@article {pmid42753439,
year = {2026},
author = {Wang, B and Zhu, K and Wang, Z and Sun, W and Zha, Y and Wang, H and Zhang, Y and Zhang, Y and Song, Y and Zhang, H},
title = {Biogeographical pattern of persistent organic pollutant-transformation genes and their hosts across global inland waters.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143613},
doi = {10.1016/j.jhazmat.2026.143613},
pmid = {42753439},
issn = {1873-3336},
abstract = {Persistent organic pollutants (POPs) remain widespread in inland waters despite decades of regulation, yet the global distribution and ecological controls of microbial POP transformation potential remain largely unresolved. Here, we analyzed 1593 metagenomic samples from inland waters across six continents to investigate the biogeography, microbial hosts, and environmental drivers of POP transformation genes (POPTGs). We identified four major POP categories, with polychlorinated POP transformation genes dominating both water and sediment habitats. Sediments harbored significantly higher POPTG richness and abundance than water columns, highlighting their role as global reservoirs of POP transformation capacity. Unexpectedly, POPTG diversity displayed hump-shaped latitudinal pattern. Proteobacteria were the dominant POPTG carriers, and widespread host taxa generally possessed broader transformation repertoires. Nearly half of POPTG-carrying species were shared between habitats, while frequent associations with mobile genetic elements suggested potential horizontal dissemination of transformation traits. Structural equation modeling revealed that host diversity, anthropogenic pressure, and mean annual temperature collectively explained 38% of POPTG abundance variation, with host diversity exerting the strongest effect. Our findings establish a global framework linking microbial ecology with POP transformation potential and provide insights into predicting natural attenuation and remediation capacity of inland waters under environmental change.},
}

@article {pmid42753600,
year = {2026},
author = {Huang, Q and Zhang, Y and Bais, C and Liu, Y},
title = {Metagenome-resolved evidence that soluble factors in granular activated carbon-amended reactor effluent reprogram propionate metabolism and methanogenic pathways.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130925},
doi = {10.1016/j.jenvman.2026.130925},
pmid = {42753600},
issn = {1095-8630},
abstract = {Granular activated carbon (GAC) enhances anaerobic digestion performance, yet the mechanisms underlying reactor-scale improvements remain incompletely understood, particularly how GAC affects biomass not attached to its surface. Here, sludge from a non-GAC up-flow anaerobic sludge blanket reactor was incubated with 0.45-μm-filtered effluents from non-GAC and GAC-amended reactors under repeated propionate loading, followed by genome-resolved metagenomics. GAC-reactor effluent increased methane yield from 64 ± 3% to 76 ± 3% (p < 0.01) in the absence of GAC particles. A non-redundant catalog of 170 quality-filtered metagenome-assembled genomes (MAGs) was recovered, enabling pathway- and gene-set quantification. Genomic potential for both major propionate-oxidation routes increased in the GAC-effluent group relative to the non-GAC group, with a larger increase for the methylmalonyl-CoA (MMC) route than for the dismutation route (1.289- versus 1.221-fold). Accordingly, the MMC-to-dismutation preference ratio was 5.60% higher in the GAC-effluent group, alongside a broader carrier base. Cobamide potential shifted toward remodeling and cobamide-dependent use rather than increased de novo corrin-ring synthesis. Candidate electron-transfer architectures were also rebalanced: PilA-associated carriers became less prominent, whereas maturation-supported multiheme cytochrome carriers increased from 22.96% to 34.90% of community abundance, although H2/formate-module carriers remained prevalent. Quorum-sensing systems underwent pathway- and carrier-specific redistribution, while all eight curated extracellular-polysaccharide modules showed higher mean gene abundance in the GAC-effluent composite. These findings show that a filter-passing effluent fraction can extend GAC-associated effects beyond direct particle contact and link enhanced methanogenesis to a broader, redistributed network of metabolic, redox, and coordination capacities. This expands the mechanistic framework of conductive-material-assisted anaerobic digestion and provides a basis for harnessing GAC-derived functions throughout the reactor.},
}

@article {pmid42753610,
year = {2026},
author = {Feng, Y and Xu, G and Wu, D and Sun, D and Shao, Q and Xu, H},
title = {Community-level eDNA decay patterns in marine zooplankton: Implications for optimizing eDNA-based marine environmental monitoring.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120341},
doi = {10.1016/j.marpolbul.2026.120341},
pmid = {42753610},
issn = {1879-3363},
abstract = {Environmental DNA (eDNA) has the potential to greatly transform marine ecological monitoring, yet its capacity for accurate biodiversity estimates is constrained by its decay process. Previous research has largely focused on laboratory-cultured single species, and thus the dynamics of mixed-species eDNA from natural communities remain poorly understood. Here, we conducted a 10-day time-series experiment to track the community-level eDNA decay process following the complete removal of zooplankton, employing an integrated approach of morphological analysis, quantitative PCR (qPCR), metabarcoding, and metagenomics. Our results reveal that the decay of marine zooplankton eDNA is a complex, heterogeneous process. Total community eDNA declined rapidly during the first two days (0-2 d), followed by a slower decline (4-10 d), as quantified by qPCR. Crucially, the taxonomic composition of the detectable eDNA pool changed substantially over time: the relative read abundance of copepods declined sharply after only two days, whereas that of medusae persisted high throughout the experiment. Furthermore, methodological comparison revealed significant discrepancies in temporal trajectories between metabarcoding and metagenomics regarding the detected community composition. To optimize eDNA-based marine environmental monitoring, we propose matching target taxa and molecular methods to the temporal scale of interest. Short-lived signals of copepods might support timely, near-snapshot assessments of recent environmental change by eDNA metabarcoding, whereas long-lived medusa eDNA appears to integrate occurrence over time. Taxon-specific signal persistence and method-dependent detectability should therefore be considered when interpreting eDNA monitoring data. This framework can strengthen the reliability of eDNA-based biodiversity assessments and support more effective marine ecosystem monitoring.},
}

@article {pmid42753987,
year = {2026},
author = {Benech, N and Guarino-Vignon, P and McLellan, P and Campidelli, C and Sergeant, M and Joubert, F and Truong, S and Barbier, P and Sandoz, E and Ruffié, P and Sedda, D and Delmeule, A and Pradat, P and Landman, C and Bourrier, A and Marchand, L and Alric, L and Scanzi, J and Cassir, N and Dureault, A and Piet, E and Gallet, S and Botelho-Nevers, E and Roussel-Gaillard, T and Cuerq, C and Ader, F and Guillet, M and Rolhion, N and Grill, JP and Lamaziere, A and Chatel, JM and Pechine, S and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 Strain for the prevention of multiple-recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.09.002},
pmid = {42753987},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Recurrent Clostridioides difficile infection (rCDI) results from persistent microbiome dysfunction and impaired colonization resistance. Although fecal microbiota transplantation (FMT) is effective, defined and scalable alternatives are needed. We evaluated whether a single commensal strain could restore key microbiome functions and prevent recurrence.

METHODS: We assessed Faecalibacterium prausnitzii EXL01 in a murine CDI model and a multicenter, open-label single-arm phase I trial including adults with ≥3 CDI episodes. Following vancomycin preconditioning, patients received oral EXL01 for 8 weeks with 8-week follow-up. Primary endpoint was safety. Secondary endpoints included recurrence at week 8. Longitudinal stool samples underwent shotgun metagenomics and metabolomics. Outcomes were benchmarked against matched FMT cohorts. Additional in vitro and murine studies of EXL01 were performed.

RESULTS: In mice, EXL01 reduced C. difficile burden and intestinal inflammation in an antibiotic-disrupted murine model. Six patients were treated; no treatment-related serious adverse events occurred. Five of six patients (83.3%) remained recurrence-free at week 8, comparable to matched FMT cohorts. EXL01 was detectable in stool up to 8 weeks post-treatment. Multi-omics analyses showed that EXL01 engraftment was correlated with restoration of bile acid metabolism, including reduced primary bile acids and increased secondary bile acids, and increased short-chain fatty acid production, particularly butyrate, despite limited taxonomic recovery. EXL01 selectively deconjugated bile acids in vitro.

CONCLUSIONS: A single, well-characterized bacterial strain was associated with restoration of key microbiome functions and low recurrence rates in high-risk rCDI. These findings support precision microbiome therapeutics targeting ecosystem function rather than taxonomic complexity. Controlled trials are ongoing. (clinicaltrials.gov; NCT06306014).},
}

@article {pmid42754030,
year = {2026},
author = {Yang, M and Luo, Y and Wu, S and Jia, W and Chen, H and He, F and Cheng, R},
title = {Oral supplementation of 6'-sialyllactose in early-life enhances cognitive function in mice via modulating gut microbiota and promoting brain myelination.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-29049},
pmid = {42754030},
issn = {1525-3198},
abstract = {This study aimed to investigate the effects of early-life oral supplementation with 6'-sialyllactose (6'-SL) on neurobehavioral development in mice and the potential mechanisms involving the microbiota-gut-brain (MGB) axis. Neonatal mice received daily oral gavage of saline or 6'-SL from birth to postnatal day (PND) 21. Behavioral tests (Y-maze, open field, light-dark box, forced swim test) were conducted from PND 37-41. Fecal metagenomics and short-chain fatty acid (SCFA) levels were assessed, and brain gene expression was analyzed by RNA sequencing and reverse transcription quantitative real-time PCR (RT-qPCR) at PND 21 and PND 42. Our findings revealed that 6'-SL supplementation enhanced cognitive function in growing mice, as evidenced by improved performance in the Y-maze test. Early-life 6'-SL supplementation exerts profound and sustained regulatory effects on the gut microbiota and SCFA. At PND 21, 6'-SL enriched Akkermansia muciniphila and elevated acetate, isobutyrate, and isovalerate, while suppressing Enterococcus. At PND 42, Akkermansia muciniphila and Escherichia were further enriched, while Alistipes and Duncaniella were inhibited. Meanwhile, acetate, isobutyrate and propionate levels remained elevated. Notably, these changes were observed not only at the end of the intervention but also persisted at PND 42, indicating a sustained long-term effect of 6'-SL supplementation. In contrast, most myelin genes were altered only to a small extent at PND 21, compared with their marked upregulation in the PFC at PND 42 (Mbp, Mog, Olig1, Sox10, Egr2, Vegfa). Correlation analysis revealed that the abundance of Akkermansia muciniphila was positively correlated with isobutyrate levels, Escherichia showed a positive correlation with propionate levels, while Enterococcus was negatively correlated with acetic acid. These SCFA were positively associated with myelin gene expression. Further, these genes were positively associated with cognitive performance, suggesting their potential involvement in cognitive function. Thus, 6'-SL enhances spatial cognition in early-life mice through a mechanism involving gut microbiota and SCFA modulation, subsequent upregulation the transcription of prefrontal myelination-related gene. This study provides novel insights into the mechanisms by which 6'-SL regulates early brain development via the MGB axis and offers critical theoretical support for nutritional supplementation strategies in infancy.},
}

@article {pmid42754171,
year = {2026},
author = {Palanga, E and Pinel-Galzi, A and Filloux, D and Pinault, A and Kpemoua, KE and Ali, E and Julian, C and Richard, D and Poulicard, N and Roumagnac, P and Hébrard, E},
title = {New insights into phylogenetic diversity of maize yellow mosaic virus revealed by viral sequences from Togo.},
journal = {Virus research},
volume = {},
number = {},
pages = {199804},
doi = {10.1016/j.virusres.2026.199804},
pmid = {42754171},
issn = {1872-7492},
abstract = {Maize yellow mosaic virus (MaYMV) (Polerovirus MAYMV, Solemoviridae) is an emerging virus with a global distribution in maize and other cereals. Transmitted by aphids in a circulative, non-propagative manner, MaYMV forms icosahedral particles and possesses a positive-sense, single-stranded RNA genome. Three distinct phylogenetic groups of MaYMV have been described in Asia, East Africa and Latin America. In this study, 19 genomes from Togo and Burkina Faso were sequenced using Virion-Associated Nucleic Acid-Based Metagenomics (VANA) combined with classical RT-PCR to constitute the first dataset of West African MaYMV genomic sequences. Phylogenetic analyses of global dataset of 92 genomic sequences revealed two sub-lineages within the African strain. We also identified 15 recombinant MaYMV genomes involving intra- and inter-continental exchanges. A comparative analysis of non-recombinant sequences was conducted and identified 19 molecular signatures in proteins P0, P1, P4 and P5. Notably, residue K/R 253 in P5 was lineage-specific and is located near conserved polero- and luteovirus residues known to be involved in aphid interactions, suggesting a potential role in viral transmission.},
}

@article {pmid42754770,
year = {2026},
author = {Petri, RM and Ricci, S and Jelinski, M and Hund, A},
title = {Observational study of the microbiome of perforated abomasal ulcers in unweaned beef calves in Canada.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42754770},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Abomasum/microbiology/pathology ; *Cattle Diseases/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Stomach Ulcer/veterinary/microbiology ; Canada ; Bacteria/classification/genetics/isolation & purification ; Male ; *Microbiota ; },
abstract = {In western Canada, perforating abomasal ulcers (AU) are generally diagnosed postmortem in beef calves up to 2 months of age. Certain microbes have been associated with AU, but the evidence is circumstantial. Thus, analyzing the abomasal microbiome in calves with and without AU may provide insight into the etiology of the disease. Using 16S rRNA gene sequencing, abomasal tissues from Western Canadian beef calves, with (n = 27) and without AU (n = 17), were analyzed for microbial diversity. No significant differences were seen between microbiomes of AU and CON calves despite numerical differences in abundance. Therefore, a subsample of 18 tissues (12 AU, 6 CON) were analyzed using untargeted metagenomic sequencing for determination of phylogeny, and the presence of antimicrobial resistance genes (ARGs). Staphylococcaceae (1.5%), Campylobacteraceae (1.4%) and Enterobacteriaceae (1.4%) were seen across all samples. Differential abundance analysis revealed Streptomyces spp. REN17 to be less abundant in AU calves, suggesting a potential association between Streptomyces spp. and calf gut health. An ARG associated with polymyxin resistance was found to be differentially abundant in calves with a history of antimicrobial therapy. Although differences were observed in the predicted metabolic functions among groups, none reached statistical significance. In our study, no consistent microbial signature associated with AU was identified, despite the differential abundance of individual taxon, nor did prior antimicrobial therapy associate to the growth of specific microbiota. To better understand the potential role of the abomasal microbiota in AU etiology and the impact of early life interventions in beef calves, a larger sample size is needed.},
}

Animals
Cattle
*Abomasum/microbiology/pathology
*Cattle Diseases/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Stomach Ulcer/veterinary/microbiology
Canada
Bacteria/classification/genetics/isolation & purification
Male
*Microbiota

@article {pmid42754901,
year = {2026},
author = {Zhou, C and Fu, B and Hou, X and Wu, WM and Khan, A and Li, C and Han, H and Li, X},
title = {Untapped enzymatic potential: dehalogenase- and peroxidase-driven PVC degradation by gene carriers in Tibetan plateau pikas.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42754901},
issn = {2049-2618},
mesh = {Animals ; *Lagomorpha/microbiology/metabolism ; Biodegradation, Environmental ; *Polyvinyl Chloride/metabolism ; *Hydrolases/metabolism/genetics ; Tibet ; Rhodococcus/enzymology/genetics/metabolism ; *Microplastics/metabolism ; *Peroxidase/metabolism/genetics ; *Bacteria/classification/genetics/enzymology/isolation & purification ; },
abstract = {BACKGROUND: Wide distribution of polyvinyl chloride microplastics (PVC-MPs) has been documented in remote regions such as the Qinghai-Tibet Plateau (QTP). Microbial degradation of plastics is frequently coupled with lignocellulose-degrading enzymatic machinery. As a ubiquitous biological sampler on the QTP, the herbivore plateau pika (Ochotona curzoniae), which harbors diverse lignocellulose-degrading enzymes, represents a promising reservoir for novel PVC-degrading enzymes.

RESULTS: In this study, a PVC-MPs feeding trial of plateau pikas revealed gut microbiota recruitment of plastic degraders. Subsequent enrichment experiment yielded a PVC-degrading consortium that depolymerized PVC into long-chain alkanes, with Rhodococcus and Leifsonia identified as PVC-response specialist and generalist, respectively. Multi-omics analysis supported a putative degradation pathway initiated by haloalkane dehalogenase (HLD) and involving oxidases. Furthermore, novel RhHLD (from Rhodococcus MAG) released 11.5 mg L[-1] chloride ions from PVC films, whereas dye-decolorizing peroxidase LeDyP from Leifsonia MAG generated PVC-degrading intermediates. Analysis of 39 metagenomic datasets further confirmed that haloalkane dehalogenase and dye-decolorizing peroxidase are prevalent in the gut of wild pikas.

CONCLUSIONS: This study elucidates the PVC-degrading potential of herbivore gut microbiota and expands the catalytic toolkit for plastic bioremediation, underscoring the bioprospecting potential in extreme ecosystems Video Abstract.},
}

Animals
*Lagomorpha/microbiology/metabolism
Biodegradation, Environmental
*Polyvinyl Chloride/metabolism
*Hydrolases/metabolism/genetics
Tibet
Rhodococcus/enzymology/genetics/metabolism
*Microplastics/metabolism
*Peroxidase/metabolism/genetics
*Bacteria/classification/genetics/enzymology/isolation & purification

@article {pmid42755253,
year = {2026},
author = {Gupta, KH and Israni, AK and Onyeaghala, G},
title = {Gut microbial metabolism of immunosuppressive drugs: from metagenomic associations to functional enzyme biomarkers.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001314},
pmid = {42755253},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: Inter-individual variability in immunosuppressant exposure remains a major challenge in transplantation. Pharmacogenomics and host-related factors contribute to this variability, with increasing evidence suggesting that the gut microbiome is also an important determinant of drug metabolism. This review summarizes recent advances in microbiome-mediated metabolism of immunosuppressive drugs like tacrolimus and mycophenolate and highlights emerging functional approaches to identify clinically relevant microbial enzymes.

RECENT FINDINGS: Microbial β-glucuronidases contribute to the enterohepatic recirculation of mycophenolic acid by deconjugating mycophenolic acid glucuronide, influencing systemic exposure and gastrointestinal toxicity. In parallel, gut bacteria such as Faecalibacterium prausnitzii can directly metabolize tacrolimus into less active metabolites, potentially contributing to variability in drug exposure and dose requirements. Recent studies further demonstrate that metaproteomic and enzyme activity-based approaches provide greater functional resolution than metagenomics alone for identifying microbiome-associated drug metabolism pathways.

SUMMARY: Current evidence supports a significant role for the gut microbiome in immunosuppressant pharmacokinetics and functional microbial enzymes represent promising biomarkers of immunosuppressant disposition. Moving beyond gene-level associations toward the functional characterization of microbial enzymes through the integration of metaproteomics, metabolomics, and enzyme activity assays with pharmacokinetic modeling may facilitate development of microbiome-based biomarkers and microbiome-guided precision dosing strategies in transplantation. Future integration of microbiome-derived functional data into therapeutic drug monitoring and pharmacokinetic models may improve individualized immunosuppressive therapy and transplant outcomes.},
}

@article {pmid42755618,
year = {2026},
author = {Li, L and Luo, Y and Liu, S and Liang, C and Ruan, H and Peng, P and Huang, Z},
title = {Genome-resolved gut metagenomics identifies an Escherichia coli-Collinsella signature associated with Wagner 4 gangrenous diabetic foot ulcers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1893357},
pmid = {42755618},
issn = {1664-3224},
mesh = {Humans ; *Escherichia coli/genetics ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Gastrointestinal Microbiome/genetics ; *Actinobacteria/genetics ; Metagenome ; Male ; Female ; Feces/microbiology ; },
abstract = {Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1-3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1-3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. To prioritize robust candidates, we combined two complementary approaches: random forest (RF) stability selection, which identified 24 MAGs with reproducibly high classification importance across resampled folds, and covariate-adjusted MaAsLin2 differential-abundance testing. Intersecting the results of both approaches prioritized three MAGs supported by each method: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG signature (out-of-bag AUC = 0.703) retained much of the discriminatory information captured by the broader 24-MAG RF classifier, with concordant, opposing abundance directions across classifier interpretation, differential-abundance testing, and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli-Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response, or recovery.},
}

Humans
*Escherichia coli/genetics
*Diabetic Foot/microbiology
*Metagenomics/methods
*Diabetes Mellitus, Type 2/complications/microbiology
*Gastrointestinal Microbiome/genetics
*Actinobacteria/genetics
Metagenome
Male
Female
Feces/microbiology

@article {pmid42755623,
year = {2026},
author = {Xu, Z and Wang, Y and Zhang, X and Guo, F and Chen, J and Geng, H and Li, Y and Gao, Y},
title = {Application of metagenomic next-generation sequencing in gastrointestinal infections in children after allogeneic hematopoietic stem cell transplantation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1868295},
pmid = {42755623},
issn = {2235-2988},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Child, Preschool ; Male ; Child ; Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Viruses/classification/isolation & purification/genetics ; Transplantation, Homologous/adverse effects ; *Gastrointestinal Diseases/microbiology/diagnosis/etiology/virology ; Diarrhea/microbiology ; Adolescent ; Bacterial Infections/microbiology/diagnosis ; },
abstract = {BACKGROUND: Gastrointestinal infections are the leading cause of death for pediatric patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT). Conventional microbiological testing (CMT) often fails to identify the pathogens, resulting in delayed diagnosis and poor treatment outcomes. Metagenomic next-generation sequencing (mNGS) offers a promising method that does not require cultivation, but its application in this specific situation has not been fully studied.

METHODS: 185 fecal samples were collected from 96 children who underwent HSCT and suffered from diarrhea. All samples were simultaneously subjected to mNGS and CMT testing. The diagnostic performance, pathogen spectrum and prevalence of gastrointestinal infection pathogens were systematically analyzed and compared.

RESULTS: Compared with CMT, mNGS detected significantly more bacteria, viruses and atypical pathogens. Among the pathogens detected by mNGS in the 185 fecal samples, the predominant bacteria were Pseudomonas spp. (28 cases), Clostridioides spp. (28 cases), Campylobacter spp. (25 cases), Acinetobacter spp. (16 cases), and Staphylococcus aureus (13 cases). Clostridioides spp. exhibited a significantly higher detection rate in fecal samples from patients receiving CsA-based combination therapy (p=0.01099) and those with bone marrow from unrelated donors (p=0.03188). Pseudomonas aeruginosa (p = 0.03038) and Campylobacter spp.(p = 0.00549) were detected significantly more frequently in patients within the early phase (1-30 days). The detection rate of Adenovirus was markedly decreased during the intermediate phase (31-100 days) (p = 0.01458). Furthermore, Polyomavirus showed a significantly increased detection rate in patients with short-term diarrhea (1-3 days) (p=0.03451).

CONCLUSION: Our findings highlight the substantial superiority of mNGS over CMT in pathogen detection, with a broader coverage encompassing bacteria, viruses, and atypical organisms. It uncovers complex polymicrobial and viral-bacterial co-infections, delineates infection dynamics linked to immune reconstitution. Integrating mNGS into the diagnostic workflow holds great potential for enabling precision antimicrobial therapy and improving outcomes in this high-risk population.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Child, Preschool
Male
Child
Feces/microbiology/virology
Infant
Bacteria/classification/isolation & purification/genetics
Viruses/classification/isolation & purification/genetics
Transplantation, Homologous/adverse effects
*Gastrointestinal Diseases/microbiology/diagnosis/etiology/virology
Diarrhea/microbiology
Adolescent
Bacterial Infections/microbiology/diagnosis

@article {pmid42755660,
year = {2026},
author = {Wei, W and Yan, P and Wang, F and Wang, Q and Li, C and Bai, X and Zhang, Y and Bao, Y and Li, J and Yu, K},
title = {Sarcopenia in patients with active ulcerative colitis: associations with serum metabolites and gut microbiota.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1942104},
pmid = {42755660},
issn = {2296-861X},
abstract = {BACKGROUND: Sarcopenia has garnered increasing attention in ulcerative colitis (UC) owing to its association with adverse clinical outcomes; however, its pathogenesis in the context of UC remains insufficiently characterized.

METHODS: Hospitalized patients aged 18-70 years with active UC were consecutively enrolled at the Department of Gastroenterology, Peking Union Medical College Hospital, and age-matched healthy controls (HCs) were recruited. Body composition was assessed by bioelectrical impedance analysis (BIA), and muscle strength was evaluated by handgrip strength. Sarcopenia was diagnosed in accordance with the Asian Working Group for Sarcopenia (AWGS) 2025 consensus. Serum high-sensitivity C-reactive protein (hsCRP) of patients was recorded at admission. Intestinal barrier function was evaluated by serum diamine oxidase (DAO). Serum metabolites were profiled by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Gut microbiota composition and functional pathways were analyzed using metagenomic sequencing.

RESULTS: Fifty-seven patients with active UC and 35 HCs were enrolled. The prevalence of sarcopenia, myopenia, and low muscle strength in the UC cohort was 40.4, 50.9, and 64.9%, respectively. Serum hsCRP was significantly higher in UC patients with sarcopenia (p = 0.011), whereas serum DAO showed no significant difference between UC patients with and without sarcopenia. Primary bile acids (BAs), conjugated BAs, and conjugated primary BAs were significantly increased, while hippuric acid, valerylcarnitine, and 2-methylbutyrylcarnitine were significantly decreased, in sarcopenic relative to non-sarcopenic UC patients (all p < 0.05). However, the association between serum hippuric acid and sarcopenia was not significant after adjusting for disease activity and hsCRP. At the genus level, Bacteroides and Streptococcus were the most prominently decreased and increased taxa in sarcopenic UC patients, respectively. Metagenomic functional analysis revealed that the relative abundance of the protein digestion and absorption pathway was significantly lower in sarcopenic UC patients (p = 0.030).

CONCLUSION: UC-related sarcopenia exhibits notable associations with systemic inflammation, gut dysbiosis, and perturbations in circulating metabolites, including BAs and acylcarnitines.},
}

@article {pmid42755900,
year = {2026},
author = {Wu, T and Wang, G and Xu, N and Xu, K and Chen, G},
title = {Case Report: A cluster of cases with rash associated with Chlamydia pneumoniae infection.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1922611},
pmid = {42755900},
issn = {2296-858X},
abstract = {We report a case of clustered rashes among teenagers associated by Chlamydia pneumoniae (CP) infection. Most patients only presented with rashes without significant fever or other respiratory tract symptoms. Metagenomic next-generation sequencing (mNGS) of blood samples identified the culprit - the nucleic acid sequence of CP was detected in the peripheral blood of the index case. The results of targeted next-generation sequencing (t-NGS) of throat swabs further supported the presence of CP. After antibiotic treatment, the patients' conditions improved. In this case, we should have a systematic understanding of rashes and mucositis caused by respiratory tract infections to facilitate further diagnosis and treatment.},
}

@article {pmid42755932,
year = {2026},
author = {Pascual, J and Martínez-Blanch, JF and Amaro, C and Roig, FJ},
title = {Editorial: Advances in immunity and microbiome: exploring key interactions and innovations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1933468},
doi = {10.3389/fimmu.2026.1933468},
pmid = {42755932},
issn = {1664-3224},
}

@article {pmid42756064,
year = {2026},
author = {Zhang, G and Huang, Y and Gong, Z and Xu, C and Ding, X and Cai, W and Wu, J},
title = {Multi-omics analyses unveil gut microbiota and metabolites signatures in deoxycholic acid-associated intestinal inflammation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917982},
pmid = {42756064},
issn = {1664-302X},
abstract = {OBJECTIVE: High-fat diet (HFD) is closely related to the increased incidence of inflammatory bowel disease (IBD), and excessive fecal deoxycholic acid (DCA) induced by HFD makes significant contribution to the colonic inflammation. However, the precise mechanisms remain unclear. This study aims to explore the association between DCA-induced alteration of gut microbiota as well as related metabolites and intestinal inflammation.

METHODS: Wild-type C57BL/6 J mice were orally administrated with or without 0.2% DCA for 12 weeks, then the alteration of gut microbiota signature and fecal metabolites were analyzed by metagenomic sequencing and widely-targeted metabolomics, respectively. The colonic tissue injury was confirmed by histopathological analysis and pro-inflammatory cytokines production was determined by qPCR and ELISA.

RESULTS: DCA administration induced gut microbiota dysbiosis and fecal metabolomic profile disturbance, accompanied with significantly increased expression of pro-inflammatory cytokines in intestine, including TNF-α, IL-6 and IL-1β, and obvious tissue damage. Specifically, α-diversity of gut microbiota was greatly reduced by excessive DCA, and abundance analysis together with linear discriminant analysis of effect size (LEfSe) identified Bacteroides and Desulfovibrio as potential biomarkers of DCA exposure. Excessive DCA significantly decreased the abundance of Eubacterium plexicaudatum, bacterium 1xD42-87 and Ruminococcus flavefaciens, which were positively correlated with the downregulation of multiple metabolites reported to possess anti-inflammatory activities, especially indoles, vitamin D3 and alpha-CEHC. Meanwhile, DCA administration dramatically increased the abundance of Parabacteroides distasonis and Bacteroide acidifacien, which were positively correlated with the upregulation of metabolites reported to have pro-inflammatory properties, including multiple bile acid metabolites such as chenodeoxycholic acid, glycochenodeoxycholic acid and lithocholic acid. Spearman correlation analysis emphasized the important effects of aforementioned microbiota and metabolites in the association between DCA and intestinal inflammation.

CONCLUSION: Our study revealed that excessive DCA led to concurrent alterations of gut microbiota and metabolites, which exhibited significant correlations with intestinal inflammation, suggesting a potential indirect regulatory pathway that may involve gut microbiota. Targeting DCA-related gut microbiota or metabolites might represent a promising intervention for HFD-associated colonic inflammation.},
}

@article {pmid42756159,
year = {2026},
author = {Jiang, P and Zhou, M and Liao, Y and Du, W and Liu, M},
title = {Associations of the gut mycobiome and its cross-kingdom interactions with estrus return in post-weaning sows revealed by metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1892244},
pmid = {42756159},
issn = {1664-302X},
abstract = {Post-weaning estrus return is a critical determinant of reproductive efficiency in the swine industry. While the gut microbiome, particularly bacteria, has been significantly associated with estrus return in sows, the role of the gut mycobiome and its cross-kingdom interactions with bacteria in this context remains largely unexplored. Here, we employed fecal metagenomics to characterize the gut mycobiome in 85 sows and investigated its association with post-weaning estrus return. A total of 22 fungal species were significantly associated with estrus return. Normal-return sows were characterized by increased abundance of Arxiozyma slooffiae (formerly Kazachstania slooffiae) and decreased abundances of Malassezia pachydermatis and Alternaria rosae. Moreover, we uncovered cross-kingdom interactions between fungi and bacteria associated with estrus return, where Arxiozyma slooffiae showed a positive correlation with Prevotella spp. enriched in normal-return sows. These interactions were predicted to involve the exchange of metabolites, including Fe[2+], thiamine, and nicotinate. Fungal biomarkers demonstrated good discriminatory power for distinguishing normal-return and non-return sows (AUC = 0.906), and the combination with bacterial biomarkers further enhanced the performance (AUC = 0.947). Integrated multi-omics analysis revealed extensive associations between gut fungi and hormones and hormone-related compounds, as well as microbial functional pathways. Notably, Arxiozyma slooffiae was positively correlated with phytoestrogens (including daidzein and genistein) and the steroid hormone biosynthesis pathway but negatively correlated with testosterone. Collectively, these findings provide comprehensive insights into the role of the gut mycobiome and its cross-kingdom interactions in sow reproductive performance.},
}

@article {pmid42756787,
year = {2026},
author = {Fang, Q and Gong, X and Mao, S and Ren, D and Chen, H and Pan, M and Huang, X and Chen, J and Chen, X and Wu, H and Zheng, Y},
title = {Pilot Surveillance Program on Pneumonia with Public Health Risk - Shanghai Municipality, China, 2024-2025.},
journal = {China CDC weekly},
volume = {8},
number = {35},
pages = {1096-1103},
pmid = {42756787},
issn = {2096-7071},
abstract = {China's surveillance for pneumonia of unknown etiology, established in 2004, is vital for identifying novel pathogens early. However, limited cases have been reported, indicating potential challenges regarding sensitivity and operational efficiency.

WHAT IS ADDED BY THIS REPORT?: A pilot surveillance program to detect pneumonia with public health risk was implemented in Shanghai between October 2024 and July 2025. The system was established using an optimized workflow involving refined case definitions, tiered laboratory testing network, and joint expert risk assessment process. Forty-six cases were identified in medical institutions at different levels, demonstrating the system's operational feasibility.

The pilot provides a framework for a proactive paradigm for monitoring emerging respiratory threats. Future surveillance should prioritize identifying case clusters and specific epidemiological links (e.g., suspicious animal contact and travel history). Applying advanced diagnostics, including metagenomic sequencing, and integrating multi-source data with information technology are crucial next steps for building a more responsive surveillance system.},
}

@article {pmid42756829,
year = {2026},
author = {Elmaghrabi, MM and Alghofaili, SA and Mahmoud, MM and ElKharashy, AK and Kulsum, SN},
title = {Metagenomic-driven predictive biosafety and contamination traceability in stem cell manufacturing: Translating outbreak genomics into regenerative medicine.},
journal = {Regenerative therapy},
volume = {33},
number = {},
pages = {101170},
pmid = {42756829},
issn = {2352-3204},
abstract = {Stem cell manufacturing and regenerative medicine laboratories are highly vulnerable to microbial contamination due to complex processing workflows, extensive manipulation, prolonged culture conditions, and continuous environmental exposure. Conventional microbiological methods remain fundamental for laboratory quality control; however, they may underestimate concealed resistance determinants, microbial diversity, contamination pathways, and transmission dynamics. Recent advances in metagenomic sequencing have transformed outbreak investigation, resistome characterization, and genomic surveillance, providing unprecedented opportunities for contamination monitoring and biosafety management. This review proposes a translational biosafety framework that integrates metagenomic surveillance with contamination traceability systems in stem cell manufacturing and regenerative medicine laboratory environments. The review discusses contamination challenges, limitations of conventional microbiological diagnostics, metagenomic surveillance approaches, predictive biosafety concepts, genomic traceability systems, corrective and preventive action (CAPA) integration, and future artificial intelligence (AI)-assisted monitoring strategies. Lessons from sequencing-based outbreak investigations involving multidrug-resistant microorganisms highlight the potential utility of metagenomic surveillance for early detection of contamination, microbial source attribution, resistome characterization, environmental monitoring, and contamination traceability. Integrating sequencing-guided diagnostics with laboratory traceability systems and CAPA-based quality management may shift biosafety practices from reactive contamination control toward proactive predictive biosurveillance. The proposed framework may strengthen contamination prevention, improve manufacturing reproducibility, support regulatory compliance, and enhance the reliability of stem cell processing and regenerative medicine applications. Future studies are needed to standardize sequencing-guided biosafety workflows and evaluate their implementation in academic, research, and clinical-grade stem cell manufacturing laboratories.},
}

@article {pmid42756860,
year = {2026},
author = {Yao, C and Lei, L and Wang, W and Jiang, L and Yang, W and Sheng, Y and Liu, Z and Qian, X},
title = {Global intI1 abundance quantifies livestock antimicrobial-resistance risk.},
journal = {Environmental science and ecotechnology},
volume = {33},
number = {},
pages = {100759},
pmid = {42756860},
issn = {2666-4984},
abstract = {Livestock farming environments are major reservoirs of antimicrobial resistance (AMR), yet scalable genetic indicators that quantitatively capture AMR risk remain limited. The class 1 integrase gene intl1 is a hallmark of class 1 integrons (CL1s), which couple gene capture with horizontal transfer capacity and have emerged as leading candidates. However, their suitability as a direct proxy for livestock-associated AMR risk has not been rigorously tested at scale. Here we show that the abundance of intI1 functions as a robust quantitative indicator of livestock-associated AMR risk. Using a custom Class 1 Integrase Database expanded by 63.5% and integrating 4017 livestock metagenomes, 9625 livestock-derived isolate genomes, and approximately 1.2 million human clinical isolate genomes, we demonstrate that intI1 abundance tracks host- and geography-dependent risk patterns, that livestock CL1s carry compact, conserved resistance-cassette arrays matching clinical spectra, and that nearly all are plasmid-borne, with their efficient dissemination facilitated by Tn402, ISCR, and IS110 family elements. A random-forest model trained on these data predicts global intI1 abundance and associated risk with high accuracy (R [2] = 0.93), revealing persistent hotspots across Asia, sub-Saharan Africa, and South America over two decades. These findings establish intI1 as a practical, single-platform proxy that can be incorporated into One Health surveillance and early-warning systems.},
}

@article {pmid42758039,
year = {2026},
author = {Agudelo, C and Nsereko, M and Ainebyona, A and Andama, A and Castro, R and Leung, SRM and Nakafeero, J and Nannyonga, G and Nolan, K and Teran, L and Wambi, P and Young, MG and Kato-Maeda, M and Cattamanchi, A and Jaganath, D and Wobudeya, E and Wolf, AR},
title = {Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciag573},
pmid = {42758039},
issn = {1537-6591},
abstract = {BACKGROUND: Stool-based molecular tests provide noninvasive options for pediatric tuberculosis (TB) diagnosis, but have lower sensitivity compared to sputum-based tests. Untargeted metagenomic sequencing (mNGS) on stool could improve sensitivity and identify new gene targets for molecular testing.

METHODS: We performed shotgun mNGS on DNA isolated from stool samples of children undergoing assessment for pulmonary TB in Uganda. We defined the performance of mNGS to identify Mycobacterium tuberculosis (Mtb) against a microbiological reference standard (MRS, TB if sputum Xpert Ultra or culture positive) and a composite reference standard (TB if confirmed or unconfirmed TB). We also compared accuracy of mNGS against stool-based Xpert Ultra. Finally, we identified enriched genomic loci among Mtb classified reads.

RESULTS: We analyzed 176 stool samples of children with a median age of 3.6 years (IQR, 1-6 years). Against the MRS, the sensitivities of mNGS with positive TB defined as ≥ 1, 2, or 5 sequence fragments were 35.5% (95% CI 19%-55%), 25.7% (12%-45%), and 19.4% (13%-25%) respectively, and specificities 92.64% (87%-96%), 97% (93%-99%), and 99.3% (96%-100%). Stool Xpert Ultra had similar sensitivity (22.6%) to stool mNGS considering all samples tested. In a head-to-head comparison, stool mNGS had lower sensitivity than stool Xpert Ultra (38.5% vs. 53.8%, difference -15.3%, 95% CI 14-68 to 25-81). mNGS utilized rRNA, virulence proteins and membrane proteins not targeted in current PCR-based platforms.

CONCLUSIONS: Metagenomic sequencing of stool DNA did not increase sensitivity of TB detection, but identified novel targets for molecular testing that may support development of more sensitive tests.},
}

@article {pmid42758297,
year = {2026},
author = {Xu, H and Zhong, T and Li, J},
title = {The link of oral microbiome diversity to stroke risk: Evidence from the National Cohort Study in the United States.},
journal = {The International journal of neuroscience},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/00207454.2026.2736054},
pmid = {42758297},
issn = {1563-5279},
abstract = {OBJECTIVE: To assess whether oral microbiome diversity and periodontal health are independently associated with stroke prevalence in a U.S. adult cohort, with implications for risk stratification in physical medicine and rehabilitation.

METHODS: We analyzed cross-sectional data from 4,438 adults in the National Health and Nutrition Examination Survey (NHANES) 2009-2012, using survey-weighted logistic regression to evaluate associations between stroke and oral microbiome β-diversity (unweighted UniFrac), α-diversity (Shannon, Simpson), and clinical periodontal measures (probing depth, clinical attachment loss, and tooth count), adjusting for age, sex, race/ethnicity, education, income, smoking, alcohol consumption, body mass index, and diabetes.

RESULTS: In crude models, each 1-mm increase in mean probing depth was associated with higher stroke odds (odds ratio [OR] = 1.89, 95% confidence interval [CI] = 1.39-2.56), as was each 1-mm increase in clinical attachment loss (OR = 1.50, 95% CI = 1.32-1.71); each additional tooth was associated with lower odds (OR = 0.91, 95% CI = 0.88-0.94). After stepwise adjustment, attachment loss (OR = 1.23, 95% CI = 1.04-1.46; P = 0.017) and tooth count (OR = 0.96, 95% CI = 0.92-0.99; P = 0.024) remained significant, whereas probing depth did not (OR = 1.30, 95% CI = 0.90-1.88; P = 0.156). A threshold effect was observed at approximately 1.46 mm for probing depth. β-Diversity clusters did not differ in stroke prevalence after adjustment (global P = 0.61), and neither α-diversity index was significant in the stepwise- or fully-adjusted models (Shannon fully-adjusted OR = 1.29, 95% CI = 0.97-1.72; P = 0.081). Periodontal associations were consistent across sex and age strata; the non-significant findings in younger participants were attributable to limited statistical power.

CONCLUSION: Clinical periodontal measures, particularly attachment loss and tooth count, were associated with stroke prevalence independently of traditional cardiovascular risk factors, whereas oral microbiome diversity indices were not. These measures may serve as readily accessible markers for refining stroke risk assessment. The cross-sectional design precludes causal inference, and findings require validation in prospective cohorts with adjudicated stroke outcomes and metagenomic profiling before clinical translation. Nevertheless, these results support integrating oral health assessment into routine stroke risk evaluation and highlight periodontal inflammation as a potentially modifiable contributor to cerebrovascular disease.},
}

@article {pmid42758523,
year = {2026},
author = {Lan, G and Li, X and Lu, Z and Zhang, Y and Feng, F and Liu, J and Wu, W and Liu, J and Zhou, Y and Gu, J and Ma, R and Qi, D},
title = {Gut Microbiome Functional Reprogramming Reflects Divergent Social Strategies in a Wild Primate.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70185},
pmid = {42758523},
issn = {1749-4877},
support = {2025JZG01//Foundation for Non-Invasive Research on Golden Snub-Nosed Monkeys in Baihe Nature Reserve/ ; CAZG2025C13//Chengdu Research Base of Giant Panda Breeding/ ; 32570615//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a critical interface between host physiology and environmental challenges, yet its role in mediating behavioral strategies in socially complex mammals remains unclear. Using metagenomic sequencing of wild golden snub-nosed monkeys (Rhinopithecus roxellana), we investigated how social status (one-male unit [OMU] leaders vs. all-male unit [AMU] individuals) and seasonal variation (winter-spring [WS] and summer-autumn [SA]) shape gut microbial structure and function. We found that seasonal shifts drive primary microbial restructuring, but social status exerts a strong influence, particularly during the SA mating season. OMU leaders maintained stable microbial communities enriched in energy conservation and cellular maintenance pathways including methane metabolism and peptidoglycan biosynthesis. In contrast, AMU individuals exhibited highly plastic microbiomes potentially suited for competition, with enhanced functions in environmental sensing (e.g., flagellar assembly and two-component systems) and nitrogen metabolism. AMU gut microbiomes also showed reduced diversity in SA, indicating specialization for competitive readiness. These results demonstrate that the gut microbiome is functionally compartmentalized by social status, providing distinct metabolic toolkits that align with divergent behavioral strategies-investment in unit fitness for OMU leaders versus risk-taking for AMU individuals. Our study reveals the gut microbiome is closely associated with social adaptation in primate societies, serving as a dynamic indicator of divergent behavioral strategies.},
}

@article {pmid42758594,
year = {2026},
author = {Khoo, BY and Sadasiv, MS},
title = {A clinician's guide to infectious diseases diagnostics: principles, pitfalls, and stewardship.},
journal = {Postgraduate medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/postmj/qgag134},
pmid = {42758594},
issn = {1469-0756},
abstract = {Accurate interpretation of infectious diseases diagnostic tests requires a comprehensive understanding of test principles, performance characteristics, and the cognitive discipline of diagnostic stewardship. While contemporary modalities range from traditional culture to high-throughput metagenomics, postgraduate trainees may struggle to reconcile complex laboratory data with the clinical context. This educational primer aims to bridge the gap between laboratory science and bedside decision-making. We first distinguish between analytical (limit of detection) and clinical sensitivity, emphasizing how disease prevalence dictates predictive values. We then move beyond theoretical limitations to identify clinician-modifiable pre-analytical variables, such as specimen collection techniques, that directly affect diagnostic test performance. A core framework for Diagnostic Stewardship is introduced, focusing on the test-treatment threshold and the critical distinction between organism detection and active infection. Through illustrative case studies, we apply clinical reasoning strategies to resolve common pitfalls, including serological cross-reactivity, polymerase chain reaction inhibition in critical samples, and prozone phenomena. Enhanced diagnostic competence requires more than memorizing test characteristics; it demands the integration of stewardship principles, awareness of cognitive biases, and active collaboration with other healthcare professionals. This review provides a structured approach for trainees to navigate the complexities of modern infectious disease diagnostics. Key messages Infectious disease tests should be interpreted in light of the syndrome, pre-test probability and the timing, and type of specimen tested. NAAT positivity detects nucleic acid, not necessarily viable organisms or active disease. Most avoidable microbiological diagnostic errors begin before the sample reaches the laboratory. Discordant test results should trigger a deliberate diagnostic pause and, when needed, discussion with the laboratory.},
}

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42759123,
year = {2026},
author = {Guo, X and He, Z and Wang, X and Ren, H and Ren, B and Zhang, J and Liu, P and Song, Z and Zhao, B},
title = {Sustained nitrogen release and nitrogen-cycling functional genes jointly shape NH3-N2O loss trade-offs under long-term controlled-release fertilization.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130951},
doi = {10.1016/j.jenvman.2026.130951},
pmid = {42759123},
issn = {1095-8630},
abstract = {Simultaneously mitigating ammonia (NH3) volatilization and nitrous oxide (N2O) emissions without compromising crop productivity remains a critical challenge in sustainable nitrogen management. Drawing on a long-term field experiment established in 2013, this study integrated multi-year gaseous nitrogen loss measurements with metagenomic sequencing to assess the performance of polymer-coated fertilizer (PCF) and sulfur-coated fertilizer (SCF) relative to conventional urea (CU) in intensive maize production. Both coated urea treatments substantially suppressed NH3 losses relative to CU, with PCF achieving consistent reductions of 72.3%-92.8% and SCF showing more variable reductions of 28.8%-89.7%. However, sustained nitrogen release from coated urea concurrently stimulated N2O production, with increases of 8.3%-114.3% under PCF and 15.5%-88.9% under SCF. Critically, NH3 mitigation substantially outweighed the N2O penalty, enabling PCF to reduce the combined NH3 and N2O losses by 39.8%-69.5% and yield-scaled losses by 45.9%-70.9%, respectively, while enhancing crop yield by 4.7%-11.2%. Soil enzyme assays and metagenomic analyses suggested that NH3 suppression was associated with reduced urease activity and enrichment of archaeal ammonia oxidation and downstream nitrification genes under PCF, whereas elevated N2O emissions were correlated with sustained soil inorganic nitrogen replenishment that appeared to override concurrent declines in denitrification genes. These findings suggest that PCF reduces the combined NH3 and N2O losses while sustaining crop productivity, although the N2O penalty outweighed the climate benefit of NH3 mitigation in three of four years. The net environmental performance of controlled-release fertilizers therefore depends on the indicators evaluated and was associated with nitrogen release dynamics and the corresponding functional gene networks.},
}

@article {pmid42759371,
year = {2026},
author = {Ge, L and Yang, S and Zeng, X and Huang, Y and Lai, H and Wang, Y and Mei, Y and Zhao, N},
title = {Unlocking the metabolomics and metagenomics code of phenyl moiety chromophore profiles underlying naturally occurring yellow color of dry-salted radish.},
journal = {Food chemistry},
volume = {529},
number = {},
pages = {151190},
doi = {10.1016/j.foodchem.2026.151190},
pmid = {42759371},
issn = {1873-7072},
abstract = {The aim of this study was to investigate the molecular basis and the role of biotic and abiotic factors in the development of naturally occurring yellow color of dry-salted radish by analyzing color, physicochemical properties, amino acid profile, glucosinolates and myrosinase activity, metabolomics and metagenomics. Results showed that metabolites of phenyl-containing amino acids (Trp, Phe, Try, carboline, indole, pyrrolidone), curcuminoids (curcumin, gingerol), polyphenols and flavonoids were the major chromophores for color of dry-salted radish. Additionally, chromophore formation involved assistance with pyrrole-containing compounds, glucosinolates and isothiocyanates. Low Aw (<0.7) was the key abiotic factor to facilitate the chromophore formation by enriching the genera of Lactiplantibacillus, Lacticaseibacillus, Pediococcus, Levilactobacillus and Halomonas, and promoted gene functions linked to metabolism of Trp, Phe, Try, curcuminoids, polyphenol, flavonoid, phenyl, pyrrolidone, transport of amino acid and ions, hyperosmotically responsive system. Capitalizing on this finding would empower the development of dry-salted vegetables with appealing and stable color.},
}

@article {pmid42748823,
year = {2026},
author = {Yang, R and Liu, C and Liu, J and Liu, Y and Wang, C and Guo, D and Zhou, J and Tai, X and Zhang, G and Zhang, B},
title = {Antibiotic resistome patterns across wheat soil microdomains under cadmium exposure and their associations with rhizosphere metabolite profiles.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143642},
doi = {10.1016/j.jhazmat.2026.143642},
pmid = {42748823},
issn = {1873-3336},
abstract = {The co-contamination of heavy metals and antibiotic resistance genes (ARGs) poses an increasing challenge to agroecosystems, yet its relationships with rhizosphere metabolism and microbial communities remain poorly understood. We integrated metagenomic sequencing, untargeted metabolomics, and absolute qPCR in a wheat pot experiment to characterize resistome patterns across unplanted bulk soil (O), root-zone soil (PS), and rhizosphere soil (PR) under three Cd treatments. At the booting stage, observed ARG subtype richness and total TPM-normalized ARG abundance were higher in root-associated compartments, whereas responses to cadmium within PR were heterogeneous and non-monotonic. Absolute qPCR broadly supported enrichment of selected resistance genes in root-associated soils. Community analyses identified Pseudomonadota and Actinomycetota as potential ARG-associated taxa. Metabolomic differentiation between PR and O was substantially greater than the differences among Cd treatments within PR, while metabolite-ARG associations partly reflected compartment-level covariation. ARG and metal resistance gene abundances showed strong covariation relationship, and contig-level analysis identified genetic contexts consistent with potential linkage among resistance determinants across both control and Cd-amended treatments. Overall, spatial differentiation among soil microdomains was more consistent than treatment-associated Cd patterns. These findings identify the wheat rhizosphere as an important zone of ARG enrichment under Cd exposure while highlighting the need for host-resolved and functional validation.},
}

@article {pmid42749142,
year = {2026},
author = {Zhang, Y and Wang, H and Ling, Y and Wang, H and Wang, S and Wang, X and Liu, F},
title = {Carbon-sulfur regulation for deep nitrogen removal in Arundo donax straw/elemental sulfur-amended surface flow constructed wetlands: Metagenomic and metabolomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135874},
doi = {10.1016/j.biortech.2026.135874},
pmid = {42749142},
issn = {1873-2976},
abstract = {Plant-derived carbon can sustain heterotrophic denitrification in low carbon-to-nitrogen (C/N) constructed wetlands, but how the relative loading of elemental sulfur (S[0]) and solid carbon regulates mixotrophic nitrogen removal remains unclear. In this study, six surface flow constructed wetlands (SFCWs) amended with different Arundo donax straw/S[0] ratios were operated for 96 days to treat simulated secondary effluent. Under the tested conditions, the 1:1 ratio (450 g/450 g) showed the best performance, with a stable-period total inorganic nitrogen (TIN) removal efficiency of 77.6 ± 5.7 % and a relatively low net SO2-4 accumulation per unit TIN removed (1.47 mg SO2-4/mg N). Insufficient S[0] weakened late-stage NO-3-N removal; the excess S[0] configuration showed HS[-]/S[2-] accumulation and was associated with a higher risk of dissimilatory nitrate reduction to ammonium without improving nitrogen removal; and carbon-limited configurations showed insufficient electron donor availability. Vertical profiles showed that carbon release and NO-3-N reduction were concentrated in the lower layers. Metagenomic analysis showed that the 1:1 configuration enriched representative functional taxa, including hydrolytic/fermentative bacteria (Clostridium), sulfur-transforming bacteria (Sulfuritalea, Thiobacillus), and nitrogen reduction-related taxa (Azonexus). Functional gene abundances suggested greater potential for anaerobic carbon oxidation and sulfur transformation in the 1:1 configuration. Metabolomic analysis indicated substrate-associated changes in sulfur-related metabolites and in pathways related to nicotinamide adenine dinucleotide and coenzyme A. Network analysis further showed that carbon metabolism and sulfur transformation were closely associated with nitrogen removal performance. These results provide new insights into substrate regulation of mixotrophic denitrification in SFCWs treating low C/N wastewater.},
}

@article {pmid42749360,
year = {2026},
author = {Zhang, K and Gorelik, MG and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G},
title = {Divergent microbial preludes to necrotising enterocolitis defined by gut phages and bacterial resistomes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338976},
pmid = {42749360},
issn = {1468-3288},
abstract = {BACKGROUND: Translating microbiome correlations into robust predictive features for complex gut disorders remains elusive, partly due to oversimplified models of pathogenesis and neglect of the virome, a key player in microbial ecosystems. Necrotising enterocolitis (NEC), a devastating disease of preterm infants with no reliable clinical predictors, exemplifies this challenge.

OBJECTIVE: To determine the predictive potential of the gut prophageome and polymicrobial aetiologies for NEC.

DESIGN: We applied integrated metagenomic and metatranscriptomic analyses and machine learning to 1825 longitudinal stool samples from 43 preterm infants who later developed NEC and 86 gestational age-matched and birthweight-matched controls across three US hospitals. We characterised gut prophageome acquisitions and their association with clinical exposures, including antibiotics, diet and pharmacotherapies. To predict NEC risk, we integrated pre-onset prophageome, antibacterial resistome and bacteriome profiles with neonatal pathology, stratifying the cohort by disease onset timing (early: ≤40 days; late: >40 days) for separate analysis.

RESULTS: NEC cases exhibited distinct viral diversity trajectories before disease onset. Early-onset NEC was best predicted by phage-bacterial interaction signatures (75% accuracy, 81% sensitivity). Metatranscriptomics revealed increased phage DNA abundance with low gene expression, suggesting a lysogenic lifestyle that may stabilise pathobionts. These phages encode metabolic genes potentially enhancing pathobiont resilience. Late-onset NEC was best predicted by antibacterial resistome profiles (83% accuracy).

CONCLUSION: The gut prophageome serves as both a source of pre-symptomatic predictive signals and an active modulator of NEC pathogenesis, with distinct microbial mechanisms driving early-onset and late-onset disease. These polymicrobial etiologies inform strategies for early detection, risk stratification and the development of microbiome-targeted preventive and therapeutic interventions.},
}

@article {pmid42749361,
year = {2026},
author = {Qian, Z and Han, J and Lyu, B and Ainiwaer, A and Zhao, Q and Wang, S and Cheng, J and Li, Y and Sun, Y and Zhang, X and Lu, Y},
title = {Longitudinal gut microbiome dynamics during immunotherapy identify microbial features of clinical benefit in advanced primary liver cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339115},
pmid = {42749361},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiome has been linked to immune checkpoint inhibitor (ICI) outcomes, but the temporal dynamics of microbial communities during treatment remain poorly characterised.

OBJECTIVE: To characterise gut microbiome trajectories during ICI therapy and evaluate whether on-treatment microbial states improve the identification and generalisability of pretreatment biomarker signatures.

DESIGN: We performed a large prospective longitudinal shotgun metagenomic study of 315 patients with advanced primary liver cancer receiving ICI-based therapy, profiling 777 serial stool metagenomes collected at baseline and at approximately 3-month intervals on treatment. Responders (durable clinical benefit ≥6 months) contributed extended follow-up beyond 18 months. On-treatment windows were used for feature discovery; baseline-trained models were evaluated across all nine public ICI cohorts (n=1204).

RESULTS: Responders showed higher baseline alpha diversity and distinct community structure. Longitudinal profiling revealed marked ecological remodelling during therapy in both response groups, characterised by reduced network connectivity, increased modularity and strong time point specificity of discriminatory species. Using the on-treatment contrast at ~6 months (T2) as a discovery window, we identified a 16-species panel. A baseline model built from this panel outperformed models based on baseline-only feature discovery and generalised across nine public ICI studies. The resulting gut microbiome-derived immunotherapy outcome score stratified overall and progression-free survival in the discovery cohort (HRs 0.49 and 0.44) and across multiple external datasets, including stable-disease subsets.

CONCLUSION: The gut microbiome undergoes structured ecological remodelling during ICI therapy; on-treatment longitudinal windows improve pretreatment signature portability and support microbiome-guided stratification in immuno-oncology.},
}

@article {pmid42749373,
year = {2026},
author = {Gao, H and Shen, J and Chen, D and Mol, BW and Hu, W and Liang, Z and Bai, X and Han, X and Zhu, J and Wang, H and Liu, X and Su, C and Chen, Y and Weng, R and Liu, Y and Li, W and Zhang, D},
title = {Labour induction in low-risk women at 39 weeks of gestation: a randomised trial in China (LIRIC) - protocol of an open label, randomised controlled trial.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e123251},
pmid = {42749373},
issn = {2044-6055},
mesh = {Humans ; Female ; Pregnancy ; China ; *Labor, Induced/methods ; *Cesarean Section/statistics & numerical data ; Randomized Controlled Trials as Topic ; Infant, Newborn ; Gestational Age ; Adult ; Infant ; Pregnancy Trimester, Third ; Perinatal Mortality ; },
abstract = {INTRODUCTION: The A Randomized Trial of Induction Versus Expectant Management (ARRIVE) first demonstrated that elective induction of labour (IOL) at 39 weeks in low-risk pregnancies reduced the likelihood of caesarean section (CS) without compromising perinatal safety; however, the generalisability of these findings remains debated, leading to uncertainty in clinical practice. The Labour Induction in Low-risk Women at 39 Weeks of Gestation: a Randomised Trial in China (LIRIC) aims to evaluate whether 39-week elective IOL reduces CS rates compared with expectant management while exploring its impact on infant neurodevelopment and multiomics profiles.

METHODS AND ANALYSIS: This is a single-centre, open-label, randomised controlled trial in China. A total of 1074 low-risk pregnant women (nulliparous or multiparous) will be randomly assigned (1:1 ratio) to either 39-week IOL or expectant management. The primary outcome is the CS rate. Secondary outcomes include a composite of severe neonatal morbidity and perinatal mortality and infant neurodevelopmental scores (Bayley Scales of Infant Development; Bayley-4 and Ages and Stages Questionnaires; ASQ-3), among others. Data analysis will follow the intention-to-treat principle. Biospecimen will be collected for metagenomic and metabolomic analyses, with results to be reported separately.

ETHICS AND DISSEMINATION: The protocol has been approved by the Ethics Committee of Women's Hospital, School of Medicine, Zhejiang University. Informed consent will be obtained from all participants. Results will be disseminated via peer-reviewed journals, and standardised infant developmental reports will be provided to participants to enhance study benefit.

TRIAL REGISTRATION NUMBER: NCT07082530.},
}

Humans
Female
Pregnancy
China
*Labor, Induced/methods
*Cesarean Section/statistics & numerical data
Randomized Controlled Trials as Topic
Infant, Newborn
Gestational Age
Adult
Infant
Pregnancy Trimester, Third
Perinatal Mortality

@article {pmid42749445,
year = {2026},
author = {Agusetyaningsih, I and Lestari, DA and Pandupuspitasari, NS and Setiaji, A and Philco, SV and Sugiharto, S},
title = {Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {3},
pages = {100775},
doi = {10.1016/j.jgeb.2026.100775},
pmid = {42749445},
issn = {2090-5920},
abstract = {Antibiotic resistance is a growing global health concern, with poultry systems acting as important reservoirs of antibiotic resistance genes (ARGs). However, resistome and functional profiles of indigenous chickens raised under traditional systems remain underexplored. This study aimed to characterize the antibiotic resistome, virulence factor genes, and metabolic potential of gut microbiota in Indonesian Kedu chickens using a shotgun metagenomic approach. Digesta samples from five gastrointestinal segments of 21 healthy adult chickens were analyzed through high-throughput sequencing. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Antibiotic Resistance Genes Databases (ARDB), while virulence factors and functional genes were annotated using Virulence Factor Database (VFDB), Clusters of Orthologous Groups (COG), and Carbohydrate-Active EnZymes (CAZy) databases. Results revealed a diverse resistome dominated by multidrug resistance and efflux pump mechanisms, with prominent genes associated with fluoroquinolone, tetracycline, β-lactam, and glycopeptide resistance. The detection of clinically relevant ARGs suggests that genetic determinants associated with antimicrobial resistance are present in the gut microbiota of traditionally raised Kedu chickens, although metagenomic data alone cannot determine whether these genes are actively expressed or confer phenotypic resistance. Virulence factor analysis showed functions related to adherence, immune evasion, iron acquisition, quorum sensing, and efflux activity, reflecting strong microbial adaptability. Functional profiling demonstrated enrichment in translation, carbohydrate and amino acid metabolism, genome maintenance, and cell envelope biogenesis. Additionally, CAZyme analysis indicated a high capacity for complex polysaccharide degradation, supporting efficient utilization of fiber-rich traditional diets. In conclusion, this study provides a comprehensive metagenomic overview of antibiotic resistance and functional potential in Kedu chicken gut microbiota, emphasizing the importance of incorporating indigenous poultry into antimicrobial resistance surveillance within a One Health framework.},
}

@article {pmid42750334,
year = {2026},
author = {Zhang, S and Xiao, L and Mo, G},
title = {[Progress in the application of bronchoalveolar lavage fluid in the diagnosis of infectious lung diseases].},
journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology},
volume = {42},
number = {9},
pages = {844-850},
pmid = {42750334},
issn = {1007-8738},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/cytology/immunology ; *Lung Diseases/diagnosis/microbiology/immunology ; },
abstract = {Bronchoalveolar lavage fluid (BALF) contains diverse cellular components and pathogens, directly reflecting the local immune status at sites of pulmonary infection. By detecting pathogens such as bacteria, fungi, and viruses within these samples and analyzing changes in the immune cell composition and cytokine levels, it will help to assess the immune microenvironment of infected lung regions and to predict disease prognosis. In recent years, the application of artificial intelligence in BALF analysis has significantly enhanced the efficiency of cell classification and counting. Combined with molecular diagnostic methods such as metagenomic next-generation sequencing, this approach deeply explores the diagnostic value of immune cells, pathogens, and their molecular characteristics in BALF for infectious lung diseases. It will provide more precise support for early disease identification, personalized treatment, and clinical decision-making.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology/cytology/immunology
*Lung Diseases/diagnosis/microbiology/immunology

@article {pmid42750336,
year = {2026},
author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YPR},
title = {Alamandine/MrgD pathway modulates gut-bone marrow axis in ageing.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70656},
pmid = {42750336},
issn = {1476-5381},
support = {AG056881/NH/NIH HHS/United States ; P20GM103442/NH/NIH HHS/United States ; U42 OD010918/NH/NIH HHS/United States ; },
abstract = {BACKGROUND AND PURPOSE: Ageing is associated with colon epithelial barrier disruption and up-regulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in ageing via modulating gut-BM axis.

EXPERIMENTAL APPROACH: Mice, 2-3 (Young) or 22-24 months (Old), were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Faecal microbiome was analysed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Caecal or serum bacterial metabolites were analysed and the caecal supernatants (CS) were tested for myelopoietic potential.

KEY RESULTS: MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in ageing was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels and this was antagonized by NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the microbiota with decreased Bacillota/Bacteroidota in ageing. Ala decreased the CD80[+] and increased CX3CR[+] macrophages in the Old colons. Old-CS induced myelopoiesis in BM cells with higher number of pro-inflammatory macrophages, which was prevented by Ala treatment.

CONCLUSIONS AND IMPLICATIONS: Targeting Ala/MrgD pathway is a promising approach for ameliorating the inflammatory stress in ageing by restoring homeostasis in the gut-BM inter-organ communication.},
}

@article {pmid42750565,
year = {2026},
author = {Pothikamjorn, TL and Gonzales, JA},
title = {Molecular biomarker profiling in noninfectious uveitis: a chronological review of discovery.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
pmid = {42750565},
issn = {1531-7021},
abstract = {PURPOSE OR REVIEW: Noninfectious uveitis (NIU) encompasses a heterogeneous group of immune-mediated intraocular inflammatory diseases whose complexity has driven systematic molecular biomarker discovery. This review presents NIU molecular biomarkers organized by biological category; autoantigens, human leukocyte antigens (HLA) and genetic markers, cellular immune subsets, cytokines, chemokines, and multiomics platforms including proteomics, microbiome metagenomics, metabolomics, and single-cell transcriptomics with each category presented in strict chronological order of landmark discovery.

RECENT FINDINGS: We present a review organized along two nested timelines. Categories are presented in the order they historically emerged in the field, and within each category, landmark discoveries appear in chronological sequence. This allows the reader to trace how each biomarker category evolved: from foundational autoantigen identification in experimental uveitis models, through the genomic revolution of HLA association studies, into cellular immunophenotyping, cytokine profiling of aqueous humor, chemokine mapping of intraocular trafficking, and finally the emerging omics platforms that may potentially anchor precision medicine in NIU. Each biomarker is paired in line with its linked targeted therapeutic.

SUMMARY: Biomarker research has transformed the understanding of NIU from a clinically defined syndrome into a group of molecularly distinct immune disorders. Advances spanning autoantigens, genetics, immune-cell profiling, cytokines, chemokines, and multiomics have revealed novel pathogenic mechanisms and therapeutic targets. Integration of these biomarkers with targeted therapies may accelerate the transition toward precision medicine in uveitis care.},
}

@article {pmid42750609,
year = {2026},
author = {Ma, X and Zhong, L and Wang, T and Zhang, Y and Liu, X and Ma, S and Dang, D},
title = {Clinical and etiological characteristics of severe community-acquired pneumonia: A two-center retrospective analysis from Xi'an and Jiaxing in China.},
journal = {The Journal of international medical research},
volume = {54},
number = {9},
pages = {3000605261489324},
doi = {10.1177/03000605261489324},
pmid = {42750609},
issn = {1473-2300},
mesh = {Humans ; *Community-Acquired Pneumonia/microbiology/epidemiology ; Male ; Female ; Retrospective Studies ; China/epidemiology ; Aged ; Severity of Illness Index ; Anti-Bacterial Agents/therapeutic use ; Sputum/microbiology ; *Community-Acquired Infections/microbiology ; },
abstract = {ObjectiveThis study was conducted to evaluate the baseline clinical profile, causative pathogens, and treatment patterns of severe community-acquired pneumonia across two medical centers (Xi'an and Jiaxing) from January 2023 to August 2025.MethodsWe extracted data regarding medical profile, demographic characteristics, comorbidities, laboratory parameters, treatments during hospitalization, and outcomes for these patients from electronic records. Pathogens were detected using a combination of sputum culture/throat-swab polymerase chain reaction with metagenomic next-generation sequencing or targeted next-generation sequencing.ResultsAmong the 204 severe community-acquired pneumonia patients, majority were men (72.55%, 95% confidence interval: 66.05%-78.21%); the age range of the population was 65-79 years (41.18%, 95% confidence interval: 34.65%-48.03%), and chronic obstructive pulmonary disease was the predominant chronic pulmonary condition, present in 28.92% of the study participants. Laboratory evaluations revealed high illness severity scores (Acute Physiology and Chronic Health Evaluation II score: 19.00 (14.00, 24.00) and Sequential Organ Failure Assessment score: 7.00 (6.00, 10.00)). Pathogens were identified using metagenomic next-generation sequencing or targeted next-generation sequencing of blood/sputum/bronchoalveolar lavage fluid and polymerase chain reaction of sputum culture/throat-swab in 117 and 85 cases, respectively. Klebsiella pneumoniae was the most common pathogen, present in 20.10% of the participants (95% confidence interval: 15.18%-26.13%), followed by coronavirus 2019 (16.18%, 95% confidence interval: 11.76%-21.85%), and influenza A virus (12.75%, 95% confidence interval: 8.85%-18.02%). Most frequently administered medicines were β-lactam/β-lactamase-inhibitor combinations (89.22%) and carbapenems (60.78%). All patients received respiratory support, with 15.69% undergoing continuous renal-replacement therapy and 5.39% receiving extracorporeal membrane oxygenation. The in-hospital mortality rate was 38.73% (79/204, 95% confidence interval: 32.31%-45.56%).ConclusionSevere community-acquired pneumonia, which is most often caused by K. pneumoniae in our region, regularly complicates chronic obstructive pulmonary disease and other chronic pulmonary diseases, requires broad-spectrum antibiotics and life-support, and is associated with a relatively high mortality rate.},
}

Humans
*Community-Acquired Pneumonia/microbiology/epidemiology
Male
Female
Retrospective Studies
China/epidemiology
Aged
Severity of Illness Index
Anti-Bacterial Agents/therapeutic use
Sputum/microbiology
*Community-Acquired Infections/microbiology

@article {pmid42750770,
year = {2026},
author = {Saha, S and Dutta, M and Bosu, A},
title = {Reframing Technology and Ethics in Corneal Xenotransplantation: A Scoping Review of Standards and Safety in Ophthalmology.},
journal = {Health care science},
volume = {},
number = {},
pages = {},
pmid = {42750770},
issn = {2771-1757},
abstract = {Xenotransplantation offers a potential solution to the critical global organ shortage by allowing the transplantation of organs from non-primate animals to humans. To address the critical barriers of biological safety, zoonotic infections, and immunological rejection, this review evaluates current innovations in genetically engineered donor species strategies and assesses existing ophthalmological standards, employing specific expression of human regulatory proteins (hCD46/hCD55) and genetically modified triple knockout (GGTA1/B4GalNT2/CMAH), biophysical thresholds, porcine cytomegalovirus screening, bacterial/mycotic cultures, and DNA sequencing for unidentified organisms. Employing a snowball strategy across PubMed Central, ResearchGate, and Wiley Online Library, 47 articles were selected and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews. The feasibility of xenotransplantation relies heavily on advancements in donor technology and genotype transparency, animal husbandry and biosafety, infectious testing and surveillance, recipient monitoring and lifetime surveillance, biosafety incident and response plan, data governance, sharing and oversight, and animal welfare and social license, necessitating pathogen observation, biosecure storage, bioexclusion monitoring, and good manufacturing practice-style manual, quantitative polymerase chain reaction for porcine cytomegalovirus, porcine reproductive and respiratory syndrome virus, hepatitis E virus, alongside porcine endogenous retrovirus-A/B/C; metagenomic sequencing initially, followed by 1, 3, 6, and 12 months, and subsequently once every year, systematic and preliminary persistent sampling evaluations, independent data safety monitoring board, collaborative guidelines, encrypted databases, and data retention. The integration of endothelium-protective human genes, including hA20 or hHO-1, into genetically altered donor corneas in non-human primate xenografts, is expected to minimize initial post-transplant endothelial cell density loss by ≥ 20% compared to existing models. While clustered regularly interspaced short palindromic repeats-based modifications offer transformative potential for xenotransplantation, their reliability currently depends on establishing stringent biosafety standards.},
}

@article {pmid42750901,
year = {2026},
author = {Musleh, L and Montilli, M and Ammendolia, MG and Sciarra, A and Riccioli, A and Maurizi, L and Longhi, C},
title = {More than an infection: the ecological puzzle of recurrent urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1927507},
pmid = {42750901},
issn = {2235-2988},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology ; Recurrence ; Microbiota ; Reinfection/microbiology ; Host Microbial Interactions ; Dysbiosis ; Urinary Tract/microbiology ; },
abstract = {Recurrent urinary tract infections (rUTIs) represent one of the most common infectious conditions worldwide, yet their pathophysiology extends far beyond repeated episodes of acute bacterial cystitis. Increasing evidence indicates that recurrence may arise through overlapping mechanisms including reinfection from intestinal or periurethral reservoirs, intracellular bacterial persistence, microbial dysbiosis, impaired mucosal immunity and chronic inflammatory remodelling of the bladder microenvironment. Current diagnostic frameworks remain largely based on symptom-based definitions and standard urine culture, approaches that incompletely capture the biological complexity of recurrent disease. This limitation is evident even at the definitional level, where clinically pragmatic categories often fail to reflect the heterogeneous mechanisms underlying recurrence. Advances in expanded urine culture techniques, metagenomics and metabolomics have reshaped the understanding of the urinary tract as a dynamic ecological system interconnected with vaginal, intestinal and prostatic microbial compartments. These approaches have identified diverse microbial communities, virulence-associated functional profiles and host-microbe interactions linked to recurrence-prone phenotypes. Significant challenges continue to persist in elucidating the biological mechanisms driving recurrence. Addressing these gaps is essential to improve disease characterization and support the development of more effective diagnostic and therapeutic approaches.},
}

Humans
*Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology
Recurrence
Microbiota
Reinfection/microbiology
Host Microbial Interactions
Dysbiosis
Urinary Tract/microbiology

@article {pmid42751327,
year = {2026},
author = {De La Hoz, A and Kovac, V and Woolley, AE and Issa, NC and Letourneau, A and Baden, LR and Hammond, SP and Little, JS},
title = {Plasma Microbial Cell-Free DNA Sequencing for the Diagnosis of Chronic Disseminated Candidiasis in Patients with Hematologic Malignancies.},
journal = {Open forum infectious diseases},
volume = {13},
number = {9},
pages = {ofag543},
pmid = {42751327},
issn = {2328-8957},
abstract = {Diagnosis of chronic disseminated candidiasis (CDC) is frequently delayed because clinical manifestations are nonspecific and conventional diagnostic tests have limited sensitivity. We describe a series of 19 CDC cases in which plasma microbial cell-free DNA sequencing was performed due to diagnostic uncertainty. Results influenced antifungal management in most cases.},
}

@article {pmid42751339,
year = {2026},
author = {Segura, MG and Schwem, B and Sakamuri, RM and Grimes, CZ and Horne, M and Wanger, A and Truong, TT and Lieberman, JA and Litvinseva, AP and Ostrosky-Zeichner, L and Smith, DJ},
title = {Molecular Evidence of Autochthonous Environmental Acquisition of Fonsecaea Pediatric Infection in the United States.},
journal = {Open forum infectious diseases},
volume = {13},
number = {9},
pages = {ofag529},
pmid = {42751339},
issn = {2328-8957},
abstract = {Fonsecaea species cause chromoblastomycosis and phaeohyphomycosis, but links between environmental exposure and infection are poorly defined. We describe a 4-year-old boy with finger swelling after oak tree laceration in Houston, Texas. Broad-range polymerase chain reaction identified F. pedrosoi or F. monophora, and metagenomic sequencing of tree bark and soil detected Fonsecaea DNA.},
}

@article {pmid42751541,
year = {2026},
author = {Victor, MP and Al Shehri, N and Grevskott, DH and Alarif, WM and Ali, AM and Marathe, NP},
title = {High-throughput sequencing dataset of raw and treated wastewater from Jeddah, Saudi Arabia.},
journal = {Data in brief},
volume = {68},
number = {},
pages = {113174},
pmid = {42751541},
issn = {2352-3409},
abstract = {Wastewater is a major point source of pollution and antimicrobial resistance (AMR) in the environment. The aim of this study was to determine the microbiota and antimicrobial resistance genes present in both the influent and effluent from a biological wastewater treatment plant situated in Jeddah Second Industrial City, Saudi Arabia, using metagenomics. Water samples were collected, and the DNA extracted from these samples was subjected to metagenomic sequencing (one influent and one effluent) using Illumina NovaSeq. Our analysis yielded ∼88 Gigabases. The predominant bacterial genera identified were Actinomycetota, Psuedomonadota, and Bacillota, and β-lactamases emerged as the most common class of resistance genes. Eventhough these are unreplicated single observations they are expected to be a valuable resource for researchers focusing on wastewater studies, especially in the middle East, offering insights into bacterial diversity and the spectrum of resistomes associated with these microbial communities.},
}

@article {pmid42751774,
year = {2026},
author = {Shao, J and Hung, W and Yin, P and Huang, P and Zhao, W and Yu, L and Tian, F and Chen, W and Xu, J and Zhai, Q and Li, J and Zhao, J},
title = {Efficacy of Bifidobacterium animalis subsp. lactate BL-99 in relieving functional constipation: a randomized placebo-controlled clinical trial.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03175c},
pmid = {42751774},
issn = {2042-650X},
abstract = {Current therapies for functional constipation (FC) often exhibit limited long-term efficacy. Probiotics, particularly Bifidobacterium animalis subsp. lactis BL-99 (BL-99), may offer a novel approach to alleviate FC symptoms. This randomized, double-blind, placebo-controlled trial (No. WXSY-YXLL-AF/SC-11/01.0) enrolled 41 FC patients who completed the full 6-week study. Participants were randomly assigned to receive either BL-99 (1 × 10[11] colony-forming units per day) or placebo for 4 weeks in this population trial. After completing the 4-week intervention period, administration was discontinued and participants entered a 2-week observation following-up period for continued monitoring. Primary endpoint data collected after trial completion were the changes in the Patient Assessment of Constipation Symptoms (PAC-SYM, 12-item scale) score, evaluated on the first day (0 day), the 28th day (week 4), and the 42th day (week 6). Secondary outcomes included fecal metagenomic profiling to evaluate gut microbiota alterations. After 4 weeks of intervention, the BL-99 group demonstrated significant reductions in PAC-SYM scores compared to the placebo, particularly in domains of "abdominal discomfort" (Δ = 1.8 vs. 0.9, p = 0.007) and "pain during defecation" (Δ = 2.1 vs. 1.0, p = 0.003). These improvements persisted at the 2-week post-treatment follow-up (p < 0.05). Metagenomic analysis revealed that BL-99 enriched Bifidobacterium and Faecalibacterium while suppressing Clostridium species, shifting gut microbiota composition closer to that of the healthy controls. Functional annotation highlighted significant downregulation of infection-related pathways (e.g., bacterial invasion and LPS biosynthesis) and metabolic disease-associated pathways (e.g., insulin resistance) in the BL-99 group (q < 0.05). This trial suggests that 4-week BL-99 supplementation effectively alleviates FC symptoms, partially through microbiota modulation and metabolic pathway regulation. The sustained post-treatment effects warrant further investigation into its long-term benefits.},
}

@article {pmid42752346,
year = {2026},
author = {Pothikamjorn, TL and Doan, TA and Hinterwirth, A and Stewart, JM and Gonzales, JA},
title = {Metagenomic Deep Sequencing Identifies Gene Mutations Associated with Chemotherapeutic Resistance in Vitreoretinal Lymphoma.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/09273948.2026.2677102},
pmid = {42752346},
issn = {1744-5078},
abstract = {PURPOSE: To identify gene mutations associated with chemotherapeutic resistance in patients with vitreoretinal lymphoma (VRL) using metagenomic deep sequencing (MDS) of intraocular specimens.

METHODS: Patients with VRL confirmed by cytopathology and immunohistochemistry, flow cytometry, and/or polymerase chain reaction for MYD88, were included. Intraocular specimens underwent MDS of the host genome. Gene mutations were identified and cross-referenced with the Catalogue of Somatic Mutations in Cancer database to determine associations with chemotherapeutic resistance.

RESULTS: Forty-nine patients with VRL underwent MDS, with six specimens from four patients revealing eight gene mutations associated with chemotherapeutic resistance. Four specimens from three patients harbored mutations associated with methotrexate resistance, the mainstay of VRL treatment. In one patient, serial sampling from the initial vitrectomy and two subsequent recurrences revealed distinct resistance-associated mutations at each time point. Despite multi-agent therapy including rituximab, consolidation regimens, and lenalidomide, this patient ultimately succumbed to the disease, whereas the other three patients remained in long-term remission.

CONCLUSIONS: Our findings demonstrated that specific gene mutations associated with chemotherapeutic resistance may be harbored by VRL. The detection of different resistance mutations at sequential time points in one patient may reflect clonal selection, treatment pressure, or variable detection sensitivity. The ability to easily sample ocular fluid and detect different mutations associated with tumor recurrence or persistence may provide insights into tumor pathogenesis and could inform prognosis and influence treatment decisions. These findings establish a foundation for developing targeted PCR assays for identified resistance genes, which could transform clinical practice in VRL.},
}

@article {pmid42752928,
year = {2026},
author = {Maurya, S and Sharma, P and Yadav, BNS and Gupta, GP and Tiwari, N and Yadav, RK},
title = {Fungi to the rescue: recent advances, mechanistic insights and omics-based perspectives in heavy metal mycoremediation.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42752928},
issn = {1432-072X},
mesh = {Biodegradation, Environmental ; *Metals, Heavy/metabolism ; *Fungi/metabolism/genetics ; Multiomics ; Proteomics ; *Environmental Pollutants/metabolism ; },
abstract = {Heavy metal (HM) contamination arising from rapid industrialization poses critical threats to global ecosystem integrity and public health. Conventional physicochemical approaches are limited by high costs, incomplete removal, and toxic waste generation, necessitating sustainable alternatives. Mycoremediation, which harnesses the remarkable, diverse capacities of fungi to tolerate and mitigate HM stress through sophisticated biological mechanisms, has emerged as a promising and sustainable approach to address HM pollution. This review examines the sources and ecotoxicological impacts of HM pollution, alongside the intracellular and extracellular mechanisms underlying fungal tolerance and removal, including biosorption, precipitation, membrane transport, antioxidant defense, chelation, bioaccumulation, and biotransformation. It further synthesizes fungal-based bioremediation strategies, while examining how metagenomic, metatranscriptomic, transcriptomic, proteomic, and metabolomic approaches are advancing understanding of fungal community structure and active detoxification pathways. This work uniquely integrates community- and isolate-level multi-omics data, explicitly bridges mechanistic understanding with omics-driven insights, and extends this into translational roadmap for applied bioremediation.},
}

Biodegradation, Environmental
*Metals, Heavy/metabolism
*Fungi/metabolism/genetics
Multiomics
Proteomics
*Environmental Pollutants/metabolism

@article {pmid42753294,
year = {2026},
author = {Saleh, ZH and El Enbaawy, MI and Kamal, MA and Mahmoud, H and Hassan, M},
title = {Heat stress, respiratory dysbiosis, and poultry pathobiome: A comprehensive review of chronic respiratory disease in chickens.},
journal = {Veterinary microbiology},
volume = {322},
number = {},
pages = {111225},
doi = {10.1016/j.vetmic.2026.111225},
pmid = {42753294},
issn = {1873-2542},
abstract = {The poultry respiratory microbiome is increasingly recognized as a critical determinant of poultry health, mucosal immunity, and host resistance to opportunistic pathogens. Chronic Respiratory Disease (CRD) exerts a severe economic toll on the global broiler industry. While conventionally attributed to specific etiological agents such as Mycoplasma gallisepticum, disease progression is fundamentally tied to broad ecological dysbiosis within the respiratory tract. This comprehensive review synthesizes current knowledge on the functional roles and compositional dynamics of the poultry respiratory microbiome in both healthy and diseased states. Notably, we acknowledge the emerging threat of climate change, elucidating how heat stress physically and immunologically disrupts the respiratory mucosal microenvironment, acting as a primary catalyst for microbiome destabilization and CRD susceptibility. By shifting the paradigm from a single-pathogen model to a comprehensive pathobiome perspective, we detail the microbial shifts that characterize CRD. Furthermore, because investigating this low-biomass environment presents unique analytical challenges, we critically evaluate current technical methodologies. We address critical bottlenecks in sample collection, DNA extraction biases, and the comparative efficacy of 16S rRNA amplicon versus shotgun metagenomic sequencing. Ultimately, this synthesis provides a foundational framework for optimizing diagnostic methodologies and developing microbiome-targeted interventions -such as next-generation probiotics- to mitigate CRD in an era of escalating environmental stressors.},
}

@article {pmid42753435,
year = {2026},
author = {Xue, P and Huang, B and Wang, Y and Zhao, L and Mao, L},
title = {Environmental fate and risk of diverse oxygenated isomeric prothioconazole biotransformation products in soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143509},
doi = {10.1016/j.jhazmat.2026.143509},
pmid = {42753435},
issn = {1873-3336},
abstract = {Isomeric biotransformation products (TPs) of organic pesticides substantially expand structural diversity and may exhibit distinct environmental behaviors compared with their parent compounds. However, the formation mechanisms and ecological risks of such isomers (regioisomers) in soil remain poorly understood. In this study, the triazole fungicide prothioconazole (PTC) was incubated in agricultural soil, and 21 isomeric TPs were identified and classified into six structural groups using high-resolution mass spectrometry (HR-MS) based on diagnostic fragmentation patterns. These secondary oxygenated isomeric TPs were derived from three primary intermediates (PTC-desthio, PTC-dehydrated, and PTC-S-methyl) via site-selective oxygenation. Toxicity predictions indicated substantial variability among isomers, with certain hydroxylated derivatives exhibiting higher predicted ecotoxicity than others, challenging the assumption that biotransformation necessarily leads to detoxification. Metagenomic analysis showed that PTC exposure significantly altered the soil microbial community, enriching genes associated with xenobiotic degradation and central carbon metabolism. Notably, functional microbial shifts, particularly involving the genus Acinetobacter, were strongly associated with specific isomer profiles. These results suggest a potential link between microbial metabolic responses and the formation of structurally diverse isomeric TPs. The widespread occurrence of such isomers highlights that assessments based solely on parent compounds may underestimate the environmental fate and risks of PTC in agroecosystems.},
}

@article {pmid42709897,
year = {2026},
author = {Guss, HD and Francioli, YZ and Grover, EN and Hill, A and Zou, W and Wade, KJ and Pike, H and Gopalan, SS and Yang, L and Bo, Z and Pollock, DD and Carlton, EJ and Castoe, TA},
title = {Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014202},
doi = {10.1371/journal.pntd.0014202},
pmid = {42709897},
issn = {1935-2735},
mesh = {Animals ; Humans ; *Schistosoma japonicum/genetics/isolation & purification/classification ; China/epidemiology ; Genetic Variation ; *Schistosomiasis japonica/epidemiology/parasitology/transmission/prevention & control ; Genome, Helminth ; Snails/parasitology ; Metagenomics ; Disease Eradication ; },
abstract = {In China, sustained snail control, environmental management, and mass drug administration with praziquantel reduced schistosomiasis to near-elimination levels, yet re-emergence in Sichuan Province during the early 2000s exposed vulnerabilities in elimination efforts. We used population genomics to investigate the multi-scale population processes underlying Schistosoma japonicum re-emergence in Sichuan. We sequenced whole genomes from 270 miracidia collected from 53 human hosts across 17 villages in 2007, one year after re-emergence was documented. Population genomic analyses identified a broadly cohesive regional schistosome population with weak geographic structuring. Genome-wide diversity remained substantial, and demographic reconstructions revealed no recent decline in effective population size, suggesting that parasite populations had not undergone regional demographic collapse prior to re-emergence and were likely maintained in non-human reservoir hosts. At finer spatial scales, several villages exhibited reduced genomic diversity and elevated inbreeding, consistent with localized transmission maintained by relatively small founding populations. Estimates of pairwise genetic relatedness revealed dense within-village sibling clusters alongside second- and third-degree relationships spanning villages, and rare first- and second-degree cross-village links, supporting predominantly local transmission embedded within a connected regional transmission network. Genomic inference of minimum reproducing worm pairs identified substantial heterogeneity in host-level worm burden, ranging from one to eleven adult worm pairs, although uneven sampling limited absolute estimates. Together, these findings indicate that parasite persistence in this near-elimination setting was sustained by interacting processes operating across multiple biological scales, including diverse regional parasite populations, localized transmission networks connecting villages, and marked heterogeneity in host-level worm burden. More broadly, this work demonstrates how population genomics can reconstruct otherwise hidden patterns of parasite persistence and transmission, providing a valuable complement to conventional epidemiological surveillance in complex, multi-host parasite systems.},
}

Animals
Humans
*Schistosoma japonicum/genetics/isolation & purification/classification
China/epidemiology
Genetic Variation
*Schistosomiasis japonica/epidemiology/parasitology/transmission/prevention & control
Genome, Helminth
Snails/parasitology
Metagenomics
Disease Eradication

@article {pmid42743804,
year = {2026},
author = {Chen, ZY and Gao, FZ and Li, P and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Multi-omics evidence reveals robust airborne-human resistome connectivity driven by high-risk ARGs and mediated by Staphylococcus.},
journal = {Environment international},
volume = {216},
number = {},
pages = {110525},
doi = {10.1016/j.envint.2026.110525},
pmid = {42743804},
issn = {1873-6750},
abstract = {Airborne microbiomes are considered an important source of human antimicrobial resistance (AMR) exposure, yet multi-omics evidence linking airborne and human nasal resistomes remains limited. Here, we integrated metagenomic sequencing and whole-genome sequencing of antibiotic-resistant Staphylococcus isolates to investigate the connectivity between air and human nasal resistomes in dairy farm environments. Metagenomic taxonomic profiling showed that Staphylococcus was prominent in total suspended particles (TSP) and consistently detected across all samples. Among environmental reservoirs, TSP resistomes exhibited the strongest similarity to human nasal resistomes. This connectivity was supported by multiple lines of evidence, including highly similar resistome profiles, extensive homologous antibiotic resistance gene (ARG) pairs, strain-level similarity of resistant Staphylococcus isolates, and conserved mobile ARG genetic contexts. Notably, this connectivity was primarily driven by high-risk ARGs, while Staphylococcus was frequently associated with mobile ARGs and represented the only shared pathogenic genomes carrying both ARGs and virulence factor genes between airborne and nasal samples. Although lower ARG diversity, nasal resistomes exhibited higher ARG burden, risk scores, antibiotic-resistant bacterial genome abundance, and prevalence of resistant Staphylococcus. Occupational exposure further increased total and high-risk ARG burdens among farm workers. Together, these findings indicate that TSP can serve as an important route of occupational AMR exposure, with high-risk ARGs and Staphylococcus contributing to connectivity between airborne and nasal resistomes. Incorporating the host microbiome may therefore provide a more complete assessment of human-associated AMR exposure within a One Health framework.},
}

@article {pmid42743807,
year = {2026},
author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C},
title = {Involvement of cross-genus phages in bacterial resistance to chlorine disinfection.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126886},
doi = {10.1016/j.watres.2026.126886},
pmid = {42743807},
issn = {1879-2448},
abstract = {Chlorine disinfection resistance in pathogenic microorganisms poses severe environmental concerns and public health risks. While phages play critical roles in host adaptation to environmental stress, how poly-host phages contribute to bacterial resistance to chlorine disinfectants remains poorly understood. Here, we investigated shifts in the population dynamics, transcriptional profiles, and function potentials of cross-genus phage-bacterial communities under exposure to chlorine disinfectants in a continuously operated anaerobic-anoxic-oxic system over a 92-day period, using integrated metagenomic and metatranscriptomic approaches. In the presence and absence of chlorine disinfectants, the genomic abundance and diversity of phage and bacterial communities showed similar variation trends, and the community structures of both exhibited clear differences. A strong significant positive correlation was observed between phage and bacterial diversity under chlorine exposure (R = 0.975, p = 0.00,057), whereas no significant correlation was detected in the absence of chlorine disinfection (R = -0.314, p = 0.613), suggesting that chlorine disinfectants may enhance phage-bacteria interactions. Host-associated phages exhibited high consistency with their corresponding putative hosts in terms of genomic abundance (M[2] = 0.0945, p = 0.001) and transcript abundance (M[2] = 0.3668, p = 0.001), and they were also significantly correlated with cross-genus phages in both genomic abundance (R = 0.97, p < 2.2e-16) and transcript abundance (R = 0.83, p < 2.2e-16), which collectively suggests the critical role of cross-genus phages in the resistance of microbial communities to chlorine disinfectants. Bipartite association network analysis shows that cross-genus phages carry highly homologous genes to their putative hosts and may be involved in the horizontal transfer of these genes among bacteria. These homologous genes are involved in DNA repair, redox balance regulation, environmental stress adaptation and efflux pump functions, suggesting a synergistic role between cross-genus phages and their putative hosts in chlorine resistance. Our findings reveal that cross-genus phages can contribute to the resistance of bacterial communities to chlorine disinfectants, providing the theoretical foundation for evaluating the role of poly-host phages in microbial communities.},
}

@article {pmid42743809,
year = {2026},
author = {Chen, S and Wu, H and Chen, Y and Wang, F and Zhang, Y and Chen, N},
title = {An inundation threshold regulates nitrate reduction pathways in mangrove sediments.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126911},
doi = {10.1016/j.watres.2026.126911},
pmid = {42743809},
issn = {1879-2448},
abstract = {Estuarine hydrological regimes are increasingly altered by dam operations and extreme climate events, reshaping inundation in intertidal wetlands. However, how inundation regulates nitrate (NO3[-]) fate remains unclear. We conducted an 18-month, elevation-controlled marsh-organ experiment with Avicennia marina-planted and unvegetated sediments across a 0 %-65 % gradient in mean inundation frequency. We combined [15]N isotope tracing and metagenomics to quantify NO3[-] reduction pathways and associated microbial attributes. In unvegetated sediments, increasing inundation reduced the contribution of denitrification (DNF) from 62 % to 48 % and increased dissimilatory nitrate reduction to ammonium (DNRA) from 25 % to 34 %. In planted sediments, NO3[-] reduction shifted nonlinearly at approximately 24 % mean inundation frequency. Below this threshold, DNF dominated, contributing 83 %-87 % of NO3[-] reduction, whereas DNRA contributed only 2 %-6 %. Above the threshold, DNF declined to 45 % at the highest inundation frequencies, while DNRA increased to 42 %-48 %, indicating a shift from nitrogen removal toward retention. This transition coincided with plant failure, more reducing conditions, and changes in microbial community and functional profiles. Plant survival was associated with DNF-related taxa (e.g., Pseudomonas and Flavobacterium), nirK, and oxidative metabolism, whereas plant failure was associated with DNRA-related taxa (e.g., Shewanella and Geobacter), nrfA, and fermentative metabolism. These findings identify a vegetation-dependent inundation threshold beyond which nitrogen removal declines and nitrogen retention increases in mangrove sediments.},
}

@article {pmid42743975,
year = {2026},
author = {Pang, SJL and Wee, SK and Yap, EPH},
title = {Phage bioinformatics tools: a review of computational approaches for bacteriophage research.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42743975},
issn = {1477-4054},
support = {//Research Center for Excellence IDMxS/ ; //NTU Research Scholarship/ ; },
mesh = {*Computational Biology/methods ; *Bacteriophages/genetics ; Metagenomics/methods ; Machine Learning ; Genome, Viral ; *Software ; },
abstract = {Rising clinical interest in phage therapy and the exponential growth of metagenomic sequence catalogues have driven a rapid expansion of bacteriophage bioinformatics. More than 80 dedicated tools, mostly published since 2020, now span identification, assembly, annotation, taxonomy, lifestyle prediction, defence-system detection, and host prediction. Aimed at experienced practitioners and developers, this review synthesizes the field through the lens of three successive computational paradigms: sequence homology, bounded by database completeness; machine learning, constrained by labelled training data; and foundation models, which now achieve Matthews correlation coefficients above 0.95 in identification tasks and, through structure-informed prediction, raise functional annotation to over half of phage genes. Furthermore, we map the upstream components, namely, gene callers, homology engines, protein language models, and structural search tools, that underpin most downstream pipelines, exposing shared infrastructure and ecosystem-level fragility when dependencies change. To translate this into practice, we propose web-based and command-line reference workflows calibrated to user expertise and sample types. Finally, we set an agenda for the next wave of tool development. Roughly half of phage genes still resist functional annotation despite structural methods; no broadly generalizable strain-level host predictor exists for phage therapy; varying true-positive rates (0%-97%) underscore the absence of standardized community benchmarks analogous to Critical Assessment of Structure Prediction or Critical Assessment of Metagenome Interpretation. As generative genome models begin designing synthetic phages, progress will depend less on producing standalone tools than on rigorous evaluation, interoperable infrastructure, and clinically meaningful prediction targets.},
}

*Computational Biology/methods
*Bacteriophages/genetics
Metagenomics/methods
Machine Learning
Genome, Viral
*Software

@article {pmid42744171,
year = {2026},
author = {Xu, X and Yin, J and Peng, D and Li, J and Yang, Z and Qiao, L and Xu, J and Hu, X and Ren, Y and Cheng, B and Mu, Y},
title = {Enrofloxacin metabolism and antibiotic resistance in Monopterus albus differs between pond cage and greenhouse micro-flow aquaculture systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125688},
doi = {10.1016/j.envres.2026.125688},
pmid = {42744171},
issn = {1096-0953},
abstract = {Enrofloxacin (ENR) is a fluoroquinolone antibiotic widely used in aquaculture, yet its metabolic fate and resistance selection dynamics remain poorly characterized. Here, we investigated ENR metabolism, tissue distribution, withdrawal periods, gut microbial communities, and antibiotic resistance genes (ARGs) in Monopterus albus reared under pond net cage (PNC) and greenhouse micro-flow (GMF) systems following a 5-day medicated feed treatment (20 mg ENR/kg body weight). Eight ENR metabolites were tentatively identified, with ciprofloxacin (CIP) as the predominant metabolite. The GMF system significantly shortened the estimated withdrawal period to 4050 °C·d compared to 5550 °C·d for PNC (about 30% reduction). Critically, the PNC withdrawal period exceeded the current Chinese regulatory standard of 500 °C·d by more than 10 folds, revealing a substantial gap between existing guidelines and on-farm food safety requirements. Sediment analysis showed that 7.8% of the administered ENR dose persisted as a long term environmental reservoir. Metagenomic sequencing revealed that even a single ENR treatment induced an approximately 10-fold increase in fluoroquinolone resistance genes by day 60 post-treatment, with cross-resistance extending to multiple other antibiotic classes. Aeromonadaceae and Enterobacteriaceae were identified as the primary ARG hosts, and ARG abundance was significantly correlated with mobile genetic element prevalence, suggesting enhanced horizontal gene transfer potential. These findings demonstrate that aquaculture system design profoundly influences antibiotic fate and resistance selection, and that current withdrawal standards are inadequate for scaleless species. System-specific withdrawal guidelines and strengthened antimicrobial stewardship are urgently needed to mitigate environmental and food safety risks from aquaculture antibiotic use.},
}

@article {pmid42744253,
year = {2026},
author = {Dessai, U and Reynolds, JL and Kabera, C and Alt, L and Birhane, MG and Boxrud, D and Caidi, H and Ceric, O and Chandler, JC and Cook, K and Cooley, LA and Folster, JP and Ford, L and Fortenberry, GZ and Francois Watkins, LK and Franklin, AB and Franklin, AM and Frye, JG and Garland, JL and Ge, B and Harbottle, H and Haro, J and Huebner, KL and Kissler, B and Logan, N and Medley, A and Merrill, A and Miller, RA and Ottesen, A and Rockwell, CA and Shaw, S and Shivley, C and Simmons, M and Tadesse, DA and Tagg, KA and Tyson, GH and Webb, HE and Whichard, JM and Zhao, S and McDermott, PF and Tate, H},
title = {National Antimicrobial Resistance Monitoring System: Three Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100917},
doi = {10.1016/j.jfp.2026.100917},
pmid = {42744253},
issn = {1944-9097},
abstract = {Antimicrobial resistance (AMR) occurs when bacteria and other microorganisms adapt in ways that make medicines less effective, causing infections that are harder to treat and more likely to spread. According to the Centers for Disease Control and Prevention (CDC), AMR infections affect millions of Americans each year and contribute to thousands of deaths (CDC, 2019). After three decades of operation, the U.S. National Antimicrobial Resistance Monitoring System (NARMS) stands as a model of sustained, collaborative public health surveillance. What began in 1996 as an effort to track resistance in Salmonella and E. coli O157 has evolved into a One Health surveillance network monitoring AMR across the farm-to-fork continuum. Through a partnership among CDC, the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), state and local health departments, and universities, NARMS has become the backbone of foodborne AMR surveillance in the United States. The past decade has been particularly transformative. NARMS explored new sampling to include companion animals, minor livestock, aquaculture, surface water, and wildlife. Whole-genome sequencing (WGS) revolutionized the program's capabilities, enabling timely identification of emerging pathogens and revealing how resistance genes spread. Near real-time public dashboards make NARMS data accessible to researchers, clinicians, regulators, and policymakers. NARMS data shape decisions about new animal drug approvals, guide stewardship programs, and inform clinical treatment guidelines nationwide. As NARMS enters its fourth decade with a 2026-2030 strategic plan, the program will leverage artificial intelligence and metagenomics while expanding surveillance to fill remaining gaps ensuring this vital system continues to protect the food supply and both human and animal health from AMR.},
}

@article {pmid42744979,
year = {2026},
author = {},
title = {Ambient temperature is encoded in the metagenome of microbial communities.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42744979},
issn = {2058-5276},
}

@article {pmid42744981,
year = {2026},
author = {Yu, T and Yuan, S and Wang, Y and Wang, F},
title = {Evidence of direct methane production from long-chain fatty acids by thermophilic Archaeoglobi.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42744981},
issn = {2058-5276},
support = {42230401//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42276139//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methanogenic degradation of long-chain fatty acids has traditionally been thought to occur through syntrophic partnerships between fatty acid-degrading bacteria and methanogenic archaea. However, recent genomic evidence suggests that certain archaea may independently carry out the entire process. Here we report the enrichment of an archaeon from the class Archaeoglobi, Candidatus Methanoglobus sphaerolipidus DLY3, from hot spring sediments in Tengchong, China. The results of selective enrichment, growth experiments, microscopy, stable isotope tracing, metagenomics and metatranscriptomics suggest that Ca. M. sphaerolipidus directly converts long-chain fatty acids to methane. This transformation involves the beta-oxidation pathway, the Wood-Ljungdahl pathway and methanogenic methyl-coenzyme M reductase and methyltransferase complexes-a process we term liparotrophy. In addition to oleic acid, Ca. M. sphaerolipidus is also capable of utilizing methanol as a substrate for methanogenesis. Our findings expand the known substrate range for methanogenic archaea beyond carbon dioxide reduction, acetoclastic methanogenesis, methylotrophy, methyl reduction, methoxydotrophy and the recently reported alkylotrophy.},
}

@article {pmid42745084,
year = {2026},
author = {Chen, Y and Zhou, J and Yuan, L and Xie, M and Wang, J and Zheng, J and Zhou, L and Zhang, D and Han, D},
title = {Clinical and Genomic Insights into the Allodiploid Hybrid Pathogen Aspergillus latus: A Retrospective Case Series.},
journal = {Mycopathologia},
volume = {191},
number = {5},
pages = {},
pmid = {42745084},
issn = {1573-0832},
support = {2024ZD0533100 & 2024ZD0533106//National Science and Technology Major Project/ ; 82472371//National Natural Science Foundation of China/ ; },
mesh = {Retrospective Studies ; *Aspergillus/genetics/isolation & purification/classification/drug effects/cytology ; Humans ; China ; Antifungal Agents/pharmacology ; *Aspergillosis/microbiology/pathology/diagnosis ; High-Throughput Nucleotide Sequencing ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; Metagenomics ; },
abstract = {Aspergillus latus is an emerging cryptic allodiploid hybrid pathogen within Aspergillus section Nidulantes that closely resembles related species and therefore prone to misidentification by routine diagnostic methods. Therefore, its true clinical burden is likely underestimated. In this study, we retrospectively characterized five patients with A. latus infections identified by metagenomic next-generation sequencing (mNGS) at a tertiary hospital in China. Clinical manifestations varied according to host immune status, ranging from a subclinical pulmonary lesion in an immunocompetent individual to aggressive disease in highly immunocompromised patients. Conventional microbiological methods showed limited sensitivity and consistently misidentified the isolates as A. nidulans, whereas mNGS enabled accurate detection of A. latus together with complex co-infections. Three viable clinical isolates were recovered for morphological characterization, antifungal susceptibility testing, and whole-genome sequencing (WGS). All tested isolates demonstrated reduced susceptibility to echinocandins but remained susceptible to mold-active triazoles and amphotericin B. Furthermore, WGS and macrosynteny analyses confirmed their allodiploid hybrid nature, revealing a mosaic genome derived from A. spinulosporus and an A. quadrilineatus-related lineage. Collectively, these findings highlight that A. latus may be missed by routine diagnostic methods and may exhibit a distinct antifungal susceptibility profile. Molecular approaches such as mNGS and WGS may therefore help achieve accurate species-level identification and support targeted antifungal therapy. Given this small retrospective case series, larger prospective and multicenter studies are needed to validate these observations and better define the epidemiology, clinical spectrum, and therapeutic implications of this emerging allodiploid hybrid pathogen.},
}

Retrospective Studies
*Aspergillus/genetics/isolation & purification/classification/drug effects/cytology
Humans
China
Antifungal Agents/pharmacology
*Aspergillosis/microbiology/pathology/diagnosis
High-Throughput Nucleotide Sequencing
Microbial Sensitivity Tests
Whole Genome Sequencing
Metagenomics

@article {pmid42745387,
year = {2026},
author = {Kunnummal, SP and Abdulla, A and Khan, M},
title = {Novel Ferulic Acid Esterase From Human Gut Microbiome: Cloning and Application in Crop Residue Valorization.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70208},
pmid = {42745387},
issn = {1470-8744},
support = {5/7/1741/CH/Adhoc/2021-RMBCH//Indian Council of Medical Research/ ; },
abstract = {Ferulic acid esterases (FAEs) are enzymes that interact with esterified components of plant cell walls, facilitating the release of free ferulic acid (FA) from plant materials. Therefore, they hold significant importance across multiple industries, including pharma, food, and cosmetics. This investigation involved the cloning, expression, and characterization of FAE from the human fecal metagenome. Sequence analysis revealed that the cloned gene was approximately 750 bp in length and contained an open reading frame encoding a protein of 252 amino acids. The resulting recombinant protein displayed a molecular weight of 28 kDa and 49.7% identity with the chlorogenic acid esterase from Lactobacillus helveticus. The hydrolytic activity of the recombinant FAE was validated using p-nitrophenyl-ferulate (pNPF) as the substrate, with optimal activity at a pH of 7 and a temperature of 35°C. The enzyme showed stability within a pH range of 5.0-7.0 and temperatures from 5°C to 35°C. High-performance liquid chromatography (HPLC) results indicated that the FAE enzyme could release up to 49.7% of total alkali-extractable FA from dehydrated rice bran, followed by wheat bran and sugarcane bagasse. The total phenolic content of sugarcane bagasse increased by approximately 100% after in situ enzymatic fermentation compared with the chemically extracted fraction. These results indicate that cloned FAE can be used as a potential biocatalyst in industrial applications.},
}

@article {pmid42745810,
year = {2026},
author = {Huang, H and Fu, Y and Liu, E and Bai, K and Li, J and Liu, C and Deng, Y and Xu, F},
title = {Application of metagenomic next-generation sequencing in children with pneumonia of unknown etiology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1922924},
pmid = {42745810},
issn = {2235-2988},
mesh = {Humans ; Female ; Male ; Child, Preschool ; *High-Throughput Nucleotide Sequencing/methods ; Infant ; *Metagenomics/methods ; Retrospective Studies ; Child ; Adolescent ; *Pneumonia/microbiology/diagnosis/etiology ; Bacteria/genetics/classification/isolation & purification ; Coinfection/microbiology ; Immunocompromised Host ; Viruses/genetics/classification/isolation & purification ; },
abstract = {OBJECTIVE: To investigate the pathogen spectrum and clinical application value of metagenomic next-generation sequencing (mNGS) in lower respiratory tract specimens from children with pneumonia of unknown etiology.

METHODS: A retrospective analysis was conducted on children hospitalized in the intensive care unit (ICU) and respiratory department ward of Children's Hospital of Chongqing Medical University from January 2025 to December 2025. All enrolled cases presented negative results for conventional respiratory pathogen tests and received mNGS testing of lower respiratory tract specimens for etiological identification. The mNGS findings and clinical data of the included children were analyzed.

RESULTS: A total of 92 children were enrolled, including 54 males and 38 females, with ages ranging from 2 months to 13 years and 8 months. Causative pathogens were detected in 77 cases (83.7%). The clinically adjudicated etiological diagnosis rates of bacteria, viruses, fungi and atypical pathogens were 75.0% (69/92), 37.0% (34/92), 13.0% (12/92) and 5.4% (5/92), respectively. Thirty-eight cases were complicated with polymicrobial infection, among which bacterial-viral infection was predominant, accounting for 23.1% (24/92). Children with immunocompromised conditions exhibited higher incidences of clinically adjudicated bacterial, fungal and polymicrobial infection than immunocompetent patients. The most common clinically confirmed causative pathogens in immunocompromised children were Streptococcus pneumoniae, human cytomegalovirus, Haemophilus influenzae, Stenotrophomonas maltophilia and Enterococcus faecalis. Treatment regimens were adjusted in 58 cases (63.0%) based on mNGS findings, switching to pathogen-targeted anti-infective therapy.

CONCLUSION: For pediatric pneumonia with negative conventional etiological tests, mNGS of lower respiratory tract specimens significantly enhances pathogen detection rates, effectively identifies polymicrobial infection and opportunistic pathogens. Immune status serves as a critical stratification factor influencing pathogen spectrum and infection patterns, with immunocompromised children being more susceptible to opportunistic infections. Adjustment of anti-infective regimens based on mNGS results can effectively facilitate personalized anti-infective therapy.},
}

Humans
Female
Male
Child, Preschool
*High-Throughput Nucleotide Sequencing/methods
Infant
*Metagenomics/methods
Retrospective Studies
Child
Adolescent
*Pneumonia/microbiology/diagnosis/etiology
Bacteria/genetics/classification/isolation & purification
Coinfection/microbiology
Immunocompromised Host
Viruses/genetics/classification/isolation & purification

@article {pmid42745851,
year = {2026},
author = {Yue, Z and Sheng, S and Peng, L and Xu, W and Zhang, J and Wu, D and Liu, B and Li, Q and Dong, R and Cheng, H and Zou, Y},
title = {Impact of Chamaecrista rotundifolia cover cropping on soil elemental cycling in karst agroecosystems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1906173},
pmid = {42745851},
issn = {1664-302X},
abstract = {Karst desertification causes severe soil erosion, hydrological imbalance, and biodiversity loss, thereby threatening ecosystem resilience and agricultural productivity. Soil carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling underpin ecosystem stability, yet how agricultural management practices regulate multi-element cycling in degraded karst agroecosystems remains poorly understood. Here, we conducted a four-year field trial in a karst mango orchard in southwestern China and integrated metagenomic sequencing with comprehensive soil environmental profiling to investigate how C. rotundifolia cover cropping reshapes soil elemental cycling. Compared with conventional tillage (CK), C. rotundifolia cover cropping (Y) significantly (p < 0.05) altered topsoil microbial functional profiles and nutrient availability. Carbon cycling potentials, including gene associated with aerobic respiration (cox1/3), fermentation, and CO2 assimilation-were enriched under C. rotundifolia cover cropping. Nitrogen cycling potentials were enhanced through increased representation of genes involved in denitrification (nirK/S, nosZ), nitrogen acquisition, and nitrate reduction (nirA, narB), while phosphorus cycling was promoted through enrichment of the PhoR-PhoB phosphate regulatory system. Sulfur transformation potentials were also altered, with increased representation of genes involved in sulfate reduction, oxidation, and sulfonate utilization. Cover cropping substantially improved soil fertility, increasing SOC (+35.4%), NH4 [+]-N (+31.8%), TN (+35.1%), and AP (+105.9%), while reducing exchangeable Al[3+] concentration by 60.9%. Microbial community restructuring was characterized by decreased Actinobacteriota and Chloroflexota and increased Bacteroidota and Proteobacteria, which exhibited central roles in elemental cycling networks. Mantel analyses identified exchangeable Al[3+] as a dominant environmental constraint shaping microbial communities involved in C, N, P, and S cycling. Collectively, these findings demonstrate that C. rotundifolia cover cropping enhances karst soil resilience through a coupled microbial-geochemical pathway, in which improved soil chemical conditions and microbial functional reorganization jointly restore elemental cycling capacity.},
}

@article {pmid42745968,
year = {2026},
author = {Liu, X and Chen, R and Li, Y and Li, D and Xu, Z},
title = {Next-generation sequencing in the etiological diagnosis of severe childhood pneumonia.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1864412},
pmid = {42745968},
issn = {2296-2360},
abstract = {Pneumonia is the leading cause of death for children, particularly those aged 3-5 years old. The majority of the 740,000 annual global deaths of children under five years old occurred in developing countries in 2019. Severe childhood pneumonia (SCAP) causes death and disability in children, as it may trigger pleural effusion, respiratory failure, bacteremia and multiple organ failure. Traditional pathogen detection techniques including microscopy, culture and polymerase chain reaction (PCR) feature narrow detection coverage, lengthy detection cycles and low sensitivity. These defects frequently lead to undetermined infectious etiology, forcing clinicians to administer empirical broad-spectrum antibiotics. Metagenomic next-generation sequencing (mNGS) has emerged as an innovative, high-throughput, untargeted detection technology in recent years, which greatly promotes the etiological diagnosis of infectious diseases. Published meta-analyses show that the pathogen detection rate of mNGS using bronchoalveolar lavage fluid (BALF) samples collected from children can reach 85.83%, which is markedly higher than the 49.97% detection rate of conventional testing approaches. This review systematically elaborates how mNGS reconstructs the cognition of pathogen spectrum in children with severe pneumonia: this technology accurately identifies complex mixed infection patterns, detects pathogens that cannot be captured by traditional testing, and redefines the clinical boundary between microbial colonization and invasive infection. Combined with latest clinical research data, this paper analyzes the core value of mNGS in optimizing treatment schemes, reducing irrational antibiotic use and realizing precision therapy for severe pneumonia in children. Meanwhile, the current limitations and future development directions of this technology are discussed.},
}

@article {pmid42746154,
year = {2026},
author = {Huang, L and Wang, L and Wang, X and Zhang, X and Yu, X and Yang, J and Zhang, W and Yang, J and Ji, W and Cao, Y and Zheng, Y and Gai, W and Jiang, M and Liang, Y},
title = {Metagenomic Next-Generation Sequencing Analysis of Pathogens in Infected Wounds from Dog and Cat Bites - China, 2021-2025.},
journal = {China CDC weekly},
volume = {8},
number = {34},
pages = {1055-1062},
pmid = {42746154},
issn = {2096-7071},
abstract = {Dog and cat bites frequently develop polymicrobial wound infections requiring prompt and appropriate antimicrobial treatment. However, conventional culture-based methods often fail to identify all pathogens, particularly anaerobic and fastidious microorganisms.

WHAT IS ADDED BY THIS REPORT?: This study used metagenomic next-generation sequencing (mNGS) to analyze infected dog- and cat-bite wounds. Distinct microbial profiles were identified between dog and cat bites, and between domestic and stray animals. Anaerobes were predominant in both groups.

These findings highlight the value of mNGS and support empirical antimicrobial strategies to improve infection management and reduce complications.},
}

@article {pmid42746171,
year = {2026},
author = {Zhang, J and Wu, S and Deng, C and Zhang, E and Yu, B and Luo, A and Sun, C and Zhang, H and Zheng, C and Zhou, H and Li, W and Lu, J and Chen, Q and Fan, R and He, X and Ye, B and Shi, X and Wang, P and Wei, J},
title = {Epidemiological Investigation and Source Tracing of an Inhalation Anthrax Case with Traceability to Yunnan Province - Guangdong Province, China, March 2026.},
journal = {China CDC weekly},
volume = {8},
number = {33},
pages = {1037-1041},
pmid = {42746171},
issn = {2096-7071},
abstract = {Anthrax is a zoonotic disease caused by the bacterium Bacillus anthracis (B. anthracis). Inhalation anthrax, caused by inhalation of B. anthracis spores, is the rarest and most fatal form of anthrax. Historically, naturally acquired inhalation anthrax cases have mainly been associated with occupational exposure to infected animals or animal products, such as in wool mills or tanneries.

WHAT IS ADDED BY THIS REPORT?: This report documents the first case of inhalation anthrax in China that was linked to environmental exposure in a historically endemic area, without direct contact with sick animals or animal products. The case was reported in Guangdong Province, however, the source was traced to the patient's newly built residence in Zhenxiong County, Yunnan Province, where environmental samples tested positive for B. anthracis nucleic acid. Three anthrax outbreaks have occurred in this region since 1990.

In anthrax-endemic areas, environmental exposure to contaminated soil or dust can pose a significant risk of anthrax infection, even without direct animal contact. Although rare, inhalation anthrax can occur naturally as B. anthracis spores can survive extreme environmental conditions in the soil or hay for long periods. As it is difficult to distinguish acute pulmonary infection from inhalational anthrax, severe cases were frequently initially suggested by metagenomic sequencing of the alveolar fluid, with similar findings reported for meningeal anthrax in the cerebrospinal fluid.},
}

@article {pmid42746328,
year = {2026},
author = {Kuzuya, K and Maeda, Y and Funakoshi, K and Mizuno, Y and Fujimoto, K},
title = {Autoimmune disease-associated pathobionts: mechanisms and therapeutic potential of phage-based approaches.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1884094},
pmid = {42746328},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/therapy/immunology/microbiology ; Animals ; *Phage Therapy/methods ; *Gastrointestinal Microbiome/immunology ; *Bacteriophages/immunology ; Bacteria/immunology/virology ; Host Microbial Interactions/immunology ; },
abstract = {The gut microbiota is a critical regulator of systemic immune homeostasis; accumulating evidence implicates specific commensal bacteria, termed "pathobionts," in autoimmune disease pathogenesis. However, the definition of pathobionts remains context-dependent, as their effects are influenced by host genetics and host-microbe interactions. In this review, we summarize representative pathobionts supported by functional evidence in selected extraintestinal autoimmune diseases and discuss how these mechanisms may inform phage-based microbiome-targeted interventions. Mechanistically, pathobionts contribute to autoimmune disease through multiple pathways, including molecular mimicry, induction of intestinal T helper 17 and T follicular helper cell responses, disruption of regulatory T cell homeostasis, intestinal barrier dysfunction, and bacterial translocation from the gut to extraintestinal sites. These processes highlight the central role of gut-associated lymphoid tissue in initiating systemic autoimmunity, and targeting disease-associated microbes represents a promising therapeutic strategy. Whole-phage therapy, which enables highly specific bacterial elimination, has shown efficacy in preclinical immune-mediated disease models, but may be affected by variable in vivo replication, bacterial receptor-mediated resistance, anti-phage immune responses, and ecological effects on the resident microbiome. Phage-derived enzymes that lyse bacterial cell walls, such as endolysins, represent a complementary therapeutic modality that specifically targets bacterial peptidoglycan through cell wall-binding and catalytic domains. Collectively, these findings support the concept that pathobiont-targeted interventions, particularly phage-based strategies, may provide microbiome-directed, immunosuppression-sparing therapeutic approaches for selected patient subsets.},
}

Humans
*Autoimmune Diseases/therapy/immunology/microbiology
Animals
*Phage Therapy/methods
*Gastrointestinal Microbiome/immunology
*Bacteriophages/immunology
Bacteria/immunology/virology
Host Microbial Interactions/immunology

@article {pmid42746344,
year = {2026},
author = {Chooklin, S and Chuklin, S},
title = {Beyond the Pancreas: The Gut Microbiota in Acute Pancreatitis - From Mechanisms to Therapeutic Perspectives.},
journal = {Clinical and experimental gastroenterology},
volume = {19},
number = {},
pages = {636881},
pmid = {42746344},
issn = {1178-7023},
abstract = {Acute pancreatitis is a heterogeneous inflammatory disease in which severe forms are frequently complicated by intestinal barrier failure, dysbiosis, bacterial translocation, infected necrosis, systemic inflammation, and organ dysfunction. Growing clinical and experimental evidence suggests that the gut microbiota may contribute to disease progression and represents a potential, although incompletely validated, therapeutic target. Importantly, acute pancreatitis-associated dysbiosis involves not only taxonomic shifts but also functional metabolic reprogramming, including reduced short-chain fatty acid production, altered microbial bile acid transformation, and disturbances in amino acid and lipid metabolism that may contribute to barrier dysfunction and systemic inflammation. This review synthesizes current evidence on microbiota-oriented strategies in acute pancreatitis, with emphasis on clinical applicability, mechanistic rationale, and safety. This narrative review integrates clinical guidelines, randomized trials, meta-analyses, cohort studies, metagenomic and metabolomic investigations, and experimental studies published mainly between 2002 and 2026. Among clinically supported strategies, early oral or enteral nutrition has the strongest evidence base and may help preserve mucosal integrity while limiting the ecological consequences of fasting and critical illness. Antimicrobial stewardship is also fundamental, because unnecessary antibiotic exposure may aggravate dysbiosis, impair colonization resistance, and promote resistant organisms. Selective digestive decontamination has historical clinical evidence but is not established for routine contemporary practice. Prebiotics, dietary fibers, postbiotics, and metabolite-oriented approaches are mechanistically promising, but clinical evidence remains limited. GV-971 is currently supported predominantly by preclinical experimental data. Probiotics and synbiotics require caution, particularly in predicted severe disease, because clinical benefits are inconsistent and important safety concerns have been reported. Fecal microbiota transplantation and washed microbiota transplantation remain investigational and should not be used routinely outside controlled protocols. At present, microbiota-oriented management should prioritize evidence-based supportive measures, particularly early oral or enteral nutrition and rational antimicrobial use. Future studies should combine clinical outcomes with standardized microbiome, metabolome, barrier, and resistance endpoints to determine whether direct microbiota modulation can become a safe and reproducible component of personalized therapy.},
}

@article {pmid42746455,
year = {2026},
author = {Abril, AG and Freire, J and Magadán, S and Villa, TG and Pazos, M and Carrera, M},
title = {A metagenomic analysis of the gut microbiota in a mouse model of fish allergy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1886359},
pmid = {42746455},
issn = {1664-302X},
abstract = {BACKGROUND: Fish are among the most frequent causes of immunoglobulin E (IgE)-mediated food allergies (Type I). Currently, there is no known cure for fish allergy and individuals who are sensitized have to practice strict, lifelong avoidance of fish products in their diets. The relationship between gut microbiome and food allergies is currently a major topic of discussion; these pathologies involve the development of dysbiosis, which is a microbial imbalance resulting from immune-related mechanisms. Recent studies have provided evidence that individuals suffering from food allergies, display an intestinal microbiota with a different microbial composition compared to healthy subjects.

OBJECTIVES AND METHODS: In this work, we have described for the first time the differences in microbiome composition in a mouse model of fish allergy with previous sensitization to the main allergen, beta-Parvalbumin (β-PRVB), compared to mouse individuals without allergic response.

RESULTS: The metagenomic analysis has shown differences in taxonomic composition between the treatments. Regarding phyla, an increase in the relative abundance of Patescibacteria, specifically Saccharimonas genus and Candidatus_Saccharimonas group, were observed in the allergic animals (Prvb_Alum group) when compared to the other groups. In contrast, the relative abundance of the RF39 group (Bacilli), Atopobiaceae family, Erysipelotrichaceae, and the Coriobacteriaceae_UCG-002 group, was higher in the animals that did not develop an allergic response, despite being exposed to the allergen (Prvb group). Furthermore, an increase in the relative abundance of Lachnospiraceae ASF356 group was observed in the control group compared to the other treatments. This family, has been reported to be inversely associated with the progression of intestinal inflammation and anaphylactic diseases. For the first time, the gut microbiota composition of individual mice with and without fish allergies is described in detail in this work. This study may shed light on the potential contribution of gut microbiota to the onset and avoidance of food allergies.},
}

@article {pmid42746483,
year = {2026},
author = {Liu, F and Luo, J and Feng, L and Xia, Y and Chen, X and Xu, Y and Liu, Y},
title = {The association between neonatal respiratory distress syndrome and gut microbiota dysbiosis: evidence from metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1925400},
pmid = {42746483},
issn = {1664-302X},
abstract = {OBJECTIVE: Neonatal respiratory distress syndrome (NRDS) is a common and life-threatening respiratory disorder that affects newborns, significantly impacting their health and survival rates. In recent years, the potential role of the gut-lung axis in NRDS has garnered increasing attention; however, the specific mechanisms involved remain unclear. This study aimed to investigate the association between NRDS and gut microbial composition and functional profiles using shotgun metagenomic sequencing.

METHODS: This case-control study recruited 25 infants diagnosed with NRDS and 15 healthy newborns, all aged between 2 and 6 days. Fecal samples were collected from all participants for subsequent metagenomic sequencing and bioinformatics analysis.

RESULTS: There was no significant difference in α-diversity between the NRDS group and the control (CON) group (p = 0.3335). However, β-diversity exhibited a significant difference (p = 0.001). In the NRDS group, the gut microbiota was enriched with Bacillota, Klebsiella, and Enterococcus, while Bifidobacterium and butyrate metabolism-related bacteria (Bacteroides/Butyricicoccus) were significantly reduced (p < 0.05). Functional analysis indicated that Staphylococcus aureus infection and the Phosphotransferase system (PTS) pathway were enriched in the NRDS group, whereas Butanoate metabolism and Glutathione metabolism were significantly enriched in the CON group. A 10-species classifier achieved 96% AUC for NRDS prediction.

CONCLUSION: NRDS was associated with differences in gut microbial composition and shotgun-metagenomic functional profiles. These preliminary findings characterize group-level microbial differences but do not establish whether the observed alterations preceded or resulted from NRDS. Longitudinal studies are required to clarify their temporal relationship and clinical relevance.},
}

@article {pmid42746583,
year = {2026},
author = {Saadeh, JE and Saad, R and Assaf, F and Osman, R and Chami, AA and Harb, BA and Ghanem, W and Badra, M and Moucharafieh, R},
title = {Current Concepts in Periprosthetic Joint Infection: Modern Biomarkers, Microbiome Insights, Molecular Diagnostics, and Emerging Prevention Strategies.},
journal = {Orthopedic research and reviews},
volume = {18},
number = {},
pages = {634292},
pmid = {42746583},
issn = {1179-1462},
abstract = {AIM: Periprosthetic joint infection (PJI) remains one of the leading causes of revision arthroplasty and is associated with substantial morbidity, mortality, and healthcare costs. Diagnosis remains challenging because of heterogeneous clinical presentations, the limited sensitivity of conventional inflammatory markers in chronic and low-grade infections, culture-negative cases, and biofilm-mediated pathogen persistence. This narrative review summarizes recent advances in the diagnosis and prevention of PJI, with a particular focus on synovial and serum biomarkers, microbiome-related susceptibility, molecular diagnostics, artificial intelligence, and emerging anti-biofilm and implant-surface technologies. Synovial biomarkers, including alpha-defensin, leukocyte esterase, calprotectin, and D-lactate, have demonstrated improved diagnostic performance, particularly in equivocal and culture-negative cases. However, none has sufficient evidence to replace established diagnostic criteria, and current data support their use as adjunctive tools in selected clinical scenarios rather than as standalone tests. Serum biomarkers beyond erythrocyte sedimentation rate and C-reactive protein, such as fibrinogen and protein fraction alterations, may provide additional diagnostic value but require further validation and standardized diagnostic thresholds. Molecular approaches, particularly metagenomic next-generation sequencing, improve pathogen detection in complex infections but remain limited by cost, protocol variability, and challenges in distinguishing clinically relevant pathogens from contaminants. Preventive strategies targeting bacterial adhesion and biofilm formation through local antibiotic delivery, surface modification, and nanotechnology-enabled implants are promising, although long-term efficacy, safety, and cost-effectiveness remain to be established. Overall, PJI management is evolving toward integrated, multimodal diagnostic strategies and biologically informed prevention. Current evidence supports the selective clinical use of synovial biomarker testing as an adjunctive tool within established diagnostic criteria, while continued research is needed before widespread routine implementation can be recommended.

Modern synovial biomarkers provide valuable adjunctive information that may improve diagnostic confidence in challenging periprosthetic joint infection cases when incorporated into a multidisciplinary diagnostic approach involving clinical assessment, laboratory evaluation, microbiological analysis, and established consensus criteria. Emerging preventive strategies targeting biofilm formation and host-microbe interactions represent promising approaches, although their ability to reduce revision rates and improve patient outcomes requires further clinical validation.},
}

@article {pmid42747097,
year = {2026},
author = {Listmann, L and Peters, C and Labecot, A and Rousseau, R and Baux, C and Santelia, ME and Manirakiza, E and Grimsley, N and Yau, S and Gourbiere, S and Schaum, CE and Piganeau, G},
title = {Bridging the gap between genomic, phenotypic, and modeling data in picophytoplankton-virus interactions.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70229},
pmid = {42747097},
issn = {1529-8817},
support = {ANR-10-LABX-0041//Agence Nationale de la Recherche/ ; ANR-18-EURE-0019//Agence Nationale de la Recherche/ ; ANR-21-CE02-0026//Agence Nationale de la Recherche/ ; ANR-21-CE20-0041//Agence Nationale de la Recherche/ ; 2154/8-1//Deutsche Forschungsgemeinschaft/ ; 2154/9-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {We present a comprehensive synthesis of recent developments in methodological approaches to combine experimental and genomic studies of picophytoplankton-virus interactions. This synthesis will not only enhance our understanding of these relationships but also stimulate new hypotheses for the interpretation of metagenomic data and enrich current modeling efforts. Marine picophytoplankton are significant primary producers despite their low contribution to biomass. Pan-oceanic metagenomic studies have revealed an astounding genetic diversity within these communities and the astronomical abundance of viruses that infect them. Despite recent advances in understanding the genetic and genomic diversity of picophytoplankton and viruses, the interpretation of these data relies heavily on ecological and physiological insights. Specifically, our understanding of the mechanisms and dynamics governing host-virus interactions is limited because the current wealth of sequence data has not yet been matched with corresponding life-history traits. Linking phenotypes to genotypes in picophytoplankton-virus systems is also essential for accurately modeling their interactions and their impact on the global carbon cycle. Ultimately, the synergy of the three domains allows for a mechanistic interpretation of environmental data.},
}

@article {pmid42747125,
year = {2026},
author = {Saavedra-Benítez, D and Ampuero, M and Gaggero, A and Chnaiderman, J},
title = {Synchronized Detection of Adenovirus F41 in Wastewater and Fecal Samples Confirms a Small Outbreak in Santiago, Chile.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71148},
doi = {10.1002/jmv.71148},
pmid = {42747125},
issn = {1096-9071},
support = {1181656//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {Chile/epidemiology ; *Wastewater/virology ; *Feces/virology ; Phylogeny ; Humans ; *Adenoviridae Infections/epidemiology/virology ; *Disease Outbreaks ; Genome, Viral ; *Adenoviruses, Human/isolation & purification/genetics/classification ; *Adenoviridae/isolation & purification/genetics/classification ; },
abstract = {We conducted systematic surveillance of circulating viruses in two cities in Chile through regular wastewater analysis between 2018 and 2021. Samples were concentrated, nucleic acids were extracted, and the samples were analyzed by massive sequencing. After bioinformatic processing, we detected a significant number of Adenovirus F41 genomes in samples collected during a specific period (January-March 2020), particularly in treatment plants from Santiago de Chile. To confirm whether the virus was circulating in the city during that period, we analyzed stool pools collected at one of the city's main pediatric hospitals. We detected Adenovirus F41 sequences only in the same period as in wastewater. Phylogenetic analysis showed that the virus detected in wastewater and stool samples was almost identical and classified as Lineage 2B. These results demonstrated the effectiveness of wastewater surveillance for detecting enteric viruses in the community, shed light on the efficiency of treatment processes, and revealed a small outbreak of a virus strain previously reported in Europe.},
}

Chile/epidemiology
*Wastewater/virology
*Feces/virology
Phylogeny
Humans
*Adenoviridae Infections/epidemiology/virology
*Disease Outbreaks
Genome, Viral
*Adenoviruses, Human/isolation & purification/genetics/classification
*Adenoviridae/isolation & purification/genetics/classification

@article {pmid42747196,
year = {2026},
author = {Lou, D and Cui, J and Duan, J and Zhou, B and Wang, Y and Wang, D and Tan, J and Duan, H},
title = {Genomic prospecting and biochemical characterization of a novel thermostable 3-quinuclidinone reductase from hot spring metagenomes for efficient biocatalysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0149026},
doi = {10.1128/aem.01490-26},
pmid = {42747196},
issn = {1098-5336},
abstract = {This study presents the discovery and characterization of a novel thermophilic 3-quinuclidinone reductase (ScQR) identified through metagenomic mining of hot spring environments. ScQR, a member of the short-chain dehydrogenase/reductase (SDR) superfamily, was heterologously expressed in Escherichia coli, and its catalytic properties were systematically characterized. The enzyme demonstrates exceptional thermal stability, retaining 86% of its activity after 48 hours at 70°C. Furthermore, K[+] and Mg[2][+] ions significantly enhanced ScQR's activity at specific concentrations. Structural analysis revealed that ScQR adopts a typical SDR fold with a conserved catalytic triad (S141-Y155-K159), and it is NAD(H) dependent. Enzyme assays indicated that ScQR is highly stereoselective for (R)-3-quinuclidinol, with no activity against its enantiomer, (S)-3-quinuclidinol. The enzyme exhibits optimal activity at pH 9 and 85°C, making it a promising candidate for industrial applications requiring high thermal stability. Molecular dynamics simulations further revealed that ScQR preserves global structural integrity up to 360 K, whereas higher temperatures induce destabilization, predominantly in the C-terminal region and residues 95-100. In addition, structure-guided computational design enabled by LigandMPNN and UniKP yielded three ScQR variants with improved substrate affinity and catalytic efficiency while maintaining the overall fold and function. This work underscores the power of metagenomics with structure-driven protein design in discovering novel enzymes with unique catalytic properties from extreme environments and establishes ScQR as a promising biocatalyst for biotechnological and pharmaceutical applications.IMPORTANCEThis study reports the discovery of ScQR, a novel thermophilic 3-quinuclidinone reductase identified via metagenomic mining. ScQR represents one of the most heat-resistant members of the SDR superfamily discovered to date, maintaining 86% activity after 48 hours at 70°C. These findings establish ScQR as a robust biocatalyst for high-temperature pharmaceutical applications and demonstrate a scalable workflow for optimizing enzymes from extreme environments, offering significant value to the fields of biocatalysis and protein engineering.},
}

@article {pmid42747298,
year = {2026},
author = {Nguyen, MH and Schatz, MC},
title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag687},
pmid = {42747298},
issn = {1367-4811},
abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.

RESULTS: We present Perseus, a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.

Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus.},
}

@article {pmid42747315,
year = {2026},
author = {Sun, W and Li, Y and Liu, X and Yu, S and Li, W and Wang, H and Geng, H and Li, L and Hu, J and Huo, J and Zhang, W and Fu, J and Jin, X and Li, H and Zhou, X and Zhu, X},
title = {Gut microbiota functional remodeling and butyrate depletion amplify anti-Ro/La antibody-driven type I interferon activation in neonatal lupus.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2728464},
doi = {10.1080/19490976.2026.2728464},
pmid = {42747315},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Interferon Type I/immunology ; Infant, Newborn ; *Autoantibodies/immunology/blood ; *Lupus Erythematosus, Systemic/immunology/microbiology ; *Butyrates/metabolism ; Female ; Bacteria/classification/genetics/isolation & purification/metabolism ; Male ; },
abstract = {The early-life gut microbiome may influence susceptibility to antibody-mediated neonatal autoimmunity, but the underlying mechanisms remain poorly understood. We investigated whether gut microbial functional capacity and metabolites influence autoantibody-dependent immune activation in 90 neonates, including healthy controls, anti-Ro/La-exposed neonates without neonatal lupus erythematosus (No-NLE), and neonates with NLE (n = 30 per group). Shotgun metagenomic profiling demonstrated progressive remodeling of the neonatal gut microbiome across the three groups, with anti-Ro/La exposure associated with depletion of early-life commensal-associated taxa, including Bifidobacterium, Rothia, and Clostridium, and enrichment of taxa with opportunistic potential, including Klebsiella and Enterococcus, with greatest ecological divergence in neonates with NLE. Functional profiling identified altered microbial carbohydrate-processing capacity, marked by enrichment of glycosyltransferase family 4 (GT4) and depletion of GT2 in NLE. These alterations coincided with broad reductions in plasma short-chain fatty acid metabolites, most prominently butyrate, together with increased serum immunoglobulin G (IgG) and interferon-α (IFN-α) and decreased complement component 4 (C4). A GT4-Klebsiella-Rothia-IFN-α signature distinguished NLE from No-NLE (AUC = 0.883; 95% CI, 0.799-0.967). In functional assays, pooled bacteria-depleted fecal filtrates from neonates with NLE potentiated IFN-α production by neonatal peripheral blood mononuclear cells in the presence of anti-Ro/La-positive plasma. Conversely, sodium butyrate suppressed anti-Ro/La-associated IFN-α production and reduced 28 inflammation-related proteins, including CXCL10, ADA, and PD-L1, involved in cytokine, IL-17, and TNF signaling. Together, these findings provide functional evidence supporting a microbiota-associated butyrate-type I interferon pathway that may amplify maternal autoantibody-dependent immune activation and contribute to the clinical manifestation of NLE.},
}

Humans
*Gastrointestinal Microbiome
*Interferon Type I/immunology
Infant, Newborn
*Autoantibodies/immunology/blood
*Lupus Erythematosus, Systemic/immunology/microbiology
*Butyrates/metabolism
Female
Bacteria/classification/genetics/isolation & purification/metabolism
Male

@article {pmid42747396,
year = {2026},
author = {Huang, Y and Feng, X and Hu, X and Sun, Y and Song, Z and Xie, M and Liao, T and Liu, X and Lv, X and Liu, R and Liu, Q and Voolstra, CR and Luo, H},
title = {Environmental Gradients as a Dominant Force in the Macroevolution of a Host-Associated Marine Bacterium.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag244},
pmid = {42747396},
issn = {1751-7370},
abstract = {Natural selection is imposed by both abiotic environmental filtering and biotic interactions, yet their relative roles in shaping the deep phylogeny of widespread, generalist host-associated bacteria remain unclear. Here, we integrate large-scale phylogenomics, environmental sequencing, functional genomics, and global metagenomic analysis to demonstrate that tidal zonation overrides host association as the dominant macroevolutionary force structuring the marine bacterial genus Ruegeria. Analysis of 533 genomes and 74 global coastal metagenomes reveals that the intertidal-subtidal boundary structures the deepest phylogenetic splits, driving the repeated evolution of distinct ecotypes through independent zonation transitions across global coastlines. These ecotypes possess divergent genomic toolkits: intertidal strains are enriched for genes coding for stress resistance and anaerobic metabolism, whereas subtidal strains specialize in high-affinity nutrient scavenging. Our findings establish that predictable physicochemical gradients act as filters that generate foundational diversity from which specialized host symbionts subsequently emerge, reframing how environmental gradients shape microbial evolution at the eco-evolutionary interface.},
}

@article {pmid42747454,
year = {2026},
author = {Bi, K and Sandoval, M and Nguyen, T and Perez, I and Ghosh, L and Krause, T and Cazaban, CG and Pasco, R and Meyers, L and Wu, F and Rios, J and Tisza, M and Clark, J and Maresso, A and Boerwinkle, E and Bauer, C},
title = {Temporal Alignment of Wastewater Signals with Clinical Indicators of Respiratory Illness Postpandemic, Texas, USA.},
journal = {Emerging infectious diseases},
volume = {32},
number = {13},
pages = {43-52},
doi = {10.3201/eid3213.260141},
pmid = {42747454},
issn = {1080-6059},
mesh = {Texas/epidemiology ; Humans ; *Wastewater/virology ; *COVID-19/epidemiology/diagnosis ; SARS-CoV-2/isolation & purification/genetics ; *Influenza, Human/epidemiology/diagnosis ; *Respiratory Syncytial Virus Infections/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; },
abstract = {In the COVID-19 postpandemic era, declining clinical testing for SARS-CoV-2 has led to the exploration of complementary early detection methods. We evaluated metagenomic wastewater-based epidemiology (WBE) in Texas, USA, by comparing viral signals with the National Syndromic Surveillance Program tracked emergency department visits and Texas All-Payer Claims Database insurance claims across several Texas counties during 2022-2024. By analyzing SARS-CoV-2, influenza, and respiratory syncytial virus, we found moderate-to-strong temporal correlations between wastewater and clinical indicators. Influenza showed the most stable associations (r<0.98), whereas SARS-CoV-2 signals generally preceded clinical metrics. Respiratory syncytial virus exhibited higher geographic and temporal heterogeneity, reflecting differences in clinical data capture. Despite sampling frequency and geographic alignment challenges, metagenomic WBE consistently tracked community trends. Our findings suggest WBE can offer valuable situational awareness and a resilient complement to clinical surveillance, supporting public health preparedness in an evolving respiratory disease landscape.},
}

Texas/epidemiology
Humans
*Wastewater/virology
*COVID-19/epidemiology/diagnosis
SARS-CoV-2/isolation & purification/genetics
*Influenza, Human/epidemiology/diagnosis
*Respiratory Syncytial Virus Infections/epidemiology
*Wastewater-Based Epidemiological Monitoring

@article {pmid42747640,
year = {2026},
author = {Redding, LE and Hu, W and Daniel, S and Okumura, M and Hiehle, ME and David, MZ and Hunter, L and Cole, SD},
title = {Antimicrobial-resistant organism carriage and metagenomic characterization of the microbiome and resistome in veterinary workers.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42747640},
issn = {1573-7446},
support = {NI25AHDRXXXXG042 Formula Funds//U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Microbiota ; *Drug Resistance, Bacterial ; Hospitals, Animal ; Methicillin-Resistant Staphylococcus aureus/isolation & purification/drug effects/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Male ; Escherichia coli/drug effects/isolation & purification/genetics ; Female ; *Animal Technicians ; *Carrier State/microbiology/epidemiology ; *Veterinarians ; Feces/microbiology ; Metagenome ; RNA, Ribosomal, 16S ; Adult ; },
abstract = {BACKGROUND: Veterinary personnel work in environments with high exposure to antimicrobials and antimicrobial-resistant pathogens. However, the extent to which these occupational exposures influence their carriage of antimicrobial-resistant (AMR) organisms and the composition of their microbiome and resistome remains poorly understood. The objective of this study was to characterize AMR pathogen carriage and microbiome/resistome composition in veterinary personnel and to assess whether workplace setting and patient-related exposures were associated with detectable differences in these outcomes.

METHODS: Personnel from a large academic veterinary hospital and a convenience sample of private-practice small-animal veterinary hospitals provided nasal swabs, stool samples, and exposure survey data; environmental samples were also collected from the academic hospital. Nasal swabs were cultured for methicillin-resistant Staphylococcus aureus, and stool samples were cultured for extended spectrum cephalosporin resistance (ESCR) Escherichia coli. Samples also underwent shotgun metagenomic sequencing or 16S rRNA gene sequencing for taxonomic and antimicrobial resistance gene profiling. Alpha/beta diversity were compared across groups, beta diversity by Permutational Multivariate Analysis of Variance, linear models tested differential abundance, and logistic regression was used to assess covariates associated with MRSA and ESCR carriage. A subset of academic-hospital participants also submitted additional samples after time away (1-2 weeks) from the hospital.

RESULTS: Among academic-hospital personnel (n = 38), MRSA and ESCR-E. coli carriage prevalence were 18.4% and 11.1%, respectively. In private-practice personnel (n = 8), carriage was 12.5% and 25%, respectively. Within the academic hospital, MRSA carriage was associated with administering antibiotics to patients. Microbial composition differed modestly by worksite (R[2] = 0.02) when assessed using unweighted UniFrac metrics only, suggesting subtle site-related differences in low-abundance phylogenetically distinct taxa. Global resistome composition did not differ significantly by site or clinical exposure, although a small number of individual AMR ontologies and broad AMR gene families varied across groups, including those associated with commonly-administered oral antibiotics at the hospital. Paired on/off-clinic analyses did not show a clear directional shift after time away from the hospital.

CONCLUSIONS: Veterinary personnel carried MRSA at a notable frequency, while workplace effects on the microbiome and resistome were subtle, with limited evidence for large-scale shifts in community structure by site or patient exposure.},
}

Humans
*Microbiota
*Drug Resistance, Bacterial
Hospitals, Animal
Methicillin-Resistant Staphylococcus aureus/isolation & purification/drug effects/genetics
Animals
Anti-Bacterial Agents/pharmacology
Male
Escherichia coli/drug effects/isolation & purification/genetics
Female
*Animal Technicians
*Carrier State/microbiology/epidemiology
*Veterinarians
Feces/microbiology
Metagenome
RNA, Ribosomal, 16S
Adult

@article {pmid42747765,
year = {2026},
author = {Gueddari, NE and Philip, M and Camoin-Jau, L and Gouriet, F},
title = {Contemporary diagnostic strategies for blood culture-negative infective endocarditis: from conventional microbiology to emerging molecular and multimodality approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42747765},
issn = {1439-0973},
abstract = {BACKGROUND: Blood culture-negative infective endocarditis (BCNE) remains one of the most challenging presentations of infective endocarditis (IE) because the absence of microbiological confirmation delays diagnosis and complicates therapeutic management. BCNE may result from prior antibiotic exposure, infection with fastidious or intracellular microorganisms, fungal pathogens, or non-infectious conditions mimicking IE.

METHODS: This narrative review provides a clinically oriented overview of contemporary diagnostic strategies for BCNE based on current evidence and recent international guidelines. The diagnostic performance, limitations, and clinical applicability of biomarkers, microbiological methods, multimodality imaging, and pathological analysis were critically evaluated and integrated into practical diagnostic algorithms.

RESULTS: Targeted serology and polymerase chain reaction (PCR), particularly on excised valve tissue, remain the most clinically validated microbiological tools for routine BCNE diagnosis. Emerging molecular approaches, including droplet digital PCR (ddPCR) and metagenomic next-generation sequencing (mNGS), show promising diagnostic potential but remain insufficiently standardized for routine implementation. Echocardiography remains the first-line imaging modality, while cardiac computed tomography, 18 F-FDG PET/CT, and white blood cell SPECT/CT (WBC SPECT/CT) provide complementary diagnostic information, particularly in prosthetic valve endocarditis (PVE) and other diagnostically challenging cases. Histopathological examination combined with molecular analysis of surgical specimens remains an important complementary diagnostic approach when valve tissue is available.

CONCLUSIONS: Optimal diagnosis of BCNE requires an integrated multidisciplinary strategy combining clinical assessment, microbiology, multimodality imaging, and pathology. Future progress will depend on evidence-based diagnostic algorithms integrating emerging technologies according to their level of validation, local epidemiology, and available expertise.},
}

@article {pmid42748603,
year = {2026},
author = {Xing, BS and Wang, ZY and Zhang, ZZ and Fu, YL and Cui, YX and Wang, XC and Chen, R and Li, YY},
title = {Spatiotemporal niche differentiation enables stable autotrophic nitrogen removal in a continuous-flow system coupling microalgae, ammonia oxidizers and anammox bacteria.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126938},
doi = {10.1016/j.watres.2026.126938},
pmid = {42748603},
issn = {1879-2448},
abstract = {Natural aquatic aggregates use diel fluctuations in dissolved oxygen and microscale redox gradients to support aerobic and anaerobic processes, providing an ecological blueprint for continuous-flow microalgal-bacterial systems; however, this coupling remains difficult because photosynthetic oxygen supports ammonia oxidation but inhibits oxygen-sensitive anaerobic ammonium-oxidizing bacteria (AnAOB). In this study, a continuous-flow light-driven microalgal-bacterial system was developed. Long-term reactor operation, pathway contribution tests, extracellular polymeric substance (EPS) characterization, granule and FISH-CLSM analysis, and metagenomics were conducted to elucidate the stabilization mechanism of autotrophic nitrogen removal without external organic carbon. During 530 days of operation, the 8 h light/16 h dark regime maintained the dissolved oxygen concentration at 0.2-0.4 mg/L, while TNRE reached 86.2% before external nitrite supplementation and remained approximately 90% during the nitrite-assisted final phase. Pathway contribution tests indicated that the estimated microalgal-associated assimilation contribution was 36.48% during illumination, whereas denitrification and anammox dominated under dark conditions, contributing 40.53% and 39.67%, respectively. During reactor maturation, the average granule size peaked at 450 μm on day 400, the protein/polysaccharide (PN/PS) ratio increased from approximately 3.0 to 5.0, and the amount of tightly bound EPS protein (TB-EPS-PN) increased to approximately 35 mg/g VSS, indicating enhanced granule cohesion and resistance to disturbance. Metagenomic analysis revealed enrichment of Candidatus Kuenenia to 11.62% and coordinated increases in key nitrogen transformation genes. During reactor maturation, granule development, EPS accumulation, and the algal-bacterial association observed by FISH-CLSM were associated with increasing structural organization, while stage-dependent changes in stress- and adaptation-related genes supported a gene-EPS-structure adaptation framework. Collectively, these findings support a spatiotemporal niche‑differentiation framework in which light/dark cycling may temporally partitions nitrogen pathways, while EPS‑associated granule development and structural heterogeneity may enhance diffusion limitation and provide spatial buffering favorable for oxygen‑sensitive anaerobic functions.},
}

@article {pmid42748612,
year = {2026},
author = {Zhang, X and He, J and Lv, L and Cui, H and Wang, Y and Zhang, X and Lv, J},
title = {Methane and carbon dioxide emissions from wastewater treatment units linked to DOM stabilization and phosphonate-scavenging microbiomes.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126932},
doi = {10.1016/j.watres.2026.126932},
pmid = {42748612},
issn = {1879-2448},
abstract = {Municipal wastewater treatment plants (WWTPs) are major engineered facilities for urban carbon removal, yet methane (CH4) formation and source mechanisms in downstream stages after aeration and biological nutrient removal remain poorly resolved. Process resolved monitoring at a full-scale WWTP showed that CH4 emissions were concentrated upstream, while measurable fluxes persisted in downstream sedimentation and denitrification units. Dissolved CH4 profiles showed strong attenuation of influent derived CH4 during upstream treatment, followed by a local increase after secondary clarification. Carbon dioxide (CO2) emissions peaked in the biochemical tank, consistent with rapid oxidation of labile organic carbon. Fluorescence and molecular analyses revealed a shift in dissolved organic matter (DOM) from protein like to more humic and processed molecules, while community assembly remained predominantly deterministic despite greater stochasticity in later stages. The C-P lyase catalytic core was enriched in these units, accompanied by higher phnJ transcript abundance, candidate organophosphonate features, and genomic potential. Together with BES insensitive CH4 formation in independent microcosms, these observations supported C-P lyase mediated organophosphonate utilization as a contributing pathway to local CH4 formation. Integrated evidence indicated that DOM stabilization, deterministic community filtering, potential succinate mediated cross feeding, and phosphonate scavenging jointly shaped this process. These findings show that advanced treatment units are not CH4 hotspots, but neither are they CH4 inactive zones; process resolved GHG assessments should therefore consider persistent local CH4 generation and its association with substrate restructuring and alternative phosphorus acquisition.},
}

@article {pmid42748661,
year = {2026},
author = {Iqbal, S and Xu, Y and Ni, L and Dang, H and Luan, X and Zhang, D},
title = {Biogeographic patterns and metabolic potential of chemoautotrophic communities in cold seep sediments across subarctic to tropical regions.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108410},
doi = {10.1016/j.marenvres.2026.108410},
pmid = {42748661},
issn = {1879-0291},
abstract = {Cold seeps are hotspots of chemoautotrophic primary production, yet how chemoautotrophic community structure and dark carbon fixation (DCF) vary across climatic regions remains unclear. We combined incubation experiments and metagenomics to compare chemoautotrophic communities in cold seep sediments across northwestern Pacific marginal seas, from the subarctic Okhotsk Sea to the tropical South China Sea. Incubation experiments demonstrated higher DCF rates in tropical (1.20 μg C g[-1] day[-1]) than subarctic (0.35 μg C g[-1] day[-1]) sediments (p = 0.002). Analyses of 133 cold seep sediment metagenomes (26 in this study and 107 from NCBI, spanning 0-240 cmbsf) revealed that subarctic chemoautotrophs were dominated by Chloroflexota, Asgardarchaeota, Campylobacterota, and Thermoproteota, whereas tropical chemoautotrophs were dominated by Pseudomonadota and Asgardarchaeota, with higher alpha diversity and integrated co-occurrence networks observed in tropical sediments. Representative genes of the Calvin-Benson-Bassham (CBB) cycle, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, and the 3-hydroxypropionate (3HP) bicycle were enriched in tropical sediments, whereas reductive tricarboxylic acid (rTCA) cycle and Wood-Ljungdahl (WL) pathway genes predominated in subarctic sediments. Genome-resolved analysis showed that CBB cycle potential was concentrated in Pseudomonadota in tropical sediments and in Asgardarchaeota in subarctic sediments, and was most strongly correlated with nitrogen metabolism genes, whereas rTCA cycle potential was concentrated in Campylobacterota across both sediments, coupled strongly to sulfur metabolism. Depth profiling revealed surface communities dominated by Campylobacteria using rTCA cycle in subarctic sediments, and Alphaproteobacteria and Gammaproteobacteria using CBB cycle in tropical sediments, whereas the WL pathway predominated in Dehalococcoidia and Lokiarchaeia in the deeper layers of both regions. This study provides a comparative framework for chemoautotrophic biogeography across climatically distinct seeps.},
}

@article {pmid42748814,
year = {2026},
author = {Gao, J and Li, Y and Feng, K and Zheng, H and Li, W and Cheng, Z and Zhao, J and Li, W and Ye, L and Li, S},
title = {Decoupling biodegradation from substrate concentration via quorum sensing: A cell density-responsive strategy for robust chlorobenzene removal.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143600},
doi = {10.1016/j.jhazmat.2026.143600},
pmid = {42748814},
issn = {1873-3336},
abstract = {Chlorinated aromatic compounds are important industrial pollutants that pose persistent environmental risks due to their toxicity and recalcitrance. Biological treatment is a sustainable approach for chlorinated VOC removal. However, conventional bioremediation is constrained by an inherent dilemma in native regulatory systems: trace substrate concentrations trigger insufficient gene expression, while shock loads induce severe metabolic inhibition and cytotoxicity. To overcome these limitations, we leveraged quorum sensing (QS) to reprogram gene regulation in Pseudomonas putida, redirecting degradation control from substrate concentration to cell density. The native, pollutant-inducible promoter of the tod operon was replaced with the QS-responsive promoter PlasA, generating the engineered strain F1-QS. At low chlorobenzene concentrations, F1-QS increased tod transcription by 9.7‑fold, reduced the lag phase from 6 h to 2 h, and enhanced the degradation rate by 38.91%. Critically, this advantage extended to high pollution loads. At 325 mg/L chlorobenzene, F1-QS achieved 88.0% removal within 32 h, outperforming the wild-type strain (35.9%) by more than two-fold. In a synthetic microbial community, the F1-QS strain accelerated consortium degradation by 70.93% and maintained stable performance during long-term operation, highlighting its superior efficacy and resilience under substrate-limited conditions. Metagenomic analysis revealed that enhanced degradation performance was associated with higher abundance of key chlorobenzene degradation genes, suggesting an enhanced functional potential of the microbial consortium. This study shows that QS‑based rewiring resolves the trade‑off between weak induction at low concentrations and toxicity at high concentrations, offering a robust strategy for chlorinated VOC bioremediation.},
}

@article {pmid42003319,
year = {2026},
author = {Jaskiel, JE and Aichelman, HE and Anderson, G and Claassens, L and Fifer, JE and Hernandez, CM and Huzar, AK and Llopiz, JK and Witting, JW and Mullen, SP and Rotjan, RD},
title = {Larval Genomics as a Viable, Fisheries-Independent Tool for Investigating Population Structure in Tropical Pacific Tunas.},
journal = {Molecular ecology},
volume = {35},
number = {8},
pages = {e70335},
pmid = {42003319},
issn = {1365-294X},
support = {CI-113205//Blue Nature Alliance/ ; 55207252//Waitt Foundation/ ; },
mesh = {Animals ; *Tuna/classification/genetics ; Larva/genetics ; *Fisheries ; Pacific Ocean ; *Metagenomics/methods ; Species Specificity ; Linkage Disequilibrium ; Reproduction ; },
abstract = {Understanding how dispersal, life history, and environmental variability shape genetic connectivity in the open ocean remains a central challenge in evolutionary biology. Highly migratory marine predators like tunas have traditionally been considered genetically homogeneous across ocean basins, yet emerging genomic evidence suggests that cryptic population structure can persist even in species with high gene flow and large effective population sizes. We used 2bRAD sequencing of 348 larval and subadult skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), and bigeye tuna (T. obesus) collected from the central Pacific across 7 years of sampling to examine species boundaries, population genetic information, genetic structure, and connectivity. Larval sampling revealed consistent spawning by all three species and enabled unbiased detection of genetic patterns prior to recruitment bottlenecks. We found strong divergence amongst species, no evidence of structuring within skipjack or bigeye, and a divergent yellowfin population detected in 2 consecutive sampling years north of American Samoa. Comparisons between larvae and subadults suggest that sampling early life history stages can be a valuable tool for assessing population genetic information before recruitment bottlenecks, selective harvest by fisheries, adult dispersal, and selective pressures acting on adult populations, thereby contributing novel insights to the research and effective management of these species. These results highlight how larval genomics can complement traditional population genomic studies of adult tunas and reveal fine-scale structure in highly vagile species, providing new perspectives on connectivity in the open ocean.},
}

Animals
*Tuna/classification/genetics
Larva/genetics
*Fisheries
Pacific Ocean
*Metagenomics/methods
Species Specificity
Linkage Disequilibrium
Reproduction

@article {pmid42734183,
year = {2026},
author = {Chen, W and Pan, Y and Chen, M and Zhou, S and Liu, X and Sun, M and Yang, Z and Zhi, Y},
title = {Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726620},
pmid = {42734183},
issn = {1949-0984},
mesh = {Humans ; *Stroke/complications/metabolism ; Metabolomics ; Metagenomics ; *Depression/metabolism/etiology/microbiology ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Middle Aged ; Aged ; Cytokines/blood ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Biomarkers/blood ; },
abstract = {Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.},
}

Humans
*Stroke/complications/metabolism
Metabolomics
Metagenomics
*Depression/metabolism/etiology/microbiology
Female
Multiomics
Male
*Gastrointestinal Microbiome
Inflammation/metabolism
Middle Aged
Aged
Cytokines/blood
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
Biomarkers/blood

@article {pmid42734327,
year = {2026},
author = {Sahu, K and Aich, P},
title = {A robustness-first cross-disease framework supports a candidate shared microbial redox axis and disease-specific metabolic divergence in colorectal cancer, Crohn's disease, and liver cirrhosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0083626},
doi = {10.1128/msystems.00836-26},
pmid = {42734327},
issn = {2379-5077},
abstract = {UNLABELLED: Gut microbiome dysbiosis is associated with colorectal cancer (CRC), Crohn's disease (CD), and liver cirrhosis (LC), yet whether these diseases share conserved microbial vulnerabilities remains unresolved. Analytical pipeline choices alone can shift apparent performance from near-zero to near-perfect on identical data, rendering cross-disease comparison unreliable. Here, in a secondary cross-sectional analysis of public data sets, maximin optimization is introduced as a proposed pipeline-selection criterion guaranteeing worst-case performance across all tasks simultaneously. Benchmarking 1,152 preprocessing-model configurations across six tasks using gut metagenomics and serum metabolomics from CRC, CD, and LC reveals a candidate 19-species microbiome signature in which Firmicutes bacterium CAG:41 is the sole threshold-stable cross-disease taxon, depleted in all three diseases. Microbiome pathway enrichment converges on sulfur-selenium redox metabolism and B-vitamin biosynthesis, while host metabolomic responses are predominantly disease-specific. CD and LC are dominated by single discriminative taxa; CRC requires community-level integration. Exploratory external evaluation was adequately powered only for CRC (AUC = 0.769, 95% bootstrap CI 0.678-0.849); CD and LC assessments were exploratory only.

IMPORTANCE: Cross-disease microbiome comparison has lacked a principled analytical foundation: arbitrary preprocessing choices can shift apparent classification performance from near-random to near-perfect on identical data, making biological conclusions unreliable when pooled across diseases. Maximin optimization addresses this by providing a decision-theoretic guarantee that every classification task contributes valid signal, enabling the first analytically controlled cross-disease comparison of gut metagenomics and serum metabolomics across three major gut-associated diseases. The identification of Firmicutes bacterium CAG:41 as the sole threshold-stable cross-disease taxon, harboring predicted functions in sulfur-selenium metabolism, offers a concrete target for experimental characterization and prospective screening validation. The two-layer dysbiosis architecture-universal microbial vulnerability with disease-specific host metabolic responses-provides a conceptual template for cross-disease microbiome study design in other gut-associated conditions, pending prospective confirmation.},
}

@article {pmid42734355,
year = {2026},
author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Gürkan Yardımcı, G and Merritt, JL},
title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0155026},
doi = {10.1128/spectrum.01550-26},
pmid = {42734355},
issn = {2165-0497},
abstract = {Across human mucosal sites, dysbiotic inflammatory diseases are characterized by compositional shifts in the resident microbiota, in which commensal-dominated communities give way to pathobiont-enriched communities where "inflammophilic" species often predominate. Effective treatments for these complex polymicrobial infections remain limited, in part, because the ecological mechanisms driving their emergence and persistence are still poorly understood. To address this gap, we analyzed a unique cohort of pediatric patient-matched, disease-free dental plaque and odontogenic abscess specimens, providing a clinically relevant model to examine microbiome transitions from commensal to inflammophilic states. Using complementary community ecology modeling approaches and inferred metagenomic analyses, we identified microbial taxa and functional programs associated with inflammatory selective pressure and dysbiotic community emergence. Dental plaque communities are characterized by anabolic metabolic processes and carbohydrate-derived ATP generation, whereas abscess microbiomes are highly biased for catabolic metabolism, amino acid-derived ATP generation, and antimicrobial resistance. The results suggest that abscess communities are much less reliant upon interspecies metabolic complementation compared to dental plaque communities, which would imply an obligate dependence upon host inflammatory responses to provide the key metabolites required for growth. These findings support a model in which an inflammophilic community ecology is largely the net result of a combination of enhanced resistance to innate immunity and compatibility with the inflammatory nutrient environment. By defining the metabolic requirements and selective pressures governing these dysbiotic transitions, it may be possible to suppress inflammatory dysbiotic diseases using ecologically focused therapeutic strategies that exploit the limited biosynthetic capacity of commensal depleted inflammophilic communities.IMPORTANCEDysbiotic inflammatory diseases are frequently sustained by complex microbial community interactions, but the ecological processes involved remain poorly understood. In this study, we leveraged pediatric patient-matched, disease-free dental plaque and odontogenic abscess clinical specimens to examine how oral microbial communities shift from health-associated to inflammation-associated states. We found that abscess microbiomes are enriched for features consistent with adaptation to inflammatory environments, including antimicrobial resistance, catabolic metabolism, and utilization of host-derived nutrients. These findings support a model in which host inflammation functions as a selective ecological pressure, favoring the establishment of metabolically specialized, inflammophilic microbial communities. By defining the ecological and functional features that distinguish abscess-associated communities from disease-free plaque microbiota, this work provides a framework for understanding inflammatory dysbiosis and for developing ecological strategies to disrupt pathobiont-enriched communities while promoting the restoration of stable, health-associated microbiota.},
}

@article {pmid42734361,
year = {2026},
author = {Luo, G and Zhao, J and Xie, L-l and Li, Y and Rao, Y-z and Sun, Y and Lu, X and Eden, J-S and Chen, L and Shi, M},
title = {Library strategies differentially shape microbial, functional, and host signals in clinical metagenomic sequencing.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0089726},
doi = {10.1128/msystems.00897-26},
pmid = {42734361},
issn = {2379-5077},
abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly used in infectious disease diagnostics, yet how library preparation shapes the microbial, functional, and host signals recovered from clinical samples remains poorly defined. Here, we performed a within-sample parallel comparison of three mNGS library preparation strategies-DNA-based libraries (DNAlib), RNA-based libraries (RNAlib), and total nucleic acid-based libraries (TNAlib)-across a diverse range of clinical specimens spanning five sample types. Using a curated clinical infectome as a benchmark, we show that library strategies are not interchangeable but capture distinct biological dimensions of the same specimen. RNAlib provided the most comprehensive standalone recovery of the clinical infectome, with improved detection of RNA viruses and cellular pathogens, enhanced resolution of resistance and virulence signals, and preservation of infection-associated host immune signatures. DNAlib showed stronger baseline recovery of DNA viruses and broader host genome coverage, whereas the TNAlib workflow evaluated here largely behaved as an intermediate strategy rather than a consistent improvement over dedicated DNA- or RNA-based workflows. Together, these results establish that the library preparation protocol is a major determinant of how clinical mNGS data should be interpreted and provide a framework for selecting sequencing strategies according to specific diagnostic and biological questions.IMPORTANCEMetagenomic sequencing is increasingly used in infectious disease research and clinical diagnostics, but different library preparation strategies may recover fundamentally different biological signals from the same sample. These signals include not only pathogens but also background microbes, microbial functional activity, and host immune-response patterns. Here, we systematically compared DNA-, RNA-, and total nucleic acid-based metagenomic sequencing libraries using the same clinical samples processed in parallel. We found that the three strategies did not provide equivalent information. RNA-based sequencing generated the most informative single-library view of infection, particularly for RNA viruses, cellular pathogens, functional microbial signals, and host immune-response patterns. DNA-based sequencing was more effective for DNA virus and host genome recovery, whereas the total nucleic acid sequencing workflow evaluated here generally behaved as an intermediate strategy. These findings show that library preparation can substantially influence the interpretation of metagenomic data.},
}

@article {pmid42734522,
year = {2026},
author = {Liu, S and Gao, X and Wang, J and Li, Z and Liu, Y and Wang, Y and Hou, T and Liu, F and Liu, Y},
title = {PPsAMP: A Novel Computational Framework for Short Antimicrobial Peptide Identification by Fusing Fine-Tuned Semantic and Physicochemical Features via Cross-Attention.},
journal = {Journal of chemical information and modeling},
volume = {66},
number = {17},
pages = {11491-11502},
doi = {10.1021/acs.jcim.6c01300},
pmid = {42734522},
issn = {1549-960X},
support = {NA//Fundamental Research Funds for the Central Universities/ ; 20250203113SF//Science and Technology Development Plan Project of Jilin Province/ ; 62303193//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Antimicrobial Peptides/chemistry/pharmacology ; Prediction Algorithms ; },
abstract = {The widespread misuse of antibiotics has led to a global antimicrobial resistance crisis, highlighting the urgent need for novel antibacterial strategies. Short antimicrobial peptides (sAMPs), while maintaining strong antimicrobial activity, offer superior bioavailability and synthetic feasibility, thus holding great promise in the development of next-generation antibiotics. In recent years, AI-based approaches have achieved notable progress in AMP prediction; however, most existing models are trained primarily on medium and long peptides, resulting in limited accuracy and representation capability when applied to identify sAMPs. To address this problem, a novel prediction model, PPsAMP, is proposed in this paper. First, the protein language model ProtBert-BFD is fine-tuned by sAMPs and non-sAMPs to extract more discriminative representations, which are then integrated with physicochemical features through a cross-attention mechanism. The fused representation is further processed by a feature learning module to achieve the identification of sAMP. The feature learning module consists of a multihead self-attention mechanism and feedforward layers, with residual connections added to enhance generalization ability. Experimental results demonstrate that PPsAMP significantly outperforms state-of-the-art models for identifying sAMPs. Moreover, PPsAMP has identified 14,839 candidate sAMPs from environmental metagenomes, most of which have not been previously reported. The predicted MIC values indicate that they possess potential antibacterial activity. PPsAMP is freely available at https://github.com/shengxiliu/PPsAMP.},
}

*Antimicrobial Peptides/chemistry/pharmacology
Prediction Algorithms

@article {pmid42734665,
year = {2026},
author = {Naik, S and Kousar, H},
title = {Synergistic Biodegradation and Detoxification of High Alkaline Textile Effluent by Acinetobacter indicus KUHKSN-02 and Native Microbiome Aided Bioaugmentation.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42734665},
issn = {1432-0991},
mesh = {Biodegradation, Environmental ; *Acinetobacter/metabolism/isolation & purification/genetics ; *Wastewater/microbiology/chemistry ; *Microbiota ; *Water Pollutants, Chemical/metabolism ; Textiles ; Textile Industry ; Azo Compounds/metabolism ; Industrial Waste/analysis ; },
abstract = {Textile effluent is a chemically complex wastewater containing azo dyes, high alkalinity and recalcitrant organic pollutants. Its untreated discharge poses serious ecological risks and requires sustainable management before release. The comparative efficiency of monoculture treatment and native microbiome assisted bioaugmentation in real highly alkaline textile effluent remains insufficiently documented. This study evaluated the biodegradation and detoxification potential of Acinetobacter indicus KUHKSN-02, isolated from effluent-contaminated soil, under sterile monoculture and non-sterile native microbiome aided conditions. Results shown reduced pollution load evidenced by drastic decrease in physicochemical parameters by both monoculture (COD to 391 ± 6 mg/L and BOD to 18.73 ± 0.25 mg/L) and native bacterial community (COD to 194.3 ± 2.51 mg/L, BOD to 13.5 ± 0.36 mg/L, and TDS to 998.3 ± 6.5 mg/L), with a highest decolorization of 97.72%. FTIR analysis confirmed alterations in functional groups, while HR-LCMS Orbitrap detected Acid Red 18, Acid Orange 7, and Acid Yellow 36 in the raw effluent and in degradation intermediates such as aniline, 2-oxindole, anthranilic acid and betaine after treatment. The Oryza sativa phytotoxicity assay confirmed detoxification, with germination increasing from 0% in raw effluent to 73.33-93.33% after treatment. These findings demonstrate that native microbiome-aided bioaugmentation enhanced biodegradation and detoxification efficiency compared with monoculture treatment. Future studies should validate this approach under field conditions using metagenomic and metatranscriptomic analysis.},
}

Biodegradation, Environmental
*Acinetobacter/metabolism/isolation & purification/genetics
*Wastewater/microbiology/chemistry
*Microbiota
*Water Pollutants, Chemical/metabolism
Textiles
Textile Industry
Azo Compounds/metabolism
Industrial Waste/analysis

@article {pmid42735627,
year = {2026},
author = {Meng, N and Zhu, J and Yan, J and Zhao, Y and Liu, J and Li, G and Zhang, J and Wu, M and Zhou, H and Ma, Q},
title = {Unraveling anaerobic indole degradation in an acclimated sludge consortium: Candidate pathways and microbial division of labor inferred from metagenomic and metatranscriptomic analyses.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143606},
doi = {10.1016/j.jhazmat.2026.143606},
pmid = {42735627},
issn = {1873-3336},
abstract = {Indole is a widespread nitrogen-containing heterocyclic compound in manure, sludge, and wastewater systems, yet the enzymes and microbial populations involved in its anaerobic transformation remain poorly resolved. Here, we established a long-term acclimated anaerobic sludge consortium and combined degradation assays, metabolite profiling, metatranscriptomics, and genome-resolved metagenomics to investigate the functional basis of anaerobic indole degradation. After 120 days of acclimation, the consortium stably degraded 100 mg/L indole, whereas skatole was not effectively removed under the same strategy, indicating substrate-specific adaptation of the microbial community. Metabolite profiling detected oxindole, dioxindole, isatin, and anthranilic acid, supporting a putative transformation route involving pyrrole-ring oxidation and ring cleavage toward anthranilate-like intermediates. Metatranscriptomic analysis identified 16,660 differentially expressed genes after indole addition, with strong transcriptional responses involving oxidoreductases, hydrolases, cofactor-dependent redox metabolism, aromatic-CoA-related metabolism, and methane metabolism-associated pathways. Transcriptional responses highlighted the xanthine dehydrogenase-like molybdenum-enzyme system and isatin hydrolase as candidate contributors to upstream indole transformation, whereas those of abmG-like, bcrC, and oah genes were consistent with possible anthranilic acid activation and downstream CoA-type processing. MAG-resolved analysis further suggested that these candidate functions may be distributed among populations affiliated with Bacteroidota, Chloroflexota, Desulfobacterota, and Methanobacterium. Together, these findings establish a stable anaerobic indole-degrading consortium and provide a testable functional framework for syntrophic interactions linking upstream indole transformation, aromatic-CoA metabolism, and methanogenesis-associated carbon flow.},
}

@article {pmid42735789,
year = {2026},
author = {Chen, J and Wang, M and Li, W and Li, X and He, L and Li, Y and Zheng, M and Du, S and Zhou, Y and Ye, W},
title = {Comprehensive evaluation of new sequencer T20 and well-established T7 with 507 human samples.},
journal = {Genomics},
volume = {},
number = {},
pages = {111320},
doi = {10.1016/j.ygeno.2026.111320},
pmid = {42735789},
issn = {1089-8646},
abstract = {The DNBSEQ-T20x2 (T20) sequencer, developed by MGI Tech, enables cost-effective human whole-genome sequencing (WGS) at 30× coverage for less than $100 per genome. Here, we evaluate the sequencing performance and data quality of the T20 platform by benchmarking it against the established DNBSEQ-T7 (T7) sequencer using 507 samples derived from blood (N = 75), stool (N = 242), and saliva (N = 190). The T20 exhibited lower sequencing quality metrics compared with the T7, with Q20 scores of 95.76%-95.83% and Q30 scores of 87.25%-87.40%, compared with 97.81%-97.93% and 93.26%-93.60%, respectively, for T7 data. Quality differences were more evident toward the end of reads, and PCR-free libraries sequenced on the T20 showed similar reductions in quality scores. The median empirical base error rate estimated from 102 ZymoBIOMICS samples was 0.33%. The T20 demonstrated comparable coverage uniformity to the T7 and showed high concordance in microbiome composition analysis, with a median Bray-Curtis dissimilarity of 0.02. Variant calling performance was highly consistent between the two platforms. Among variants with non-missing genotype calls on both platforms, 94.92% of SNPs and 87.20% of indels showed concordant genotypes between T20 and T7. Overall, the T20 delivers reliable sequencing accuracy and reproducibility for large-scale genomic and microbiome studies, providing a cost-effective alternative for high-throughput sequencing applications.},
}

@article {pmid42735830,
year = {2026},
author = {Ma, Y and Ge, Y and Liu, C and Wang, M and Xiao, Z and Liu, X and Song, T and Zhou, Q and Xiao, L},
title = {Pathogenic microbiomes on jellyfish reveal health risks beyond envenomation.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {109307},
doi = {10.1016/j.toxicon.2026.109307},
pmid = {42735830},
issn = {1879-3150},
abstract = {Jellyfish stings pose a growing public health concern in coastal regions, yet secondary bacterial infections arising from venom-induced tissue damage remain largely unexplored. Here we used shotgun metagenomics to characterize the surface microbiomes of Rhopilema esculentum, Chrysaora quinquecirrha and Stomolophus meleagris, profiling bacterial composition, virulence factors, antibiotic resistance genes and mobile genetic elements. We observed distinct host-specific microbiome signatures, with R. esculentum harboring the highest abundance of virulence-associated genes and notable enrichment of WHO priority pathogens including Staphylococcus aureus and Acinetobacter baumannii. Resistance genes conferring tetracycline, glycopeptide and fluoroquinolone resistance were prevalent across all species. Transposases comprised over 45% of mobile genetic elements, indicating substantial horizontal gene transfer potential. Validation using newly developed TaqMan qPCR assays across eight jellyfish species including the three aforementioned and five additional species, confirming that all harbored at least one opportunistic pathogen. These findings establish jellyfish surfaces as underappreciated reservoirs of antibiotic-resistant pathogens and highlight a potential, but as yet unproven, route of pathogen exposure following envenomation.},
}

@article {pmid42735856,
year = {2026},
author = {Li, D and Hao, DC and Wang, F and Xiao, P},
title = {Integrating multiphysics simulation and biological insights to optimize fungal-bioaugmented soil microbial fuel cells.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135853},
doi = {10.1016/j.biortech.2026.135853},
pmid = {42735856},
issn = {1873-2976},
abstract = {Soil contamination by persistent herbicides like haloxyfop-P-methyl (B) poses substantial environmental risks. Microbial fuel cells (MFCs) offer a solution but require in-depth optimization. We designed a single-chamber soil MFC with a graphite felt anode and air cathode. A 2D equivalent model coupling secondary current distribution and diluted species transport was built in COMSOL Multiphysics. A specific factor (ffungi) for fungal bioaugmentation was introduced, alongside a substrate promotion-toxicity inhibition function (fB(x)) for the herbicide. The model validated the experimental performance ranking (2B + Myrothecium verrucaria (Mv) > B + Mv + Carbon fiber > B + Talaromyces > B + Mv/Talaromyces) and achieved high calibration accuracy, with relative errors below0.6% for current density(CD) and5.7% for power density (PD) across multiple groups. Parameter scans revealed that increasing ffungi linearly boosts performance, with CD and PD enhancements of approximately 2.5 times at ffungi=5. The initial pollutant concentration exhibited a non-monotonic "substrate promotion-toxicity inhibition" window based on model-predicted extrapolations beyond the experimentally tested x = 1 and x = 2 cases, suggesting an optimal concentration range (x = 2-4) that requires future experimental validation.Carbon fibers predominantly lower interfacial contact impedance and enhance the effective reaction area. Mechanistically, the simulated electrochemical behavior is consistent with the reported biological data (e.g. metagenomics and EIS), suggesting that the "xeno-fungusphere" formed by M. verrucaria promotes biofilm formation and electron transfer. The model serves as a robust tool for designing efficient fungal-augmented MFC for herbicide remediation and energy recovery.},
}

@article {pmid42735857,
year = {2026},
author = {Wang, YG and Chen, H and Sun, XX and Li, LH and Wang, ZY and Chen, R and Xing, BS},
title = {Elucidating how calcium inhibits anammox systems and a novel recovery strategy using cation exchange resin: Performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135851},
doi = {10.1016/j.biortech.2026.135851},
pmid = {42735857},
issn = {1873-2976},
abstract = {The application of anaerobic ammonium oxidation (anammox) process is hindered by the susceptibility of anaerobic ammonium-oxidizing bacteria (AnAOB) to inhibitors including excessive Ca[2+] concentrations. In this study, the mechanisms of Ca[2+] inhibition and subsequent recovery using cation exchange resin (CER) were systematically investigated by analyzing the characteristics of anammox granular sludge combined with metagenomic analysis. Under 400 mg/L Ca[2+] stress, the nitrogen removal rate (NRR) remained stable despite a sharp decrease in AnAOB abundance. This resilience was attributed to increased extracellular polymeric substance secretion for Ca[2+] sequestration and functional compensation owing to the activation of the nitrification-denitrification process. When Ca[2+] concentration raised to 800 mg/L, a dense CaCO3 precipitate layer formed on the granules, protecting the internal AnAOB but severely limiting substrate mass transfer, leading to a reduction in the NRR from 2.0 to 1.5 kg N/m[3]/d. Under this dense shield, metabolic pathways shifted toward biosynthesis, and carbon fixation and nucleotide metabolism were activated to support cellular proliferation. CER treatment removed the precipitate layer, restored mass transfer, and fully restored nitrogen removal performance. This recovery was accompanied by peak abundances of auxiliary bacteria (Fimbriimonas and Chthonomonas) and metabolic signatures, indicating a transition from stress defense to growth-oriented homeostasis. This study elucidated the response behavior of the anammox system under graded Ca[2+] stress and during the recovery process, and proposed a novel recovery method suitable for industrial application.},
}

@article {pmid42736576,
year = {2026},
author = {O'Sullivan, RJ and Nordfors, U and Saari, NJ and Majander, K and Taavitsainen, JP and Salo, K and Rohrlach, AB and Salmela, E and Lamnidis, TC and Traverso, L and Krause, J and Peltola, S and Onkamo, P},
title = {Population genomics, demography, and circum-Baltic connectivity of Early Medieval southwestern Finland.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42736576},
issn = {1474-760X},
support = {352727//Research Council of Finland/ ; 160003//Jane ja Aatos Erkon Säätiö/ ; },
mesh = {Humans ; Finland ; *Genetics, Population ; Demography ; History, Medieval ; Genomics ; DNA, Ancient ; Genome, Human ; Scandinavians and Nordic People ; *Metagenomics ; },
abstract = {BACKGROUND: Knowledge of Early Medieval Finland (1050-1250 CE) relies primarily on archaeological evidence, as contemporary sources are scarce. The available evidence indicates two distinct cultural-economic zones: coastal and inland. Using newly generated genomic data from 34 ancient individuals alongside modern Finnish genomes, we characterise Late Iron Age and Early Medieval ancestry in southwestern Finland, reconstruct demographic patterns, and place individuals within a circum-Baltic relatedness network.

RESULTS: Early Medieval ancestry in inland southwestern Finland was very similar to that of present-day inhabitants. Ancient coastal and inland individuals were genetically indistinguishable, whereas modern coastal populations showed substantially more Scandinavian ancestry, and less Baltic ancestry compared to their ancient counterparts. IBD (identity-by-descent) analyses also indicate a major genetic shift in the coastal zone since the Early Medieval Period. Effective population size increased throughout the study period and was ~ 13,000 by 1250 CE. IBD links between Scandinavia and Early Medieval Finland align with known archaeological connections. Furthermore, we identify IBD links between individuals from Early Medieval Finland and victims of the Kronan warship sinking.

CONCLUSIONS: We demonstrate nearly a millenium of population continuity in the inland zone of southwestern Finland, contrasted by a large, contemporaneous genetic shift in the coastal zone. This ancestry shift corresponds with documented medieval emigration from Sweden to Finland. The regional population rapidly expanded during this time period, likely due to new agricultural practices and favourable climatic conditions. Our circum-Baltic IBD network indicates that southwestern Finland was firmly embedded into the wider, pre-modern Baltic world.},
}

Humans
Finland
*Genetics, Population
Demography
History, Medieval
Genomics
DNA, Ancient
Genome, Human
Scandinavians and Nordic People
*Metagenomics

@article {pmid42736748,
year = {2026},
author = {Dirican, N and Yardibi, F},
title = {Scientific research dynamics on community-acquired pneumonia: Bibliometric analysis and future perspectives.},
journal = {Medicine},
volume = {105},
number = {37},
pages = {e50602},
pmid = {42736748},
issn = {1536-5964},
mesh = {*Bibliometrics ; *Community-Acquired Pneumonia ; Humans ; COVID-19/epidemiology ; *Biomedical Research/trends ; SARS-CoV-2 ; Community-Acquired Infections ; },
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is a leading cause of morbidity, mortality, and hospitalization worldwide. This study aimed to provide physicians and researchers with a comprehensive overview of the most influential publications and research trends in CAP.

METHODS: Research articles and reviews on CAP published in English and indexed in the Web of Science from 1978 to 2023 were analyzed. Network visualization and comprehensive bibliometric analyses of publication output, countries, journals, authors, cited references, and keywords were performed using CiteSpace and VOSviewer software.

RESULTS: A total of 4141 publications, including 3665 original research articles and 476 reviews, were included in the analysis. Publication output increased after 1991 and showed an overall upward trend, particularly after 2000. The United States, Spain, and China were the most productive countries. Chest published the most articles, whereas Clinical Infectious Diseases received the highest number of citations. Torres A was the most prolific author, whereas Fine MJ was the most cited. The most cited clinical studies published in the past 5 years focused on COVID-19, severe CAP (sCAP), and corticosteroid therapy. Co-citation analysis identified sCAP, healthcare-associated pneumonia, prospective cohort studies, and metagenomic next-generation sequencing as active research clusters. Keyword co-occurrence analysis identified sCAP as the largest and most prominent cluster, whereas the other current clusters included atypical pathogens, antibiotic resistance, chronic obstructive pulmonary disease, and β-lactam monotherapy.

CONCLUSIONS: This bibliometric analysis highlights the evolving research landscape of CAP and suggests that future research will increasingly focus on sCAP and its treatment, the identification of rare or emerging pathogens, rapid diagnostic technologies, appropriate initial treatment selection, personalized therapeutic strategies, and vaccination. These findings provide valuable insights into the current research hotspots on CAP and future priorities for researchers and clinicians.},
}

*Bibliometrics
*Community-Acquired Pneumonia
Humans
COVID-19/epidemiology
*Biomedical Research/trends
SARS-CoV-2
Community-Acquired Infections

@article {pmid42737259,
year = {2026},
author = {O'Bryan, CA and Stalford, B and Obe, T and Crandall, PG},
title = {Emerging Microbiological and Sensor-Based Approaches for Biofilm Detection in Meat and Poultry Processing Environments.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737259},
issn = {2304-8158},
abstract = {Biofilms remain a major challenge in meat and poultry processing because conventional sanitation verification methods provide only indirect evidence of attached microbial communities. Emerging microbiological and sensor-based technologies offer new opportunities to improve biofilm detection by providing information on biofilm structure, cellular membrane integrity, composition, and spatial distribution. This review evaluates advanced imaging techniques, molecular assays, extracellular polymeric substance (EPS)-focused analyses, and real-time sensor platforms for their potential to strengthen risk-based biofilm monitoring in meat and poultry processing environments. Confocal and epifluorescence microscopy, scanning electron microscopy, optical coherence tomography, and in situ fluorescence imaging provide detailed visualization of biofilm architecture and viability, supporting validation of routine monitoring methods and assessment of sanitation practices. Quantitative PCR, digital PCR, amplicon sequencing, and metagenomics characterize biofilm communities, identify persistent microorganisms, and evaluate sanitation effectiveness, while EPS analyses of polysaccharides, proteins, extracellular DNA, and lipids indicate biofilm maturity and resilience. Electrochemical impedance, quartz crystal microbalance, surface acoustic wave sensors, and microfluidic platforms show promise for near-real-time detection of attached biomass. Collectively, these technologies provide a framework for more targeted, data-driven biofilm surveillance that can improve sanitation verification and reduce pathogen persistence in meat and poultry processing facilities.},
}

@article {pmid42737331,
year = {2026},
author = {Olanbiwoninu, AA and Awotundun, TA and Afolabi, JF and Fashogbon, RO and Fagunwa, O},
title = {Ethnogeographic Distribution of Nigerian Fermented Foods and the Prospects for Bioeconomy Improvements.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737331},
issn = {2304-8158},
abstract = {Fermented foods and beverages represent a cornerstone of Nigerian food culture, yet their scientific documentation remains fragmented, and their potential within global bioeconomy frameworks is largely unrealised. This review addresses two interrelated gaps: the absence of a comprehensive ethnogeographic analysis of Nigerian fermented foods that integrates ecological, cultural, and agricultural drivers of regional diversity, and the limited examination of these foods as models for circular bioeconomy development. Using a narrative synthesis of peer-reviewed literature spanning 1986-2025, we systematically map the distribution of fermented tuber, cereal, legume, dairy, and fruit products across Nigeria's major geopolitical zones, demonstrating that agroecological endowment, ethnic composition, trade routes, and cross-cultural interactions shape regional variation. Beyond their socio-cultural significance, Nigerian fermented foods contribute meaningfully to food security by extending shelf life, enhancing nutrient bioavailability, and reducing post-harvest losses. This review further positions ogi (fermented maize gruel) and garri (fermented cassava granules) as model systems for circular bioeconomy integration, demonstrating how by-product valorisation can generate value-added outputs, including animal feed, bioethanol, biodegradable packaging, and organic acids. Key challenges, including food safety deficits, absence of standardised production protocols, and limited regulatory frameworks, are critically assessed. Three priority research directions are identified: metagenomics-based microbiome profiling, development of culturally appropriate starter cultures, and formulation of gender-responsive regulatory instruments. Nigerian fermented foods, properly documented and integrated into innovation systems, represent an underutilised asset for sustainable food system transformation in Sub-Saharan Africa.},
}

@article {pmid42737401,
year = {2026},
author = {Li, W and Guo, R and Zu, Z and Xu, S and Zhang, G and Dai, Y and Li, Y},
title = {Iron-Amended Pleurotus citrinopileatus Residue Composting: Lignocellulose Degradation and Microbial Functional Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737401},
issn = {2304-8158},
support = {2025ZDYFNS05//Changchun City Science and Technology Development Plan Project/ ; N/A//the Project of "Tiānchí Yīngcái" Talent Introduction Program of Xinjiang Uygur Autonomous Region/ ; N/A//NYGG/ ; },
abstract = {Spent mushroom substrate (SMS) from Pleurotus citrinopileatus cultivation is a lignocellulose-rich by-product whose efficient composting is hindered by lignocellulose recalcitrance and slow humification. This study compared the effects of Fe3O4-based magnetic powder (MP), Fe[0] beads (IB), and Fe2O3-rich crude iron ore (RI) with those of an unamended control during 30-day aerobic co-composting with chicken manure. Physicochemical characterization and metagenomic sequencing were combined to assess compost maturity, lignocellulose degradation, humic substance transformation, microbial succession, and functional potential. MP achieved the most balanced overall performance, exhibiting the highest total lignocellulose degradation (59.48%), the lowest final organic matter content (357.70 g/kg), a final C/N ratio of 13.04, and the highest germination index (151.50%). RI achieved the highest hemicellulose degradation and final contents of humic acid and total humic substances, whereas IB promoted rapid initial heating and relatively high cellulose degradation but caused greater physicochemical fluctuations. Metagenomic analyses revealed amendment-specific microbial succession and distinct CAZy-annotated gene and MetaCyc pathway profiles associated with lignocellulose transformation and carbon metabolism. Overall, Fe3O4-based magnetic powder showed the greatest potential for simultaneously promoting lignocellulose degradation, organic matter transformation, and compost maturity, providing a practical basis for the sustainable valorization of edible mushroom industry by-products.},
}

@article {pmid42737628,
year = {2026},
author = {Ghaffar, A and Abdul-Careem, MF},
title = {Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737628},
issn = {1422-0067},
support = {10036367//Egg Farmers of Alberta/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Metagenomics/methods ; *Housing, Animal ; *Metagenome ; *Bacteria/genetics/classification ; Genome, Bacterial ; Manure/microbiology ; Archaea/genetics ; Microbiota/genetics ; },
abstract = {Culture-independent techniques are playing a major role in exploring unique and novel microbial communities from complex ecosystems, leading to an outstanding impact on our basic understanding of the tree of life. Microbial communities are not extensively studied in layer chicken housing environments, particularly from the point of view of taxa carrying antimicrobial resistance genes, virulence genes and their functional potential. This study aimed to extract metagenomic-assembled genomes (MAGs) from the Illumina short-reads shotgun metagenomics sequenced data that originated from an Alberta poultry barn environment and then to study host tracking of antimicrobial resistance genes (ARGs) and the roles of genes involved in functions related to ammonia production, short-chain fatty acid (SCFA)-related pathways, sulfur metabolism, methane emission, stress and disinfectant-related pathways. A total of 251 high-quality MAGs were extracted, including 249 bacterial and two archaeal genomes from sequencing data of 30 metagenomic sequencing samples comprising 15 air and 15 manure samples collected from 15-layer farms. Interestingly 22 bacterial MAGs were not classified to species levels using GTDB-based classification. ARGs were mainly harbored by the genera Staphylococcus, Alistepes, Romboutsia, and Enterococcus. Bacteroides is a main taxon carrying ARGs in air samples. Ammonia production-related genes were mainly tracked in Staphylococcus, Ruminococcus and Corynebacterium genera. The assimilatory sulfate reduction genes responsible for sulfur metabolism and hydrogenase-related genes responsible for hydrogen cycling were traced from Staphylococcus originated from both air and manure. The current study provides characterizations of MAGs from a poultry housing environment by linking microbial taxa with virulence, resistance, and metabolic functions. The findings emphasize the role of microbiota in shaping gas emissions and AMR, with implications for poultry health and worker's safety and the ultimate aim of sustainable poultry production.},
}

Animals
*Chickens/microbiology
*Metagenomics/methods
*Housing, Animal
*Metagenome
*Bacteria/genetics/classification
Genome, Bacterial
Manure/microbiology
Archaea/genetics
Microbiota/genetics

@article {pmid42737764,
year = {2026},
author = {Kozhakhmetov, S and Vinogradova, E and Sergazy, S and Chulenbayeva, L and Kossumov, A and Kovenskiy, A and Mukhanbetzhanov, N and Ospankulova, G and Saduakhasova, S and Khamitova, D and Kamanova, S and Toimbayeva, D and Shaimenova, B and Kalemshariv, B and Aitmukhanbetov, D and Kushugulova, A},
title = {Enteral Nutrition Is Associated with a Distinct Gut Microbiome Composition and Fermentation Capacity Profile After Acute Colonic Injury in Rats.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737764},
issn = {1422-0067},
support = {BR22883587//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
mesh = {Animals ; Rats ; *Gastrointestinal Microbiome ; *Enteral Nutrition/methods ; *Fermentation ; Male ; *Colon/injuries/microbiology/pathology ; Dextran Sulfate ; Metagenomics ; Disease Models, Animal ; *Colitis/microbiology/therapy/chemically induced ; Rats, Sprague-Dawley ; },
abstract = {Enteral nutrition (EN) is known to promote mucosal healing in inflammatory bowel disease, and multi-omics data suggest that the gut microbiome mediates its therapeutic effects. However, the impact of EN and its components on the gut community during recovery from acute epithelial injury remains incompletely understood. We used whole-genome metagenomic sequencing to investigate the effect of an EN formula based on extruded amaranth flour and pea protein on the gut microbiome in a dextran sulfate sodium (DSS) rat model of acute colonic injury. Three groups were compared, as follows: an unchallenged control (n = 9) with standard chow, a colonic injury (5% DSS; n = 9) group with standard chow, and a colonic injury (5% DSS; n = 9) group with EN. Injury was confirmed histologically (median MCHI score was 2, indicating epithelial damage without inflammation). DSS caused significant weight loss. Animals receiving EN regained baseline weight faster, by day 14, whereas animals on standard chow achieved recovery only by day 21. Differences in energy intake should be further investigated to validate the effect of EN on body weight recovery. At day 21, both injury groups demonstrated higher relative abundances of Bacteroidaceae and Erysipelotrichaceae, including the mucin-degrader Allobaculum mucilyticum, compared with the control group. Conversely, Lactobacillus abundance, notably Lactobacillus acidophilus, was higher in the EN group than in both other groups, as was the inferred capacity for lactate-producing fermentation. These findings suggest that EN is associated with a distinct microbial composition and inferred metabolic profile during the post-injury period, with lactobacilli as one of the potential mediators of its effects.},
}

Animals
Rats
*Gastrointestinal Microbiome
*Enteral Nutrition/methods
*Fermentation
Male
*Colon/injuries/microbiology/pathology
Dextran Sulfate
Metagenomics
Disease Models, Animal
*Colitis/microbiology/therapy/chemically induced
Rats, Sprague-Dawley

@article {pmid42737832,
year = {2026},
author = {Wei, L and Liu, H and Shen, Z and Song, Z and Huang, S and Lin, Z and Huang, X},
title = {Epithelial Inflammatory iNOS-Nitrate Axis Enhances P. gingivalis Pathogenicity via V. parvula in Diabetes-Associated Periodontitis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737832},
issn = {1422-0067},
support = {82201056//National Natural Science Foundation of China/ ; 2023A04J2154//Guangzhou Experimental Station/ ; 2023A0505050158//China International Science and Technology Cooperation/ ; },
mesh = {Animals ; *Nitric Oxide Synthase Type II/metabolism/genetics ; *Porphyromonas gingivalis/pathogenicity ; *Periodontitis/microbiology/metabolism/pathology/etiology ; Humans ; Mice ; *Nitrates/metabolism ; Epithelial Cells/metabolism/microbiology ; *Veillonella/pathogenicity ; Male ; Gingiva/microbiology/metabolism/pathology ; Female ; *Diabetes Mellitus, Experimental/complications/microbiology ; Inflammation/microbiology/metabolism ; Virulence ; },
abstract = {The mechanisms by which host inflammatory responses reshape the pathogenic potential of oral microbiota in mucosal inflammatory diseases remain poorly defined. Metagenomic sequencing of subgingival plaque and single-cell RNA sequencing of gingival tissues were performed in patients with diabetes-associated periodontitis (DP) and non-diabetic periodontitis (P). A diabetic mouse model was used to evaluate inflammation and bone resorption following oral inoculation with Porphyromonas gingivalis (P. gingivalis), Veillonella parvula (V. parvula), or both. Human gingival epithelial cells (HGECs) were cultured under high glucose conditions with or without an iNOS inhibitor 1400 W to assess iNOS and nitrate levels. A P. gingivalis-V. parvula co-culture system with nitrate supplements was used to evaluate P. gingivalis growth and virulence. Higher abundance of P. gingivalis and V. parvula was found in DP subgingival plaque. In diabetic mice, these bacteria worsened bone resorption and increased iNOS[+] epithelial cells. Single-cell sequencing showed higher iNOS expression in DP patients, linked to V. parvula. In vitro, high glucose increased iNOS and nitrate in HGECs, and these effects were reversed by 1400 W. With V. parvula, nitrate over 200 μM enhanced P. gingivalis growth and virulence. Diabetic epithelial iNOS-derived nitrate boosts P. gingivalis pathogenicity through V. parvula, worsening periodontal inflammatory bone damage.},
}

Animals
*Nitric Oxide Synthase Type II/metabolism/genetics
*Porphyromonas gingivalis/pathogenicity
*Periodontitis/microbiology/metabolism/pathology/etiology
Humans
Mice
*Nitrates/metabolism
Epithelial Cells/metabolism/microbiology
*Veillonella/pathogenicity
Male
Gingiva/microbiology/metabolism/pathology
Female
*Diabetes Mellitus, Experimental/complications/microbiology
Inflammation/microbiology/metabolism
Virulence