communicable Diseases, Imported/diagnosis/parasitology/drug therapy
Adult
*Metagenomics/methods
Travel
Antimalarials/therapeutic use
Middle Aged
Young Adult

@article {pmid42851331,
year = {2026},
author = {Xu, Y and Zhang, Y and Li, S and Yao, H and Yang, Y and Yu, C and Zhang, S},
title = {Hepatoprotective action of Dendrobium officinale polysaccharide against MAFLD: modulation of gut microbiota-metabolite cascade controls TLR4/NF-κB inflammatory response.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1953606},
pmid = {42851331},
issn = {1663-9812},
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) threatens public health worldwide, and Dendrobium officinale polysaccharide (DOP) exhibits promising hepatoprotective potential, yet its regulatory mechanism targeting the gut microbiota-metabolite-TLR4/NF-κB inflammatory axis remains poorly defined.

METHODS: In this study, in-vivo rat and in-vitro HepG2 cell MAFLD models were established. Male Sprague-Dawley (SD) rats received 12-week high-fat diet (HFD) feeding to induce MAFLD; HepG2 cells were exposed to a 1 mmol/L free fatty acid (FFA) mixture (oleic acid/palmitic acid = 2:1) for 24 h to trigger cellular steatosis. Serum, hepatic and cellular biochemical indexes, intestinal permeability factors and inflammatory mediators were detected. Hepatic pathological lesions and lipid accumulation were evaluated via hematoxylin-eosin (HE) and Oil Red O staining. Fecal metagenomics and untargeted metabolomics were applied to profile gut microbes and differential metabolites. RT-qPCR and Western blotting were used to assess tight-junction protein expression and TLR4/NF-κB pathway activation.

RESULTS: DOP markedly alleviated hepatic lipid accumulation, restored liver function abnormalities and mitigated hepatic pathological damage. DOP reshaped the disturbed gut flora: it reduced lipopolysaccharide (LPS)-enriched Gram-negative bacteria, elevated short-chain fatty acid-producing probiotics, modified intestinal metabolites, repaired the intestinal barrier and prevented intestinal LPS leakage. Both cellular and animal experiments demonstrated that DOP down-regulated TLR4, MyD88 and NF-κB p65 levels, increased IκBα expression and suppressed downstream pro-inflammatory mediators.

DISCUSSION: Collectively, DOP confers protective effects against MAFLD through remodeling gut microbiota and intestinal metabolites, preserving intestinal-barrier integrity, and inhibiting LPS-provoked hepatic TLR4/NF-κB inflammatory activation.},
}

@article {pmid42851483,
year = {2026},
author = {Yang, C and Lin, Z and Yang, D and Xu, X},
title = {Case Report: Primary cutaneous infection caused by Microascus trigonosporus.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1963973},
pmid = {42851483},
issn = {2296-858X},
abstract = {BACKGROUND: Microascus trigonosporus is an emerging opportunistic filamentous fungus, with most reported cases involving invasive pulmonary infections in solid organ transplant recipients. Worldwide, cutaneous infections caused by this organism are extremely rare. This case highlights an unusual presentation of primary cutaneous infection in a non-transplant host.

METHODS: We report a case of a 67-year-old woman who presented with progressive skin erythema and pustules for two months, unresponsive to topical halometasone. Her medical history included glaucoma, hypertension, and coronary heart disease. The diagnostic workup included microscopic examination of skin lesion scrapings, skin biopsy for histopathology, fungal culture, and metagenomic next-generation sequencing (mNGS) for pathogen identification. The patient was treated sequentially with oral fluconazole for 2 weeks, followed by itraconazole for 8 weeks, and was followed up for 1 year.

RESULTS: Microscopic examination of skin scrapings revealed abundant, branched, and septate fungal hyphae. Skin biopsy revealed chronic inflammation with neutrophil infiltration in the superficial dermis. Fungal culture results were positive, and the isolate exhibited morphological features consistent with the genus Microascus. The pathogen was definitively identified as M. trigonosporus using mNGS. The skin lesions completely resolved after sequential antifungal therapy (fluconazole for 2 weeks, followed by itraconazole for 8 weeks). No drug-related adverse events were observed, and no recurrence was noted during the 1-year follow-up.

CONCLUSION: This case expands the disease spectrum of M. trigonosporus, demonstrating that primary cutaneous infections can occur in non-transplant hosts. mNGS facilitates the rapid identification of rare filamentous fungi in chronic, undiagnosed skin lesions, enabling earlier and more precise diagnoses.},
}

@article {pmid42851762,
year = {2026},
author = {Ye, G and Yu, X and Ismaiah, MJ and Ke, R and Zeng, Z and Wang, J and Lan, S and Yu, H and Liu, H and Xie, S and Leung, KS and Zhang, L and Lee, JC and Habimana, O},
title = {Structured succession of a cross-kingdom microbiome drives degradation and detoxification of oolong tea waste.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1871476},
pmid = {42851762},
issn = {2813-4338},
abstract = {The spontaneous aerobic degradation of oolong tea waste offers a promising but underexplored route for sustainable waste valorization. In this study, we used whole-genome metagenomic sequencing to examine microbial succession and functional gene dynamics over a 35-day degradation period. Our results uncovered a three-phase ecological progression: an initial mesophilic phase (Days 0-7) dominated by Pseudomonadota, which reached 93.4% relative abundance and specialized in simple substrate utilization; a thermotolerant transition (Days 8-15, 30-33°C) characterized by increased abundance of glycoside hydrolases (GH5, GH13); and a maturation phase (Days 16-35) marked by the emergence of lignocellulose-degrading taxa such as Cellulomonas and Microbacterium, accompanied by a 78% reduction in antibiotic resistance genes. Profiling of carbohydrate-active enzymes revealed a sequential shift from pectinases (GH28) to hemicellulases (GH43), while mobile genetic elements declined substantially during the maturation phase. These results indicate that tea waste degradation follows structured microbial succession patterns influenced by abiotic factors and suggests a potential self-purification capacity through the attenuation of antibiotic resistance genes. This study establishes a foundation for optimizing composting processes and designing targeted bioaugmentation strategies to enhance tea waste valorization.},
}

@article {pmid42851821,
year = {2026},
author = {Al-Shaarani, AAQA and Pecoraro, L},
title = {The influence of environmental factors on the diversity and structure of airborne fungal and bacterial communities.},
journal = {Mycology},
volume = {17},
number = {3},
pages = {811-836},
pmid = {42851821},
issn = {2150-1203},
abstract = {Airborne fungal and bacterial communities are key components of microbial diversity, with significant consequences for human health, environmental processes, and ecosystem stability. This review analyzes the impact of environmental factors, such as climatic conditions, air pollutants, geographical locations, seasonal variations, human activities, soil and vegetation, on the diversity and structural composition of airborne fungal and bacterial communities. By evaluating functional features and diversity of fungi and bacteria in various contexts, this review highlights the differences in the microbial community structure across urban and rural environments, indoor and outdoor settings, and geographic locations. The potential health hazard of pathogenic airborne fungi and bacteria is considered and highlighted, particularly under critical environmental conditions determined by pollution and climate change. Advanced methodologies for air sampling, molecular approaches, and metagenomic tools, are essential for investigating the dynamics of microbial communities in the environment. Future research is required to address the issues of emerging pollutants and global climate shifts and integrate the results obtained from microbial studies into urban planning, sustainable environmental management, public health programs, etc. This review seeks to increase our understanding of airborne fungal and bacterial communities and their environmental drivers, delivering insights for minimizing human health risks and improving ecosystem resilience.},
}

@article {pmid42852388,
year = {2026},
author = {Laue, HE and Fleisch, AF and Calafat, AM and Lanphear, BP and Cecil, KM and Yolton, K and Buckley, JP and Karagas, MR and Madan, JC and Willis, AD and Braun, JM},
title = {Associations of Urinary Triclosan Concentrations Across Gestation and Childhood with the Adolescent Gut Microbiome.},
journal = {Environmental health perspectives},
volume = {134},
number = {6},
pages = {672-687},
pmid = {42852388},
issn = {1552-9924},
mesh = {*Triclosan/urine ; Humans ; Female ; Pregnancy ; Adolescent ; Child ; *Gastrointestinal Microbiome/drug effects ; Child, Preschool ; Male ; Infant ; *Anti-Infective Agents, Local/urine ; Ohio ; Prospective Studies ; Feces/microbiology ; },
abstract = {Research on the influence of repeated exposure to antimicrobial chemicals, such as triclosan, on the microbiome is lacking. The goal of this study was to elucidate the associations of time-varying urinary triclosan concentrations with the adolescent gut microbiome. We used data from a prospective cohort based in Cincinnati, OH (enrolled 2003-2006, n = 146), to assess the time-varying associations of urinary triclosan concentrations with adolescent (age ∼ 12 years) gut microbiome diversity and composition. Individuals ≥ 18-years-old were recruited during the second trimester of pregnancy, and urinary triclosan concentrations were measured in pregnant women up to 2 times in pregnancy and up to 7 times in the child from ages 1 through 12 years. At age ∼ 12 years, fecal microbiome diversity and composition was characterized with metagenomic sequencing. We estimated differences in the relative abundance of prevalent (≥50%) bacterial species and gene pathways using linear regression and generalized estimating equations to assess windows of heightened susceptibility adjusted for sociodemographic characteristics. Additionally, we examined sex-specific associations by including an interaction term. The adolescent median Shannon diversity was 3.5 (IQR: 3.3, 3.5). Higher gestational triclosan concentrations with lower gut microbiome diversity [β = -0.13 per 10-fold increase (95%CI: -0.24, -0.02)]. Triclosan concentrations were also positively associated with higher abundance of antibiotic resistance genes and differential abundance of some bacterial species, with the strongest associations observed in early life and at age 12 years. We also found differences depending on sex, with more significant associations observed among males. Our findings provide insight into windows of triclosan exposure that are relevant to gut microbiome composition and the impacts of antimicrobial agents.},
}

*Triclosan/urine
Humans
Female
Pregnancy
Adolescent
Child
*Gastrointestinal Microbiome/drug effects
Child, Preschool
Male
Infant
*Anti-Infective Agents, Local/urine
Ohio
Prospective Studies
Feces/microbiology

@article {pmid42852396,
year = {2026},
author = {Si, G and Jiang, H and Peng, C and Xu, D and Zhao, S},
title = {A 20% nitrogen reduction threshold optimizes soil carbon stability and microbial functional resilience under long-term straw return in a rice-wheat rotation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1928083},
pmid = {42852396},
issn = {1664-302X},
abstract = {Reducing synthetic nitrogen (N) fertilizer while maintaining soil fertility and crop productivity is a major challenge for sustainable rice production. Straw return has been widely adopted to enhance soil organic carbon (SOC) sequestration; however, the mechanisms by which reduced N input interacts with straw return to regulate SOC stabilization remain poorly understood. Here we evaluated graded N reduction (0, 20, and 30%) under continuous straw return in a nine-year rice-wheat double-cropping experiment in central China. Soil carbon pools, aggregate stability, organic carbon functional groups, and microbial community structure and function were assessed using carbon fractionation, wet-sieving, FTIR spectroscopy, and metagenomic analyses. We found that 20% N reduction (80%NR) maintained grain yield comparable to conventional N fertilization while significantly increasing readily oxidizable organic carbon (ROOC, +18-26%), water-soluble organic carbon (WSOC, +12-21%), microbial biomass carbon (MBC, +15-24%), and carbon management index (CMI, +42-58% relative to NR). Moderate N reduction also enhanced macroaggregate-associated SOC and the relative abundance of aliphatic and aromatic carbon functional groups. Metagenomic analyses revealed that 80%NR enriched Firmicutes (+26%), Actinobacteria (+50%), and Nitrospira, reduced methanogenic archaea, and triggered a metabolic shift from CO oxidation (coxL/cutL, -15 to -22%) toward reductive carbon fixation via the Wood-Ljungdahl pathway (hdrA2, +6 to +19%). In contrast, 30% N reduction (70%NR) undermined subsurface aggregate stability and eroded microbial functional diversity, identifying 20% N reduction as an optimal threshold within the tested gradients. These findings provide a mechanistic basis for optimizing nitrogen management in sustainable rice production systems.},
}

@article {pmid42852494,
year = {2026},
author = {Li, Y and Chen, J and Lin, L and Jian, Z and Liu, L and Wang, M and Wei, J and Chen, X and Yang, M and Li, T and Xiang, L and Liao, B and Jin, X and Wang, K},
title = {Gut microbiota-derived tryptophan metabolite attenuates calcium oxalate nephropathy by suppressing renal tubular cell apoptosis through the AhR-SOCS3-STAT1 axis.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.70135},
pmid = {42852494},
issn = {1096-9896},
support = {82570894//National Natural Science Foundation of China/ ; 82270799//National Natural Science Foundation of China/ ; 2023SCUH0054//Sichuan University/ ; CZ2026001//Project of National Outstanding Medical Doctors/ ; 2023HXFH014//Clinical Research Incubation Project of West China Hospital of Sichuan University/ ; },
abstract = {Calcium oxalate (CaOx) nephropathy is a highly prevalent urological disease worldwide. Gut microbiota dysbiosis and host metabolic dysregulation are recognized as pivotal drivers in disease pathogenesis, yet the underlying mechanisms remain incompletely understood. In this study, by integrating metagenomics and metabolomics, we identified dysregulation of tryptophan metabolites in patients with CaOx nephrolithiasis, with microbiota-derived indole-3-propionic acid (IPA) as the most discriminatory differential metabolite. Oral IPA supplementation markedly reduced renal CaOx crystal deposition and tubular injury in a CaOx nephropathy murine model. Mechanistically, IPA activated the aryl hydrocarbon receptor (AhR), which translocated to the nucleus and transcriptionally upregulated suppressor of cytokine signaling 3 (SOCS3)-a negative regulator of signal transducer and activator of transcription 1 (STAT1)-thereby suppressing STAT1 phosphorylation, alleviating oxalate-induced tubular cell injury and apoptosis, and inhibiting CaOx crystal deposition. Our findings identify tryptophan metabolite alteration as a critical metabolic signature of CaOx nephropathy and demonstrate that microbiota-derived IPA attenuates oxalate-induced renal tubular cell injury and apoptosis via the AhR-SOCS3-STAT1 axis. © 2026 The Pathological Society of Great Britain and Ireland.},
}

@article {pmid42852641,
year = {2026},
author = {Zhong, L and Purushothaman, B and Tu, Q and Boopathi, S},
title = {From microbial tryptophan metabolism to crystal injury: an IPA-AhR checkpoint in calcium oxalate nephropathy.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.70134},
pmid = {42852641},
issn = {1096-9896},
support = {W2433079//National Natural Science Foundation of China/ ; 32350010//National Natural Science Foundation of China/ ; QDBSH20240102002//Qingdao Postdoctoral Funding Project/ ; 2025RC3210//Science and Technology Innovation Program of Hunan Province/ ; 2025RC4019//Science and Technology Innovation Program of Hunan Province/ ; },
abstract = {Calcium oxalate nephrolithiasis is commonly viewed as a consequence of urinary supersaturation, although crystal retention and renal injury are also influenced by gut microbiota dysbiosis and local tissue environment. In a recent study by Li et al, published in The Journal of Pathology, the authors integrated human metagenomic and metabolomic analyses with mouse and tubular cell models to identify indole-3-propionic acid (IPA) as a key gut-derived metabolite associated with kidney stone disease. Patients with calcium oxalate stones showed altered gut microbial composition and reduced serum IPA levels, which were inversely related to stone burden. In experimental models, IPA supplementation reduced renal crystal deposition, preserved kidney function, and limited tubular injury and apoptosis. Mechanistic studies showed that IPA activated aryl hydrocarbon receptor (AhR) in tubular epithelial cells, increased suppressor of cytokine signaling 3 (SOCS3) expression, and suppressed signal transducer and activator of transcription 1 (STAT1) phosphorylation and nuclear accumulation. These findings were supported by complementary activation, inhibition, knockdown, and overexpression experiments. Collectively, the data suggest that IPA protects renal epithelial cells through the AhR-SOCS3-STAT1 signaling pathway and may offer a potential therapeutic approach for calcium oxalate nephropathy. © 2026 The Pathological Society of Great Britain and Ireland.},
}

@article {pmid42852904,
year = {2026},
author = {Harrison, LB and Ahmed, JO and Coulibaly, GM and Veyrier, FJ},
title = {Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0044426},
doi = {10.1128/msystems.00444-26},
pmid = {42852904},
issn = {2379-5077},
abstract = {UNLABELLED: Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypotheses, which previously relied on PCR or culture. However, the problem of determining the presence/absence of a given species of interest is not trivial, particularly when closely related species are present in the reference database or metagenomic sample. Reference-based methods for detecting species-level taxa mostly rely on thresholding of aligned reads or mapped k-mers, or derivative metrics such as genomic coverage, creating a trade-off between recall/completeness and precision/purity. New methods for species-level profiling (YACHT, Metapresence, and sylph) have recently been published. Here, we test the performance of these methods, along with Kraken2/bracken and MetaPhlAn4, to detect related species of interest using simulated metagenomic samples from genomes in the families Mycobacteriaceae and Neisseriaceae, which contain closely related genomes. Among methods tested, Metapresence, when used with an alignment quality filter, and sylph offer the best overall performance. Sylph maintains high precision but requires a depth of coverage greater than approximately 0.1× to reliably detect a genome's presence. Metapresence has a lower limit of detection of hundreds of reads, but this is balanced against relatively lower precision. Both methods are relatively robust to the presence of reads from genomes outside the groups of interest. We demonstrate the application of these methods in two real-world data sets: a mycobacterial community in a drinking water system and the community of Neisseriaceae present in the human oral cavity.

IMPORTANCE: Detecting which bacterial species of interest are present in a given sample is fundamental to studies of microbial ecology and evolution and to applied microbiology (e.g., clinical diagnostics). Culture-dependent and culture-independent (e.g., PCR) approaches are increasingly complemented by metagenomic approaches, but methods to accurately identify specific low-abundance species-level genomes in a shotgun metagenomic sample are still being refined. Here, we comprehensively test YACHT, Kraken2/bracken, Metapresence, MetaPhlAn4, and sylph using two simulated data sets of bacterial families, Mycobacteriaceae and Neisseriaceae, that contain closely related species. Our simulations exploit natural genomic diversity to create a challenging benchmark. We demonstrate that Metapresence and sylph perform best, with the former being well suited to low-biomass host-associated data sets and the latter with environmental metagenomic samples. This study is the first extensive benchmark of these methods for this use case and demonstrates that these methods can accurately identify closely related species of interest.},
}

@article {pmid42853493,
year = {2026},
author = {Li, Y and Wu, Z and Xiang, T and Duan, B and Liu, Z and Liu, P and Wei, Y and Ling, P},
title = {Mycoplasma pneumoniae infections in the Post-COVID era: recent advances from pathogenesis to clinical management.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42853493},
issn = {1439-0973},
support = {S202310555045 and S202310555226//Hunan Provincial College Students' innovation and Entrepreneurship Training Program/ ; Z2023090//Health Research Project of Hunan Provincial Health Commission/ ; 2023GZ4043//Science and Technology Planning Project of Shaoyang City/ ; },
abstract = {M.pneumoniae is a major cause of human respiratory infection whose pathogenicity relies on adhesion proteins, secreted virulence factors, and immune evasion mechanisms. This review contextualizes these strategies within the broader phylogeny of clinically relevant Mycoplasma species while addressing the diverse extrapulmonary manifestations of M. pneumoniae. Current challenges in managing M. pneumoniae infections are multifaceted. The post-pandemic resurgence reflects a population-level immune debt resulting from prolonged non-pharmaceutical interventions, with test positivity rising sharply after restrictions were lifted and driving pneumonia outbreaks across age groups. Macrolide resistance remains persistently high in East Asia and is emerging at variable rates in other regions; routine diagnostics cannot detect resistance in real time, complicating first-line empirical therapy. Vaccine development continues to face obstacles including antigenic variation mediated by recombination between repetitive genomic sequences, the IL-17 A paradox wherein protective Th17 responses also drive vaccine-enhanced disease, and the inability of systemic vaccines to induce mucosal secretory IgA and tissue-resident memory T cells. In response, we evaluate emerging diagnostics-including metagenomic sequencing, CRISPR-Cas platforms, and host biomarkers-and discuss resistance-guided therapies involving doxycycline, quinolones, and novel agents like lefamulin and omadacycline. We further analyze vaccine development hurdles alongside the potential of mRNA-LNP platforms targeting conserved adhesin epitopes. Our findings indicate that the lag between mechanistic insight and clinical implementation remains the most pressing challenge. Future research must shift from simple mechanistic elucidation to addressing real-world clinical dilemmas, including distinguishing colonization from infection through integrated pathogen-host evaluation, exploring synergistic use of antibiotics and immunomodulators targeting the IL-17 A pathway, advancing vaccine design that circumvents IL-17 A-mediated immunopathology via conserved epitope selection and mucosal delivery, and establishing real-time surveillance networks integrating genomics and clinical phenotypes. Collectively, this work provides a practical roadmap spanning molecular pathology to clinical practice for the precise management of M. pneumoniae infections.},
}

@article {pmid42853601,
year = {2026},
author = {Mendoza-Guido, B and Rojas-Jimenez, K},
title = {Plasmidomics: studying plasmids as ecological entities beyond their hosts.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001846},
pmid = {42853601},
issn = {2057-5858},
mesh = {*Plasmids/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Symbiosis ; Evolution, Molecular ; Ecosystem ; },
abstract = {Plasmids are mobile genetic elements with autonomous replication, whose ecology extends beyond individual bacterial hosts. As molecular symbionts, they have the potential to traverse bacterial taxa and environments, disseminating adaptive genes and shaping microbial community structure through dynamics that are likely decoupled from host taxonomy. Plasmidomics - the omics discipline dedicated to the study of plasmids - has revealed that plasmid diversity and distribution respond to environmental gradients independently of their hosts, underscoring their roles as ecological entities. However, the field faces critical methodological constraints: short-read assemblies fragment plasmid sequences, culture-dependent approaches underrepresent environmental diversity and most metagenomic methods fail to capture plasmid-host associations. In addition, a universally accepted classification framework is still lacking. Advancing plasmidomics will require the integration of long-read sequencing, Hi-C proximity ligation, meta-epigenomics and ecology-informed classification frameworks grounded in genomic and functional criteria. Together, these approaches are essential to uncover the true diversity, evolutionary significance and ecological dynamics of plasmids across complex microbial ecosystems.},
}

*Plasmids/genetics/classification
*Metagenomics/methods
*Bacteria/genetics/classification
Gene Transfer, Horizontal
Symbiosis
Evolution, Molecular
Ecosystem

@article {pmid42853629,
year = {2026},
author = {Jin, JX and Ye, ZC and Zhang, GF and Wang, Y and Jiang, ZC and Lan, FL and He, YF},
title = {Geographic differentiation of the gut microbiota in Lissorhoptrus oryzophilus (Coleoptera: Curculionidae): associations with environmental gradients and predicted functional potential.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {5},
pages = {},
doi = {10.1093/jisesa/ieag111},
pmid = {42853629},
issn = {1536-2442},
support = {568//Guizhou Provincial Science and Technology Program Project/ ; 011//Innovative capabilities Buildup of Green Prevention and Control for Invasive Species in Agriculture/ ; 2017YFC1200600//National Key R&D Program of China/ ; 024//Guizhou Key Laboratory of Agricultural Biosecurity/ ; },
mesh = {Animals ; *Weevils/microbiology ; China ; *Gastrointestinal Microbiome ; Altitude ; Bacteria/classification/genetics ; Metagenomics ; },
abstract = {The rice water weevil, Lissorhoptrus oryzophilus (Kuschel), is a major invasive pest native to rice that has expanded far beyond its native North American range to establish widespread populations across Asia and Europe. However, how altitudinal gradients shape this microbial ecosystem remains unclear. We performed shotgun metagenomics to profile the gut microbiota of 3 geographically distinct populations-Pingba District (PB), Yibin City (SC), and Mudanjiang (MDJ) City-of L. oryzophilus across elevational gradients in China. Though low-abundance archaeal, fungal, and viral sequences were detected, bacterial taxa (>89% of annotated genes) dominated functional profiles. All populations were Proteobacteria-dominated, but PB was enriched in Erwiniaceae (Pantoea deleyi), while SC/MDJ were dominated by Rickettsiaceae (Rickettsia/Wolbachia). Population-specific taxa were most abundant in MDJ (19 species), followed by PB (15), with SC harboring only 1 unique species. Predicted functional profiles aligned with taxonomy: PB showed elevated amino acid/carbohydrate metabolism, carbohydrate-active enzyme, and efflux pump gene abundances. SC and MDJ shared similar functional profiles. Principal coordinates analysis revealed distinct clustering of PB across taxonomic and functional dimensions, while SC/MDJ partially overlapped. These correlative findings suggest microbial metabolic plasticity may support the weevil's persistence across heterogeneous environments, though causal links require experimental validation.},
}

Animals
*Weevils/microbiology
China
*Gastrointestinal Microbiome
Altitude
Bacteria/classification/genetics
Metagenomics

@article {pmid42841659,
year = {2026},
author = {Kovenskiy, A and Mukhanbetzhanov, N and Jarmukhanov, Z and Duisebayeva, A and Morenko, M and Kossumov, A and Chulenbayeva, L and Vinogradova, E and Popov, M and Kushugulova, A and Kozhakmetov, S},
title = {Escherichia coli-derived enterobactin is associated with delayed gut microbiome maturation in infants born to mothers with obesity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098626},
doi = {10.1128/msystems.00986-26},
pmid = {42841659},
issn = {2379-5077},
abstract = {Maternal obesity has been increasingly recognized as a factor influencing early-life microbiome development. However, its impact on the infant gut resistome and virulome remains insufficiently characterized. In this prospective longitudinal study, we investigated gut microbiome composition, antibiotic resistance genes (ARGs), and virulence factor profiles in infants born to mothers with obesity and normal weight during the first year of life. Shotgun metagenomic sequencing was performed on maternal and infant fecal samples collected at birth and at 1, 3, 6, and 12 months. Infants born to obese mothers exhibited delayed microbiome maturation characterized by early enrichment of Pseudomonadota, particularly Escherichia coli and Klebsiella pneumoniae, and reduced abundance of Bifidobacterium species. This compositional pattern was accompanied by a significantly higher ARG burden in early life, including enrichment of genes associated with antibiotic inactivation, efflux mechanisms, and β-lactam resistance. Although taxonomic differences between groups were no longer statistically detectable at the 12-month time point, where the sample size was smallest, functional disparities in the resistome persisted. Additionally, infants born to obese mothers demonstrated increased relative abundance of secretory virulence-associated genes and E. coli-derived enterobactin, suggesting enhanced iron-scavenging capacity and competitive potential of Enterobacteriaceae. Together, these findings suggest that maternal obesity is associated with altered early microbial ecological dynamics, promotes resistome expansion, and may delay transition toward a stable Bacteroidota- and Bacillota-dominated microbiome.IMPORTANCEThe first year of life is a critical window for gut microbiome development, during which early microbial disturbances may influence later health. This study shows that maternal obesity is associated not only with altered infant microbial succession but also with functional changes in the infant gut microbiome, including greater antibiotic resistance gene burden and enrichment of virulence-associated traits. The finding of increased Escherichia coli-derived enterobactin suggests that iron-scavenging mechanisms may help Enterobacteriaceae persist during early infancy and may contribute to delayed microbial maturation. By linking maternal obesity with infant microbiome development, resistome expansion, and virulence-related functions, this work provides new insight into how maternal metabolic status may shape early microbial ecology and potential microbiome-associated risks.},
}

@article {pmid42841906,
year = {2026},
author = {Hodgins, HP and Lobb, B and Peck, M and Doxey, AC},
title = {Targeted genome recovery of under-sequenced microbes from the Sequence Read Archive STAT.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001853},
pmid = {42841906},
issn = {2057-5858},
mesh = {*Genome, Bacterial ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Phylogeny ; Clostridium/genetics/classification ; Sequence Analysis, DNA/methods ; Genome, Archaeal ; High-Throughput Nucleotide Sequencing ; Databases, Genetic ; },
abstract = {Most microbial species are represented by a single genome in public databases. The lack of genomes for these 'singleton' organisms limits our understanding of their pan-genome diversity and evolution. Although the Sequence Read Archive (SRA) contains millions of sequencing datasets that could be used to expand our understanding of many species, the extent to which under-represented microbial species are present at levels sufficient for genome recovery is unclear. Here, we show that the pre-computed taxonomic profiles generated by the National Center for Biotechnology Information SRA Taxonomy Analysis Tool (STAT) can be used to identify SRA datasets containing recoverable genomes for under-represented microbes. Across >28 million SRA datasets, tens of thousands of singleton archaeal and bacterial species were detected, often at abundances consistent with successful genome recovery. Applying targeted genome recovery to 804 singleton species, we recovered genomes representing new strains for 472 species. The success rate of genome recovery correlated with STAT-derived estimates of genome coverage, demonstrating that genome recovery from the SRA is both predictable and scalable. Using the single available genome of Clostridium tarantellae as a case study, SRA data mining recovered seven additional C. tarantellae genomes, correcting assembly gaps in the reference genome, expanding its pan-genome and increasing its known host range by seven additional fish species. These findings reveal that many microbial species currently represented by a single genome are in fact widely distributed across existing sequencing data and highlight a major opportunity to systematically expand strain-level genomic diversity and pan-genomic representation for under-sampled microbial species without additional sequencing.},
}

*Genome, Bacterial
*Archaea/genetics/classification
*Bacteria/genetics/classification
Phylogeny
Clostridium/genetics/classification
Sequence Analysis, DNA/methods
Genome, Archaeal
High-Throughput Nucleotide Sequencing
Databases, Genetic

@article {pmid42842295,
year = {2026},
author = {Lin, WY and Chang, YJ and Gill, T and Ching, J and Anderson, D and Creek, DJ and Ayub, Q and Rahman, S and Chong, CW},
title = {Association of microbial pathways predicted/inferred using 16S and shotgun metagenome with faecal metabolite abundances.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001855},
pmid = {42842295},
issn = {2057-5858},
mesh = {*Feces/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Metagenomics/methods ; Humans ; Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; *Bacteria/genetics/classification/metabolism ; Metabolome ; Liquid Chromatography-Mass Spectrometry ; },
abstract = {The gut microbiome is an essential metabolic organ influencing host health through metabolite production. While metabolite production levels can be directly measured by gas or liquid chromatography, they are commonly inferred from the abundance of metagenomic functional pathways. To evaluate the accuracy of these inferences, we established a single, manually curated metabolite-pathway/enzyme mapping list as a standardized biological reference. We then compared liquid chromatography-mass spectrometry (LC-MS)-based faecal metabolites with functional pathways/enzymes inferred from four approaches: 16S rRNA gene amplicons, reference-based shotgun, de novo assembly-based contigs and de novo assembly-based metagenome-assembled genomes (MAGs). Our results demonstrate that predictive accuracy is strongly metabolite-specific and method-dependent rather than a uniform characteristic of metagenomic data. While 16S (9.9%), ref-shotgun (14.2%) and de novo-contigs (5.5%) yielded only a small fraction of well-predicted metabolites, the de novo-MAGs approach significantly outperformed other approaches, achieving a 36.9% well-predicted rate for mapped metabolites. Notably, this approach provided the most robust functional-metabolite associations for indicators of gut health. In conclusion, while microbial functional potential does not always mirror metabolic reality, high-quality genomic binning via MAGs offers a significantly more robust framework for selective metabolite prediction.},
}

*Feces/microbiology/chemistry
*RNA, Ribosomal, 16S/genetics
*Metagenome
*Metagenomics/methods
Humans
Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
*Bacteria/genetics/classification/metabolism
Metabolome
Liquid Chromatography-Mass Spectrometry

@article {pmid42842485,
year = {2026},
author = {Conchon-Kerjan, E and Rouzé, T and Robidou, L and Ingels, F and Limasset, A},
title = {Super Bloom: Fast and Precise Filter for Streaming k-Mer Queries.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261493564},
doi = {10.1177/15578666261493564},
pmid = {42842485},
issn = {1557-8666},
abstract = {Approximate membership query structures are used throughout sequence bioinformatics, from read screening and metagenomic classification to assembly, indexing, and error correction. Among them, Bloom filters remain the default choice. They are not the most efficient structures in either time or memory, but they provide an effective compromise between compactness, speed, simplicity, and dynamic insertions, which explains their widespread adoption in practice. Their main drawback is poor cache locality, since each query typically requires several random memory accesses. Blocked Bloom filters alleviate this issue by restricting accesses for any given element to a single memory block, but this usually comes with a loss in accuracy at fixed memory. In this work, we introduce the Super Bloom Filter, a Bloom filter variant designed for streaming k-mer queries on biological sequences. Super Bloom uses minimizers to group adjacent k-mers into super-k-mers and assigns all k-mers of a group to the same memory block, thereby amortizing random accesses over consecutive k-mer queries and improving cache efficiency. We further combine this layout with the findere scheme, which reduces false positives by requiring consistent evidence across overlapping subwords. We provide a theoretical analysis of the construction of Super Bloom filters, showing how minimizer density controls the expected reduction in memory transfers, and derive a practical parameterization strategy linking memory budget, block size, collision overhead, and the number of hash functions to robust false-positive control. Across a broad range of memory budgets and numbers of hash functions, Super Bloom consistently outperforms existing Bloom filter implementations, with several-fold time improvements. As a practical validation, we integrated it into a Rust reimplementation of BioBloom Tools, a sequence screening tool that builds filters from reference genomes and classifies reads through k-mer membership queries for applications such as host removal and contamination filtering. This replacement yields substantially faster indexing and querying than both the original C++ implementation and Rust variants based on Bloom filters and blocked Bloom filters. The findere scheme also reduces false positives by several orders of magnitude, with some configurations yielding no observed false positives among 109 randomly queried k-mers. Code is available at https://github.com/EtienneC-K/SuperBloom and https://github.com/Malfoy/SBB.},
}

@article {pmid42843234,
year = {2026},
author = {Su, K and Wu, D and Xia, Y and Tian, S and Li, C and Ji, J and Guo, Y and Zhao, X and Huang, J and Hu, S and Ye, J},
title = {Prediction of age using shotgun metagenomic sequencing and random forest algorithm based on cadaveric colon.},
journal = {Forensic science international},
volume = {390},
number = {},
pages = {113154},
doi = {10.1016/j.forsciint.2026.113154},
pmid = {42843234},
issn = {1872-6283},
abstract = {Age estimation is important for the identification of unknown cadavers in forensic practice. Previous studies have shown that gut microbiota is associated with host age, but most evidence has been derived from fecal samples of living individuals. In this study, shotgun metagenomic sequencing was performed on mid-colon tissue samples from 76 cadavers to explore age-associated taxonomic and predicted functional patterns in cadaveric colon microbiota and to evaluate their potential value for forensic age estimation. After quality control and taxonomic annotation, 3980 microbial species were identified. Descriptive differences among age groups were observed in microbial composition, alpha diversity, species-enrichment patterns, co-occurrence network structure, and KEGG functional profiles; however, a multivariable PERMANOVA did not detect a statistically significant association between age group and overall species-level community composition after accounting for postmortem sampling interval, cause-of-death category, and sex. The complete random forest pipeline was re-evaluated using repeated nested five-fold cross-validation, with all data-dependent filtering, transformation, feature selection, and hyperparameter tuning restricted to the outer training data. The resulting out-of-fold performance was limited (R[2] = 0.005, MAE = 13.686 years, and RMSE = 17.741 years), and predictions showed regression toward the cohort mean. Overall, this study provides preliminary evidence that cadaveric colon microbiota contains age-associated microbial signals, but these findings should be interpreted as exploratory. Larger cohorts and independent external validation are needed before microbiome-based age prediction can be applied in forensic practice.},
}

@article {pmid42843345,
year = {2026},
author = {Zhao, S and Haryono, MAS and Lai, CWM and Seah, F and Tang, YL and Lim, M and Febriana, E and Lee, MH and Tan, KS and Fu, JH and Yip, JK and Preshaw, PM and Williams, RBH and Toh, SA and Lee, JWJ and Goh, CE},
title = {Oral microbial nitrate metabolism is associated with lower prevalence of prediabetes.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103092},
doi = {10.1016/j.xcrm.2026.103092},
pmid = {42843345},
issn = {2666-3791},
abstract = {The oral microbiome is a key microbial interface for dietary or oral nitrate metabolism, yet its role in early glycemic dysregulation remains poorly defined. In a population-based cohort (n = 472), we perform metagenomic profiling of tongue dorsum microbiomes and identify 11 taxa and nine microbial pathways associated with prediabetes. Among these, Rothia mucilaginosa and microbial nitrate reduction emerge as the only taxon and the strongest pathway associated with lower prediabetes prevalence. Individuals without prediabetes show higher salivary nitrate and nitrite concentrations, supporting enhanced oral nitrate bioavailability. Functional characterization of an isolated Rothia mucilaginosa strain demonstrates its capacity to mediate both nitrate-nitrite-NO and nitrate-nitrite-NH4[+] pathways under oxygen-limited conditions. Incorporating nitrate metabolism-associated microbial features into clinical risk factors improves risk stratification for progression to prediabetes. These findings support oral nitrate metabolism as a microbial pathway linking oral ecology to systemic metabolic health and suggest that tongue cleaning may modulate microbial functions involved in this pathway.},
}

@article {pmid42843534,
year = {2026},
author = {Wang, P and Xiao, Z and Lin, C and Li, S and Chen, K and Ma, X and He, D},
title = {Acetate-driven reorganization of Fe(III) mineral interfaces suppresses Anammox bacteria-associated Feammox.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136022},
doi = {10.1016/j.biortech.2026.136022},
pmid = {42843534},
issn = {1873-2976},
abstract = {Fe(III)-coupled anaerobic ammonium oxidation (Feammox) couples NH4[+]-N oxidation to Fe(III) reduction, yet the involvement of anaerobic ammonium-oxidizing bacteria (AnAOB) in complex enrichment systems and the mechanism underlying organic inhibition remain unclear. Here, using a Feammox-acclimated anaerobic ammonium oxidation (Anammox) enrichment exposed to different acetate loadings, we combined continuous-flow operation, isotope tracing, microscopic characterization, and integrated metagenomic and metatranscriptomic analyses to clarify the functional attribution of AnAOB-associated Feammox and the mechanism underlying its inhibition. Although acetate was readily consumed, NH4[+]-N removal decreased from 100% to 72.1 ± 9.5% and 61.2 ± 9.3%, respectively. [15]NH4[+]-N tracing, Raman spectroscopy, and inhibitor assays supported a close association between AnAOB and Fe(III)-dependent NH4[+]-N conversion. 16S ribosomal ribonucleic acid (rRNA) gene sequencing further indicated the dominance of Candidatus (Ca.) Brocadia under Feammox conditions, and metagenome-assembled genome (MAG)-resolved multi-omics resolved three Brocadia-like candidate Feammox-AnAOB populations, namely MAG288, MAG18, and MAG274. Among them, MAG288 showed nearly 100% average nucleotide identity to the extracellular electron transfer (EET)-capable Ca. Brocadia sp. BROELEC01, supporting a BROELEC01-like genetic basis for EET. Mechanistically, acetate-associated Feammox inhibition was not explained by depletion of the bulk Fe(III) inventory. Acetate exposure coincided with heterotrophic expansion and increased coverage of Fe(III) mineral surfaces by filament-like structures. Together with the redox signals associated with extracellular polymeric substances (EPS) and MAG-resolved transcriptional responses, these observations suggest that acetate may impair access of candidate Feammox-associated AnAOB to solid-phase Fe(III). Potential trophic restructuring may have further reinforced this interface-limitation response. Collectively, acetate-driven Fe(III) interface reorganization limits AnAOB-associated Feammox.},
}

@article {pmid42843535,
year = {2026},
author = {Chen, H and Lin, C and Wei, Y and Ji, J and Yu, H and Wu, S and Liu, Z and Shi, L and Chen, J and Wang, J},
title = {Spatiotemporally targeted electron-donor impulse dosing sustains carbon-efficient partial nitritation-partial denitrification-anammox nitrogen removal.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136023},
doi = {10.1016/j.biortech.2026.136023},
pmid = {42843535},
issn = {1873-2976},
abstract = {Single-stage partial nitritation-anammox (PN/A) is constrained by stoichiometric nitrate accumulation, which limits theoretical nitrogen removal efficiency to approximately 89%. Bulk or continuously supplied electron-donor dosing can enhance nitrate reduction, but reactor-wide donor exposure may increase donor demand, intensify heterotrophic competition, and limit control over donor delivery to specific nitrate-reducing niches in single-stage PN/A systems. In this study, spatiotemporally targeted electron-donor impulse dosing (STID) using a separate donor inlet and short pulses was implemented and evaluated over 156 days of continuous operation in a single-stage airlift internal circulation partitioned bioreactor. Across all 56 sodium acetate (NaAc)-dosing days, total nitrogen removal efficiency averaged 94.4 ± 5.9%, compared with 61.8 ± 11.6% across the 100 PN/A-only days. Metagenomic analyses showed enrichment of partial denitrifiers, especially Thauera, and increased abundance of nitrate-reduction genes (narG/H/I and napA/B), while the PN/A-associated genera Nitrosomonas and Ca. Brocadia were maintained. Abundances of amoA/B/C and hzs/hdh indicated the genetic potential for ammonia oxidation and anammox, while independent activity assays showed that ammonia-oxidizing and anammox activities were retained. Across all 56 dosing days, cumulative external donor input was 1.20-1.23 g NaAc per g N removed, equivalent to 0.94-0.96 g chemical oxygen demand-equivalent per g N removed. Overall, STID repeatedly improved nitrogen removal across three dosing periods, supporting its use as an operating strategy for continuous single-stage PN/A.},
}

@article {pmid42844256,
year = {2026},
author = {Legrand, M and Nguyen, H and Calfee, CS and Lu, Y and Harhay, M and Liu, K and Chen, D and Bernholz, J and Matthay, M and Mebazaa, A and Pickkers, P and Rojas, E and Perez, AR},
title = {Plasma proteomics defines two reproducible subphenotypes of sepsis-associated acute kidney injury with distinct outcomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42844256},
issn = {2041-1723},
support = {R01-GM151494-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 DK139484/DK/NIDDK NIH HHS/United States ; R35 HL177135/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Acute Kidney Injury/blood/etiology/mortality/drug therapy ; *Sepsis/complications/blood/mortality ; *Proteomics/methods ; *Blood Proteins/metabolism ; Critical Illness ; Phenotype ; Male ; Female ; Oxidative Stress ; Inflammation/blood ; },
abstract = {Sepsis is the leading cause of acute kidney injury in critically ill patients, and this complication carries a high risk of death. The biology underlying it varies between patients, which may explain why treatments have not succeeded. Here we show, using an ensemble method that groups patients by patterns across hundreds of blood proteins in three independent groups of patients, that sepsis-associated acute kidney injury comprises two reproducible subphenotypes. One subphenotype shows widespread activation of inflammation, metabolism, and oxidative stress; the other shows a quieter profile. Patients in the inflammatory subtype have higher mortality, more complications, and fewer days alive and out of the intensive care unit. A simple seven-protein test reproduces these groupings and identifies them accurately in separate cohorts. In a randomized trial, the drug ilofotase alfa appears to benefit the inflammatory subtype but not the other, suggesting that this classification could guide future treatment.},
}

Humans
*Acute Kidney Injury/blood/etiology/mortality/drug therapy
*Sepsis/complications/blood/mortality
*Proteomics/methods
*Blood Proteins/metabolism
Critical Illness
Phenotype
Male
Female
Oxidative Stress
Inflammation/blood

@article {pmid42844282,
year = {2026},
author = {Zhou, S and Philo, SE and Saldana, MA and Vela, JD and Smith, AL and Stadler, LB},
title = {Plasmid-Host Networks Reveal Persistent Mobile Elements Across Wastewater Treatment.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42844282},
issn = {2041-1723},
support = {R21AI190938//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21AI190938//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; NAS Grant G10001728//National Academies of Sciences, Engineering, and Medicine | National Academy of Sciences (NAS)/ ; NAS Grant G10001728//National Academies of Sciences, Engineering, and Medicine | National Academy of Sciences (NAS)/ ; NAS Grant G10001728//National Academies of Sciences, Engineering, and Medicine | National Academy of Sciences (NAS)/ ; W9132T-23-2-0002//United States Department of Defense | United States Army | U.S. Army Corps of Engineers (US Army Corps of Engineers)/ ; W9132T-23-2-0002//United States Department of Defense | United States Army | US Army Corps of Engineers | Engineer Research and Development Center (U.S. Army Engineer Research and Development Center)/ ; W9132T-23-2-0002//United States Department of Defense | United States Army | US Army Corps of Engineers | Engineer Research and Development Center (U.S. Army Engineer Research and Development Center)/ ; No. EEC-2133504//National Science Foundation (NSF)/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; Gene Transfer, Horizontal ; *Water Purification ; Metagenomics ; Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; *Interspersed Repetitive Sequences/genetics ; Drug Resistance, Bacterial/genetics ; Host Specificity/genetics ; Bacteria/genetics ; },
abstract = {Plasmids drive horizontal gene transfer and antimicrobial resistance spread in water resource recovery facilities, yet their in situ dynamics in complex microbial communities remain poorly characterized. We apply Hi-C metagenomics to resolve plasmid-host associations across influent, activated sludge, and effluent at three facilities. We identify 944 plasmid clusters with facility- and stage-specific distributions. Plasmid host range narrows from influent to effluent, indicating that treatment selectively constrains plasmid-host associations. Persistent plasmid clusters with detectable mobility markers show a trend toward broader, less modular host networks than those with no detected markers. Hi-C-supported antibiotic resistance gene associations highlight Burkholderiaceae and Rhodocyclaceae as prominent hosts of beta-lactam, tetracycline and sulfonamide resistance genes across facilities. These findings indicate that wastewater treatment narrows plasmid host range while maintaining dominant plasmid-carrying taxa and adaptive mobile elements, providing a framework for understanding plasmid persistence across treatment systems.},
}

*Plasmids/genetics
*Wastewater/microbiology
Gene Transfer, Horizontal
*Water Purification
Metagenomics
Sewage/microbiology
Anti-Bacterial Agents/pharmacology
*Interspersed Repetitive Sequences/genetics
Drug Resistance, Bacterial/genetics
Host Specificity/genetics
Bacteria/genetics

@article {pmid42844285,
year = {2026},
author = {Pearman, JK and Sissons, J and Kanyi Kihika, J and Waters, S and Rees, ABH and Howarth, JD and Vandergoes, MJ and Wood, SA},
title = {Divergent microbial functional pathways and declining redundancy in lake sediments across eutrophication gradients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42844285},
issn = {2041-1723},
support = {CAWX2305//Ministry of Business, Innovation and Employment (MBIE)/ ; C05X1707//Ministry of Business, Innovation and Employment (MBIE)/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Eutrophication ; *Geologic Sediments/microbiology/chemistry ; New Zealand ; Phosphorus/metabolism ; Ecosystem ; *Microbiota/genetics ; *Bacteria/metabolism/genetics/classification ; Nitrification ; Denitrification ; Metagenomics ; Nitrogen/metabolism ; },
abstract = {Microbial communities underpin nutrient cycling across aquatic ecosystems and are strongly influenced by human disturbance, yet the implication for functional redundancy remains poorly understood. Lake eutrophication is a global threat to freshwater systems, primarily driven by human activities within lakes and surrounding catchments. We hypothesize that eutrophication alters functional redundancy of key metabolic pathways in lake sediments. To test this, we conducted a national scale metagenomic study of surface sediments from 144 New Zealand lakes spanning a broad nutrient gradient. Increasing eutrophication is associated with reduced taxon-based functional redundancy, the potential of multiple species to perform the same function, indicating a narrower taxa pool supporting core functions. In contrast, abundance-based functional redundancy, characterized by the abundance of organisms that can perform the function, showed pathway-specific responses across trophic gradients. For example, nitrification and denitrification have greater abundance-based functional redundancy under higher nutrient conditions, whereas phosphorus transport shows reduced redundancy. By eroding microbial functional redundancy, eutrophication may increase susceptibility of microbial communities to environmental perturbations, potentially compromising their ability to sustain key metabolic processes. As lakes play key roles in biogeochemical cycles, the lower stability of vital biogeochemical pathways in lake sediments is likely to have an impact across ecosystems globally.},
}

*Lakes/microbiology/chemistry
*Eutrophication
*Geologic Sediments/microbiology/chemistry
New Zealand
Phosphorus/metabolism
Ecosystem
*Microbiota/genetics
*Bacteria/metabolism/genetics/classification
Nitrification
Denitrification
Metagenomics
Nitrogen/metabolism

@article {pmid42844352,
year = {2026},
author = {Dalton, KR and Lee, M and Fisher, JA and Richards-Barber, M and Beane Freeman, LE and Jones, RR and London, SJ},
title = {Residential proximity to intensive animal agriculture associates with increased prevalence of antimicrobial resistance in homes.},
journal = {Journal of exposure science & environmental epidemiology},
volume = {},
number = {},
pages = {},
pmid = {42844352},
issn = {1559-064X},
abstract = {BACKGROUND: Antimicrobial resistance (AMR), a global public health threat, affects rural communities disproportionately due to their unique regional exposures, including proximity to animal feeding operations (AFOs), a source of AMR genes.

OBJECTIVE: We evaluated residential proximity to AFOs and the presence of AMR genes in the home dust resistome, the collection of antimicrobial resistant genes within a microbial community.

METHODS: We conducted metagenomic sequencing of 534 bedroom dust samples to characterize the resistome for a subset of homes of Iowa participants in the US Agricultural Health Study. We examined the association between the presence of AMR genes in dust samples and the total number of AFOs and distance-weighted number of livestock animal units (AUs) within 2, 5, and 10 km of participant homes, using data from the Iowa Department of Natural Resources.

RESULTS: Homes that were closer to a greater number of AFOs and AUs had increased odds of the presence of AMR genes in the dust, including genes resistant to multiple classes of antimicrobials.

SIGNIFICANCE: We found that AFOs were positively related to the composition of the indoor home dust resistome, which may serve as a potential environmental reservoir of antimicrobial resistance with implications for the health of household occupants.

IMPACT: This study is the first to detect a positive association between the presence of antimicrobial resistance (AMR) genes in the indoor home dust resistome and residential proximity to animal feeding operations (AFOs), a known reservoir and possible source of AMR in rural communities. Our results indicate that both distance and density were important components of AFO-related AMR risk in rural residential environments. Overall, this suggests that environmental exposures can shape the indoor home dust resistome, which may have implications for the health of inhabitants and increase the risk of AMR infections.},
}

@article {pmid42844483,
year = {2026},
author = {Carter, MM and Liu, Z and Olm, MR and Martin, M and Sprockett, DD and Ghadermazi, P and Trumble, BC and Kaplan, H and Stieglitz, J and Rodriguez, DE and Relman, DA and Sonnenburg, ED and Gurven, M and Good, BH and Sonnenburg, JL},
title = {Prehistoric global migration of vanishing gut microbes with humans.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42844483},
issn = {1476-4687},
abstract = {The gut microbiome is crucial for health and is affected strongly by lifestyle[1]. Many microorganisms commonly found in non-industrialized populations are disappearing or have become extinct in industrialized populations[2-6]. Studying which microorganisms have been long-term residents of the human gut and may have co-evolved with humans[2,7,8] could provide insights into how microbial biodiversity loss affects human health. However, the genetic complexities of microbial evolution and the plasticity of gut microbiome composition have made it challenging to resolve the evolutionary history of these long-term associations. Here we performed deep metagenomic sequencing of the Tsimane horticulturalists of Bolivia and compared their gut microbiomes with those of the Hadza hunter-gatherers of Tanzania[3]. These two populations, whose ancestors have been separated for tens of thousands of years, share 1,231 microbial species, most of which are rare in or absent from industrialized populations. Population genetic analyses of 636 of the shared species revealed patterns of microbial divergence and gene flow consistent with prehistoric human co-migration, with estimated split times that approximately align with human migration out of Africa and into the Americas. Our findings indicate that a diverse gut microbiome co-migrated with humans worldwide and has persisted over millennia. However, many of these species are now vanishing from industrialized populations and the consequences for human health remain uncertain.},
}

@article {pmid42844520,
year = {2026},
author = {Katara, A and Chand, S and Chaudhry, V and Vishwakarma, S and Dubey, RC and Chandra, H and Shilbayeh, SAR and Khan, SU and Vohra, S and Poddar, NK and Khan, S},
title = {Analysis of bacteriophage diversity in Ganga river ecosystem: insights from metagenome-based sequencing.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42844520},
issn = {1618-1905},
support = {PNURSP2026R814//Princess Nourah Bint Abdulrahman University/ ; DST/2022/1012//DST- FIST project/ ; },
abstract = {Water from the Ganga River and its tributaries is the main freshwater resource in the northern parts of India and has experienced rigorous ecological deterioration because of the continuous discharge of untreated polluted industrial and household effluents, resulting in increased chemical and microbial loads of pollution. Water is an essential requirement for millions of people and supports a complex ecosystem that includes a variety of microbial species. Among them, bacteriophages are essential for controlling bacterial populations and the dynamics of microbial communities. The knowledge of the diversity and functions of bacteriophages is poorly understood in the River Ganges. Using cutting-edge metagenomic techniques, we explore the diversity of viruses, specifically the bacteriophages in the river, offering a real picture of bacteriophage populations and their ecological functions. Metagenomic datasets were produced by high-throughput sequencing and were used to determine bacteriophage sequences, viral genome similarity, and potential functions. Initial findings demonstrated a significant degree of diversity among bacteriophages. The results demonstrated three families of phage (Casjensviridae, Rountreeviridae, and Peduoviridae).The bacteriophages of these families were identified to infect a variety of bacteria. The results offer important insights into the bacteriophage ecology of freshwater ecosystems, highlighting the necessity for deeper investigation into phage-bacterial interactions in aquatic environments. Gaining a deeper understanding of bacteriophage diversity and their roles in the Ganges can aid in developing phage-driven approaches for environmental monitoring and management, especially in tackling issues like pollution, eutrophication, and antibiotic resistance. These metagenomic results present a genomic basis for investigating environmental bacteriophage and viruses in sustainable water quality management and the generation of bacteriophage-based therapeutic interventions.},
}

@article {pmid42844624,
year = {2026},
author = {Yoon, J and Lee, B and Yoo, KC and Kwak, MJ and Song, HJ and Hwang, CY and Chung, Y and Kim, K and Kwon, SK and Song, JY and Yoon, HS and Kim, JF},
title = {Novel Antarctic chemolithotroph drives iron biomineralization.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42844624},
issn = {2049-2618},
mesh = {*Iron/metabolism ; *Geologic Sediments/microbiology/chemistry ; Antarctic Regions ; *Biomineralization ; Oxidation-Reduction ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; *Chemoautotrophic Growth ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Iron, the most abundant redox-active metal in the Earth's crust, is coupled to numerous biogeochemical cycles. However, the mechanisms of iron oxidation and the organisms involved remain incompletely understood. Banded iron formations (BIFs) are a major reservoir of iron ore in the Precambrian sedimentary record, yet the biological contribution to their genesis remains a subject of unresolved debate. While large-scale BIF deposition largely ceased after the Proterozoic, microbial activity in modern Holocene sediments under fluctuating redox conditions provides a unique opportunity to examine mechanisms reminiscent of ancient iron cycling. Here, we report the stratigraphic sequence of microbiome profiles recorded in laminated facies with iron-containing crystalline illite in the embayment sediments beneath the Larsen C Ice Shelf (LCIS) in Antarctica during the Holocene.

RESULTS: LCIS sediments record microbial community shifts tightly coupled to environmental changes throughout the Holocene. Metagenomic analyses revealed three dominant microbial phases corresponding to geological facies boundaries. The open marine setting (phase A) showed higher taxonomic richness, whereas the sub-ice shelf sediments (phases B and C) were largely anoxic and characterized by diverse chemolithoautotrophic metabolisms. Keystone taxa including uncultured members of Thermodesulfovibrionia, as well as unique microbial communities and metabolisms, were evident in the aphotic, anoxic seawater; metagenomic analyses further revealed chemolithotrophy. The Thermodesulfovibrionia bacterium, visualized using fluorescence in situ hybridization and designated as "Candidatus Mariimomonas ferrooxydans", formed a novel clade in the phylum Nitrospirota. Metagenome-assembled genome analysis identified a putative outer-membrane Fe(II) oxidase, Cyc2, whose Fe(II)-oxidation activity was experimentally confirmed.

CONCLUSION: Our findings document the interaction between microbiome and environment, illustrating how LCIS sediments preserve a dynamic record of microbial community responses to environmental transitions. These results provide critical insights into microbial iron mineralization, echoing the biogeochemistry of the geologic past, particularly synglacial iron formation during the Neoproterozoic Snowball Earth. Video Abstract.},
}

*Iron/metabolism
*Geologic Sediments/microbiology/chemistry
Antarctic Regions
*Biomineralization
Oxidation-Reduction
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
*Chemoautotrophic Growth
RNA, Ribosomal, 16S/genetics
Phylogeny
Metagenomics/methods
Seawater/microbiology

@article {pmid42844723,
year = {2026},
author = {Noland, E and Conner, K and Brame, B and Petersen, A and Thaiwong-Nebelung, T},
title = {EXPRESS: Metagenomic Oxford Nanopore sequencing of feline aural inflammatory polyps for pathogen discovery.},
journal = {Journal of feline medicine and surgery},
volume = {},
number = {},
pages = {1098612X261497556},
doi = {10.1177/1098612X261497556},
pmid = {42844723},
issn = {1532-2750},
abstract = {ObjectivesFeline aural inflammatory polyps (FIAP) have been proposed to be induced by chronic viral or bacterial infections; however, the cause is still unknown. The aim of this study was to investigate potential etiologies of these polyps using metagenomic sequencing.MethodsPolyp tissue was collected from 13 cats following routine traction and avulsion procedures. Total nucleic acid was extracted and subjected to a host (feline) nucleic acid depletion protocol. Additionally, the Sequence-Independent Single-Primer Amplification (SISPA) method was used to enrich for low-abundance RNA viral genomes. Sequencing was conducted on the Oxford Nanopore MinION sequencing platform. Non-feline sequencing reads were taxonomically classified against custom bacterial/viral databases to calculate relative genus-level abundances.ResultsTaxonomic classification of sequencing reads identified various bacteria across samples and, in some samples, rare viruses. However, no common microbial sequences were associated with polyps to suggest a specific infectious etiology. Bacterial communities were dominated by Pseudomonadota, Actinomycetota, and Bacillota phyla, with Pseudomonadota and Actinomycetota being more frequently dominant. Lasallevirus was detected in few samples with unknown clinical relevance. Culture and sequencing showed partial concordance in identifying bacteria in some cases.Conclusions and relevanceNo common microbial-associated sequences found to be associated with polyp samples; therefore, no suspect causative agent was identified. 16S and ITS metagenomic sequencing on FIAP may help further elucidate if microbial population shifts have a role in polyp development and recurrence and/or persistence of inflammation leading to polyp development.},
}

@article {pmid42844853,
year = {2026},
author = {Chen, J and Deng, W and He, J and Niu, S and Xing, S and Liao, X},
title = {Source tracking and transmission of antibiotic resistance genes mediated by core microbiota in black soldier fly larvae bioconversion of doxycycline-contaminated hen manure.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70366},
pmid = {42844853},
issn = {1744-7917},
support = {32072783//National Natural Science Foundation of China/ ; 2020B1212060060//Science and Technology Program of Guangdong Province, China/ ; CARS-40//Modern Agro-industry Technology Research System/ ; },
abstract = {Black soldier fly larvae (BSFL) bioconversion of doxycycline-contaminated hen manure raises concerns about antibiotic resistance gene (ARG) transmission. Although core microbiota in gut may participate in ARG dynamics, the relative contributions of microbiota from manure and baseline larval gut to the BSFL gut resistome remain unclear. Using metagenomics, amplicon sequencing, and cultivable bacteria analysis, we found that: (1) Providencia, Klebsiella, Enterococcus, and Escherichia-Shigella dominated the BSFL gut and served as primary ARG hosts; (2) Fecal filtrate intervention drastically altered gut microbiota and ARG profiles, suppressing Klebsiella (by 95.56%) and Escherichia-Shigella (to < 0.5%) while enriching Providencia (3.53 fold increase) and Enterococcus, with increased ARGs such as tet(59) and qnrD1. Long-read metagenomic analysis indicated that viable manure-borne bacteria, rather than cell-free fecal filtrate, delivered structurally intact ARG-MGE units as key carrier of mobile resistance cassettes; (3) Source tracking (FEAST) assigned the majority of ARBs (> 90%) and their ARGs in the BSFL gut to the baseline BSFL gut source, with manure-derived ARBs contributing 4.80%. Culture-based 16S rRNA gene homology provided evidence consistent with possible manure-to-gut transfer of selected Escherichia-Shigella and Enterococcus. The BSFL gut resistome was more strongly associated with the baseline BSFL microbiota than with manure, but manure still represented a detectable source of ARB and ARG introduction. FEAST source assignments should be interpreted as composition-based bioinformatic estimates rather than definitive proof of origin, due to lack of direct functional tracing. These findings have critical implications for assessing the ecological safety of BSFL-based waste valorization.},
}

@article {pmid42845172,
year = {2026},
author = {Xu, Q and Song, Y and Yu, H and Wang, Y and Gu, HF},
title = {Gut Microbiota Modulation by Abelmoschus manihot (L.) Improves Circulating Metabolites and Alleviates Diabetic Nephropathy in db/db Mice.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e5630909},
pmid = {42845172},
issn = {2314-6141},
support = {CPU20200228//Suzhong Pharmaceutical Group Co. Ltd/ ; },
mesh = {Animals ; *Diabetic Nephropathies/drug therapy/microbiology/blood/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Abelmoschus/chemistry ; Male ; Metabolomics ; Metabolome/drug effects ; Diabetes Mellitus, Experimental/drug therapy ; *Plant Extracts/pharmacology ; Diabetes Mellitus, Type 2/drug therapy ; Disease Models, Animal ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; },
abstract = {BACKGROUND: Huangkui capsule (HKC), derived from the ethanol extract of Abelmoschus manihot (L.) flowers, is widely used in China for treating kidney diseases, including diabetic nephropathy (DN). Our previous study demonstrated that HKC modulates the intestinal microbiota and circulating metabolites in non-obese diabetic mice, a type 1 diabetes model. To further explore its efficacy, we evaluated HKC in db/db mice, a well-established type 2 diabetes and DN model.

METHODS: An HKC cohort studied in 2022 was compared with historical Ctrl and DN cohorts studied in 2021. Shotgun metagenomic sequencing was performed to characterize intestinal microbiota changes, while liquid chromatography-mass spectrometry (LC-MS)-based plasma metabolomics was used to identify alterations in circulating metabolites. The biological functions of the altered microbiota and plasma metabolites were analyzed, and the potential association between the intestinal microbiome and plasma metabolome was evaluated.

RESULTS: Compared with the historical DN cohort, the HKC cohort had higher abundances of Streptococcaceae, Streptococcus, and Massilimaliae and lower abundances of Alloprevotella and Prevotellamassilia in exploratory comparisons. In the HKC-versus-DN comparison, the archived gene set enrichment analysis reported 15 pathways with nominal positive enrichment. Additionally, 12 plasma metabolites were upregulated and 14 downregulated, including branched-chain amino acids (DL-leucine, DL-valine, D-isoleucine), organic acids (N-methyl-α-aminoisobutyric acid, guanidineacetic acid), and choline.

CONCLUSION: In db/db mice, the cohort receiving A. manihot (L.)-derived HKC had lower urinary albumin-to-creatinine ratio (UACR) and different intestinal microbiota and plasma metabolite profiles than the historical DN cohort, highlighting its therapeutic potential for DN.},
}

Animals
*Diabetic Nephropathies/drug therapy/microbiology/blood/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Abelmoschus/chemistry
Male
Metabolomics
Metabolome/drug effects
Diabetes Mellitus, Experimental/drug therapy
*Plant Extracts/pharmacology
Diabetes Mellitus, Type 2/drug therapy
Disease Models, Animal
Mice, Inbred C57BL
*Drugs, Chinese Herbal/pharmacology

@article {pmid42845237,
year = {2026},
author = {Shannon, E and Devotta, H and Ndwandwe, C and Kim, S and Yao, L and Kareem, L and Walters, A and Korpela, K and Hurley, S and Lunjani, N and Koc, F and Mathur, H and Ambikan, A and Neogi, U and Friess, L and van Sinderen, D and Stanton, C and Venter, C and Walter, J and Hourihane, J and O'Mahony, L},
title = {Gut microbial metabolism of peanuts generates immunoregulatory metabolites.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2743944},
doi = {10.1080/19490976.2026.2743944},
pmid = {42845237},
issn = {1949-0984},
mesh = {Humans ; *Arachis/metabolism/immunology/microbiology/chemistry ; Bifidobacterium/metabolism/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Leukocytes, Mononuclear/immunology ; Fermentation ; Infant ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fatty Acids, Volatile/metabolism ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Interleukin-10/immunology ; Cytokines ; },
abstract = {Early life introduction of potentially allergenic foods such as peanuts is important for the prevention of food allergy. We hypothesized that peanut consumption may indirectly influence the immune system via effects on gut microbiota composition and metabolism. In vitro human fecal fermentations with peanuts were performed. Changes in taxa and metabolism were measured using 16S rRNA gene sequencing and untargeted metabolomics respectively. Ten Bifidobacterium strains were cultured in vitro in the presence of peanuts and human peripheral blood mononuclear cells (PBMCs) were used to assess culture supernatant immunomodulatory effects. Fecal samples were sequenced from children at 12 months (n = 343) using whole genome metagenomic sequencing. An online questionnaire was used to collect dietary data. Human fecal bioreactor fermentation of peanut flour, previously subjected to in vitro simulated gastrointestinal digestion, resulted in significant production of short-chain fatty acids (SCFA), associated with increased relative abundance of Megasphaera and bifidobacteria. 188 metabolites were significantly altered following peanut fermentation. Bifidobacterium longum subspecies longum strain 160 efficiently metabolized peanut associated with secretion of indole-3-lactic acid (ILA). Following growth on peanuts, bifidobacterial supernatants enhanced IL-10 secretion, but reduced TNF-alpha and IL-5 secretion from stimulated PBMCs. Peanut consumption by 12-month-old children was associated with significant changes in gut microbiota composition including increased levels of Prevotella buccae, Megasphaera micronuciformis and Blautia wexlerae. Peanuts are metabolized by microbes generating immunoregulatory metabolites such as SCFAs and ILA. These metabolites may represent one potential mechanism underlying the allergy-protective effects of early peanut consumption, which requires further validation in high-risk allergy cohorts.},
}

Humans
*Arachis/metabolism/immunology/microbiology/chemistry
Bifidobacterium/metabolism/genetics
Feces/microbiology
*Gastrointestinal Microbiome
Leukocytes, Mononuclear/immunology
Fermentation
Infant
*Bacteria/classification/genetics/metabolism/isolation & purification
Fatty Acids, Volatile/metabolism
RNA, Ribosomal, 16S/genetics
Female
Male
Interleukin-10/immunology
Cytokines

@article {pmid42845342,
year = {2026},
author = {Rising, K and Karp, R and Baker, A and Metz, S and Sweet, M and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the staghorn coral, Acropora cervicornis (Lamarck, 1816) (Scleractinia: Acroporidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {613},
pmid = {42845342},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Acropora cervicornis (staghorn coral; Cnidaria; Anthozoa; Scleractinia; Acroporidae). The genome sequence has a total length of 328.68 megabases. Most of the assembly (99.07%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.26 kilobases. Gene annotation of this assembly by Ensembl identified 24,579 protein-coding genes. From the metagenome data, we recovered two bins, of which one was a high-quality MAG.},
}

@article {pmid42845384,
year = {2026},
author = {Huang, Z and McGrath, PM and Ferdinand, DC and McCormick, BA and Ward, DV and Bucci, V and Haran, JP},
title = {Gut community-level analysis reveals an altered balance between Phocaeicola vulgatus and Bacteroides fragilis in Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.12.743985},
pmid = {42845384},
issn = {2692-8205},
abstract = {Gut microbiome differences in Alzheimer's disease (AD) are typically cataloged taxon by taxon, yet bacterial competition and cross-feeding make species' roles dependent on the entire community. We analyzed 274 stool metagenomes from 119 older adults (18 with AD) as communities, retaining 22 recurring across 1,000 runs. Using our AI framework, we identified 15 species differing in abundance in AD, particularly the commensal Phocaeicola vulgatus (Cohen's d -0.91, 95% CI [-1.23, -0.59]), a finding robust to repeated sampling. It correlated negatively with its sister species, Phocaeicola dorei (r -0.57), suggesting possible niche competition; this replicated in an independent cohort (r -0.43). P. vulgatus was depleted in AD and the opportunistic pathogen Bacteroides fragilis enriched, shifting their balance toward B. fragilis (d -0.70), a modestly reproduced AD-associated pattern (d -0.24). Our findings suggest that AD-associated gut microbiome variation extends beyond taxon-specific abundance to the balance between specific species within a community matrix.},
}

@article {pmid42845442,
year = {2026},
author = {Ragheb, M and Kiguchi, Y and Lin, JD and Hoffman, FT and Daigh, L and Chakraborty, M and Doyle, B and Grieshop, MP and Lin, A and Maghini, D and Spees, K and Bintu, L and Bassik, MC and Bhatt, AS},
title = {A microproteome screen identifies immunomodulatory bacterial microproteins encoded in expanded gene arrays in Leptotrichia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.11.744246},
pmid = {42845442},
issn = {2692-8205},
abstract = {The human microbiome exerts broad influence in health and disease with associative studies implicating the microbiome in influencing immunity, cancer outcomes, and neurodegeneration. However, the molecular mediators of microbe-host communication remain poorly defined. Bacterial microproteins from the microbiome represent a largely uncharacterized class of potential regulators of host immunity. Here, we utilize functional genomics to interrogate 3,552 microproteins in order to identify novel microbial-immune interactions. We constructed a microproteome library from microbial metagenomic datasets, expressed it in macrophages and assayed for immunomodulatory activity. We identify several bacterial microproteins that drive macrophage M1 polarization. Among the strongest hits are a cluster of structurally related microproteins from Leptotrichia species, which are oral Gram-negative commensals associated with differential cancer outcomes. Genomic analysis reveals that Leptotrichia species encode these putative immunomodulatory microproteins in tandem arrays of up to 44 copies. These genes encode microproteins with varying sequences but conserved predicted structures. In an orthogonal approach, we demonstrate that bacterial expression of Leptotrichia microproteins influences macrophage cell state and function. As a whole, our findings identify novel microbial microproteins with immunomodulatory activity and provide a framework for future discovery of host-microbe interactions that influence human health.},
}

@article {pmid42845473,
year = {2026},
author = {LaFranchi, B and Maison, DP and Vinden, J and Rodriguez, AE and Tout, A and Grimbert, L and Velazquez, E and Vudali, U and Poblano, BA and Dalhuisen, T and Cattle, J and Figueroa, TR and Fudotan, Y and Luna, M and Ryder, D and Deswal, M and Abel, BS and Lynch, J and Lipford, A and Razi, N and Steifman, CB and McCann, HN and Kataria, N and Girling, V and Thomas, R and Wang, C and Deitchman, AN and Patel, S and Traglia, M and Tseng, ZH and Szabo, G and Laszik, Z and Farrow, A and Zwart, N and Sumimoto, N and Servellita, V and Hoh, R and Fehrman, EA and Kelly, JD and Martin, JN and Deeks, SG and Chiu, CY and Somsouk, M and Peluso, MJ and Henrich, TJ},
title = {Multiomic and Spatial Profiling of Colorectal Tissue Reveals Viral Persistence and Immune Dysregulation in Long COVID.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.07.743616},
pmid = {42845473},
issn = {2692-8205},
abstract = {Long COVID (LC) - a chronic condition characterized by persistent, debilitating symptoms following SARS-CoV-2 infection - has emerged as a major public health challenge. Although many interrelated mechanisms have been proposed as drivers of LC, the root causes have yet to be identified, posing significant challenges for therapeutic development. While many blood-based studies have been conducted, they have not yielded conclusive mechanistic insights into LC pathogenesis. Attention has therefore turned toward direct tissue investigation, with the gastrointestinal (GI) tract becoming a major focus due to evidence that virus or viral components can persist at this site for months to years following an episode of COVID-19. Here, we performed a high-dimensional characterization of colorectal tissue and peripheral blood in a highly characterized cohort of 44 people with LC and 13 recovered controls. We profiled SARS-CoV-2 persistence, host immune responses, and tissue inflammation using bulk and single-cell RNA sequencing, nCounter RNA probe hybridization, quantitative PCR, metagenomic next-generation sequencing, plasma proteomics, high-dimensional spectral flow cytometry, in situ-hybridization/immunohistochemistry, and single-cell digital spatial omics. Our results support a model in which LC is driven by long-term immune dysregulation and perturbations of the regulatory gut immune environment which imply ongoing viral persistence, although direct viral detection was only observed in a subset of participants. Specifically, we identify a tissue-based transcriptional environment in which SARS-CoV-2 activates innate myeloid immune signaling, driving chronic inflammation while simultaneously downregulating pathways responsible for immune-mediated clearance of infected cells, including antigen presentation, phagocytosis, cytotoxic immune cell trafficking, and granzyme production. Importantly, signatures in peripheral blood are considerably weaker than those observed in tissue. Together, these findings provide a direct biological rationale for therapeutic strategies in LC aimed at enhancing or redirecting cytotoxic immune function to overcome immune dysregulation and clear persistent viral reservoirs.},
}

@article {pmid42845486,
year = {2026},
author = {De Santiago, A and Han, MK and Hargadon, SB and Marcellino Barros, M and Brito De Jesus, S and Pereira, TJ and Bik, HM},
title = {Marine nematodes exhibit widespread symbiosis, novel chemoautotrophy, and evolutionary conservation of holobiont taxa.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.12.744518},
pmid = {42845486},
issn = {2692-8205},
abstract = {Microbial symbioses drive the evolutionary and functional diversification of eukaryotic clades, from single-celled protists to large invertebrates. However, our knowledge of host-associated assemblages (the "holobiont") is limited in microscopic animal phyla with a body size <1mm, due to practical challenges such as low biomass and difficult taxonomy of host species. Marine nematodes represent an ideal case study for rapidly advancing our knowledge of bacterial-animal symbioses, representing a globally abundant invertebrate group with strong links to terrestrial and model organism species within the same phylum. Here, we sequenced the holobionts of 220 marine nematodes and generated 815 metagenome-assembled genomes (MAGs) of host-associated bacteria/archaea. Our data indicates that 20-34% of marine nematodes harbor an obligate intracellular symbiont, often with multiple endosymbionts co-occurring within the same host. Three bacterial phyla (Pseudomonadota Bacteroidota, and Verrucomicrobiota) account for three-quarters of all nematode-associated MAGs, and the majority of these holobiont MAGs represent deeply divergent lineages in the prokaryotic tree of life. The Flavobacteriaceae (a core microbiome taxon in C. elegans and other terrestrial nematodes), were consistently recovered across phylogenetically diverse marine nematode lineages, suggesting evolutionary conservation of holobiont taxa across marine and terrestrial environments. We also report a novel chemoautotroph family (Ca. Thionematobacter) recovered from nematode hosts in both deep-sea and shallow-water habitats, and report the first confirmed instance of Cardinium endosymbionts from marine invertebrates. Finally, ∼65% of nematode-associated MAGs are able to degrade chitin, via hexosaminidase, implying that benthic invertebrate holobionts make significant contributions to global carbon cycling. These results underline the importance of evaluating symbiosis in microscopic marine invertebrates, and accelerating our understanding of animal evolution and ecosystem dynamics in vast benthic habitats.},
}

@article {pmid42845900,
year = {2026},
author = {Zhang, Z and Zhou, D and Tao, X},
title = {Case Report: A neonatal case of Elizabethkingia anophelis sepsis complicated by meningitis and intestinal necrosis: a triumph of multidisciplinary management.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1920161},
pmid = {42845900},
issn = {2296-2360},
abstract = {This case reports a 10 day old neonate with fulminant Elizabethkingia anophelis sepsis presenting as disseminated infection involving meningitis and intestinal necrosis. Pathogen identification was achieved on hospital day 2 by metagenomic next generation sequencing and confirmed by blood and cerebrospinal fluid cultures, enabling antimicrobial susceptibility guided therapy. The infant was treated with cefoperazone sulbactam plus levofloxacin on day 3, switched to levofloxacin plus trimethoprim sulfamethoxazole (TMP SMX) on day 10, and stepped down to oral TMP SMX on day 24, completing a 42 day course (24 days intravenous and 18 days oral). Concurrently, three surgical interventions, including bowel resection, burr hole drainage, and Ommaya reservoir placement, were performed to address intestinal perforation and intracranial complications. At 4 months of corrected age, the infant showed age appropriate neurodevelopment with no recurrence or sequelae. This successful outcome underscores that prompt diagnostics, susceptibility driven antibiotic optimization, and a coordinated multidisciplinary surgical medical approach are essential for managing life threatening neonatal Elizabethkingia anophelis infections, even in the setting of severe multisystem involvement.},
}

@article {pmid42846008,
year = {2026},
author = {Wang, X and Li, J and Zhuge, Y and Chen, R and Gao, Q and Zhao, Y and Jin, Q and Zhang, Y},
title = {NDM-Producing Escherichia coli subdural empyema mimicking chronic subdural hematoma: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1930920},
pmid = {42846008},
issn = {2296-858X},
abstract = {BACKGROUND: Subdural empyema is a life-threatening intracranial infection that may mimic chronic subdural hematoma on non-contrast computed tomography (CT), delaying diagnosis and source control. Intracranial infection caused by New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli is rare and may be overlooked when bloodstream infection appears microbiologically controlled.

CASE PRESENTATION: An 82-year-old man presented with fever and progressive neurological deterioration. Chest computed tomography (CT) suggested right lower lobe pneumonia, whereas serial head CT scans showed a left frontotemporoparietal subdural collection that was repeatedly interpreted as chronic subdural hematoma. Blood culture yielded multidrug-resistant Escherichia coli, and blood metagenomic next-generation sequencing (mNGS) detected E. coli together with blaNDM and other resistance determinants. Despite microbiologically guided antimicrobial therapy and subsequent clearance of blood cultures, fever, impaired consciousness, and enlargement of the subdural lesion persisted. Burr-hole exploration on March 22 revealed yellow purulent material rather than hematoma, establishing the anatomical diagnosis of subdural empyema and providing source control. Conventional culture of the surgically obtained subdural pus also yielded multidrug-resistant E. coli, while pus mNGS detected E. coli, blaNDM, blaCTX-M, and mcr-1. At the latest follow-up, the patient was undergoing further rehabilitation at a rehabilitation hospital. His vital signs were stable, and his Glasgow Coma Scale score was 15.

CONCLUSION: Negative follow-up blood cultures do not exclude persistent compartmentalized intracranial infection. In bacteremic patients with neurological deterioration and an enlarging subdural collection, subdural empyema should be reconsidered and timely source control should not be delayed.},
}

@article {pmid42846102,
year = {2026},
author = {Chu, H and Dong, S and Zhang, Y and Duan, R and Li, L},
title = {Neurosyphilis presenting as status epilepticus and hemiplegia diagnosed by metagenomic next-generation sequencing: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {32},
number = {5},
pages = {311},
pmid = {42846102},
issn = {1792-1015},
abstract = {The current study aimed to present a diagnostically challenging case of neurosyphilis manifesting with atypical neurological symptoms, emphasizing the importance of clinical vigilance and advanced diagnostics in avoiding misdiagnosis and inappropriate intervention. In the present study, a case of neurosyphilis, initially misdiagnosed and treated as acute cerebral infarction, is reported. Diagnostic analyses included serial brain magnetic resonance imaging (MRI), continuous electroencephalography (EEG) monitoring and metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) for pathogen identification. The results revealed that the patient presented with status epilepticus and hemiplegia. Follow-up MRI after transfer revealed extensive patchy cortical and subcortical white matter abnormalities in the right cerebral hemisphere. Notably, a thalamic signal abnormality observed on pre-thrombolysis diffusion-weighted imaging had notably diminished. EEG demonstrated periodic lateralized epileptiform discharges (PLEDs). CSF mNGS definitively identified 883 specific sequences of Treponema pallidum. Despite targeted anti-syphilitic and antiepileptic therapy, the patient's consciousness failed to improve, with persistent PLEDs on EEG. The patient was later discharged against medical advice due to pulmonary infection and hypotension and was subsequently confirmed deceased. In conclusion, the current case illustrates the markedly diverse and misleading presentations of neurosyphilis, which can mimic other acute neurological conditions. It underscores the need for maintaining a high index of suspicion and utilizing comprehensive diagnostic tools, including mNGS, to ensure accurate diagnosis and prevent the consequences of missed diagnosis or incorrect treatment.},
}

@article {pmid42847686,
year = {2026},
author = {Lane, KR and Meyer-Kaiser, KS and Collens, AB and Leal, CV and Collins, AG and Herrera, S and Hansel, CM},
title = {Deep-sea siliceous sponges harbor distinct and functionally diverse microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0174726},
doi = {10.1128/aem.01747-26},
pmid = {42847686},
issn = {1098-5336},
abstract = {Sponges, phylum Porifera, are long-lived and basal-branching metazoans that play important roles in ocean biogeochemistry and host diverse microbial communities. Siliceous sponges form a major clade of the Porifera; however, their microbiome is not well characterized, particularly in the deep ocean. Here, we used shotgun metagenomics to investigate the composition of the microbial communities of 13 siliceous sponges collected from four sites near Puerto Rico from depths ranging from 400 to 1,900 meters. Nine of the sponges in this study are from five sponge families that have not previously been sequenced using shotgun metagenomics. We assembled a total of 176 metagenome-assembled genomes from 20 bacterial phyla and 1 archaeal phylum. Ammonia-oxidizing archaea (AOA) Nitrosopumilaceae dominated most siliceous sponge microbial communities and was strikingly the sole symbiont associated with one sponge (Farrea). Overall, microbiome diversity was relatively low across siliceous sponges, except for a Phloeodictyidae, which is likely a high microbial abundance (HMA) sponge. Our results suggest that host sponge phylogeny may shape microbial community structure, with limited evidence for an environmental role. The sponge-associated microbial communities contained genetic capabilities for diverse metabolic functions, particularly contributing to the carbon, nitrogen, and sulfur cycles. In addition to the AOA, evidence of potential for microbial autotrophy was found through the presence of genes for RuBisCO, methanotrophy, and ATP citrate lyase. These results reveal both conserved relationships and metabolic flexibility across siliceous sponge lineages, suggesting unique evolutionary dynamics and demonstrating the importance of microbial metabolism to sponge host health and nutrient cycling in the oligotrophic deep ocean.IMPORTANCEMarine sponges, emerging ~600 million years ago, have close relationships with microorganisms, but the microbiome of deep-sea siliceous sponges is not well understood. Siliceous sponges play essential roles in deep-sea ecosystems by providing habitats for other metazoans and mediating carbon, nitrogen, and sulfur cycling; however, they remain some of the least-studied sponges. By shotgun sequencing DNA from 13 siliceous sponges collected near Puerto Rico, this study found that host sponge phylogeny is linked to microbial community composition and structure. Ammonia-oxidizing archaea dominated the microbial communities associated with marine sponges, likely playing key roles in utilizing metabolic byproducts and supporting host health. Other microbes also contributed to nutrient cycling and contained the potential to fix carbon, suggesting metabolic flexibility, which may benefit sponge hosts in low-resource environments. These findings emphasize the ecological importance of siliceous sponge-microbe symbioses and contribute to our understanding of the drivers shaping their structure and function.},
}

@article {pmid42847688,
year = {2026},
author = {Stroek, R and Gabriëls, M and Winkelhorst, M and van den Broek, M and Pabst, M and Jourdin, L and Daran, J-M and Bajic, D},
title = {Integrated multi-omics and metabolic modeling links structure to function in high-performing electrosynthetic biofilm communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0080326},
doi = {10.1128/msystems.00803-26},
pmid = {42847688},
issn = {2379-5077},
abstract = {Microbial electrosynthesis (MES) is a promising technology for the valorization of CO2 into industrially relevant building blocks. The high-performing MES systems in terms of production rates of acetate (12.5-19.7 mmol L[-1]catholyte day[-1]), butyrate (1.9-12.2 mmol L[-1]catholyte day[-1]), and caproate (0.6-0.9 mmol L[-1]catholyte day[-1]) discussed in this study consist of mixed microbial communities. However, the microbial community members, metabolic pathways, and interactions driving product formation in MES communities remain poorly understood. To overcome these challenges, we conducted a comprehensive characterization of three high-performing MES communities, combining multi-omics with metagenome-scale metabolic modeling. Using a high-resolution metagenomic pipeline, we reconstructed high-quality genomes of 25 metagenome-assembled genomes present in our reactors, including six fully circular genomes. We report the presence of Clostridium aromativorans for the first time in a gas-fermenting system. In particular, our findings identified three acetogenic species, Eubacterium limosum, Sporomusa sphaeroides, and C. aromativorans, as key contributors to the production of acetate, butyrate, and caproate via the Wood-Ljungdahl and the reverse β-oxidation pathways. In addition, we found genes related to lactate and ethanol production from acetyl-CoA, along with proteomic evidence of lactate production. This paves the way for investigating the role of cross-fed metabolites such as lactate and ethanol as electron donors in chain elongation. Finally, meta-genome-scale metabolic modeling suggests that the communities might be sustained by the cross-feeding of specific cofactors such as pyridoxine, pantothenate, biotin, and thiamin. This study provides key insights into the structure and function of electrosynthetic communities, bringing us closer to the rational engineering of MES systems.IMPORTANCEMicrobial electrosynthesis (MES) offers a promising route to transform CO2 and renewable electricity into valuable platform chemicals. However, the microbial ecology governing the assembly and function of these systems remains poorly understood, limiting our ability to engineer them. By integrating high-resolution multi-omics with metabolic modeling, this study provides a systems-level framework to dissect the structure and function of electrosynthetic microbial communities. Understanding which organisms drive carbon fixation and chain elongation, how electrons and intermediates are transferred within the biofilm, and how metabolic dependencies structure these communities is essential for improving productivity and product specificity in MES. More broadly, this work highlights how integrated multi-omics approaches can resolve the functional organization of complex microbial ecosystems and provides methodological advances that are broadly applicable to the study and engineering of microbial communities in autotrophic, electricity-driven biotechnologies.},
}

@article {pmid42847700,
year = {2026},
author = {Singh, VY and Gadekar, VP and Sasikumar, S and Lokshanan, RMR and Senthamizhan, V and Prithiviraj, B and Sinha, H and Raman, K},
title = {Microbial communities on station and train surfaces in Chennai Metro: insights into urban transit microbiome.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043326},
doi = {10.1128/msphere.00433-26},
pmid = {42847700},
issn = {2379-5042},
abstract = {UNLABELLED: Urban public transport systems, particularly metro networks, serve as key hubs for microbial transmission, yet the urban microbiome in densely populated regions like India remains poorly characterized. Understanding these environments is crucial for public health, especially in light of the COVID-19 pandemic and growing concerns about antimicrobial resistance (AMR). This study is the first of its kind to investigate the microbial communities and the presence of AMR genes in the Chennai Metro system. We collected 96 surface swabs from 12 metro stations across two lines, focusing on surfaces that people frequently touch, such as handrails, kiosks, banisters, and ticket counters. Of the collected samples, 47 met quality control standards and were subjected to shotgun metagenomic sequencing, and 41 samples with more than 1 million reads were included in our analysis. Our findings indicate that surface type significantly influences microbial community structure, with kiosks exhibiting the highest microbial diversity. Comparative analysis with global urban data sets revealed unique microbial patterns specific to Chennai, including nine species that were notably more prevalent in our samples than in other urban transit systems worldwide. Furthermore, through pangenome analysis, we generated high-quality metagenome-assembled genomes that elucidated the adaptive strategies of dominant microbial species in this urban environment. Despite their relatively low abundance, several AMR families were widely distributed across the data set, with over 80% of samples containing at least one associated AMR gene, including families linked to rifamycins, multidrug resistance, and sulfonamides. This study lays a foundation for understanding the urban microbiome in India, emphasizing distinct regional characteristics and underscoring the need for sustained monitoring to mitigate disease transmission risks in high-density transit settings.

IMPORTANCE: Densely populated urban transit systems are critical hubs for microbial exchange, yet the mass transit microbiomes of Indian cities remain largely uncharacterized, representing a significant gap in global surveillance. Our study provides the first comprehensive metagenomic analysis of the Chennai Metro, a high-traffic transit network serving millions. Our findings highlight the unique environmental drivers shaping urban microbiota in India. Chennai, with over 12 million residents and a metro system serving over 105 million passengers annually, is an ideal yet uncharacterized environment for studying microbial dynamics, surface-microbe interactions, and environmental antimicrobial resistance reservoirs.},
}

@article {pmid42848247,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Tumor microenvironment and gut microbiome in immunotherapy resistance in gastric cancer: clinical questions, biological mechanisms, and evidence-based therapeutic perspectives.},
journal = {Medical oncology (Northwood, London, England)},
volume = {43},
number = {11},
pages = {},
pmid = {42848247},
issn = {1559-131X},
mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/drug therapy/therapy/pathology ; *Tumor Microenvironment/immunology ; *Drug Resistance, Neoplasm/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Immunotherapy/methods ; },
abstract = {Immune checkpoint inhibitors (ICIs) have improved systemic therapy for advanced gastric and gastroesophageal junction cancer, yet primary and acquired resistance remain common and are incompletely explained by established tumor biomarkers. This narrative review evaluates the connected roles of the tumor microenvironment (TME), host immunity, and the gut microbiome in shaping ICI resistance in gastric cancer. We performed a structured PubMed search through 28 August 2026 and prioritized gastric cancer-specific clinical and translational evidence, supplemented by systematic reviews, meta-analyses, and mechanistically relevant studies from other tumor types when necessary. Within the gastric cancer TME, cancer-associated fibroblasts, myeloid cells, regulatory T cells, extracellular matrix remodeling, hypoxia, angiogenesis, and T-cell exhaustion can promote immune exclusion or dysfunction. Microbial diversity, microbial metabolites, antibiotics, proton pump inhibitors, defined live biotherapeutics, fecal microbiota transplantation, and diet may influence systemic antitumor immunity, but most human evidence is retrospective, cross-sectional, or derived from non-gastric cancers. Clinically, antibiotic stewardship, reassessment of unnecessary acid suppression, and nutritional optimization are reasonable supportive measures, whereas routine probiotic supplementation, Clostridium butyricum MIYAIRI 588 for ICI sensitization, and fecal microbiota transplantation remain investigational in gastric cancer. Future studies should integrate longitudinal exposures, serial TME profiling, stool metagenomics, medication use, nutritional status, and clinical outcomes. The TME-gut microbiome axis is therefore a biologically plausible framework for biomarker-guided research, but current evidence does not justify empiric microbiome-directed anticancer therapy in gastric cancer.},
}

Humans
*Stomach Neoplasms/immunology/microbiology/drug therapy/therapy/pathology
*Tumor Microenvironment/immunology
*Drug Resistance, Neoplasm/immunology
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Immunotherapy/methods

@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.},
}