@article {pmid41998770,
year = {2026},
author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH},
title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {41998770},
issn = {1756-994X},
support = {NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Emerging evidence suggests that maternal-prenatal gut microbiome disturbances shape offspring allergic outcomes through modulation of the in utero immune environment. Yet, no comprehensive clinical studies in human mother–offspring dyads have deconvoluted the maternal-prenatal gut microbiome and systemic immune-metabolome signatures underlying offspring allergic predisposition.

METHODS: We performed a longitudinal nested case–control study involving 128 well-characterized mother–offspring dyads from defined cases (offspring with atopic dermatitis (AD); n = 64) and controls (offspring without AD; n = 64). Maternal stool and blood samples were collected at multiple time points during gestation for multi-omic profiling. Structural and functional gut microbiome composition was characterized via metagenomic sequencing, while systemic metabolome and serum immune milieu were profiled using targeted plasma metabolomics and Olink proximity extension assays, respectively. In offspring early-life, stool samples were collected longitudinally up to 6 months of age for gut microbiome and metabolome analyses.

RESULTS: Mothers of AD infants exhibited longitudinal enrichments of gut Klebsiella pneumoniae, Roseburia intestinalis, Clostridioides difficile and Bilophila sp. 4_1_30, alongside depletions in gut Clostridium sp. CAG:678, Romboutsia timonensis, Akkermansia muciniphila, Blautia hansenii and Alistipes ihumii during pregnancy. These taxonomic shifts were associated with systemic metabolomic alterations, including elevated branched-chain amino acids and immune-related metabolites (e.g., creatine, ornithine), and a concurrent pro-inflammatory TH2-skewed immunological milieu marked by increased interleukin-4 (IL-4) and IL-5 and decreased CXCL11. In early life, AD infants harbored a dysbiotic gut microbiome characterized by persistent enrichments of potentially pathogenic Escherichia coli and K. pneumoniae, along with depletion of short chain fatty acid-producing Bacteroides species and beneficial colonizers. Integrated multi-omic analyses across the prenatal-postnatal axis indicated that the impaired establishment of gut microbiome in AD infants may, in part, be attributed to the (1) potential transmission of maternally originated Klebsiella and (2) immunomodulatory effects of a maternal-prenatal pro-inflammatory, TH2-skewed milieu during gestation.

CONCLUSIONS: Our study uncovers a distinct maternal-prenatal gut microbiome and systemic metabolome–immune signature that predisposes offspring to AD by disrupting early-life gut microbial establishment. These findings highlight the gestational period as a critical window for preventive strategies targeting the maternal microbiome or systemic immune-metabolic axes to mitigate allergic disease susceptibility in offspring.

TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov (NCT 03531658).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01655-5.},
}

@article {pmid42202790,
year = {2026},
author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R},
title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102835},
doi = {10.1016/j.xcrm.2026.102835},
pmid = {42202790},
issn = {2666-3791},
abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.},
}

@article {pmid42203111,
year = {2026},
author = {Wang, L and Bai, L and Li, H and Zhang, P and He, F},
title = {A Case of Imported Infection in China: Initially Treatment-unresponsive Schistosomiasis Coinfection with Bladder Tuberculosis.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101157},
doi = {10.1016/j.ijmmb.2026.101157},
pmid = {42203111},
issn = {1998-3646},
abstract = {Schistosoma haematobium, endemic to sub-Saharan Africa, causes urogenital disease, differing from Schistosoma japonicum, which affects the hepatointestinal system and is the only endemic schistosome in China. A Chinese male with persistent hematuria after prolonged occupational exposure in Angola was initially attributed to S. japonicum. Following failed treatment, metagenomic sequencing confirmed S. haematobium infection, and subsequent urethral resection detected Mycobacterium tuberculosis DNA, establishing concurrent bladder tuberculosis. This case highlights the need for molecular diagnostics in patients with hematuria after sub-Saharan exposure and the immunomodulatory risks posed by helminth infections.},
}

@article {pmid42203372,
year = {2026},
author = {McCann, P and Megaw, J and Gobert, GN},
title = {Parasite-associated microbiomes: An unseen microenvironment.},
journal = {Advances in parasitology},
volume = {131},
number = {},
pages = {31-70},
doi = {10.1016/bs.apar.2026.03.001},
pmid = {42203372},
issn = {2163-6079},
mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; },
abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.},
}

Animals
Humans
*Microbiota
*Host-Parasite Interactions
*Parasites/microbiology/physiology
Symbiosis

@article {pmid42203690,
year = {2026},
author = {Fullam, A and Prasoodanan Pk, V and Kuhn, M and Bork, P and Schmidt, TSB},
title = {microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag343},
pmid = {42203690},
issn = {1367-4811},
abstract = {MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.

RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories.

AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305,626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues.

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

@article {pmid42203770,
year = {2026},
author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M},
title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73297-5},
pmid = {42203770},
issn = {2041-1723},
support = {1026-00386B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; },
abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.},
}

@article {pmid42203854,
year = {2026},
author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I},
title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42203854},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; },
abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.},
}

Humans
Female
Pregnancy
*Saliva/microbiology
*Microbiota/genetics
*Metagenomics/methods
Adult
*Mouth/microbiology
Shotgun Sequencing
Cross-Sectional Studies
Metagenome
Bacteria/genetics/classification

@article {pmid42204574,
year = {2026},
author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N},
title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.},
journal = {Annals of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ana.78243},
pmid = {42204574},
issn = {1531-8249},
support = {RF1AG075922/GF/NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; R01NS097723/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; },
abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026.},
}

@article {pmid42204631,
year = {2026},
author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH},
title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07471-5},
pmid = {42204631},
issn = {1756-3305},
support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.

METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples (n = 46) was investigated by metagenomic shotgun sequencing and comparatively analysed at the phylum, genus, and species levels. In addition, the prevalence of potential pathogen DNA in head lice samples (n = 204) was assessed using real-time PCR with stringent negative controls.

RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722 genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level, DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial DNA from these taxa.

CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB microbiome in head lice. The high proportion of unannotated genes (>95%) underscores the limited representation of louse-associated microbial genomes in public databases and suggests  substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may suggest prior exposure, mechanical carriage, or residual DNA from blood meals. These exploratory findings contribute new insights into the microbiota associated with human lice.},
}

@article {pmid42204733,
year = {2026},
author = {Fang, Q and Liu, J and Xuan, C and Li, C and Jiang, X and Zhang, S and Li, Q and Liu, X and Liu, Q and Zhang, L and Wang, Y and Cui, J and Qu, Y and Zhang, J and Li, P and Chen, X},
title = {Targeting the gut‒kidney axis for lupus nephritis treatment: multimechanism regulatory strategies and evidence from Traditional Chinese medicine.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {42204733},
issn = {1749-8546},
support = {2022YFC3602000//the National Key Research and Development Program of China/ ; 82274327//the National Natural Science Foundation of China/ ; 32141005//the National Natural Science Foundation of China/ ; },
abstract = {Lupus nephritis (LN) treatment remains challenging because of the limited efficacy and substantial side effects of conventional immunosuppressive therapies. Traditional Chinese medicine (TCM), with its holistic and multitarget approach, offers unique therapeutic potential. The emerging gut-kidney axis theory provides a new framework for understanding LN pathogenesis by linking gut dysbiosis and intestinal barrier injury to renal inflammation. This review systematically examines the role of gut-kidney axis dysregulation in LN progression and establishes connections between the TCM spleen-kidney correlation theory and this modern concept. Accumulating evidence suggests that TCM compounds and active ingredients alleviate renal injury and improve LN through multiple mechanisms. TCM compounds modulate the gut microbiota composition, enhance intestinal barrier integrity, reduce endotoxin translocation, and suppress systemic inflammation. These findings position the gut-kidney axis as a critical target for TCM intervention. Through multicomponent synergy, TCM restores gut homeostasis and inhibits aberrant immune responses. Future studies should integrate multiomics approaches, including metagenomics and metabolomics, and prospective clinical trials should dynamically track the gut microbiota and metabolite profiles in LN patients. Such investigations will clarify the precise mechanisms by which TCM modulates the gut-kidney axis and facilitate the development of personalized TCM-based therapeutic strategies.},
}

@article {pmid42204882,
year = {2026},
author = {Jiang, Y and Zhao, J and Chen, Z and Jiang, N and Lu, C and Zhang, Y and Chen, H},
title = {Long-Term Effects of Straw-Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote-Fungus-Protist Interactions and Metagenomic-Metabolite Linkages.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70339},
doi = {10.1111/1462-2920.70339},
pmid = {42204882},
issn = {1462-2920},
support = {2022YFD1500302//National Key Research and Development Program of China/ ; 42277282//National Natural Science Foundation of China/ ; 2022A1515010861//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20250604174440054//Shenzhen Natural Science Foundation in Basic Research Fund/ ; JCYJ20220530150201003//Shenzhen Natural Science Foundation in Basic Research Fund/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism/genetics/physiology ; Metagenomics ; *Charcoal ; *Carbon Sequestration ; Bacteria/metabolism/genetics/classification ; *Fertilizers/analysis ; China ; Microbiota ; Carbon/metabolism ; Metagenome ; },
abstract = {Here, we conducted a seven-year field experiment in black soils of Northeast China to evaluate the effects of carbon (C) management, that is, control, straw return (SD), straw-biochar (BC), and a combined amendment (SDBC), with three fertilization levels (N0: unfertilized control, N60: 60% of conventional rates, N100: conventional rates) on soil microbiomes, metagenomics, and metabolomics. Results showed that BC significantly elevated soil total C (+15%), total N (+10%), and NH 4 + $$ {\mathrm{NH}}
_4^{+}
$$ (+63%) relative to controls. Microbial community analyses revealed that SD increased prokaryotic richness but reduced protist diversity, whereas BC and SDBC suppressed fungal diversity. Integrated metagenomic and metabolomic profiling uncovered microbial functional adaptations to rich-C conditions under BC and SDBC, characterized by downregulated C metabolism-related genes and concurrent accumulation of lipid-associated metabolites. Crucially, BC decreased the abundance of bacterial virulence factors, contrasting with SD elevating pathogenic potentials. Among three fertilization levels, the reduced rates of N60 optimized microbial network complexity and minimized pathogen invasion risks more effectively than conventional rates of N100 without compromising soil fertility. Collectively, by deciphering prokaryote-fungus-protist interactions and metagenomic-metabolite linkages, our research highlights that straw-derived biochar application and optimized fertilization offers a sustainable strategy to foster beneficial microbial associations, suppresses pathogenic potential, and enhances carbon storage.},
}

*Soil Microbiology
*Soil/chemistry
*Fungi/metabolism/genetics/physiology
Metagenomics
*Charcoal
*Carbon Sequestration
Bacteria/metabolism/genetics/classification
*Fertilizers/analysis
China
Microbiota
Carbon/metabolism
Metagenome

@article {pmid42205184,
year = {2026},
author = {Wang, X and Wang, H and Liu, J and Zhang, H and Zhou, XJ},
title = {Gut Virome Characteristics and Network Alterations in IgA Nephropathy.},
journal = {Kidney international reports},
volume = {11},
number = {7},
pages = {106550},
pmid = {42205184},
issn = {2468-0249},
abstract = {INTRODUCTION: Emerging evidence implicates gut microbiota dysbiosis in the pathogenesis of IgA nephropathy (IgAN), yet the contribution of the gut virome remains unexplored. This study aimed to characterize virome signatures and virus-microbiota interactions in IgAN.

METHODS: We performed a rigorously matched case-control study including 32 patients with biopsy-proven IgAN and 32 healthy controls. Fecal viral-like particles and bacterial communities were profiled using metagenomic sequencing and full-length 16S ribosomal RNA (rRNA) sequencing. Statistical analysis included diversity, differential abundance, network analysis, and correlation with clinical indices.

RESULTS: IgAN subjects displayed significant reductions in gut virome richness (severe IgAN vs. healthy controls, P = 0.03), with a lower relative abundance of Caudoviricetes in severe IgAN (P = 0.045) and enrichment of Tectiliviricetes in mild disease (P = 0.03). We identified 113 differentially abundant bacteriophage contigs (82 up, 31 down; false discovery rate < 0.05); key predicted hosts shifted toward Bacteroides, Clostridium, and Roseburia in IgAN, whereas Faecalibacterium and Alistipes prevailed in controls. Viral and bacterial alpha diversity correlated in healthy controls but not in IgAN (r = 0.38, P = 0.03 vs. r = 0.04, P = 0.81). IgAN virome encoded more glyco-modifying enzymes (P < 0.05), with strong correlations to estimated glomerular filtration rate (eGFR) (r = 0.65, P = 0.001). Viral and bacterial alpha diversity were significantly correlated with proteinuria and gross hematuria (r = 0.18-0.25, - < 0.05).

CONCLUSION: This study describes potential alterations in gut virome diversity, bacteriophage composition, bacteriome-virome relationships, and predicted functional profiles in IgAN, suggesting potential relevance of the gut virome to intestinal ecological alterations.},
}

@article {pmid42205574,
year = {2026},
author = {Liao, G and Xiao, J and Zhang, B and Wang, S and Wan, X and Zhang, C and Lyu, C and Yan, B and Zhao, Y and Kang, C and Zhang, Y and Yuan, F and Zhao, Z and Chen, Y and Guo, L and Zhang, Y},
title = {Enhancement of genetic potential for soil carbon and nitrogen cycling by organic fertilizer substitution improves the ecological environment for licorice cultivation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758116},
pmid = {42205574},
issn = {1664-302X},
abstract = {BACKGROUND: Excessive chemical fertilizer application has become a core bottleneck restricting the green and sustainable cultivation of Glycyrrhiza uralensis (licorice). Partial organic fertilizer substitution can improve soil microecology and licorice growth traits, yet its regulatory effects on microbial functional genes mediating soil carbon (C) and nitrogen (N) cycling remain unclear.

RESULTS: Using metagenomic sequencing, we investigated the effects of six fertilization regimes [100% organic fertilizer (OF100), 100% chemical fertilizer (OF0), and organic-inorganic combinations (OF25, OF50, OF75)] on the genetic potential of soil C and N cycling, as well as soil properties and licorice growth traits in bulk and rhizosphere soils of licorice. Organic substitution significantly altered the abundance of C and N cycling-related functional genes: OF100 significantly increased the abundance of genes associated with methane oxidation (pmoA/amoA), carbon degradation (pel, cbh) and nitrification (pmoB/amoB), while OF0 significantly upregulated the methanogenesis-related gene mttA and downregulated nitrogen degradation genes; optimized fertilization (OF50) significantly reduced the abundance of genes linked to excessive carbon degradation (malZ) and nitrogen loss genetic potential (nirK), and markedly increased the abundance of genes for carbon fixation (pccA) and nitrogen mineralization (GDH). PERMANOVA revealed that soil compartment (bulk vs. rhizosphere) explained 62.87% of the total variation in functional gene profiles, which was 5.67 times higher than the contribution of fertilization regime (11.10%).

CONCLUSION: Rational organic-inorganic fertilization effectively regulates soil microbial functional genes related to C and N cycling, optimizes soil nutrient cycling potential, reduces nutrient loss risk, and enhances nutrient supply efficiency for licorice growth. These findings provide a scientific basis for fertilizer management optimization and sustainable cultivation of licorice.},
}

@article {pmid42205899,
year = {2026},
author = {Patil, BL and Shanmugaraj, C and Madhusudan, M},
title = {Metagenomic profiling of endophytic microbiomes associated with fruit pulp and seed kernels of different mango varieties reveals conservation of bacterial communities in seed kernels.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {222},
pmid = {42205899},
issn = {2190-572X},
abstract = {UNLABELLED: Bacterial and fungal communities associated with mango pulp and seed kernels from eight Indian mango varieties were profiled using 16 S rRNA and ITS amplicon sequencing. Bacterial diversity was consistently higher in seed kernels (647 ± 238 OTUs) than in pulp tissues (196 ± 112 OTUs). Seed kernel-associated bacterial communities were dominated by Firmicutes (35.8-44.0%) and Bacteroidota (16.8-35.8%) and showed high compositional consistency across varieties, with core genera including Prevotella, Ruminiclostridium, and Lachnoclostridium. In contrast, pulp-associated bacterial communities were enriched in Proteobacteria (6.5-88.5%) and Actinobacteria (4.4-34.6%) and exhibited pronounced inter-varietal variability, particularly in the relative abundance of Bacteroidota (0.8-53.8%). Fungal communities displayed lower richness (14-72 OTUs) and higher variability, with Candida kruisii (15-67%) and Hanseniaspora uvarum (up to 86%) as dominant taxa. Non-metric multidimensional scaling and hierarchical clustering revealed clear tissue-driven segregation of bacterial communities, whereas fungal assemblages showed weaker tissue-associated structuring. Seed kernels harbored approximately 3.3-fold more unique bacterial OTUs than pulp tissues, with the Amrapali seedkernel exhibiting the highest richness (789 OTUs). Across varieties, 82% of kernel-associated bacterial OTUs were shared, compared with 31% in pulp, indicating a conserved kernel microbiome and a more variable, cultivar-specific pulp microbiome. These results highlight strong tissue-level compartmentalization of mango-associated bacterial communities across cultivars.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04848-2.},
}

@article {pmid42205903,
year = {2026},
author = {Hameed, A and Ghate, SD and Shastry, RP},
title = {Fecal functional metagenomics reveals increased gut Bacillota/Pseudomonadota (Firmicutes/Proteobacteria) ratio and altered bacterial CAZyme profile in human colorectal cancer.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {230},
pmid = {42205903},
issn = {2190-572X},
abstract = {UNLABELLED: Gut microbial dysbiosis has been implicated in the onset and/or progression of colorectal cancer (CC). We recently identified the emergence of low-abundance bacterial taxa affiliated with the phylum Bacillota in the gut microbiome of CC patients, as revealed by 16S rRNA gene amplicon sequencing. Here, we subjected the fecal samples from CC (n = 4) and healthy control (HC, n = 4) participants to functional metagenomics using the Illumina Novaseq 6000 platform. Metagenome-assembled genomes (MAGs) showed compositional differences among bacterial phylotypes in CC and HC. Species observed, richness (Chao1), and diversity (Shannon's) were high in CC, whereas species abundance peaked in HC. The Bacillota to Pseudomonadota ratio was high (> 3-fold) in CC (2.45) as compared to HC (0.70). MAGs revealed a decline in the distribution frequency of COGs involved in carbohydrate transport and metabolism (G), inorganic ion transport and metabolism (P), and unknown function (S) in CC. However, CC and HC samples exhibited marginal variations in terms of G/P (1.29 and 1.18, respectively) and G/S (0.35 and 0.40, respectively) ratios. Analysis further revealed a significant increment in glycosyltransferases GT1, GT2 and GT4, particularly in CC. In contrast, the glycoside hydrolases GH5 and GH9 declined in CC. GT/GH ratios were found to increase > 2-fold in CC (3.94) compared with HC (1.37). The present pilot-scale dataset-specific work reflects perseverance of Bacillota, significant decline in Pseudomonadota, a stable G/P and G/S ratios and enrichment of glycosyltransfererases in CC. Further transcriptomic-based studies in larger cohorts are warranted to gain insights into the implications of dysbiosis and its pathophysiological relevance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04882-0.},
}

@article {pmid42206066,
year = {2026},
author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R},
title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.},
journal = {Infectious medicine},
volume = {5},
number = {2},
pages = {100260},
pmid = {42206066},
issn = {2772-431X},
abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.

METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.

RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 × 10⁻⁵ and 1.2 × 10⁻⁵, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 × 10⁻⁵ and 1.1 × 10⁻⁴ in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid‑mediated ARGs and Cr, and between transposon‑mediated ARGs and Cr/V. The MP of transposon‑mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid‑mediated ARGs but positively with insertion sequence‑mediated ARGs. Ni concentration was positively associated with the MP of IS‑mediated VFGs.

CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.},
}

@article {pmid42206150,
year = {2026},
author = {Sun, K and Wang, F and Niu, T and Wang, H and Liu, Y and Guo, L and Wang, X and Hou, X},
title = {Metagenomic and metabolomic insights into the rhizosphere of Paeonia suffruticosa 'Luoyang Hong' across a continuous cropping chronosequence.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1754999},
pmid = {42206150},
issn = {1664-462X},
abstract = {The cultivation of Paeonia suffruticosa 'Luoyang Hong', a valuable ornamental crop, faces significant challenges due to replanting issues. However, the dynamics of its rhizosphere micro-ecosystem under continuous cropping remain poorly understood. This study systematically investigates the successional patterns of the rhizosphere micro-ecosystem over a 12- to 42-year chronosequence to identify the underlying drivers of these issues. Using an integrated multi-omics approach combining metagenomics and non-targeted metabolomics, we deciphered the rhizosphere mechanisms associated with replanting issues in Paeonia suffruticosa 'Luoyang Hong'. Based on differential changes in metabolites within the soil and root systems, key substances such as succinic acid, trans-ferulic acid, vanillic acid, and Leu-Val-Arg-Lys were identified. The microbial succession demonstrated a distinct temporal progression. Initially, at the 12-year stage, the rhizosphere was enriched with beneficial bacterial genera. However, around the 20-year stage, the abundance of these beneficial genera significantly declined. Subsequently, at the 34-year stage, the community shifted to a dominance of genera associated with organic matter degradation. Finally, at the 42-year stage, a partial recovery of certain beneficial genera and their functions was observed. Despite this recovery, the overall system continued to exhibit signs of continuous degradation. Integrated multi-omics analysis further revealed significant positive correlations, such as that between N,N-dimethyldodecylamine N-oxide and several differential microbial genera, underscoring the complex interactions between metabolites and microbes. Our findings provide a systematic perspective on the micro-ecological dynamics in the rhizosphere of Paeonia suffruticosa 'Luoyang Hong', offering deeper insights into replanting issues and supporting future mitigation strategies.},
}

@article {pmid42206286,
year = {2026},
author = {Oladejo, OA and Ibiwoye, DO and Faniyi, AA and Ayoola, MO and Oguntunji, AO and Ayansina, AD and Dahunsi, SO},
title = {Dynamics of enzyme and metabolic profile of broilers fed black soldier fly (Hermetiailucens) larvae-based diets.},
journal = {Biochemistry and biophysics reports},
volume = {46},
number = {},
pages = {102618},
pmid = {42206286},
issn = {2405-5808},
abstract = {This study investigated the impact of replacing fishmeal with black soldier fly larvae meal (BSFLM) on growth performance, microbial enzyme activity, and metabolic functions in broiler chickens. A total of fifty Arbor Acre Plus chicks were distributed across five dietary groups, including a control (100% fishmeal) and four diets containing increasing levels of BSFLM (25%, 50%, 75%, and 100%) in a completely randomized design. Broilers were reared over eight weeks, and cecal samples were subjected to 16S rRNA metagenomic sequencing to profile gut microbial enzyme activities and metabolic functions. Results revealed a progressive increase in microbial enzyme abundance and functional metabolic pathways with higher BSFLM inclusion, particularly in the 50% (T3) and 100% (T5) groups. Key enzymes, including ABC-2-type ATP-binding proteins, RNA polymerase sigma factors, and carbohydrate-active enzymes, were significantly upregulated, supporting enhanced carbohydrate fermentation, amino acid biosynthesis, and central carbon metabolism. Metabolic pathway analysis indicated a dietary shift from carbohydrate-driven fermentation in the control group to a more protein- and lipid-centered metabolism in BSFL-fed birds, with T3 showing a balanced metabolic profile and T5 exhibiting hyper-metabolic activity. These findings demonstrate that BSFLM can replace fishmeal without compromising gut health and may even enhance microbial functionality, with a 50% replacement emerging as an optimal inclusion level to sustain balanced microbial metabolism.},
}

@article {pmid42206340,
year = {2026},
author = {Huerta, AI and Joglekar, P and Totsline, N and D'Amico-Willman, KM and Ritchie, DF},
title = {Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1951},
pages = {},
doi = {10.1098/rstb.2025.0124},
pmid = {42206340},
issn = {1471-2970},
support = {//National Institute of Food and Agriculture/ ; //Foundation for Food and Agriculture Research/ ; },
mesh = {*Bacteriophages/physiology/genetics ; *Plants/virology/microbiology ; *Microbiota ; *Biological Evolution ; },
abstract = {Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.},
}

*Bacteriophages/physiology/genetics
*Plants/virology/microbiology
*Microbiota
*Biological Evolution

@article {pmid42206370,
year = {2026},
author = {Chen, L and Lin, L and Wang, Z and Yu, L and Ren, B and Zhou, S and Wang, P and Li, Y and Lu, E and Dong, Z},
title = {Fusobacterium nucleatum-Derived Isoleucine Exacerbates Aneurysm by Inducing Ferroptosis in Vascular Smooth Muscle Cells.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.126.324050},
pmid = {42206370},
issn = {1524-4636},
abstract = {BACKGROUND: Bacterial communities and their metabolites are increasingly recognized as key contributors to cardiovascular disease, yet their role and mechanistic involvement in abdominal aortic aneurysm (AAA) pathogenesis remain insufficiently defined.

METHODS: Dental plaques from patients with AAA and matched healthy controls were subjected to metagenomic sequencing, and corresponding plasma samples underwent untargeted metabolomic profiling. In vivo, mice were topically exposed in the oral cavity to Fusobacterium nucleatum (Fn) followed by AngII (angiotensin II) infusion to evaluate its impact on AAA progression. A homologous recombination-based ilvE deletion strategy was used to confirm the role of Fn in isoleucine biosynthesis. Molecular assays were performed to assess ferroptosis-related signatures and histone acetylation in smooth muscle cells, while chromatin immunoprecipitation-quantitative polymerase chain reaction verified the specific acetylation target. In addition, dietary restriction of isoleucine was introduced in the AAA murine model to explore therapeutic relevance.

RESULTS: Patients with AAA showed a marked enrichment of Fn in dental plaque, and topical application of Fn aggravated AngII-induced AAA in mice. Elevated plasma isoleucine concentrations were observed in both human AAA and experimental models. Genetic deletion of ilvE in Fn diminished bacterial isoleucine release and mitigated AAA development in mice. Mechanistic analyses revealed that Fn-derived isoleucine promoted ferroptosis in smooth muscle cells through H3K9ac (histone H3 lysine 9 acetylation)-dependent transcriptional activation of ACSL4 (acyl-CoA [coenzyme A] synthetase long-chain family member 4), a core regulator of ferroptosis. Dietary isoleucine restriction in the AngII-induced model reduced H3K9ac, suppressed ferroptosis, and alleviated aneurysmal progression.

CONCLUSIONS: Fn-derived isoleucine drives ferroptosis in smooth muscle cells via H3K9ac-mediated activation of ACSL4, delineating a microbiota-metabolite-epigenetic axis in AAA pathogenesis and nominating dental plaque Fn abundance and circulating isoleucine as exploratory biomarker candidates requiring larger, independent validation.},
}

@article {pmid42206586,
year = {2026},
author = {Yeo, S and Park, H},
title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681840},
doi = {10.1080/19490976.2026.2681840},
pmid = {42206586},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation & purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation & purification/classification/genetics ; },
abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.},
}

Humans
*Gastrointestinal Microbiome
Feces/microbiology
*Enterococcus faecium/isolation & purification/classification/genetics
Metagenomics/methods
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Bifidobacterium/isolation & purification/classification/genetics

@article {pmid42190464,
year = {2026},
author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A},
title = {Age, strain, and gut section shape the microbiome of commercial laying hens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107152},
doi = {10.1016/j.psj.2026.107152},
pmid = {42190464},
issn = {1525-3171},
abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.},
}

@article {pmid42190784,
year = {2026},
author = {Qadeer, A and Nazir, MJ and Muhammad, S and Azim, R and Wang, Q and Hussain, MM},
title = {Decoding heavy metal tolerance in rice: Nucleic acid-based technologies shaping global food security.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152693},
doi = {10.1016/j.ijbiomac.2026.152693},
pmid = {42190784},
issn = {1879-0003},
abstract = {Global rice production is critically threatened by heavy metal contamination, particularly cadmium (Cd) and arsenic (As), which compromises yield, diminishes grain nutritional quality, and exposes billions of consumers to nephrotoxic and carcinogenic risks. Conventional remediation strategies (soil amendments, water management, phytoremediation) are prohibitively expensive, temporally protracted, and fundamentally reactive, while conventional breeding is constrained by linkage drag, polygenic trait architecture, and absence of natural alleles that restrict toxic metal uptake from essential mineral nutrition. This review critically examines how nucleic acid-based technologies have fundamentally reconfigured the discovery-to-deployment pipeline for heavy metal tolerance in rice. We trace the progression from early QTL mapping and positional cloning of transporters through population-scale GWAS and pan-genomics, which have resolved the full allelic series at these loci, to contemporary CRISPR-mediated genome editing, that generated transgene-free, field-validated low-accumulating lines. Transcriptomic, epigenomic, and metagenomic tools have further illuminated the dynamic stress response, non-coding regulatory networks, and rhizosphere microbiome contributions to metal exclusion. Translational case studies including Japan's marker-assisted deployment of OsHMA3 for Cd mitigation and South Asia's development of OsLsi2-edited low-As lines demonstrate that these technologies are not merely academic instruments but operational solutions. However, specificity-versus-essentiality dilemma, multi-metal antagonism (Cd/As redox conflict), and profound regulatory divergence (SDN-1 exemption in the Americas, Japan, and India versus GMO classification in the EU) remain formidable barriers. We conclude that nucleic acid technologies constitute the cornerstone of a second Green Revolution focused on grain quality and safety, contingent upon sustained investment in synthetic biology, digital integration, and internationally harmonized governance frameworks.},
}

@article {pmid42190825,
year = {2026},
author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J},
title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124845},
doi = {10.1016/j.envres.2026.124845},
pmid = {42190825},
issn = {1096-0953},
abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.},
}

@article {pmid42190956,
year = {2026},
author = {Xia, R and Cui, B and Li, G and Zhou, H and Luo, W and Xu, Z},
title = {Integrated metagenomics unravels the microbial mechanisms driving greenhouse gas and odor emissions during composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134984},
doi = {10.1016/j.biortech.2026.134984},
pmid = {42190956},
issn = {1873-2976},
abstract = {While composting is widely used for the resource recovery of organic waste, it is complicated by greenhouse gas and odor emissions. An integrated analysis of emission characteristics and elemental metabolism mechanisms is essential for targeted control strategies. Using integrated metagenomics and modular network analysis, this study identified the biotic and abiotic factors driving gaseous emissions. Results showed that methane (CH4) and nitrous oxide (N2O) emissions mainly occurred during the mesophilic and cooling stages, whereas ammonia (NH3) and hydrogen sulfide (H2S) peaked at the thermophilic stage. Initially, acidogens (e.g. Klebsiella) and methanogens (e.g. Methanobacterium) promoted CH4 production via aceticlastic (e.g. ackA gene) and hydrogenotrophic (e.g. frhB gene) pathways. Meanwhile, nitrate-reducing bacteria and denitrifiers converted nitrate nitrogen to N2O via assimilatory/dissimilatory reduction and denitrification pathways, respectively. As temperature increased into the thermophilic stage, CH4 and N2O production decreased due to the thermal inhibition of acidogens and nitrate-reducing bacteria. However, intense mineralization of organic nitrogen/sulfur compounds released ammonium and sulfate ions, leading to NH3 volatilization and microbial H2S production by sulfate-reducing bacteria (e.g. Desulfitibacter) via synergistic assimilatory/dissimilatory sulfate reduction pathways. Reduced thermal inhibition at the cooling stage restored activity of acidogens and methanogens, which drove CH4 emission via all four pathways. Denitrifiers (e.g. Pusillimonas) with nirS and norC genes and nitrifiers (e.g. Devosia) with hao genes were also enriched, increasing N2O production. Nevertheless, N2O was ultimately reduced to N2 by denitrifiers carrying nosZ at the mature stage. These findings provide fundamental insights for developing targeted strategies to mitigate gaseous emissions during composting.},
}

@article {pmid42191017,
year = {2026},
author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Caracciolo, AB and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V},
title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2026.05.013},
pmid = {42191017},
issn = {1876-4347},
abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7,959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.},
}

@article {pmid42192344,
year = {2026},
author = {Liu, L and Su, P and Gong, F and Wang, A and Wang, X and Yang, L and Mo, W and Jiang, T},
title = {Diagnosis and management of mixed Chlamydia abortus and psittaci pneumonia guided by metagenomic next-generation sequencing: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13691-y},
pmid = {42192344},
issn = {1471-2334},
support = {2023SK4077//the China Hunan Provincial Clinical Medical Technology Demonstration Base for Cardiac Arrest Diseases/ ; },
abstract = {BACKGROUND: Chlamydia abortus primarily causes abortion and stillbirth in animals and is associated with pregnancy-related complications in humans. However, it is an extremely rare cause of pneumonia in humans. While Chlamydia psittaci is a well-established respiratory pathogen, pneumonia resulting from a co-infection with both species has not been previously reported.

CASE PRESENTATION: A 57-year-old male presented with fever, cough, and shortness of breath. Imaging revealed extensive pulmonary inflammation and consolidation, which rapidly progressed to respiratory failure. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) confirmed a mixed infection with Chlamydia abortus and Chlamydia psittaci. Following the early initiation of targeted doxycycline therapy, the patient's clinical symptoms and pulmonary imaging showed significant improvement, leading to a full recovery and hospital discharge.

CONCLUSIONS: To our knowledge, this study reports the first case of atypical pneumonia caused by a mixed Chlamydia abortus and Chlamydia psittaci infection in a male patient, thereby expanding the clinical spectrum of these zoonotic pathogens. The case exhibited a "clinical-imaging dissociation," characterized by severe radiographic changes alongside relatively mild clinical symptoms. When conventional diagnostic methods failed to identify the pathogens, mNGS provided a rapid and precise diagnosis. Guided by this result, early targeted therapy with doxycycline achieved a marked therapeutic effect, preventing progression to severe disease and an adverse outcome.

TRIAL REGISTRATION: Not applicable.},
}

@article {pmid42192666,
year = {2026},
author = {Liu, L and Wang, M and Wang, X and Liu, Y and Li, Z},
title = {Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050444},
pmid = {42192666},
issn = {2079-6382},
support = {242300420230//Natural Science Foundation of Henan Province/ ; },
abstract = {Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation.},
}

@article {pmid42192676,
year = {2026},
author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW},
title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050456},
pmid = {42192676},
issn = {2079-6382},
support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; },
abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.},
}

@article {pmid42192677,
year = {2026},
author = {Carneiro, PAM and Santos, LRD and Jardim, R and Silva, CBDGE and Araújo, FR and Dávila, AMR},
title = {Resistome and Mobilome Profiling of Raw Cow and Buffalo Milk from the Brazilian Amazon via Shotgun Metagenomics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050454},
pmid = {42192677},
issn = {2079-6382},
support = {408696/2024-9//Beef Cattle National Science and Technology Institute/CNPq/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a global health threat, with raw milk serving as a potential reservoir for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). This study characterized the resistome and mobilome of raw milk from cows (Bos taurus) and water buffalo (Bubalus bubalis) in the Brazilian Amazon, a region where unpasteurized dairy consumption is culturally ingrained. Methods: Using shotgun metagenomic sequencing, we analyzed 32 pooled milk samples from extensive and semi-intensive farms in the Manaus Metropolitan Region. Results: Sequencing yielded over 3.1 million contigs. While cow milk showed a higher prevalence of positive samples (80%), buffalo milk exhibited a significantly higher abundance and diversity of ARG-associated contigs (301 contigs vs. 85 in cows). Clinically relevant genes were identified, including AbaQ, ArnT, and KpnF, alongside complex multi-AMR cassettes co-occurring with plasmids and widespread viral sequences (dominated by Caudoviricetes). Integrons were ubiquitous in cattle and highly prevalent in buffalo samples. Conclusions: These findings indicate that raw milk in the Amazon harbors a rich reservoir of resistance determinants and MGEs, likely driven by farm-level antibiotic usage. This underscores a critical food safety risk and highlights the need for One Health-based surveillance in the region.},
}

@article {pmid42192724,
year = {2026},
author = {Skotareva, AE and Sokolova, EA and Voronina, EN},
title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050502},
pmid = {42192724},
issn = {2079-6382},
support = {125012300671-8//Russian state-funded project/ ; },
abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.},
}

@article {pmid42193165,
year = {2026},
author = {Liang, Y and Wang, H and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y},
title = {High-Fiber Diet Supplemented with N-Carbamylglutamate Modulates Uterine Microbiota, Metabolites, and Transcriptome to Improve Reproductive Efficiency in Sows.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antiox15050542},
pmid = {42193165},
issn = {2076-3921},
support = {No.2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025M780240//China Postdoctoral Science Foundation/ ; NO.2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; },
abstract = {Uterine microbiome homeostasis and antioxidant capacity are critical for sow fertility. While high-fiber diets and N-carbamylglutamate (NCG) individually enhance sow fertility, their synergistic effects on the antioxidant status, microbiota, metabolites, and transcriptome remain unclear. Here, sows were assigned to the low-fiber (3.73%) or high-fiber (7.46% crude fiber) group, each without or with 0.05% NCG, throughout the 114-day gestation. Sex hormones and antioxidants in serum were detected. Multi-omics approaches were employed to investigate the impact of a high-fiber diet supplemented with NCG (H + N) on uterine microbiota, metabolites, and gene expression profiles. The study revealed that H + N significantly increased total antioxidant capacity (T-AOC) level in serum. Metagenomic analysis revealed an increased abundance of Clostridium disporicum in the uterine microbiota. Plasma metabolomics identified hydroxylysine as a key metabolite mediating this effect, and this metabolite was positively correlated with elevated abundance of Clostridium disporicum. Subsequent transcriptomic profiling revealed activation of the PI3K-Akt signaling pathway, closely linked to improved T-AOC level. Overall, these findings demonstrated that H + N could modulate the uterine microbiota (specifically Clostridium disporicum), increase hydroxylysine production, and activate the PI3K-Akt signaling pathway. These effects further enhanced hormonal activity and antioxidant capacity, ultimately improving sow reproductive efficiency.},
}

@article {pmid42193259,
year = {2026},
author = {Zhang, MY and Ke, ZZ and Deng, PL and Qin, YY and Mo, SL and Qiu, LT and Xu, JJ and Tong, CX and Song, JL},
title = {Rhamnocitrin Ameliorates the Intestinal Fibrosis in DSS-Induced Colitis Mice by Modulating Host-Metabolites and Remodeling the Gut Microbiome.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antiox15050639},
pmid = {42193259},
issn = {2076-3921},
support = {82273630//National Natural Science Foundation of China/ ; 81960590//National Natural Science Foundation of China/ ; 81760589//National Natural Science Foundation of China/ ; 81560530//National Natural Science Foundation of China/ ; },
abstract = {Ulcerative colitis (UC) is characterized by barrier disruption, microbiota dysbiosis, fibrosis, and impaired autophagy. We investigated the effects of Rhamnocitrin (Rha) in dextran sulfate sodium (DSS)-induced chronic UC mice using histological analysis, molecular assays, and multiomics profiling. Rha alleviated weight loss and colon shortening; improved mucus secretion and tight junction protein expression; suppressed NLRP3 inflammasome activation; activated autophagy via AMPK activation and consequent Akt/mTOR inhibition; and attenuated colonic fibrosis. Multiomics analysis integrating 16S rRNA sequencing, metagenomics, and metabolomics revealed that Rha remodels the gut microbiota and is associated with elevated levels of beneficial metabolites, including butyrate in the colon, glutamate and γ-aminobutyric acid in the liver, and α-linolenic acid in the serum. Correlation analysis revealed close associations between microbiota and metabolite alterations, and improved barrier integrity, reduced inflammation, and attenuated fibrosis. These findings suggest that Rha ameliorates chronic UC by modulating autophagy, microbiota composition, and host metabolism across the gut-liver axis.},
}

@article {pmid42193752,
year = {2026},
author = {Guo, T and Wan, B and Ye, Y and Zhang, Y and Mao, M and Li, R and Fang, Y and Lu, Y and Shao, R and Wu, Y and Wang, Y and Wu, J and Yang, H},
title = {A Prevotella-Rich Gut Microbiota and Microbial CAZymes Are Associated with Half-Diving Length in Ducks.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/ani16101460},
pmid = {42193752},
issn = {2076-2615},
support = {2024YFF1000900//National Key Research and Development Program of China/ ; 32302739//National Natural Science Foundation of China/ ; 32360830//National Natural Science Foundation of China/ ; 20243BCE51147//Ganpo Juncai Support Program/ ; QN2023015//Ganpo Juncai Support Program/ ; 20232ACB215003//Natural Science Foundation of Jiangxi Province/ ; },
abstract = {The gut microbiota is closely associated with host growth by nutritional metabolism and immune homeostasis. Half-diving length, a key indicator of duck development and production efficiency, correlates with economic traits like body weight and slaughter yield, yet its link to gut microbiota remains unclear. This study combined metagenomic and metabolomic analyses to explore the association between gut microbiota and duck half-diving length. We found distinct microbial communities between ducks with high (H) and low (L) half-diving lengths: the H group had more carbohydrate-active enzymes (CAZymes) genes (p < 0.05), especially glycoside hydrolases (GHs), and was enriched in MAG3173 (Prevotella sp000431975), which features complete carbohydrate and amino acid metabolic pathways and key CAZymes. Metabolomics revealed slightly higher short-chain fatty acids (SCFAs) levels in the H group, but glycerophospholipids, particularly phosphatidylinositol (PI), were significantly upregulated (p < 0.05). The Prevotella-rich microbial structure in the H group is potentially linked to enhanced polysaccharide degradation capacity and altered SCFAs abundance. This metabolic shift may be associated with host energy supply and lipid metabolic profiles, thereby influencing duck growth. Collectively, this study found significant correlations between duck half-diving length and gut microbial composition, functional capacity, and intestinal metabolic signatures. The study proposes the hypothesis of a potential Prevotella-CAZymes-glycerophospholipid metabolism axis, which might offer a theoretical reference and candidate microbial targets for understanding the microbe-phenotype association in waterfowl.},
}

@article {pmid42193766,
year = {2026},
author = {Qiu, G and Bai, H and Shi, J and Xue, Y and Wang, T and Qin, S and Zhou, X and He, K},
title = {Metagenomic and Metabolomic Analysis of Intestinal Excrement Differences Between Natural Hatching and Artificial Peeling out of the Shell in Nipponia nippon.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/ani16101472},
pmid = {42193766},
issn = {2076-2615},
support = {ZJXRDQ-2025-JC28//the Project for Enhancing the Reproductive Capacity of the Red-crowned Crane/ ; },
abstract = {The Nipponia nippon is a critically endangered species, and its breeding efforts are of vital importance for its conservation. Although artificial shell removal is sometimes employed in current breeding programs to increase survival rates, it may also have unknown impacts on chicks' development. To investigate the influence of artificial shell removal on the gut microbiota composition in Nipponia nippon, metagenomic sequencing and untargeted LC-MS/MS analyses were performed. Samples from the early, mid, and late stages of natural hatching (ZE, ZM, ZL) and artificial shell removal (RE, RM, RL) were compared. Results indicated that the natural hatching groups formed a unique, highly diverse, and stable community by the late stage (ZL). Conversely, artificial peeling caused the microbial community succession to stagnate at an intermediate state. The RL group experienced a sharp decline in alpha diversity and a significant enrichment of opportunistic pathogens, such as Edwardsiella, Clostridium, and Fusobacterium. Functionally, the microbial community in the RL group remained in a stage of expanding basic functions rather than reaching an advanced equilibrium state. Metabolomic analysis confirmed this developmental arrest, revealing abnormal accumulations of organic acids, such as citric acid, and indole derivatives in the RL group. This indicates metabolic dysregulation, stress, and altered microbial-host chemical signaling. Furthermore, the significant biomarker Edwardsiella was strongly correlated with multiple differential metabolites in the RL group. Ultimately, these results indicate that artificial peeling intervention disrupts environmental adaptation and induces metabolic alterations in the intestinal development of the Nipponia nippon chicks.},
}

@article {pmid42193830,
year = {2026},
author = {Zhou, K and Shi, H and Kong, X and Ma, W and Kang, J and Che, H and Hua, Y},
title = {Wuwei Jianpi San Improves Growth Performance and Immune Status in Yaks Through Modulation of Rumen Microbiota and Host Metabolism.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/ani16101539},
pmid = {42193830},
issn = {2076-2615},
support = {CARS-37, CARS-07G-13//China Agriculture Research System of MOF and MARA/ ; No. Gaufx-03J01//Fuxi Foundation of Gansu Agricultural University/ ; 24YFNA016//Gansu Provincial Key Research and Development Program - Agriculture Field/ ; KJZC-2025-14//Modern Cold and Drought Characteristic Agricultural Science and Technology Sup-port Project of Gansu Province/ ; },
abstract = {To investigate the effects of Wuwei Jianpi San (WJPS), a Chinese herbal compound feed additive, on rumen microecology, host metabolism, and immune function in healthy yaks (Bos grunniens), and to determine the optimal supplementation level, 32 yaks with similar initial body weight were randomly assigned to four groups: a control group and three groups receiving 0.5%, 1.0%, or 2.0% WJPS for 90 days. Growth performance, hematological indices, serum antioxidant and immune parameters, tryptophan metabolites, ruminal short-chain fatty acids (SCFAs), and rumen microbiota were analyzed. WJPS supplementation improved growth performance, as shown by a reduced feed-to-gain ratio in all treated groups and tended to increase average daily gain in the 2.0% group. It also enhanced hematological, antioxidant, and immune status, evidenced by increased white blood cell (WBC) and lymphocyte (Lym) counts and elevated interleukin-2 (IL-2), immunoglobulin G (IgG), and superoxide dismutase (SOD) levels. Moreover, 2.0% WJPS increased total SCFAs, acetate, and n-butyrate, while WJPS reduced kynurenine pathway metabolites, including kynurenine, 3-hydroxykynurenine, and quinolinic acid. Metagenomic analysis showed that WJPS tended to shape rumen microbial composition by increasing Bacillota and decreasing Bacteroidota, and these microbial changes were associated with host immune indices and tryptophan metabolism. Overall, 2.0% WJPS showed the best comprehensive effect.},
}

@article {pmid42195821,
year = {2026},
author = {Wang, X and Liu, X and Han, G and Erdene, K and Bai, C and Cao, Q and Zheng, Y and Hai, L and Ao, C},
title = {Allium mongolicum Regel-Mediated Rumen Microbiota Intervention Modulates Hepatic Metabolome to Reduce 4-Alkyl Branched-Chain Fatty Acids in Lamb Longissimus Thoracis Muscle.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101617},
pmid = {42195821},
issn = {2304-8158},
support = {32260839//National Natural Science Foundation of China/ ; },
abstract = {Deposition of three key 4-alkyl branched-chain fatty acids (KBCFA), including 4-methyloctanoic acid (MOA), 4-ethyloctanoic acid (EOA), and 4-methylnonanoic acid (MNA), causes the gamey flavor in sheep meat. This study integrated metagenomics and metabolomics to evaluate how Allium mongolicum Regel (AMR) supplementation (15 g/d) and rumen fluid transplantation (RFT) modulate rumen microbiota and hepatic metabolism to reduce KBCFA in lamb longissimus thoracis muscle. The experiment consisted of two phases. In Phase I, twelve 3-month-old male Dorper × Small Tailed Han sheep (25 ± 1 kg) were selected as the rumen donor group. These sheep were supplemented with 15 g/d/head of AMR powder in their basal diet until the end of the experiment. In Phase II, thirty 3-month-old male Dorper × Small Tailed Han sheep (23 ± 2 kg) were randomly assigned to one of three groups (n = 10 per group): the control group (STG), which was fed the basal diet and received a physiological saline transplant; the AMR group, which was fed the basal diet supplemented with 15 g/d/head of AMR powder and received a physiological saline transplant; and the rumen fluid transplant group (RTG), which was fed the basal diet and received a rumen fluid transplant from the donor group. Compared to the STG, results showed that the MOA, EOA, and MNA in the AMG decreased by 64.51%, 54.72%, and 49.34%, respectively. Similarly, the MOA, EOA, and MNA in the RTG were reduced by 63.13%, 56.17%, and 49.60%, respectively (p < 0.001). For the rumen metagenome, AMR enriched the genus Prevotella, while RFT increased Butyrivibrio. Hepatic metabolomics revealed a distinct shift where AMR elevated amino acid derivatives and RFT enhanced carnitine-related metabolites. These alterations indicate a potential metabolic shift associated with amino acid metabolism and mitochondrial β-oxidation, rather than lipid elongation. We postulate that this coordinated regulation across the rumen-liver-muscle axis may alter the availability of lipogenic precursors for KBCFA synthesis, ultimately contributing to improved meat flavor.},
}

@article {pmid42195847,
year = {2026},
author = {Song, D and Yang, L and Zhang, C},
title = {Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101643},
pmid = {42195847},
issn = {2304-8158},
support = {32460269//National Natural Science Foundation of China/ ; MTXYTD202501//The Science and Technology Innovation Team of Moutai Institute/ ; Qiankehe Platform Talent-ZDSYS [2023] 007//Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation industry/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Industry Group Co., Ltd./ ; },
abstract = {Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems.},
}

@article {pmid42195939,
year = {2026},
author = {Chen, P and Du, G and Chen, J and Fang, F},
title = {Construction of Synthetic Microbial Community with Core Microorganisms for Soy Sauce Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101736},
pmid = {42195939},
issn = {2304-8158},
support = {32172182//National Natural Science Foundation of China/ ; },
abstract = {Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce.},
}

@article {pmid42196007,
year = {2026},
author = {Duo, Q and Zhao, Y and Osman, H and Shao, W and Zhao, Y},
title = {Correlation Between Microbial Communities and Volatile Organic Compounds in Camel Milk at Different Lactation Stages in Xinjiang, China.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101804},
pmid = {42196007},
issn = {2304-8158},
support = {2023B02034-1//Xinjiang Academy of Agricultural Sciences/ ; XJARS-11-09//Xinjiang Academy of Agricultural Sciences/ ; xjnkywdzc-2026002-10//Xinjiang Academy of Agricultural Sciences/ ; },
abstract = {The aroma of camel milk is a key sensory indicator for evaluating its quality and flavor. Camel milk collected at different lactation stages exhibits unique flavor characteristics. However, no systematic study has yet explored the aroma characteristics and variation patterns of camel milk across these stages. This study employs HS-SPME-GC-MS, multivariate statistical analysis, and metagenomics to systematically reveal differences in aroma formation in camel milk across lactation periods and their interactions with microbial communities. A total of 577 metabolites is detected. Through OPLS-DA screening, 24 key differential flavor compounds are identified. ROAV analysis indicates that 2,4-undecadienal and (E)-2-undecenal are the main contributors to the fatty, creamy, fresh green, and citrus aromas of camel milk. Some compounds are more abundant in colostrum, while others are richer in mature milk. For microbiota, colostrum is dominated by Proteobacteria, Psychrobacter, and Janthinobacterium, whereas mature milk is dominated by Acinetobacter and Moraxella. Mature milk shows significantly higher alpha diversity and species richness. Spearman correlation analysis shows that core bacterial groups such as Enterococcus and Lactococcus are significantly positively correlated with characteristic flavor compounds, including aldehydes and lactones. This finding suggests that HS-SPME-GC-MS, combined with multivariate analysis, effectively distinguishes patterns associated with microbes and flavor metabolites in camel milk at different lactation stages, which provides a theoretical basis for quality control and further processing of camel milk.},
}

@article {pmid42196140,
year = {2026},
author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL},
title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104155},
pmid = {42196140},
issn = {1422-0067},
support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; },
mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth & development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; },
abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.},
}

Animals
*Biofouling
*Microbiota
Larva/microbiology
Biofilms/growth & development
Quorum Sensing
Ecosystem
*Aquatic Organisms/microbiology

@article {pmid42196196,
year = {2026},
author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L},
title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104213},
pmid = {42196196},
issn = {1422-0067},
support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; },
abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/metabolism
*Metagenomics/methods
*Metabolomics/methods
Male
*Gastrointestinal Microbiome/genetics
Female
Aged
Middle Aged
Feces/microbiology
Multiomics
Metabolome
Biomarkers
RNA, Ribosomal, 16S/genetics
China
Case-Control Studies

@article {pmid42196214,
year = {2026},
author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT},
title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104232},
pmid = {42196214},
issn = {1422-0067},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; },
abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/genetics
*Protein Interaction Maps
*Deep Learning
Phenotype
*Gastrointestinal Microbiome
*Protein Interaction Mapping/methods
*Host Microbial Interactions

@article {pmid42196222,
year = {2026},
author = {Zhang, X and Cai, L and Bai, Y and Peng, F},
title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104238},
pmid = {42196222},
issn = {1422-0067},
support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; },
abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.},
}

*Metagenomics/methods
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
Nutrients

@article {pmid42196433,
year = {2026},
author = {Zeng, Y and Lau, EYT and Ye, S and Lu, J and Zhang, R and Hu, R and Liang, JQ},
title = {Fecal Cloacibacillus porcorum Improves Non-Invasive Diagnosis of Colorectal Adenoma in the Hong Kong Population.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104457},
pmid = {42196433},
issn = {1422-0067},
support = {MRP/058/20//ITF-MRP, Hong Kong/ ; N/A//Hong Kong Ph.D. Fellowship Scheme (HKPFS)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; *Feces/microbiology ; Female ; Hong Kong/epidemiology ; Male ; Middle Aged ; Aged ; Biomarkers, Tumor/genetics ; Metagenomics ; ROC Curve ; },
abstract = {We previously developed a four-marker panel for the diagnosis of colorectal cancer (CRC) and adenoma. This study aimed to identify novel bacterial markers to improve adenoma detection using metagenomics and qPCR. Candidate markers were identified from metagenomic data (n = 492) using ANCOM-BC2 and Spearman's rank correlation analysis and were subsequently validated in an independent cohort (n = 426). Diagnostic performance was assessed both individually and in combination with our previously identified markers and FIT. Metagenomic analysis identified 21 candidate markers that increased along the normal-adenoma-carcinoma axis. Two top candidates, Cloacibacillus porcorum (Cp) and Intestinimonas butyriciproducens, were validated via qPCR and showed significant correlations with metagenomic abundances (both p < 0.0001). ROC analysis demonstrated that Cp levels significantly distinguished CRC and adenoma from controls, whereas I. butyriciproducens distinguished only CRC. The prevalence of Cp was significantly higher in adenoma and CRC than in controls (all p < 0.05). Multivariate analysis confirmed that Cp was independently associated with CRC and adenoma diagnoses. Adding Cp to the four-marker panel improved diagnostic sensitivity from 44.8% to 58.7% for adenoma and from 85.7% to 88.6% for CRC (specificity = 85%). When further combined with FIT, Cp improved sensitivity from 47.6% to 64.3% for adenoma and from 95.2% to 96.2% for CRC (specificity = 84.6%). C. porcorum is a novel bacterial marker that may aid in the non-invasive diagnosis of colorectal adenoma.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
*Adenoma/diagnosis/microbiology
*Feces/microbiology
Female
Hong Kong/epidemiology
Male
Middle Aged
Aged
Biomarkers, Tumor/genetics
Metagenomics
ROC Curve

@article {pmid42196657,
year = {2026},
author = {Zafar, I and Shafiq, S and Khan, MS},
title = {Wastewater Treatment Challenges and Circular Reuse for One Health Sustainability: A Review.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {5},
pages = {},
doi = {10.3390/ijerph23050563},
pmid = {42196657},
issn = {1660-4601},
mesh = {*Wastewater/analysis ; *One Health ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Humans ; *Recycling ; Environmental Monitoring ; },
abstract = {Wastewater is a complex and dynamic issue, particularly at the human-animal-environment interface, bearing biological and chemical hazards that may serve as a resource for transmission pathways for pathogens, antimicrobial resistance (AMR) determinants, heavy metals, pharmaceutical residues, per- and polyfluoroalkyl substances (PFAS), and microplastics. Rising global health issues necessitate effective wastewater treatment and advanced research to support risk-informed circular management within a one health framework, incorporating wastewater-based epidemiology (WBE), multi-omics approaches, nanobiotechnology, and green technologies. Inadequate wastewater treatment and uncontrolled discharge result in the generation of more than 380 billion cubic meters of wastewater annually worldwide, contributing to ecological degradation, the spread of AMR, and long-term toxicological risks. Despite significant advances in wastewater treatment, several challenges remain, including complex contaminant mixtures, limited detection and monitoring technologies, variable treatment efficiency, and weak regulatory and governance frameworks. This review highlights key wastewater treatment issues and presents recent advances in WBE and multi-omics approaches, such as metagenomics, resistome profiling, virome analysis, and chemical fingerprinting for contaminant monitoring and public health risk assessment. This review also examines circular reuse strategies focused on water reclamation, nutrient recovery, bioenergy production, and resource recovery, with particular emphasis on nature-based systems, hybrid biological-physicochemical treatment platforms, and green nanobiotechnology as promising approaches to improve treatment performance while minimizing environmental impacts. In conclusion, this review highlights the importance of integrated and sustainable wastewater management approaches within the One Health framework to address emerging challenges and promote environmental resilience, public health protection, and circular resource recovery.},
}

*Wastewater/analysis
*One Health
*Waste Disposal, Fluid/methods
*Water Purification/methods
Humans
*Recycling
Environmental Monitoring

@article {pmid42197004,
year = {2026},
author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH},
title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.},
journal = {Nutrients},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/nu18101544},
pmid = {42197004},
issn = {2072-6643},
support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.

METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.

RESULTS: The results showed that the a-FMT group recovered α diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.

CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.},
}

Animals
*Dysbiosis/therapy/chemically induced/microbiology
*Fecal Microbiota Transplantation/methods
*Mannans/pharmacology
*Anti-Bacterial Agents/adverse effects
Mice
*Gastrointestinal Microbiome/drug effects
Male
*Physical Conditioning, Animal
Mice, Inbred C57BL

@article {pmid42197026,
year = {2026},
author = {Alsinani, Y and Rostamkhani, F and Shirvani, H},
title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.},
journal = {Nutrients},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/nu18101565},
pmid = {42197026},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Exercise/physiology
Fatty Acids, Volatile/metabolism

@article {pmid42197087,
year = {2026},
author = {Yang, H and Li, J and Ren, S and Chai, X and Lu, J and Yan, H and Lu, Y},
title = {Gut Microbiota Changes Following Aerobic Exercise in Malnourished Octogenarians: An Assessor-Blinded Intervention Study Stratified by Nutritional Status.},
journal = {Nutrients},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/nu18101627},
pmid = {42197087},
issn = {2072-6643},
support = {2020YFC2002902//Beijing Sport University/ ; },
mesh = {Humans ; Aged, 80 and over ; *Nutritional Status ; Female ; Male ; *Malnutrition/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Nursing Home Residents ; Feces/microbiology ; Nutrition Assessment ; Nursing Homes ; },
abstract = {BACKGROUND/OBJECTIVES: Global population aging is associated with a rising prevalence of malnutrition among adults aged ≥80 years. Gut dysbiosis is linked to immune decline and impaired nutrient absorption, and aerobic exercise may enhance microbial diversity. This study investigated gut microbiota changes after a 12-week aerobic exercise intervention in octogenarians stratified by nutritional status.

METHODS: A total of 129 nursing home residents (≥80 years) were classified via the Mini Nutritional Assessment Short-Form (MNA-SF) into a healthy group (HG, MNA-SF ≥ 11) and a malnourished group (MG, MNA-SF < 11). Both groups underwent a 12-week brisk walking intervention (three sessions/week, 1 h/session, 40-60% heart rate reserve). Fecal samples were collected at baseline and post-intervention and were analyzed via shotgun metagenomic sequencing.

RESULTS: A total of 36 participants completed the intervention (HG = 17, MG = 19). Within-group baseline-to-post-intervention analysis showed no significant changes in alpha or beta diversity in the MG. However, post-intervention between-group comparison revealed higher microbial richness and diversity in the MG vs. the HG, with enrichment of taxa including Faecalibacterium prausnitzii and Streptococcus salivarius. Functional analysis revealed significant enhancements in metabolic pathways related to amino acid biosynthesis, protein synthesis, and quorum sensing in the MG. In contrast, the HG showed limited shifts in microbial diversity but an increase in species involved in carbohydrate metabolism.

CONCLUSIONS: After 12 weeks, the malnourished group showed higher post-intervention microbial richness and diversity than the healthy group, with differences in taxonomic and predicted functional profiles. Without a non-intervention control group, the microbiota differences observed during the 12-week aerobic exercise period can only be considered observational associations, not causal. Additionally, the high dropout rate (72.1%) limits the generalizability of the findings.

CLINICAL TRIAL REGISTRATION: The Chinese Clinical Trial Registry on 19 October 2022 (ChiCTR2200064801).},
}

Humans
Aged, 80 and over
*Nutritional Status
Female
Male
*Malnutrition/microbiology/therapy
*Gastrointestinal Microbiome/physiology
*Exercise/physiology
Nursing Home Residents
Feces/microbiology
Nutrition Assessment
Nursing Homes

@article {pmid42197123,
year = {2026},
author = {Rojas-Flores, SJ and Liza, R and Nazario-Naveda, R and Díaz, F and Delfin-Narciso, D and Cardenas, MG and Cabanillas-Chirinos, L},
title = {Mapping the Convergence of Frontier Technologies for Major Environmental Challenges: A Chemical and Molecular Perspective on the Use of AI for Climate Action and Antimicrobial Resistance.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {10},
pages = {},
doi = {10.3390/molecules31101571},
pmid = {42197123},
issn = {1420-3049},
mesh = {*Artificial Intelligence ; *Climate Change ; Metagenomics ; Humans ; *Drug Resistance, Microbial ; },
abstract = {The planet faces the critical interconnected challenges of climate change and antimicrobial resistance (AMR); these two crises mutually reinforce each other, threatening global health and ecosystem stability. This study conducts a systematic documentary analysis to map the convergence and identify the structural gaps between two key technological domains: artificial intelligence (AI) for climate action and molecular methods for AMR. The methodology was based on a corpus of 179 scientific documents indexed in Scopus (2010-2025), analyzed with data science tools to identify trends, collaborations, and impact. Quantitative results revealed clear leadership by the United States, accounting for 37.4% of publications, followed by China (26.8%); this leadership reflects the concentration of high-throughput molecular surveillance infrastructure and data science clusters essential for monitoring the environmental resistome. In terms of scientific impact, Spain showed the highest average, with 32.8 citations per article. The most influential work, a review on food security and sustainability, accumulated 275 citations. Network analysis identified authors such as Zhu, Yongguan, with 240 citations in total, as central nodes in international collaborations. Thematically, metagenomics and machine learning emerged as mature and interconnected research cores. This analysis confirms a solid yet still fragmented relationship between the two fields. The analysis reveals that, while metagenomic tools dominate the current literature, a gap persists in correlating genotypic resistance potential with functional phenotypic expression under changing climatic stressors. The results confirm a solid yet still fragmented foundation, highlighting the need for hybrid platforms that transition from descriptive bibliometrics to functional integration for designing systemic solutions. Future work should prioritize the development of hybrid platforms, such as intelligent biosensors, and collaborative governance frameworks that accelerate effective responses to these dual crises.},
}

*Artificial Intelligence
*Climate Change
Metagenomics
Humans
*Drug Resistance, Microbial

@article {pmid42197331,
year = {2026},
author = {Manoharan, RK and Shin, HD and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and La, IJ and Lee, DH and Han, KI and Srinivasan, S},
title = {Shotgun Metagenomic Analysis of Gut Microbiota and Antibiotic Resistance Genes in a High-Fat Diet Mouse Model Treated with Heat-Killed Lactiplantibacillus plantarum beLP1.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050944},
pmid = {42197331},
issn = {2076-2607},
abstract = {The gut microbiota is a central regulator of metabolic function, and its disruption by a high-fat diet (HFD) is strongly linked to obesity and metabolic impairment. This study evaluated the potential of heat-killed Lactiplantibacillus plantarum beLP1 (beLP1[®]) in alleviating HFD-induced metabolic and microbial imbalances in mice. Male C57BL/6N mice were fed an HFD for 10 weeks, with or without daily oral supplementation of beLP1 (≥3 × 10[10] cells). Compared with untreated HFD mice, beLP1 supplementation reduced serum triglycerides by 35% and lowered liver enzymes AST and ALT by 17% and 36%, respectively. Blood glucose levels remained similar to the HFD group throughout the study period. Shotgun metagenomic analysis revealed that beLP1 restored gut microbial diversity, increased beneficial taxa such as Akkermansia and Faecalibaculum high. and reduced pro-inflammatory species including Streptococcus sp., Mucispirillum schaedleri and Clostridium cocleatum. These microbial changes were associated with partial normalization of the Firmicutes/Bacteroidota ratio and improvements in antibiotic resistance gene (ARG) profiles. Specifically, in silico analysis of the short-chain fatty acid (SCFA) synthesis pathways indicated that the potential for acetate and propionate production was maximized in the beLP1 group, resulting in the highest relative abundance among all groups. This functional enhancement directly correlated with the enrichment of key SCFA-producing taxa, particularly Akkermansia muciniphila, confirming that increased bacterial abundance suggests an enhanced functional potential for SCFA production. Furthermore, beLP1[®] induced a selective modulation of gut ARGs, significantly reducing specific subtypes such as tetracycline and multidrug efflux genes, despite a slight increase in vancomycin resistance markers. Overall, our findings suggest that beLP1[®] attenuated the rate of body weight gain during the initial weeks of HFD exposure and significantly improved markers of hepatic stress and lipid metabolism.},
}

@article {pmid42197333,
year = {2026},
author = {Zhao, Z and Wang, X and Wen, F and Zhao, F and Zhang, M and Menghe, B},
title = {Integrated Metagenomic and Metabolomic Profiling Identifies Predictive Biomarkers for Overweight Status in a Mongolian Population.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050946},
pmid = {42197333},
issn = {2076-2607},
support = {2018YFE0123500//Special Funds for International Science and Technology Cooperation of China/ ; },
abstract = {Mongolians have high overweight prevalence linked to their nomadic lifestyle and diet, but gut microbiota studies in this population are scarce. This study used fecal metagenomic and serum metabolomic analyses of 96 Mongolian participants (normal-weight n = 55, overweight n = 41) to characterize gut microbiome alterations and identify weight-related biomarkers. The analyses revealed that Parabacteroides distasonis, Barnesiella intestinihominis, and Alistipes onderdonkii were significantly reduced in overweight individuals (p < 0.05). Concurrently, the metabolites such as beta-cryptoxanthin, p-cresol, and ribothymidine were significantly down-regulated in the overweight group (p < 0.05). Random forest models from the three datasets showed a strong diagnostic ability for microbial families (AUC > 0.70). A subsequent integrated multi-kingdom classifier that combined microbiota and metabolite data achieved the highest performance (AUC = 0.818). Key features with high predictive contributions were identified, including Lactobacillus crispatus, Alistipes onderdonkii, and Parabacteroides distasonis, and metabolites, such as beta-cryptoxanthin, p-cresol, and picolinic acid. These results show the random forest model has high predictive value for distinguishing normal weight and overweight individuals. In summary, this study identified specific gut microbiota and serum metabolomic profiles linked to overweight in Mongolians. Multi-omics integration established a diagnostic biomarker model, laying a theoretical basis for microbiome-targeted weight management interventions.},
}

@article {pmid42197335,
year = {2026},
author = {Naranjo-Moran, J and Ratti, MF and Vera-Morales, M},
title = {Microorganisms from Antarctica: A Review of Their Potential in the Bioremediation of Hydrocarbon-Contaminated Soils.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050948},
pmid = {42197335},
issn = {2076-2607},
abstract = {Antarctica's extreme cryospheric conditions impose severe thermodynamic constraints on the natural attenuation of hydrocarbon pollutants. Despite the Antarctic Treaty System's protections, the footprint of human logistics has left persistent reservoirs of petroleum hydrocarbons that threaten endemic biodiversity. This review critically synthesizes the state-of-the-art in Antarctic bioremediation, moving beyond traditional culture-dependent studies to integrate recent multi-omics breakthroughs (2020-2025). We analyze the molecular mechanisms limiting bioavailability in frozen soils and highlight the adaptive strategies of psychrophilic consortia, including the modification of membrane fluidity and the expression of cold-active enzymes (e.g., RHDs, AlkB). Notably, we discuss emerging findings on novel long-chain alkane degradation genes (almA, ladA) identified in 2025, which challenge previous assumptions about recalcitrance. Furthermore, the review evaluates the engineering bottlenecks of in situ versus ex situ strategies, emphasizing the synergistic potential of bacterial-fungal co-cultures and the ecological necessity of "climate-smart" remediation to mitigate methane emissions from thawing permafrost. By bridging the gap between fundamental microbial genetics and applied field engineering, we propose a roadmap for the next generation of biotechnological solutions in the warming polar environment.},
}

@article {pmid42197351,
year = {2026},
author = {Huang, W and Liang, J and Chan, P and Liu, Z and Guo, L},
title = {Probiotics Exert Colonization Resistance Against F. nucleatum subsp. polymorphum: Disruption by Antibiotics and Underlying Molecular Mechanisms.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050965},
pmid = {42197351},
issn = {2076-2607},
support = {81670982//National Natural Science Foundation of China/ ; },
abstract = {Fusobacterium nucleatum (F. nucleatum), a key oral pathogen, promotes colorectal cancer (CRC) progression via gut translocation. Although gut probiotics provide colonization resistance against pathogens, antibiotic-induced dysbiosis may facilitate F. nucleatum integration and increase the risk of CRC. The mechanisms underlying probiotic-F. nucleatum antagonism and antibiotic modulation remain unclear. A 33-strain probiotic consortium and F. nucleatum subsp. Polymorphum (F. polymorphum) ATCC 10953 were co-cultured. The inhibitory effects of probiotics on F. nucleatum and the impacts of antibiotics (ABXs) on the microbial community structure in the co-culture system and on the probiotic-mediated inhibition of F. nucleatum were evaluated using spent medium assays, plate confrontation tests, growth curves, qRT-PCR, metagenomic sequencing, and transcriptomics. Hydrogen peroxide/pH/lysine assays and coaggregation models were performed to probe the associated mechanisms. Probiotics strongly inhibited the growth of F. nucleatum in a dose-dependent manner, primarily via organic acids, while F. nucleatum enriched amino acid/vitamin biosynthesis pathways without major growth suppression. Antibiotics weakened probiotic antagonism, shifted species abundance (↓ L. plantarum, ↑ L. paracasei), induced adaptive stress responses in F. nucleatum (↑ nucleotide metabolism, propanediol degradation, pdxS), and reduced lysine biosynthesis. Lysine supplementation restored probiotic abundance and disrupted F. nucleatum coaggregation. Multi-strain probiotics exert potent colonization resistance effects against F. nucleatum, mainly through organic acids and metabolic interference. Antibiotic-induced dysbiosis impairs this protective effect and may promote the persistence of F. nucleatum, which has been implicated in CRC risk. Targeted probiotic strategies may offer novel preventive approaches.},
}

@article {pmid42197355,
year = {2026},
author = {Feletti, R and Mori, A and Zaffagnini, A and Castilletti, C and Pomari, E},
title = {The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050969},
pmid = {42197355},
issn = {2076-2607},
support = {PE00000007, INF-ACT//EU funding within the MUR PNRR/ ; 5MIL-VISA L1P17//Italian Ministry of Health/ ; },
abstract = {The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including the fraction of unclassified viral "dark matter"; (ii) describe virome alterations in chronic infections; and (iii) explore site-specific virome dynamics across respiratory, intestinal, and genito-urinary tracts in both chronic and acute infections. In chronic viral infections such as HIV, HBV, HCV, and HPV, a recurrent feature is the expansion of Anelloviridae-particularly torque teno virus-reflecting impaired immune surveillance rather than direct pathogenicity, suggesting their potential as surrogate biomarkers of immune competence. Evidence on virome changes in chronic bacterial and parasitic infections remains limited, highlighting a critical knowledge gap. Acute infections are associated with compartment-specific shifts in eukaryotic viruses and bacteriophage communities, often paralleling changes in bacterial populations and inflammatory responses, with implications for disease severity. Despite advances in metagenomic approaches, a substantial proportion of viral sequences remains unclassified, limiting functional interpretation. Nevertheless, virome profiling provides an ecosystem-level perspective, offering insights beyond single-pathogen detection and supporting emerging applications in diagnostics, immune monitoring, prognosis, and infectious disease surveillance.},
}

@article {pmid42197366,
year = {2026},
author = {Huang, Z and Chen, S and Fan, A and Chen, Y and Cai, Q and Zeng, T and Zheng, W and Yang, Y},
title = {Iron-Containing Flocs Derived from Environmental Emergency Response Influenced Nitrogen Cycling Driven by Microorganisms in River Sediments.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050980},
pmid = {42197366},
issn = {2076-2607},
support = {PM-zx703-202204-155//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PM-zx097-202506-204//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; },
abstract = {In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl3), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl3 caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level.},
}

@article {pmid42197381,
year = {2026},
author = {Li, X and Liang, X and Hao, P and Wu, J and Liu, D},
title = {Compound Yeast Culture Reshapes Gut Microbiota and Functional Pathways to Enhance Antioxidant Capacity and Immune Homeostasis in Suckling Calves.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050995},
pmid = {42197381},
issn = {2076-2607},
support = {2022YFDZ0051//Inner Mongolia Autonomous Region Science and Technology Project/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Autonomous Region/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; },
abstract = {Diarrhea in suckling calves is associated with impaired growth, oxidative stress, immune dysfunction, and intestinal microbial dysbiosis. This study evaluated the effects of compound yeast culture (CYC) supplementation on growth performance, fecal characteristics, antioxidant capacity, immune function, and gut microbiota in diarrheic Holstein calves. Thirty-six approximately 7-day-old calves were enrolled, including 12 healthy calves (CON) and 24 diarrheic calves randomly assigned to a diarrhea group (DIA) or a CYC-supplemented group (DIA-YC; 50 g/d for 30 days). The experimental period lasted 60 days. Compared with the DIA group, calves in the DIA-YC group showed significantly higher average daily feed intake and average daily gain (ADG) during days 31-60 and across the entire period (p < 0.05), with a trend towards increased body weight. Fecal scores were significantly elevated in diarrheic calves during the early and mid-stages but were markedly reduced by CYC supplementation from days 7 to 30; no significant difference was observed between DIA-YC and CON during days 16-30 (p > 0.05). Diarrheic calves exhibited oxidative stress, characterized by decreased total antioxidant capacity (T-AOC) and increased malondialdehyde (MDA). CYC supplementation significantly increased T-AOC, superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) activities, while reducing MDA levels (p < 0.05). Immune analysis showed higher serum IgG and IL-10 levels and lower TNF-α levels in the DIA-YC group, along with improved intestinal barrier indicators, including diamine oxidase (DAO) activity and endotoxin levels. Metagenomic analysis revealed that diarrhea reduced microbial richness and diversity and altered community structure, whereas CYC partially restored microbial diversity and increased beneficial genera such as Prevotella, Coprococcus, Ruminococcus, and Parabacteroides. Functional analysis indicated that CYC enhanced pathways related to immune regulation, energy metabolism, and antioxidant function. CYC supplementation alleviates oxidative stress and immune dysfunction by modulating gut microbiota, thereby improving growth performance and reducing diarrheal severity in calves.},
}

@article {pmid42197408,
year = {2026},
author = {Qie, T and Lin, D and Fan, Q and Sun, G and Wang, H and Liu, Z and Liu, X},
title = {Responses of Soil Nitrogen-Cycling Microbial Communities and Functional Potential to Grazing Intensities in Alpine Meadows.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051022},
pmid = {42197408},
issn = {2076-2607},
support = {KLGE202209//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 32260354//National Natural Science Foundation of China/ ; KLGE-2024-01//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 2023-QN-46//Lanzhou Science and Technology Bureau/ ; 2500011004//Gansu Agricultural University/ ; },
abstract = {Although grazing is a key driver of nitrogen cycling in alpine meadow soils, a systematic understanding of how different grazing intensities shape the structure and functional potential of soil nitrogen-cycling microbial communities remains lacking. In this study, soil samples were collected under five grazing intensities (no grazing, light grazing, moderate grazing, heavy grazing, and extreme grazing) and metagenomic sequencing was employed to analyze variations in nitrogen-cycling microbial communities and functional genes. The results showed that bacteria were the dominant group in nitrogen-cycling communities (relative abundance: 93.99-98.98%), with significant community differentiation across grazing intensities. Light grazing maintained relatively high microbial diversity, whereas moderate and heavy grazing led to more pronounced differences in community composition. Functional gene analysis identified 41 nitrogen-cycling-related genes, primarily involved in denitrification, nitrate reduction, and ammonia assimilation. Light grazing enhanced nitrate reduction and glutamate synthesis; moderate grazing exhibited the strongest ammonia assimilation potential; heavy grazing significantly increased denitrification activity, indicating an elevated risk of nitrogen loss; and under extreme grazing, both the number and abundance of nitrogen-cycling functional genes declined markedly, with functional composition becoming simplified. Collectively, light grazing is more conducive to maintaining the balance between soil microbial diversity and nitrogen-cycling function in alpine meadows, whereas overgrazing disrupts the equilibrium between microbial communities and nitrogen metabolism. This study provides a microbiological basis for the restoration of degraded alpine meadows and sustainable grazing management.},
}

@article {pmid42197422,
year = {2026},
author = {Shaik, SM and Schiro, G and Laubitz, D and Madan, JC and Kelley, CP and Daines, M and Rice, SA and Ghishan, FK and Kiela, PR},
title = {Functional Shifts in Gut Microbiota and Associated Metabolites Suggest Gut-Brain Axis Dysregulation in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS).},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051036},
pmid = {42197422},
issn = {2076-2607},
support = {NA//Alex Manful Fund/ ; RFGA2022-010-23//Arizona Department of Health Services/ ; },
abstract = {Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host-microbiome interactions in modulating neuro-immune functions via gut-brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut-brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe-metabolite networks allied to gut-brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut-brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders.},
}

@article {pmid42197470,
year = {2026},
author = {Zheng, Y and Wu, R and Feng, H and Wu, X and Yang, Y},
title = {Temperature Elevation Alters the Gut Antibiotic Resistome and Carbohydrate-Active Enzymes in the Desert Lizard Eremias roborowskii.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051084},
pmid = {42197470},
issn = {2076-2607},
support = {32560265//National Natural Science Foundation of China/ ; 32260118//National Natural Science Foundation of China/ ; 2023TSYCQNTJ0034//the second group of Tianshan Talent Training Program: Youth Support Talent Project/ ; XJAUGRI2025030//Xinjiang Agricultural University Graduate Research Innovation Program/ ; },
abstract = {In the context of global warming, the resulting persistent thermal stress has become a critical environmental factor influencing the structural and functional homeostasis of gut microbiota in reptiles. In this study, Eremias roborowskii, a desert lizard endemic to the extreme heat conditions of the Turpan Basin, was selected as an ideal model for evaluating the ecological impacts of global warming. Meanwhile, a 60-day controlled laboratory experiment was conducted, exposing the lizards to normal (30 °C ± 1 °C), elevated (37 °C ± 1 °C), and high (42 °C ± 1 °C) temperatures to reflect future climate scenarios. Using shotgun metagenomic sequencing, the gut microbiota was characterized to investigate the dynamics of the antibiotic resistance genes (ARGs) and carbohydrate-active enzymes (CAZymes) under heat stress. The results reveal that elevated temperature selectively promotes heat-tolerant gut microbiota, such as Tetragenococcus and Faecalicatena, by altering host energy metabolism and modulating heat stress adaptation to maintain intestinal homeostasis. Moreover, the observed increase in resistome diversity and richness under elevated temperature may be attributed to temperature-induced shifts in gut microbial composition, particularly the enrichment of heat-tolerant ARG-carrying bacterial taxa. Metabolic changes in CAZymes were caused by gut microbiota remodeling, which optimized carbon utilization and preferentially allocated cell wall synthesis and repair. Furthermore, the pentose phosphate pathway and amino acid biosynthesis pathways were upregulated, providing NADPH for antioxidant defense and precursors for protein synthesis, respectively, thereby contributing to the maintenance of microbial cellular homeostasis. Our study provides a theoretical basis for understanding functional gene adaptation strategies in wildlife microbiomes due to climate change.},
}

@article {pmid42197480,
year = {2026},
author = {Duran Yunga, ER and Rodriguez Coyago, ML},
title = {Structure and Function of the Dental Plaque Microbiome in Eubiosis: A Systematic Review of Ethnic-Racial Influences.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051095},
pmid = {42197480},
issn = {2076-2607},
abstract = {While a conserved core microbiome is shared across healthy individuals, significant interindividual taxonomic variation exists; however, the specific influence of genetic ancestry on supragingival plaque structure in eubiosis remains unclear. This systematic review analyzed evidence regarding taxonomic variations in supragingival plaque associated with ethnicity in systemically healthy populations. A search was conducted in PubMed, Scopus, ScienceDirect, and Scielo following PRISMA 2020 guidelines, covering literature up to October 2025. Cross-sectional studies using genomic sequencing or metagenomics were included, with quality assessed via the GRADE system. Six studies met eligibility criteria. Results identified a universal core microbiome structurally dominated by Corynebacterium spp. and Streptococcus spp. However, distinct ethnic-specific taxonomic signatures emerged, such as the enrichment of Fusobacterium spp. in African Americans and Corynebacterium spp. in Caucasians, alongside the exclusive presence of Sneathia spp. in Burmese individuals. Although a basal microbial architecture necessary for homeostasis exists, ethnicity acts as a biological filter defining distinctive bacterial profiles and differential susceptibilities. These findings suggest that while the core microbiome is conserved, the composition of peripheral species in the dental plaque hedgehog structure varies according to ancestry. This supports a transition from standardized dental care to personalized medicine oriented towards the patient's biological heritage.},
}

@article {pmid42197517,
year = {2026},
author = {Albastaki, A and Smith, J},
title = {Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051132},
pmid = {42197517},
issn = {2076-2607},
abstract = {Studying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the community is described. Three approaches now dominate soil microbiome research: short-read 16S rRNA amplicon sequencing on Illumina platforms, full-length 16S sequencing on Oxford Nanopore Technologies (ONT) platforms (particularly the R10.4.1 flow cell), and long-read shotgun metagenomics. Each has distinct biases that shape the recovered community, yet researchers routinely select a method based on cost, understanding, or local expertise rather than on a clear knowledge of what each approach methodically over- or under-represents. Here, we review head-to-head benchmarking studies that have applied two or more of these methods to the same soil or directly comparable samples. We show that while long-read and short-read 16S approaches generally converge on dominant taxa and on between-sample differences, they disagree substantially on alpha diversity estimates, rare taxon detection, and the relative abundances of entire phyla. The R10.4.1 flow cell chemistry has narrowed but not eliminated the accuracy gap with Illumina, and shotgun metagenomics reveals systematic biases in both short and long-read assembly that depend on population diversity within the sample. We synthesise this evidence into an evidence-based decision framework tied to specific research questions and recognise the gaps in soil-specific benchmarking that limit current methods. Rather than asking which platform is "best," we argue that method choice should be framed as an important part of study design, with the biases of the chosen method acknowledged and, where possible, controlled for.},
}

@article {pmid42197550,
year = {2026},
author = {Zhang, S and Li, G and Zhu, E and Zhao, Y and Yang, X and Huang, S and Zheng, Z},
title = {Rhizosphere Microbial Community and Metagenomic Annotation Responses in a Vallisneria natans-Sediment Microcosm Exposed to Trifluenfuronate and Fluopyram.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051166},
pmid = {42197550},
issn = {2076-2607},
support = {2023YFD1700403//the National Key Research and Development Program of China/ ; 2024R054//Zhejiang Shuren University/ ; },
abstract = {Rhizosphere microorganisms play central roles in nutrient cycling and contaminant transformation in sediment-associated freshwater systems, yet their responses to newer pesticides remain insufficiently characterized. In this study, a 28-day Vallisneria natans-rhizosphere sediment microcosm was used to compare the effects of trifluenfuronate and fluopyram at nominal concentrations of 0.01, 0.1, and 1 mg L[-1]. Bacterial community composition was assessed using 16S rRNA gene sequencing, and shotgun metagenomic data were used to evaluate relative functional annotation patterns. Plant physiological traits and rhizosphere sediment enzyme activities were measured as ecological context for interpreting microorganism-associated responses. Fluopyram, particularly at 1 mg L[-1], produced clearer ordination-level shifts in rhizosphere bacterial community composition than trifluenfuronate, although pairwise treatment separation was not statistically resolved after multiple-testing correction. Annotation-based metagenomic profiles also differed between the two pesticides: stronger exposure was associated with reduced relative signals for several xenobiotic-, transport-, and regulation-related annotations, while high-dose fluopyram showed a methane-metabolism-related annotation signal and high-dose trifluenfuronate showed relative enrichment of secondary-metabolism-related annotations. These microbial and annotation-profile responses coincided with stronger inhibition of V. natans growth and greater suppression of rhizosphere sediment enzyme activities under fluopyram exposure. Overall, fluopyram induced more consistent microorganism-associated response patterns than trifluenfuronate in the tested rooted macrophyte-sediment microcosm. The results highlight the sensitivity of rhizosphere microbial communities and metagenomic annotation profiles to pesticide exposure in sediment-associated freshwater systems.},
}

@article {pmid42197616,
year = {2026},
author = {Wang, W and Yang, W and Song, W and Huang, S and Lai, J and Zhou, Z and Wang, P and Wang, B},
title = {Rhizosphere Microbial Effects on Soil Quality of Pinus massoniana and Schima superba Mixed Plantations.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/plants15101482},
pmid = {42197616},
issn = {2223-7747},
support = {2023YFD2200902//National R&D Program of China/ ; CAFYBB2024ZA021//Fujian Sanming Demonstration and Model Construction Project of China/ ; },
abstract = {This study aimed to reveal the rhizosphere microbial community structure, carbon-nitrogen-phosphorus (C-N-P) nutrient cycling processes, and functional gene characteristics of Pinus massoniana and Schima superba in mixed forests. Furthermore, we sought to elucidate the microbial mechanisms by which mixed-species afforestation enhances soil quality improvement, providing a theoretical basis in soil microbiology for the cultivation of these mixed forests. The research subjects included pure P. massoniana plantations (CLPs), pure S. superba plantations (CLSs), and individual P. massoniana (HJP) and S. superba (HJS) trees within mixed plantations (HJLs). We collected rhizosphere and bulk soil samples to analyze their physicochemical properties and enzyme activities. Metagenomic sequencing was employed to profile the rhizosphere microbial communities and functional genes involved in C-N-P cycling. Furthermore, by integrating a functional gene co-occurrence network analysis with structural equation modeling (SEM), we systematically elucidated the coupling relationships among the stand types, soil properties, microbial communities, and nutrient cycling. Mixed planting significantly improved soil quality; compared to the CLP and CLS forests, the nitrate nitrogen (NO3[-]-N) content in the mixed forest soils increased by 121.01% and 120.10% (p < 0.05), and the activity of urease (URE) also significantly increased by 123.99% and 49.56%, respectively. Mixing significantly altered the microbial community structure. In the bacterial community of the mixed forests, the abundance of nitrogen-fixing and potentially phosphorus-solubilizing bacteria from the genera Paraburkholderia and Burkholderia increased. In the fungal community, the arbuscular mycorrhizal fungus Rhizophagus, which possesses a nutrient absorption advantage, exhibited absolute dominance, with its relative abundance ranging from 14.84% to 88.81%. The abundances of genes associated with denitrification and phosphorus starvation regulation were significantly upregulated in the mixed forests; notably, the abundance of phosphorus starvation regulation genes in the HJSs was 18.84% higher than that in the CLSs. A co-occurrence network analysis demonstrated that the proportion of positive correlation edges in the HJP nitrogen cycling network reached as high as 75.0%, and the average degree of the HJS phosphorus cycling network (2.691) surpassed that of the CLSs. The structural equation modeling further revealed that the association strength between the fungi and phosphorus cycling genes in the mixed forests increased to R[2] = 0.915 (p < 0.01) from R[2] = 0.213 in the pure forests. This mixed planting practice transforms nutrient cycling from a resource-competitive mode to a microbially synergized mode, thereby forming an efficient endogenous nutrient cycling system. This synergistic rhizosphere microbial effect is a key internal mechanism for overcoming nutrient bottlenecks and should serve as a diagnostic indicator of soil recovery in the ecological restoration of degraded pine forests.},
}

@article {pmid42198637,
year = {2026},
author = {Malleret, B and Kwak, ML and Chavatte, JM},
title = {Accelerating Progress on Ticks and Tick-Borne Diseases in Southeast Asia: Regional Challenges, Evidence Gaps, and Priorities (2023-2025).},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/pathogens15050511},
pmid = {42198637},
issn = {2076-0817},
support = {NUHSRO/2025/017/T1/Seed-Sep24/Adhoc/01//Ministry of Education/ ; },
mesh = {Animals ; Humans ; Asia, Southeastern/epidemiology ; Evidence Gaps ; *Tick-Borne Diseases/epidemiology/prevention & control ; *Ticks/microbiology ; },
abstract = {Southeast Asia (SEA) faces persistent gaps in regional understanding and control of ticks and tick-borne diseases (TBDs) despite recent advances (2023-2025). The second international symposium on ticks and TBDs in SEA (Singapore, August 2025), following the inaugural 2023 meeting in Cambodia, served as a catalyst for regional exchange that informed this perspective. SEA's ecological and host diversity supports complex tick-host-pathogen networks, yet evidence remains fragmented due to uneven sampling that has largely focused on livestock and peri-urban environments. Key constraints include limited taxonomic resolution driven by outdated or incomplete identification keys, under-sampling of soft ticks (Argasidae), and the absence of harmonized, open-access regional reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). While MALDI-TOF MS, proteomics, AI-assisted identification, and next-generation sequencing/metagenomics are increasingly applied, their broader regional uptake is limited by the absence of harmonized, open-access reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). Broad ecological surveys and integrated animal and human surveillance remain limited, and vector competence studies are constrained by the scarcity of SEA-derived tick colonies and cell lines. Regional data and recent findings (2024-2026) confirm circulation of multiple TBPs (including Anaplasma, Babesia, Borrelia, Coxiella, Ehrlichia, Rickettsia, and Theileria) and highlight emerging viral findings, including southward reports of Bandavirus dabieense. Human infestations and non-communicable tick bite outcomes (e.g., tick paralysis and alpha-gal syndrome) are recognized but remain under-reported due to low clinical awareness and limited diagnostics. Importantly, the diagnostic chain is further disrupted by missed/insufficient specimen collection at the point of care, and by constrained capacity to identify (especially immature) ticks to species level-limitations compounded by the absence of harmonized, open-access regional reference resources. The symposium identified six priorities: (1) full completion and regional validation of tick identification keys for adults (in progress) and immatures (to be initiated), plus an open-access DNA barcode library anchored by curated, voucher-based collections from all SEA countries; (2) harmonization of molecular and proteomic diagnostic platforms, including expansion of regional MALDI-TOF MS and NGS protocols and reference databases; (3) development of tick colonies and cell lines from locally prevalent species to support vector competence, vaccine, and acaricide testing; (4) expansion of One Health surveillance with enhanced ecological sampling at wildlife-livestock-human interfaces; (5) establishment of open-access, region-wide data platforms for integrated tick, TBP, and ecological metadata sharing; and (6) sustained investment in human resources, training, and policy advocacy to raise research and public health visibility of ticks and TBDs.},
}

Animals
Humans
Asia, Southeastern/epidemiology
Evidence Gaps
*Tick-Borne Diseases/epidemiology/prevention & control
*Ticks/microbiology

@article {pmid42198700,
year = {2026},
author = {Mansour, O and Fadeev, AV and Perederiy, AA and Ksenafontov, AD and Boyarintseva, AY and Danilenko, DM and Lioznov, DA and Komissarov, AB},
title = {Whole-Genome Phylogenetic Characterization of Human Parainfluenza Virus Type 4 Circulating in St. Petersburg, Russia.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/v18050497},
pmid = {42198700},
issn = {1999-4915},
support = {TVKQ-2024-0003, registration number 124020500002-4//Ministry of Health of the Russian Federation (Project #TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing")/ ; },
mesh = {Humans ; *Phylogeny ; Russia/epidemiology ; *Genome, Viral ; Genetic Variation ; Whole Genome Sequencing ; *Parainfluenza Virus 4, Human/genetics/classification/isolation & purification ; *Rubulavirus Infections/virology/epidemiology ; },
abstract = {Human parainfluenza virus type 4 (hPIV4) remains poorly characterized compared with other hPIV serotypes and information on its genomic diversity is particularly limited for Russia and Eastern Europe. In this study, we report the first complete genome sequences of hPIV4 isolates from Russia and place them in the context of global hPIV4 genetic diversity. Eight hPIV4 viruses were isolated in cell culture from respiratory samples collected from hospitalized children in Saint Petersburg between 2017/2018 and 2023/2024. Complete viral genomes were recovered using a metagenomic whole-genome amplification approach based on SMART-9N technology. Phylogenetic analysis of 178 complete hPIV4 genomes showed clear separation into hPIV4a (n = 132) and hPIV4b (n = 46) subtypes. Based on genetic distance approach, hPIV4a formed two major clusters, with the dominant cluster B subdivided into four subclusters (B1-B4); and subcluster B4 further resolved into four genetic lineages. All Russian isolates belonged to the subcluster B4 and were distributed among multiple co-circulating lineages. In contrast, hPIV4b genomes segregated into three distinct clusters, reflecting structured genetic diversity within the subtype. Collectively, this study provides, to the best of our knowledge, the first p-distance-based framework for hPIV4 whole-genome classification and contributes new complete genome sequences for an underrepresented region.},
}

Humans
*Phylogeny
Russia/epidemiology
*Genome, Viral
Genetic Variation
Whole Genome Sequencing
*Parainfluenza Virus 4, Human/genetics/classification/isolation & purification
*Rubulavirus Infections/virology/epidemiology

@article {pmid42198703,
year = {2026},
author = {Wang, Z and Liu, Z and Zeng, J and Li, J and Cheng, J and Qi, X and Li, J and Bai, S},
title = {Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/v18050500},
pmid = {42198703},
issn = {1999-4915},
support = {423RC548//Hainan Provincial Natural Science Foundation of China/ ; KJRC2023C14//Department of Science and Technology of Hainan Province/ ; 41506139//National Natural Science Foundation of China/ ; },
mesh = {Seashore ; *Geologic Sediments/virology ; Seasons ; Metagenomics ; *Bays/virology ; *Viruses/classification/genetics/isolation & purification ; Tropical Climate ; Phylogeny ; *Virome ; },
abstract = {Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October-December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential.},
}

Seashore
*Geologic Sediments/virology
Seasons
Metagenomics
*Bays/virology
*Viruses/classification/genetics/isolation & purification
Tropical Climate
Phylogeny
*Virome

@article {pmid42198741,
year = {2026},
author = {Jia, L and De, R and Li, Z and Han, Z and Liu, L and Dong, H and Feng, S and Liu, R and Zhao, L},
title = {A Prolonged Norovirus Infection and the Molecular Evolution of Human Norovirus Within-Host in a Child with Burkitt Lymphoma.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/v18050538},
pmid = {42198741},
issn = {1999-4915},
support = {Discipline Leader -02-20//Beijing Municipal Health Commission/ ; },
mesh = {Humans ; *Burkitt Lymphoma/virology/complications ; *Evolution, Molecular ; *Norovirus/genetics/classification/isolation & purification ; Phylogeny ; *Caliciviridae Infections/virology/complications ; Genome, Viral ; Child ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Mutation ; },
abstract = {It has been reported that chronic infection of human norovirus (HuNoV) may potentially serve as a reservoir for viral variants with the possibility to evade population immunity or alter the binding sites of HBGA receptors. In this study, a child diagnosed with Burkitt lymphoma and positive for HuNoV determined by real-time PCR (qPCR) firstly in 15 August 2016, was followed up until 20 March 2018, and 26 fecal specimens and one vomitus were collected to trace the evolutionary characteristics of HuNoV by phylogenetic analysis, meta-genomics next-generation sequencing (mNGS), and temporal evolutionary analysis of VP1 among 23 specimens positive for HuNoV. There were 15 specimens with partial RdRp gene sequences forming an independent cluster with sequences of GII.P31, 14 with the region C sequences and 11 with P domain sequences of VP1 gene clustered together with HuNoV GII.4 Sydney_2012. All these sequences showed that mutations accumulated nearly in a time order, and more mutations were shown in the key epitopes A-E or near the binding sites for HBGA in subdomain P2 with higher evolutionary rates. Analysis of NGS data identified intra-host viral quasi-species, and two genome sequences of the same length from mNGS were assembled from N705, with mutations located in the region of subdomain P2 (1171 nt-1202 nt) which led to five amino acid mutations. In conclusion, the accumulated mutations of HuNoV, especially in subdomain P2, were explored in a child with Burkitt lymphoma, and the sequencing of HuNoV from immunocompromised individuals was proven critical for monitoring intra-host quasi-species evolution and potential variant emergence, providing basic data for clinical infection control.},
}

Humans
*Burkitt Lymphoma/virology/complications
*Evolution, Molecular
*Norovirus/genetics/classification/isolation & purification
Phylogeny
*Caliciviridae Infections/virology/complications
Genome, Viral
Child
Feces/virology
High-Throughput Nucleotide Sequencing
Mutation

@article {pmid42198763,
year = {2026},
author = {Kim, MJ and Kim, YJ and Ha, HJ and Park, JS and Rini, IA and Lee, S and Lee, TK},
title = {Biological Trajectory of Virophage Research and the Emergence of Marine Virophages: A Scoping Review.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/v18050560},
pmid = {42198763},
issn = {1999-4915},
support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology Promotion/ ; },
mesh = {*Virophages/genetics/physiology ; Genome, Viral ; Giant Viruses/genetics ; *Aquatic Organisms/virology ; Seawater/virology ; Metagenome ; Virus Replication ; },
abstract = {Virophages are satellite viruses that depend on the replication machinery of giant double-stranded DNA viruses and influence the structure and dynamics of viral communities through multilayered interactions among giant viruses, their hosts, and virophages. Since the discovery of the Sputnik virophage in 2008, virophages have been increasingly recognized for their roles in regulating giant virus replication, contributing to host defense mechanisms, and shaping the evolution of mobile genetic elements. However, quantitative syntheses examining how virophage research has developed over time, particularly in marine environments, remain limited. Here, we conducted a bibliometric analysis of virophage research published between 2008 and 2025 using the Web of Science Core Collection. By comparing an overall virophage research corpus with a marine virophage sub-corpus, we assessed publication and citation trends, collaboration structures, and keyword-based intellectual and thematic evolution. Our results show that virophage research has gradually transitioned from an early phase dominated by landmark discoveries and experimental model systems to a data-intensive stage driven by genome- and metagenome-based analyses and computational approaches. Although marine virophage studies represent a relatively small proportion of the total literature, they exhibit sustained citation impact and form a distinct research axis within the field. In particular, marine-focused studies emphasize metagenomic discovery, genome sequence alignment, and the analysis of mobile genetic elements such as polinton-like viruses, highlighting the role of marine environments in accelerating the intellectual transition of virophage research. Collectively, these findings demonstrate that virophage research has moved beyond a "discovery and definition" phase toward data-driven integrative interpretation, with marine virophage research emerging as a key domain for understanding the structure and evolutionary dynamics of marine viral ecosystems.},
}

*Virophages/genetics/physiology
Genome, Viral
Giant Viruses/genetics
*Aquatic Organisms/virology
Seawater/virology
Metagenome
Virus Replication

@article {pmid42199008,
year = {2026},
author = {Lépine, G and Davila, AM and Cueff, G and Pickering, G and Ichou, F and Perreau, C and Lefranc-Millot, C and Gilles, M and Thirion, F and Mariotti, F and Rémond, D and Fouillet, H and Polakof, S},
title = {Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2677951},
doi = {10.1080/19490976.2026.2677951},
pmid = {42199008},
issn = {1949-0984},
mesh = {Humans ; Male ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cross-Over Studies ; Middle Aged ; *Plant Proteins/metabolism/administration & dosage ; Adult ; Diet ; Cardiometabolic Risk Factors ; Metabolome ; Indoles/metabolism ; Bacteria/classification/isolation & purification/genetics/metabolism ; },
abstract = {This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δd28-d1) were computed (n = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δd28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (p-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., Alistipes putredinis). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.},
}

Humans
Male
*Tryptophan/metabolism
*Gastrointestinal Microbiome
Feces/microbiology
Cross-Over Studies
Middle Aged
*Plant Proteins/metabolism/administration & dosage
Adult
Diet
Cardiometabolic Risk Factors
Metabolome
Indoles/metabolism
Bacteria/classification/isolation & purification/genetics/metabolism

@article {pmid42199353,
year = {2026},
author = {Bergot, M and Lefevre, CT and Grouzdev, DS and Menguy, N and Ortet, P and Denis, Y and Viollier, E and Jézéquel, D and Monteil, CL},
title = {Magnetotactic Bdellovibrionota from a ferruginous spring.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag116},
pmid = {42199353},
issn = {2730-6151},
abstract = {Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately 100 cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.},
}

@article {pmid42199424,
year = {2026},
author = {Zhao, L and Wang, Q and Chen, J and Wang, J},
title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1767902},
pmid = {42199424},
issn = {1664-3224},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; },
abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.

METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.

RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.

CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/metabolism
Female
Multiomics
Male
*Gastrointestinal Microbiome
Child, Preschool
Metagenomics/methods
China/epidemiology
*Metabolome
Metabolomics/methods
Infant
Feces/microbiology
Bacteria/classification/genetics
Child

@article {pmid42199698,
year = {2026},
author = {Li, Q and Wang, X and Zhang, S and Wang, H and Li, X and Zhao, F},
title = {mNGS-Supported Interpretation of Staphylococcus pettenkoferi Bloodstream Infection After Intracerebral Hemorrhage: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {611927},
pmid = {42199698},
issn = {1178-6973},
abstract = {PURPOSE: Staphylococcus pettenkoferi is an uncommon coagulase-negative staphylococcus whose recovery from blood may be difficult to interpret because of the frequent contamination associated with this bacterial group. We report a case in which peripheral-blood metagenomic next-generation sequencing (mNGS) and repeated blood cultures supported clinically significant bloodstream infection after intracerebral hemorrhage.

PATIENTS AND METHODS: We described the clinical course, imaging findings, microbiological results, and antimicrobial management of an 85-year-old man admitted to the intensive care unit after intracerebral hemorrhage with intraventricular extension. Peripheral-blood mNGS and two sets of peripheral blood cultures were obtained during early fever evaluation.

RESULTS: Peripheral-blood mNGS, performed on samples obtained immediately after ICU admission and before neurosurgical intervention or intracranial device placement, detected S. pettenkoferi within 24 h. At 72 h, both peripheral blood culture sets yielded the same organism. Concordant results from mNGS and repeated peripheral blood cultures, together with the clinical context, supported clinically significant bloodstream infection rather than simple contamination. The respiratory tract was considered a presumed source in the setting of clinically suspected aspiration-related pulmonary infection, although it was not microbiologically confirmed.

CONCLUSION: This case highlights the need for cautious interpretation of uncommon coagulase-negative staphylococci recovered from blood. Peripheral-blood mNGS may provide early etiologic support, but conventional blood culture remains essential for confirmation and antimicrobial susceptibility testing.},
}

@article {pmid42200417,
year = {2026},
author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X},
title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70046},
pmid = {42200417},
issn = {1365-2583},
support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; },
abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.},
}

@article {pmid42200512,
year = {2026},
author = {Vergara, E and Khaleque, HN and Neira, G and Watkin, ELJ and Valdés, JH and Holmes, DS},
title = {Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001732},
pmid = {42200512},
issn = {2057-5858},
mesh = {Phylogeny ; *Sulfur/metabolism ; *Adaptation, Physiological/genetics ; *Rhodobacteraceae/genetics/metabolism/classification ; Genome, Bacterial ; Evolution, Molecular ; Hydrothermal Vents/microbiology ; Australia ; Oxidation-Reduction ; Italy ; Metagenome ; Pacific Ocean ; Bacterial Proteins/genetics/metabolism ; },
abstract = {This study compares predicted sulphur metabolism genes across four Acidihalobacter type strains and two metagenome-assembled genomes (MAGs), revealing genomic differences that appear to correspond to ecological specialization. Phylogenomic analysis separates the species into two clades: clade I includes Acidihalobacter ferrooxydans from a geothermal region in Italy and the two MAGs derived from deep-sea hydrothermal vents in the Pacific Ocean, while clade II comprises Acidihalobacter aeolianus and Acidihalobacter prosperus from a geothermal region in Italy and Acidihalobacter yilgarnensis from a saline and acidic drainage in Australia. Variations in sulphide/quinone oxidoreductases (SQRs) across the species, in particular in Ah. ferrooxydans and Ah. yilgarnensis, likely relate to the availability and speciation of sulphur substrates, which are strictly governed by local redox potential (Eh) and metal redox cycling in their respective habitats. Notably, only Ah. ferrooxydans (clade I) lacks the canonical sulphur/thiosulphate oxidation (Sox) system for thiosulphate oxidation found in clade II and instead encodes components of an alternative S4I pathway. We hypothesize that this difference reflects an adaptation to dynamic microniches going from highly reduced (sulphide-rich) to oxidized metastable sulphur intermediates. In contrast, the retention of the Sox system in clade II suggests a distinct strategy permitting greater metabolic versatility under fluctuating Eh-pH conditions.Differences in clade I terminal oxidases (cbb3-type cytochrome, bc1 complex) and regulatory elements appear to support further adaptation to environments with elevated H2S, setting this clade apart from clade II members. These adaptations, mainly evidenced by gene redundancy, gene loss and horizontal gene transfer, seem to reflect a unique ecological microniche and evolutionary trajectory for Ah. ferrooxydans distinct from other members of the genus, particularly from a sulphur-based energy metabolism perspective.},
}

Phylogeny
*Sulfur/metabolism
*Adaptation, Physiological/genetics
*Rhodobacteraceae/genetics/metabolism/classification
Genome, Bacterial
Evolution, Molecular
Hydrothermal Vents/microbiology
Australia
Oxidation-Reduction
Italy
Metagenome
Pacific Ocean
Bacterial Proteins/genetics/metabolism

@article {pmid42200521,
year = {2026},
author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI},
title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001739},
pmid = {42200521},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.},
}

*Metagenomics/methods
Humans
*Metagenome
*Bacteria/classification/genetics
Genome, Bacterial
Sequence Analysis, DNA/methods
Computational Biology/methods
Microbiota/genetics

@article {pmid42200658,
year = {2026},
author = {Blanchard, JL},
title = {Learning R with generative AI in a metagenomic data science course.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0034325},
doi = {10.1128/jmbe.00343-25},
pmid = {42200658},
issn = {1935-7877},
abstract = {Generative artificial intelligence (AI) tools are increasingly used by students in introductory coding courses; however, evidence-based guidance for integrating these tools into biology education remains limited. We examined student experiences with generative AI in a beginner R programming course focused on metagenomic data analysis. An anonymous survey (n = 43) captured quantitative ratings and qualitative reflections on how AI influenced learning, productivity, and problem-solving practices. Most respondents entered the course with little to no prior coding experience (79%) and reported frequent AI use throughout the semester, indicating that AI quickly became embedded in students' workflows. Students rated AI as highly helpful for suggesting R code, explaining syntax and logic, and brainstorming analyses, with over 70% endorsing each use case. However, AI errors were common: over 90% of students encountered incorrect output at least sometimes, including domain-specific misinterpretations and overcomplicated or syntactically incorrect code. Notably, students identified a need for clearer instructional support in core AI-mediated practices. The most frequent recommendation for course redesign was to introduce foundational R concepts prior to AI use, highlighting a threshold-competency principle for effective AI integration. Together, these findings suggest that generative AI can support novice coders but does not substitute for foundational instruction. Effective AI integration requires deliberate pedagogical scaffolding and reflection rather than code generation alone. These principles are likely to remain critical as AI tools become more capable and more widely adopted in undergraduate biology education.},
}

@article {pmid42200756,
year = {2026},
author = {Harrison, LB and Sohani, ZN and Lasry, D and Cheng, MP and Lee, TC and Babiker, A and Kadri, SS and Lawandi, A},
title = {Rapid Microbiological Diagnostics for Sepsis: Narrative Review of Current and Prospective Approaches.},
journal = {Critical care explorations},
volume = {8},
number = {6},
pages = {e1415},
doi = {10.1097/CCE.0000000000001415},
pmid = {42200756},
issn = {2639-8028},
mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture/methods ; Molecular Diagnostic Techniques/methods ; *Microbiological Techniques/methods ; Rapid Diagnostic Tests ; },
abstract = {OBJECTIVES: In this review, we aim to provide critical care clinicians with a concise introduction to the current and prospective tools that exist for rapid diagnostics in sepsis employed in the microbiology laboratory. Our objective is to provide a primer for clinicians to engage with their colleagues in the microbiology laboratory for the selection and implementation of new and emerging tools.

DATA SOURCES: The primary literature, restricted to peer-reviewed sources, was queried using relevant search terms (e.g., sepsis, rapid diagnostics, microbiology, etc) using PubMed and Google Scholar (until February 2025), as well as review of citations of relevant articles.

STUDY SELECTION: After initial searches, literature was screened by each author responsible for the sections of this review: blood culture-based methods (L.B.H.), nonblood culture-based molecular diagnostics (D.L.), and antigen-based methods (Z.N.S.). Titles and abstracts of individual articles were reviewed by the respective section authors and articles describing microbiological diagnostic techniques that decrease the turnaround time for the identification of microorganisms and/or antimicrobial susceptibility testing with relevance to the diagnosis of sepsis were retained.

DATA EXTRACTION: Data from individual studies was extracted by each respective section author using Zotero reference management software and synthesized narratively.

DATA SYNTHESIS: Rapid diagnostics for sepsis can be broadly divided into three categories: those applied to incubated positive blood culture specimens, and culture-independent approaches applied directly to clinical specimens, which can be further divided into those based on the direct detection of the nucleic acids of microorganisms, and those based on the detection of antigens. Blood culture-based approaches rely on biological amplification of microorganisms present but aim to measure this amplified signal directly to speed identification of microorganisms or antimicrobial resistance relative to traditional plate-culture-based workflows. Nucleic acid and antigen detection methods can be performed directly on clinical specimens, and so promise more rapid diagnostics in sepsis, but with method-specific tradeoffs in sensitivity, specificity, and interpretation.

CONCLUSIONS: Evolutionary refinements of blood culture-based diagnostic approaches have decreased time to actionable information significantly while emerging and established culture-independent approaches can reduce time to actionable information to a few hours. In aggregate these interventions may have important clinical benefits, yet significant heterogeneity exists in the applicability and availability of technologies.},
}

Humans
*Sepsis/diagnosis/microbiology
Blood Culture/methods
Molecular Diagnostic Techniques/methods
*Microbiological Techniques/methods
Rapid Diagnostic Tests

@article {pmid42201023,
year = {2026},
author = {Rehman, A and Awais, M and Baloch, HNUA and Leghari, MO and Ahmad, A and Javed, H},
title = {Sputum Liquid Biopsy for Lung Cancer Screening, Diagnosis, Subtyping, Surveillance, Response Prediction, and Prognostication: A Scoping Review.},
journal = {Medical sciences (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/medsci14020231},
pmid = {42201023},
issn = {2076-3271},
mesh = {Humans ; *Lung Neoplasms/diagnosis/pathology/metabolism ; *Sputum/metabolism ; Liquid Biopsy/methods ; Biomarkers, Tumor ; Prognosis ; *Early Detection of Cancer/methods ; },
abstract = {Background/Objectives: Liquid biopsy (LB) is transforming cancer care by enabling minimally invasive tumor profiling. While current research and clinical pathways mostly focus on blood LB, sputum represents a non-invasive, readily available respiratory specimen that may offer unique advantages for lung cancer (LC) care. Despite its potential, the maturity, breadth, and clinical applicability of sputum-based LB remain elusive. Methods: We conducted a scoping review to systematically map the existing literature on sputum LB in LC. Electronic databases were searched for studies evaluating sputum-derived biomarkers-cytologic, genomic, epigenetic, transcriptomic, proteomic, metabolomic, metagenomic, and extracellular vesicle-derived products-across the LC care continuum. Study designs, technologies, clinical contexts, and reported outcomes were extracted and synthesized qualitatively. Results: The literature demonstrated substantial heterogeneity in sputum collection, processing, and analytical platforms. Early work focused on cytometry and genetic alterations, while recent studies increasingly explore DNA methylomics, microRNAs, extracellular vesicle-derived products, and multi-omics approaches. The evidence suggests potential utility of sputum biomarkers for early detection and risk stratification, particularly in high-risk populations, with emerging data supporting roles in molecular subtyping, response monitoring, prognostication, and surveillance. However, few studies report prospective validation, direct comparison with blood-based LB, or impact on actual patient outcomes. Conclusions: Sputum LB is a promising yet underdeveloped modality in LC care. This scoping review highlights technological innovations alongside significant methodological heterogeneity and translational gaps. Future research should focus on standardization, prospective validation, impact on patient outcomes, and integration with blood- and other body fluid-based LB, as well as imaging biomarkers. This will enable incorporation of sputum-based LB into actual clinical pathways of LC care.},
}

Humans
*Lung Neoplasms/diagnosis/pathology/metabolism
*Sputum/metabolism
Liquid Biopsy/methods
Biomarkers, Tumor
Prognosis
*Early Detection of Cancer/methods

@article {pmid42201143,
year = {2026},
author = {Zhang, W and Eleftherianos, I and Mohamed, A and Smagghe, G and Chakkalakkal, G and Al-Akeel, R and Toprak, U and Tettamanti, G and Keyhani, N and Renault, D},
title = {Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag137},
pmid = {42201143},
issn = {1751-7370},
abstract = {Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.},
}

@article {pmid42201824,
year = {2026},
author = {Lin, X and Asif, M and Li, W and Zhang, B and Li, Y and Yu, Y and Jiang, X},
title = {Long-Term Straw Return Reverses Antibiotic Resistance Accumulation in Maize Rhizosphere through Integrated Soil-Microbial Mechanisms.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11371},
pmid = {42201824},
issn = {1520-5851},
abstract = {The impact of long-term agricultural cultivation on antibiotic resistance has emerged as a critical environmental concern. However, previous studies have primarily examined organic fertilizers, and the effects of sustained chemical fertilizer use combined with straw incorporation over extended periods remain poorly understood. Here, we employed a 25-year field trial combined with metagenomic analysis to investigate the differential effects of chemical fertilization and straw incorporation on soil antibiotic resistance gene (ARG) dynamics in the maize rhizosphere. Results showed that long-term cultivation progressively increased ARG and virulence factor gene (VFG) abundance. Metagenomic analyses suggested that shifts in Pseudomonas populations and microbial metabolic pathways were associated with elevated levels of ARGs in the rhizosphere. Field inoculation with a synthetic Pseudomonas community further increased the ARG abundance, accompanied by reduced genomic GC content and enrichment of specific metabolic pathways. In contrast, straw amendment treatments reduced Pseudomonas abundance and soil acidification while increasing the soil total carbon and lignin degradation functional capacity. Our findings indicate that long-term straw incorporation represents a promising strategy for controlling antibiotic resistance dissemination in agricultural systems, offering valuable insights into sustainable crop management practices.},
}

@article {pmid42201863,
year = {2026},
author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI},
title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0340244},
doi = {10.1371/journal.pone.0340244},
pmid = {42201863},
issn = {1932-6203},
mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; },
abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.},
}

Humans
*Bone and Bones/microbiology/pathology
*Metagenomics/methods
*Archaeology
*Microbiota/genetics
Bacteria/genetics/classification
Fungi/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Norway
Phylogeny

@article {pmid42201897,
year = {2026},
author = {, },
title = {Editorial Note: Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0350242},
doi = {10.1371/journal.pone.0350242},
pmid = {42201897},
issn = {1932-6203},
}

@article {pmid42202516,
year = {2026},
author = {Sun, X and Lin, Z and Ni, SQ},
title = {Multidrug-resistant bacteria contribute to core bacterial community and ARGs persistence during full-scale pharmaceutical wastewater treatment.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142513},
doi = {10.1016/j.jhazmat.2026.142513},
pmid = {42202516},
issn = {1873-3336},
abstract = {Pharmaceutical wastewater treatment plants (WWTPs) are confronted with a wide range of contaminants, resulting in the accumulation of antibiotic resistance genes (ARGs) and the evolution of multidrug-resistant (MDR) bacteria. However, the ecological roles of these MDR residents during full-scale wastewater treatment remain unclear. In this study, the core bacterial communities as well as potential MDR bacteria for industrial WWTPs were firstly categorized out. Taxa belonging to MDR bacteria were frequently detected to persist with low relative abundance across different treatment units, even in the effluent. Then, the occurrence and health risk of ARGs were evaluated. Certain abundant and prevalent ARGs, such as fabG, macB, and adeF, were found to exhibit high prevalence. Some pivotal mobile genetic elements, acting as key network hubs, can link MDR bacteria with a broad range of ARGs. Finally, the result showed that several metagenome-assembled genomes recovered from the effluents were not only classified as MDR bacteria harboring ARGs with high risk, but also served as important members of the core bacterial community. These findings provide critical insights into the ecological roles of MDR bacteria during the full-scale pharmaceutical wastewater treatment, and emphasize the urgent need for real-time monitoring of wastewater-borne MDR bacteria for ecological health.},
}

@article {pmid42202519,
year = {2026},
author = {Li, X and Wang, Y and Dang, X and Zhang, Y and Zhao, C and Hou, S and Li, B and Ma, F and Hao, L and Zhu, T},
title = {Molecular mechanism by which high temperature and RecBCD synergistically lower strand-separation barriers and promote destabilization of representative efflux-pump ARG fragments (macB/tetA) during hyperthermophilic composting.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142445},
doi = {10.1016/j.jhazmat.2026.142445},
pmid = {42202519},
issn = {1873-3336},
abstract = {Hyperthermophilic composting (HC) effectively mitigates antibiotic residues and antibiotic resistance genes (ARGs), yet the molecular basis of ARG-derived DNA destabilization under extreme heat remains unclear. Here, we established an HC system reaching 87.3 ℃ (∼360 K) and combined metagenomics, AlphaFold prediction, molecular dynamics (MD), and free-energy calculations to investigate representative efflux-pump ARG fragments (macB/tetA). HC removed oxytetracycline, enrofloxacin, and sulfamethoxazole by 98.44%, 92.34%, and 99.63%, respectively, while overall ARG abundance declined markedly. Metagenomics identified 796 ARGs, dominated by efflux mechanisms, and qPCR confirmed multi-order decreases in macB and tetA. Nucleic acid processing/degradation genes, including recD/RecBCD-related homologs, were enriched during the high-temperature phase and negatively associated with ARG abundance. Based on these data, we constructed a candidate RecBCD model from metagenomic recB/recC/recD homologs. MD showed that this model maintained overall structural integrity at 360 K. AlphaFold predicted end-loaded candidate RecBCD-DNA complexes (ipTM/pTM ≈ 0.89-0.90) with local duplex opening. Subsequent MD revealed that RecBCD-bound DNA became more flexible, displayed weakened/reorganized hydrogen-bond networks, and sampled more multistate free-energy basins. Umbrella sampling further showed that strand-separation PMFs at 360 K were ∼25-30 kJ·mol[-1] lower than at 330 K, with tetA exhibiting a lower barrier and greater thermal sensitivity than macB. Together, these results support a working model in which high temperature lowers DNA stability and strand-separation barriers, thereby facilitating candidate RecBCD-mediated loading and local processing of representative efflux-pump ARG-derived DNA fragments during HC.},
}

@article {pmid42202778,
year = {2026},
author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M},
title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.001},
pmid = {42202778},
issn = {1934-6069},
abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.},
}

@article {pmid42184943,
year = {2026},
author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Zhang, J},
title = {In situ assembly of the humic acid-protein conductive network facilitates chain elongation for medium-chain fatty acids anaerobic production from waste activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134964},
doi = {10.1016/j.biortech.2026.134964},
pmid = {42184943},
issn = {1873-2976},
abstract = {Biosynthesis of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS) is primarily limited by intracellular reductive stress (NADH accumulation) and energy shortages. This work demonstrates that humic acid (HA), functioning as a redox mediator, effectively enhances the carbon chain elongation (CE) process. Optimal HA supplementation (1000 mg/L) increased the peak MCFAs yield by 98.3%, driving a fundamental shift in the dominant product spectrum from short-chain fatty acids (SCFAs) to MCFAs. Combined metagenomic and electrochemical analyses reveal that this enhancement originates from HA-mediated spatial and metabolic integration across multiple scales. Macroscopically, HA complexes with proteins to construct a conductive biopolymer network. Functioning as a highly efficient extracellular electron sink, this network significantly accelerates transmembrane electron discharge to consume excess intracellular electrons. This rapid electron extrusion alleviates reductive stress and relieves product feedback inhibition on dehydrogenases, concurrently inducing an elevated cellular energy charge (ATP surge). Subsequently, feedback regulation driven by this high-energy state suppresses the competitive acetogenic branch (Pta-ackA pathway), effectively preventing carbon loss. Dominated by the highly enriched CE taxon Candidatus_Microthrix, the microbial consortium exhibits a robust metabolic potential to channel carbon into synergistic RBO and FAB pathways. This metabolic shift, fueled by abundant precursors and energy, effectively circumvents acidic toxicity by rapidly consuming SCFAs. These findings elucidate the critical role of HA in reshaping microbial redox homeostasis, providing a robust mechanistic foundation for high-value carbon recovery engineering from complex solid wastes.},
}

@article {pmid42185267,
year = {2026},
author = {Zhou, YL and Feng, JC and Lu, R and Chen, Z and Mara, P and Tao, X and Liu, J and Huang, Y and Hu, J and Yao, J and Edgcomb, VP and Teske, A and Wang, X and Zhang, S},
title = {Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73573-4},
pmid = {42185267},
issn = {2041-1723},
support = {42494884//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42325603//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Anaerobic methanotrophic (ANME) archaea have been primarily documented by metagenomic analysis of environmental samples. The mechanisms that drive their diversification and speciation are poorly understood. Here we analyse the phylogenomic diversity at the species and strain levels of clade ANME-1 from deep-sea cold seeps, as a model system with a well-studied phylogenetic framework. We reconstruct high-quality circular metagenomic-assembled genomes (cMAGs) and identify highly variable genomic hotspots that distinguish them. Genomic differentiation and diversification in ANME-1 is associated with genes involved in prokaryotic defense systems, transport mechanisms and methane metabolism. In addition, heterologous expression of ANME-1 hicAB operons supports their proposed role as toxin/antitoxin systems, possibly involved in mediating responses to environmental stresses.},
}

@article {pmid42185302,
year = {2026},
author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R},
title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01021-8},
pmid = {42185302},
issn = {2055-5008},
support = {2020/06077-9//São Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//São Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; },
abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.},
}

@article {pmid42185318,
year = {2026},
author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR},
title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73524-z},
pmid = {42185318},
issn = {2041-1723},
support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.},
}

@article {pmid42185326,
year = {2026},
author = {Hoggard, M and Gios, E and Tee, HS and Geoghegan, JL and Handley, KM},
title = {DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73439-9},
pmid = {42185326},
issn = {2041-1723},
abstract = {Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and traits of environmental adaptation, we analyse metagenomic and metatranscriptomic data from an estuarine salinity gradient, including water and sediment. We then expand our analysis to globally-distributed viral genomes. Viral distributions vary by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, are largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, viruses feature osmoadaptive traits similar to their prokaryote hosts. These include slightly elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities, particularly in virus major tail and capsid proteins, which are not solely explained by reliance on host machinery. Further studies are needed to determine the primary driver of these modifications in viruses (e.g. environment or host) and whether these traits restrict virus distributions beyond host-range limitation. Overall, our findings indicate that successful proliferations of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) are rare, with viruses constrained to specific ecological niches.},
}

@article {pmid42185942,
year = {2026},
author = {Wang, Y and Peng, Y and Wang, B and Di, M and Xi, M and Yao, Z and Shi, C and Feng, Q and Yin, D and Li, J and Xu, X and Zhang, R and Peng, X},
title = {A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42185942},
issn = {1674-9782},
abstract = {BACKGROUND: Under high-concentrate feeding conditions, ruminants often experience rumen microecological imbalance and dysfunction, which can impair growth performance and increase the risk of antibiotic resistance gene (ARG) dissemination.

RESULTS: To evaluate the ameliorative effects of Aspergillus niger (A. niger) cultures, fattening sheep were randomly allocated into the following five groups: a control group (CON), a control diet supplemented with 250, 500, or 1,000 mg/kg A. niger cultures (designated as LA, MA, and HA, respectively); and an antibiotic group supplemented with 5,000 mg/kg chlortetracycline premix (AN). Microbial community analysis indicated that several bacterial taxa, including Succinivibrio sp900317105, Prevotella sp002353485, Quinella sp017515635, Quinella sp015206805, and Prevotella sp900320255, were significantly enriched in the A. niger culture-supplemented groups (P < 0.05). ARG profiling showed that the abundance of tetracycline resistance genes was significantly lower in all A. niger groups compared with the CON and AN groups (P < 0.05), while β-lactam resistance genes were significantly reduced in the HA group (P < 0.05). Furthermore, the abundances of Rank I and Rank II ARGs were significantly higher in the AN group than in the other groups, whereas the abundances of Rank II and Rank IV ARGs were significantly lower in the A. niger culture groups than in the CON and AN groups. Metabolomic analysis further demonstrated that supplementation with A. niger cultures significantly decreased the concentration of N-decanoyl-L-homoserine lactone (P < 0.05) while increasing the levels of N-3-oxotetradec-7Z-enoyl-L-homoserine lactone, indole-3-methyl acetate, and indole-3-propionic acid (P < 0.05).

CONCLUSIONS: These findings suggest that A. niger cultures can reduce the abundance of ARGs and mitigate the risk of ARG dissemination by modulating the rumen microbial community and associated metabolites.},
}

@article {pmid42185948,
year = {2026},
author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P},
title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12986-3},
pmid = {42185948},
issn = {1471-2164},
support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.

RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.

CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.},
}

@article {pmid42186028,
year = {2026},
author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y},
title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01335-5},
pmid = {42186028},
issn = {1475-2891},
abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.

METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10 years) and 133 adolescents (11-17 years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.

RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.

CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.},
}

@article {pmid42186092,
year = {2026},
author = {Wang, L and Li, F and Ma, Z and Ungerfeld, EM and Zhang, T and Zhang, Z and Liu, X and Zhang, Q and Zhang, X},
title = {Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02436-3},
pmid = {42186092},
issn = {2049-2618},
support = {32308686//The National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Yeast culture (YC) supplementation is widely adopted to mitigate rumen pH depression and alleviate the inhibition of fiber degradation under starch-rich diets. Yet, the underlying microbial mechanisms, particularly how yeast culture orchestrates fibrolytic communities and affects metabolic hydrogen flow in the rumen, remain a critical knowledge gap. Accordingly, elucidating the microbial basis by which yeast culture modulates fiber degradation and hydrogen utilization under starch-rich diets is of both theoretical and practical importance.

METHODS: We conducted a study with growing lambs receiving starch-rich diets that differed only in yeast culture supplementation (CON 0%, YC 1%). We evaluated their growth performance, apparent total-tract digestibilities, rumen fermentation end-products, and the rumen metagenome.

RESULTS: The YC treatment increased the lambs' final body mass (P = 0.02), average daily gain (P = 0.03), digestibilities of neutral detergent fiber (P < 0.001) and acid detergent fiber (P < 0.001), and rumen pH (P < 0.05), and tended to increase organic matter digestibility (P = 0.09). In addition, total VFA concentrations, particularly butyrate, were higher at 6 h post-morning feeding (P = 0.01). Fibrolytic and hydrogenotrophic taxa (e.g., Ruminococcus_E and Quinella) and CAZyme families, including GH43, GH31, GH9, and GH35, were enriched by the YC treatment, as were bacteria involved in fiber degradation and butyrate production. Furthermore, none of the top five YC treatment-enriched bacterial genomes contained any hydrogenase genes, which indicates that this butyrogenic fibrolytic consortium is significantly different from the hydrogen-producing fiber-degrading microorganisms we are familiar with.

CONCLUSION: Yeast culture supplementation promoted the proliferation of a distinct butyrogenic consortium that degrades fiber while apparently disposing intracellularly metabolic hydrogen generated during fermentation, rather than releasing it as H2. These findings provide a microbial basis for understanding how yeast culture improves fermentation efficiency under starch-rich diets and suggest that selecting yeast culture products capable of promoting butyrogenic fibrolytic bacteria may be beneficial for ruminant performance and rumen stability. Video Abstract.},
}

@article {pmid42186552,
year = {2026},
author = {Méndez-Sánchez, D and Pomahač, O and Valt, M and Bourland, WA and Čepička, I},
title = {An extensive morphological and molecular characterization of the neglected class Odontostomatea (Ciliophora).},
journal = {Marine life science & technology},
volume = {8},
number = {2},
pages = {289-323},
pmid = {42186552},
issn = {2662-1746},
abstract = {UNLABELLED: Odontostomatid ciliates, known for over a century, were historically classified within various taxonomic groups of Ciliophora Doflein, 1901 until their reclassification into the class Odontostomatea. Despite the recognition of 25 valid species, most descriptions predate the advent of silver impregnation and sequencing methods. Consequently, many species were described based solely on observations of live specimens, leading to incomplete or ambiguous records. To date, redescriptions of only three species include 18S rRNA gene sequences data, and their evolutionary relationships remain unresolved. In this study, we investigated 32 populations representing 15 species-including three newly described-across the genera Discomorphella, Epalxella, Limnomylestoma gen. nov., Mircalla gen. nov., Mylestoma, Pelodinium, Saprodinium, and Tostonella gen. nov. Comprehensive analyses were conducted using in vivo microscopy, silver impregnation, and scanning electron microscopy. We also designed specific primers to amplify the partial 18S rRNA gene of various odontostomateans and retrieved additional 18S rRNA sequences from environmental metatranscriptomic and metagenomic datasets. This study represents the most extensive investigation of Odontostomatea to date, confirming the monophyly of the class by revealing the position of Epalxella, reconstructing its internal phylogeny, identifying two main odontostomatean lineages, and revealing its remarkable diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-026-00352-x.},
}

@article {pmid42186601,
year = {2026},
author = {Zhang, Z and Jia, Z and Zhang, X and Zou, W and Chen, J},
title = {Late-onset cytomegalovirus pneumonia after autologous stem cell transplantation for angioimmunoblastic T-cell lymphoma: a case report.},
journal = {Therapeutic advances in infectious disease},
volume = {13},
number = {},
pages = {20499361261450721},
pmid = {42186601},
issn = {2049-9361},
abstract = {This case report illustrates a diagnostic and therapeutic challenge in a highly immunocompromised host: severe pneumonia occurring late after autologous hematopoietic stem cell transplantation (auto-HSCT). A 57-year-old male with angioimmunoblastic T-cell lymphoma (AITL) presented with hypoxemic respiratory failure 1 year post-auto-HSCT, a timeline extending beyond the typical high-risk period for opportunistic infections. A profoundly low CD4+ T-cell count (172/µL) was identified as the key predisposing factor. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) enabled rapid, unbiased pathogen detection, confirming cytomegalovirus (CMV) pneumonia (viral load: 3.0 × 10[4] copies/mL) with Klebsiella pneumoniae coinfection. An integrated management strategy was instituted, comprising early empiric coverage for Pneumocystis jirovecii pneumonia, targeted therapy with ganciclovir and levofloxacin, and adjunctive immunomodulation using intravenous immunoglobulin and corticosteroids. This comprehensive approach resulted in full recovery, highlighting that the severity of immune suppression-rather than time since transplantation alone-determines infection risk. This case challenges the conventional time-based risk paradigm and supports immune-guided surveillance. It underscores the transformative role of mNGS in diagnosing complex infections in immunocompromised patients and advocates for a management paradigm that concurrently addresses pathogen eradication and host immune dysfunction.},
}

@article {pmid42186944,
year = {2026},
author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F},
title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70160},
doi = {10.1111/1755-0998.70160},
pmid = {42186944},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; },
abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*DNA, Environmental/genetics
*Metagenomics/methods
*Computational Biology/methods
Bayes Theorem

@article {pmid42187250,
year = {2026},
author = {Liu, X and Kwok, L-Y and Zhang, W},
title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0024426},
doi = {10.1128/spectrum.00244-26},
pmid = {42187250},
issn = {2165-0497},
abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.

IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.},
}

@article {pmid42187318,
year = {2026},
author = {Tang, Y and Lin, Z and Liu, Z and Guo, J and Yang, C and Feng, L and Wang, Y and Zhang, P and Chen, Y},
title = {Impact of Corneal Microbial Latency Detected by Metagenomic next-generation sequencing on Postoperative Recovery Following Keratorefractive lenticule extraction.},
journal = {Journal of cataract and refractive surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/j.jcrs.0000000000001979},
pmid = {42187318},
issn = {1873-4502},
abstract = {PURPOSE: To investigate the microbial species latent in corneas of healthy individuals and determine whether small incision lenticule extraction (SMILE) serves as a risk factor for pathogen reactivation.

SETTING: The Ophthalmology Department of Peking University Third Hospital, Beijing, China.

DESIGN: Prospective Cohort Study.

METHODS: Metagenomic next-generation sequencing (mNGS) was employed to analyze the microbial composition of corneal lenticules from SMILE. Based on the results, patients were categorized into Viral Group (VG) and Non-Viral Pathogen Group (NVPG). Two Matched Groups (MG1 and MG2) were established by selecting pathogen-negative individuals at a 1:4 ratio relative to two positive groups. Using SPSS to analyze baseline characteristics, preoperative ocular parameters and postoperative ocular parameters among groups.

RESULTS: Among the detected pathogens, latent Herpesviruses were identified in 9 cases (4.31%), Papillomavirus were 4 cases (1.91%), and non-viral pathogens were 20 cases (9.57%). Both VG and NVPG groups showed no significant differences in baseline characteristics or preoperative ocular parameters compared with MG groups. In postoperative ocular parameters, no significant differences were found between VG and MG1, though intergroup variations in intraocular pressure and corneal thickness were observed (p>0.05). However, NVPG demonstrated significantly poorer results than MG2 in 1 month-spherical equivalent (p=0.033) and corneal epithelial staining (p=0.044).

CONCLUSION: These findings indicate pathogen latency does not affect ocular status and SMILE surgery is unlikely to reactivate latent viruses or exerts minimal influence. Viral latency has almost no impact on postoperative recovery, while latent non-viral pathogens may interfere with postoperative recovery.},
}