@article {pmid42859003,
year = {2026},
author = {Dong, L and Luo, S and Misbahullah, SM and Xu, J and Wan, S and Gao, H and Qin, Z},
title = {Polymerization-dependent gut microbiome responses to curdlan β-1,3-glucan and its oligosaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120524},
doi = {10.1016/j.foodres.2026.120524},
pmid = {42859003},
issn = {1873-7145},
mesh = {*beta-Glucans/metabolism/chemistry ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Feces/microbiology ; *Oligosaccharides/metabolism/chemistry ; Polymerization ; Fermentation ; Dietary Fiber/metabolism ; Fatty Acids, Volatile/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {β-1,3-Glucan is a dietary fiber with microbiome-modulating potential, yet the role of polymerization degree on microbial composition and metabolism remains unclear. Curdlan is an insoluble linear β-1,3-glucan widely used as a food hydrocolloid that provides a model to examine structure-dependent microbiome responses. We compared glucose, curdlan (CBG), and curdlan-derived β-1,3-glucan oligosaccharides (OBG) using anaerobic in vitro fermentation of pooled human feces. A multi-omics approach integrating 16S rRNA sequencing, shotgun metagenomics, short-chain fatty acid (SCFA) quantification, and untargeted metabolomics was applied to resolve taxonomic, functional, and metabolic shifts. Both CBG and OBG enriched Bacteroidota and enhanced carbohydrate metabolism relative to glucose, but through distinct pathways. CBG promoted polymer-associated carbohydrate processing, with enrichment of β-1,3-glucan-degrading enzymes such as GH16, Sus-like transport systems, and polysaccharide-specialized taxa (e.g., Prevotella and Bifidobacterium), and butyrate production. In contrast, OBG favored transporter-mediated substrate uptake, broader microbial participation (e.g. Parabacteroides and Enterobacteriaceae), and a metabolite profile enriched in amino acid-derived compounds and branched-chain SCFAs. These findings demonstrate that β-1,3-glucan polymerization degree governs microbiome functional routing and highlight polymerization degree as a tunable parameter for designing microbiome-directed carbohydrate ingredients with predictable metabolic outcomes.},
}

*beta-Glucans/metabolism/chemistry
Humans
*Gastrointestinal Microbiome/drug effects/physiology
Feces/microbiology
*Oligosaccharides/metabolism/chemistry
Polymerization
Fermentation
Dietary Fiber/metabolism
Fatty Acids, Volatile/metabolism
Glucose/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42859015,
year = {2026},
author = {Yu, Z and Wang, W and Chen, F and Li, L and Luo, L and Zhong, X and Liu, D and Tang, W and Liu, X and Huang, M},
title = {Temporal dynamics and metabolic potential of microbial dark matter during dry storage of high-temperature Daqu revealed by metagenome-assembled genomes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120539},
doi = {10.1016/j.foodres.2026.120539},
pmid = {42859015},
issn = {1873-7145},
mesh = {*Metagenome ; *Alcoholic Beverages/microbiology/analysis ; *Hot Temperature ; Fermentation ; *Food Microbiology ; Metagenomics ; *Food Storage/methods ; Bacillota/genetics/metabolism ; Archaea/genetics/metabolism ; *Microbiota/genetics ; },
abstract = {High-temperature Daqu is the core starter culture for Jiang-flavor Baijiu production, whose microbial community directly shapes the enzymatic properties and flavor precursor profiles of fermentation systems. Dry storage drives microbial succession and functional maturation of Daqu, yet existing studies have predominantly focused on cultivable and well-characterized taxa, leaving the temporal dynamics and metabolic contributions of microbial dark matter (MDM) largely unexplored at the genome-resolved level. Using genome-resolved metagenomics, we reconstructed 52 medium- to high-quality metagenome-assembled genomes (MAGs) from high-temperature Daqu samples across a six-month dry storage period and identified five novel unclassified MDM lineages comprising four Bacillota-affiliated bacterial lineages and one archaeal lineage. Comparative genomic analysis revealed distinct functional differentiation between MDM lineages and dominant culturable taxa, as MDM lineages were enriched in genes associated with carbohydrate uptake and fermentative acid production and harbored a streamlined biosynthetic gene cluster (BGC) profile with uniformly high sequence novelty. Temporal dynamic analysis showed that MDM lineages from different storage microhabitats exhibited divergent succession patterns, and conventional physicochemical parameters showed limited explanatory power for MDM community variation, with only glucoamylase activity displaying a marginal association trend. This study provides genome-resolved insights into uncultured MDM lineages during high-temperature Daqu dry storage, expands the genomic repertoire of uncultured microbiota in traditional fermentation ecosystems, and offers novel perspectives for deciphering Daqu maturation mechanisms and quality regulation.},
}

*Metagenome
*Alcoholic Beverages/microbiology/analysis
*Hot Temperature
Fermentation
*Food Microbiology
Metagenomics
*Food Storage/methods
Bacillota/genetics/metabolism
Archaea/genetics/metabolism
*Microbiota/genetics

@article {pmid42859016,
year = {2026},
author = {Ji, Q and Qu, H and Chen, D and Li, Q and Zong, L and Liu, Y and Huang, Y and Gu, R},
title = {Matrix-associated spatial structure contributes to compositional stability of a complex multispecies starter culture under microbial perturbation: Insights from kefir grains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120540},
doi = {10.1016/j.foodres.2026.120540},
pmid = {42859016},
issn = {1873-7145},
mesh = {*Kefir/microbiology ; Fermentation ; *Food Microbiology/methods ; *Microbiota ; Cultured Milk Products/microbiology ; },
abstract = {Complex multispecies starter cultures can enrich the metabolic and sensory diversity of fermented foods, but industrial use is limited by compositional drift, overgrowth of dominant taxa, and vulnerability to exogenous microbial contamination. Kefir grains (KG), a matrix-encapsulated complex starter culture with stable serial propagation, provide a model for how spatial structure contributes to starter stability. We compared matrix-associated KG with free kefir-fermented milk (FKFM), representing a grain-free liquid-phase kefir microbial community, under a large-scale microbial challenge. During the acute 24 h challenge, target-taxon drift estimated from PMA-qPCR data was lower in KG than in the liquid compartments. Ten-generation serial transfer caused stronger community restructuring and Shannon diversity loss in FKFM, whereas KG showed constrained compositional adjustment and remained relatively clustered in Bray-Curtis ordination space. Species-level metagenomic tracking showed broader expansion, retention, and cumulative drift of species-level signals corresponding to exogenous challenge strains in FKFM, while more of these signals in KG followed restricted/stable trajectories. Kefir cell-free supernatant inhibited multiple challenge strains beyond the effect of low pH, indicating a contribution of diffusible inhibitory factors. SEM and live/dead staining revealed rough matrix-associated surfaces and heterogeneous cell states in KG. Together, the results support a model in which spatial structure, prior niche occupancy, and diffusible inhibition jointly contribute to the compositional stability and anti-perturbation capacity of this complex starter culture, informing the design of spatially structured synthetic starter consortia for industrial fermentation.},
}

*Kefir/microbiology
Fermentation
*Food Microbiology/methods
*Microbiota
Cultured Milk Products/microbiology

@article {pmid42859679,
year = {2026},
author = {Patsakis, M and Provatas, K and Mouratidis, I and Georgakopoulos-Soares, I},
title = {Derivation of oligonucleotide barcodes that are absent from natural sequences.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag251},
pmid = {42859679},
issn = {2635-0041},
abstract = {DNA barcodes are short synthetic sequences used to uniquely identify target molecules, samples, or objects, and are essential for a wide range of biotechnology applications including high-throughput sequencing, lineage tracing, genetic screens, massively parallel reporter assays, and DNA-based data storage. However, randomly generated barcodes are prone to off-target hybridization and cross-reactivity with endogenous biological sequences, which can compromise experimental specificity and interpretation. Barcodes derived from sequences that are entirely absent from natural genomes, termed DNA primes, offer an ideal solution by eliminating the possibility of unintended interactions with biological material. Here, we present barcodesDB, a comprehensive database of synthetic DNA barcodes systematically identified by scanning 403 199 complete organismal genome assemblies across the tree of life, together with 215 Gbp of raw metagenomic sequencing reads spanning marine, soil, polar and host-associated environments. These barcodes are absent, on either strand, from every assembly and sequencing read examined in the release described, providing maximal specificity and minimizing cross-reactivity for downstream applications. We provide an open-access web application that enables researchers to search for barcodes satisfying user-defined constraints, including GC content and substring requirements, and to query whether candidate sequences occur in nature. This resource supports robust and scalable barcode design for diverse experimental and applied contexts. Our database is publicly available at: https://barcodesdb.com/.},
}

@article {pmid42859685,
year = {2026},
author = {Chatzigiannidou, I and Taparia, T and Johansen, PL and Berzina, L and Nesme, J and Petersen, M and Sørensen, SJ and Brix, S and Kristiansen, K},
title = {Genome-resolved metagenomics reveals rare taxa and functional traits in two contrasting agricultural fields.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag268},
pmid = {42859685},
issn = {2730-6151},
abstract = {Agricultural soils harbor highly diverse and functionally rich microbial communities, yet much of their genomic potential remains unexplored. Here, we present a genome-resolved metagenomic analysis of 455 soil samples collected at different depths and seasonal stages across two Danish agricultural fields representing sandy and clay soil types. Ultra-deep shotgun sequencing enabled the recovery of 58 831 medium to high-quality prokaryotic metagenome-assembled genomes (MAGs), which were dereplicated into 56 340 strain-level MAGs and 9090 species-level genome bins (SGBs) spanning 49 prokaryotic phyla. The majority of the SGBs represented previously uncharacterized species. Functional annotation revealed extensive biosynthetic and metabolic potential, including 46 913 biosynthetic gene clusters and prevalent genes linked to nitrogen cycling. Notably, 378 MAGs harbored the nitrous oxide reductase gene nosZ. Soil type and depth strongly influenced microbial diversity and functional traits. These findings provide a resource for linking microbial traits to soil function of potential value for better sustainable agricultural practice.},
}

@article {pmid42859709,
year = {2026},
author = {de Bruijn, TEP and Doekes, HM and Kupczok, A},
title = {Temperate versus virulent phage lifestyle impacts microdiversity in soil environments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag265},
pmid = {42859709},
issn = {2730-6151},
abstract = {Bacteriophages are not only the most ubiquitous biological entity on earth, but they also display remarkable genetic diversity across and within populations. While macrodiversity has been extensively studied, the drivers of microdiversity (intra-species genetic diversity) remain poorly understood, particularly in relation to phage lifestyle. The distinguishing ability of temperate phages to integrate themselves into the host genome has an unknown influence on the microdiversity present. This difference in microdiversity could impact the adaptability of phages to (a)biotic factors. To identify a possible association between microdiversity and lifestyle, we analysed 12 existing viromics datasets focusing on soil bacteriophages, including 43 171 viral genomes in total. We found that phages predicted to be temperate consistently exhibit higher microdiversity than their virulent counterparts in 8 of 12 datasets. Of the remaining four datasets, one showed the opposite trend and three datasets did not show a significant trend at all. The detected pattern holds across multiple quality thresholds and lifestyle prediction methods. These findings suggest that lifestyle has a significant impact on genetic variation within phage populations, with potential implications for phage-host coevolution and environmental adaptability.},
}

@article {pmid42860091,
year = {2026},
author = {Chen, S and Xin, X and Yang, J and Xu, H and Zhu, X and Wang, G and Yan, W},
title = {Conductive Fe3O4 drives a stress-dependent shift in electron-transfer strategies during anaerobic tetramethylammonium hydroxide degradation.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127060},
doi = {10.1016/j.watres.2026.127060},
pmid = {42860091},
issn = {1879-2448},
abstract = {Anaerobic treatment of tetramethylammonium hydroxide (TMAH) wastewater is often constrained by metabolic disruption under high TMAH loading. Conductive Fe3O4 has shown promise for enhancing anaerobic bioprocesses; however, the dominant mechanism governing its enhancement under different metabolic conditions remains unclear. Here, anaerobic reactors were operated under stepwise increases in TMAH concentration (1-10 g/L) to compare the effects of soluble Fe[2+] and conductive Fe3O4 using reactor performance, electrochemical characterization, intracellular reducing-equivalent measurements, and integrated metagenomics and metatranscriptomics analyses. At low-to-moderate TMAH loadings (1-5 g/L), Fe3O4 and Fe[2+] exhibited comparable improvements in TMAH degradation and methane production, together with elevated soluble Fe[2+] and reduced ferredoxin, indicating that dissolved iron was the dominant contributor. Under severe TMAH stress (10 g/L), both iron amendments improved reactor performance, whereas Fe3O4 became markedly more effective than Fe[2+], achieving complete TMAH removal and over twofold higher methane production than the unamended control. Electrochemical analyses showed that Fe3O4 enhanced extracellular electron-transfer activity, accompanied by intensified riboflavin-like redox signals. Integrated metagenomic and metatranscriptomic analyses further revealed concurrent enrichment of electroactive bacteria and syntrophic methanogens, together with increased transcription of genes involved in intracellular electron metabolism, particularly those associated with F420-dependent C1 metabolism and HdrABC-MvhADG-mediated electron bifurcation. Collectively, these findings unravel a stress-dependent transition in the mechanism underlying Fe3O4 enhancement, from dissolved-iron-supported intracellular reducing-equivalent metabolism under low-to-moderate TMAH loadings to conductivity-associated coordination between extracellular electron transfer and intracellular methanogenic metabolism under severe TMAH stress. This mechanistic insight provides a basis for optimizing conductive iron mineral-assisted anaerobic treatment of high-strength TMAH wastewater.},
}

@article {pmid42860095,
year = {2026},
author = {Ju, H and Yuan, Y and Jiang, L and Song, C and Li, J and Zou, S and Korir, RK and Gin, KY and Zhang, J},
title = {Winter ice regulates antibiotic resistance dynamics through seasonal genetic reservoirs across lake compartments.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127053},
doi = {10.1016/j.watres.2026.127053},
pmid = {42860095},
issn = {1879-2448},
abstract = {Antibiotic resistance is a growing environmental and public-health threat, yet its seasonal dynamics in cold-region freshwater ecosystems remain poorly understood. Using year-round observations, metagenomic sequencing, and machine learning, we investigated antibiotic resistance genes (ARGs) across ice, water, and sediment in an ice-covered lake. Winter ice contained significantly higher abundances of ARGs, mobile genetic elements (MGEs), and microbial hosts than water and sediments. Driver analysis based on explainable machine learning showed that ARG dynamics in ice were primarily associated with MGEs, whereas ARGs in water and sediments were associated with host-related ecological processes and environmental conditions. During spring, ice-associated ARGs, MGEs, and their microbial hosts showed potential contribution to the water column, expanding resistance-risk hotspots and reorganizing associations among ARGs, MGEs, hosts, and virulence factors. These findings indicate that winter ice acts as a seasonal reservoir of antibiotic resistance, regulating spring antibiotic resistance dynamics and potential health risks.},
}

@article {pmid42860401,
year = {2026},
author = {Xu, Z and Jiang, H and Huang, W and Chan, A and Lin, Y and Chan, T and Lui, RN and Wong, MTL and Mak, JWY and Chan, FKL and Chevarin, C and Colombel, JF and Buisson, A and Ng, SC},
title = {Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn's disease: an open-label pilot study.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42860401},
issn = {2041-1723},
mesh = {Humans ; *Crohn Disease/therapy/microbiology ; Pilot Projects ; *Fecal Microbiota Transplantation/methods/adverse effects ; Female ; *Escherichia coli/genetics/physiology ; Male ; Feces/microbiology ; Adult ; *Intestinal Mucosa/microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Escherichia coli Infections/therapy/microbiology ; Young Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {Adherent-invasive Escherichia coli (AIEC) is implicated in Crohn's disease (CD) pathogenesis, but whether fecal microbiota transplantation (FMT) clears mucosal AIEC and alters fecal and mucosal microbiomes has not been studied. In this open-label pilot study, thirty adults with CD and seropositivity for serum anti-E.coli antibody (AEcAb) received a single colonoscopic FMT from one of two donors (ClinicalTrials.gov identifier NCT05611866). The primary outcome was adverse events (AEs) within 12 weeks after FMT; secondary outcomes included changes in mucosal AIEC, clinical measures, and fecal and mucosal microbiome profiles. Shotgun metagenomic sequencing for fecal samples and 16S rRNA sequencing for ileal mucosal samples were performed at baseline and after FMT. Baseline AEcAb levels were higher in patients with mucosal AIEC colonization (p = 0.019) and remained elevated after FMT. No FMT-related serious adverse events were reported. FMT was associated with mucosal AIEC decolonization in all 8 evaluable baseline-positive patients. Mucosal alpha diversity increased after FMT (p = 0.023), which correlated with reduced fecal calprotectin (p = 0.034). Microbial pathway profiles in CD patients resembled those of their respective donors with reduced donor-recipient dissimilarity post-FMT (p = 0.030), particularly among recipients with mucosal AIEC decolonization (p = 0.039). In conclusion, this open-label pilot study demonstrates the feasibility of FMT for modulating mucosal AIEC colonization in CD and highlights the importance of capturing microbial changes at the disease site that may be undetectable in fecal samples.},
}

Humans
*Crohn Disease/therapy/microbiology
Pilot Projects
*Fecal Microbiota Transplantation/methods/adverse effects
Female
*Escherichia coli/genetics/physiology
Male
Feces/microbiology
Adult
*Intestinal Mucosa/microbiology
Middle Aged
RNA, Ribosomal, 16S/genetics
*Escherichia coli Infections/therapy/microbiology
Young Adult
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid42860710,
year = {2026},
author = {McAleese, K and Vather, M and Vargas, SO and Sharma, TS and Elisofon, SA and Guenther, G},
title = {Successful Liver Transplantation in a Child With Invasive Aspergillus terreus Cholangitis Identified via Plasma Metagenomic Next-Generation Sequencing.},
journal = {Pediatric transplantation},
volume = {30},
number = {10},
pages = {e70490},
doi = {10.1111/petr.70490},
pmid = {42860710},
issn = {1399-3046},
mesh = {Humans ; *Liver Transplantation ; Female ; *Cholangitis/microbiology/surgery/diagnosis ; *Aspergillus/genetics/isolation & purification ; *Biliary Atresia/surgery ; High-Throughput Nucleotide Sequencing ; *Aspergillosis/diagnosis/surgery ; Child, Preschool ; Metagenomics ; *Postoperative Complications/diagnosis/surgery/microbiology ; Antifungal Agents/therapeutic use ; Voriconazole/therapeutic use ; Portoenterostomy, Hepatic ; },
abstract = {BACKGROUND: Ascending cholangitis, one of the most common complications in patients with biliary atresia (BA) after Kasai hepatoportoenterostomy (HPE), impacts native liver survival. Typically, enteric bacterial flora are the source of infection, and fungal infections of the biliary tree are rare.

CASE REPORT: We report the case of a 3-year-old female with BA status post Kasai HPE who developed Aspergillus terreus cholangitis (complicated by hepatic vein thrombus) identified through plasma metagenomic next-generation sequencing (NGS) of microbial cell-free deoxyribonucleic acid (DNA). Despite improvement in galactomannan (GM) antigen indices while on antifungal therapy with voriconazole and anticoagulation, she experienced complications with the extension of septic thrombus and persistent cholestasis; thrombus tissue sampling later confirmed the diagnosis and antimicrobial sensitivities. Ultimately, native liver explantation succeeded in achieving source control with sustained normalization of GM indices after the completion of voriconazole. Post-transplant, she received routine immunosuppression and infection prophylaxis per institutional protocol and remains well without infectious complications more than 1 year later.

DISCUSSION: This case highlights the important role of newer molecular diagnostic tools in facilitating timely species-level pathogen identification and initiation of targeted therapy (in this case, 35 days prior to confirmed tissue diagnosis), particularly in circumstances where the risk-to-benefit ratio of invasive tissue sampling is unfavorable. Despite the significant morbidity associated with invasive fungal infection, transplantation followed by standard immunosuppression is a reasonable therapeutic option with successful outcomes in patients who are otherwise suitable transplant candidates.},
}

Humans
*Liver Transplantation
Female
*Cholangitis/microbiology/surgery/diagnosis
*Aspergillus/genetics/isolation & purification
*Biliary Atresia/surgery
High-Throughput Nucleotide Sequencing
*Aspergillosis/diagnosis/surgery
Child, Preschool
Metagenomics
*Postoperative Complications/diagnosis/surgery/microbiology
Antifungal Agents/therapeutic use
Voriconazole/therapeutic use
Portoenterostomy, Hepatic

@article {pmid42861590,
year = {2026},
author = {Deng, LR and Zhong, YM and Zhu, SF and Wu, ZY and Chen, FJ and Huang, CY and Wu, QY and Tomlinson, B and Tan, HE and Li, YH},
title = {Anemoside B4 from Pulsatilla chinensis Ameliorates Ulcerative Colitis by Inhibiting Inflammatory Responses via the Modulation of the Gut Microbiota-Immune Interplay.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-29},
doi = {10.1142/S0192415X26500849},
pmid = {42861590},
issn = {1793-6853},
abstract = {We previously demonstrated that anemoside B4 (AB4) exerts a beneficial effect in a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis (UC). In this study, we further explored the mechanism of AB4 against UC from the perspective of gut microbiota-immune interplay. The gut microbiota was depleted in two DSS-induced colitis models to investigate the modulatory effects of the gut microbiome on immune responses and the activity of AB4. In parallel, adoptive transfer of CD4[Formula: see text]CD62L[Formula: see text] T cells into Rag1-deficient (Rag1[-/-]) mice was used to elucidate the alterations in the gut microbiota associated with immune-mediated colitis as well as the modulation by AB4. qPCR, ELISA and western blotting were used to determine the inflammatory responses of mice with colitis, while immunohistochemistry and flow cytometry were employed to determine the CD4[Formula: see text] T cell function and the underlying mechanism. Metagenomic sequencing analysis was used to detect changes in the intestinal microbiota. The depletion of the gut microbiota attenuated disease severity and immune responses in mice with DSS-induced acute and chronic colitis. Notably, the inhibitory effects of orally administered AB4 on colitis progression and immune responses were abrogated. In addition, colitis induced by adoptive transfer of CD4[Formula: see text]CD62L[Formula: see text] T cells into Rag1[-/-] mice was accompanied by CD4[Formula: see text] T cell engraftment and alterations in gut microbiota. Remarkably, all these pathological changes were significantly attenuated by AB4. Crucially, we found that AB4 suppresses the proliferation, migration, and differentiation of CD4[Formula: see text] T cells, which provides a mechanistic basis for its immunosuppressive effects. Collectively, these findings indicate that the gut microbiota and the immune system, particularly CD4[Formula: see text] T cells, interact with each other in the initiation of colitis. We show that, by targeting this gut microbiota-immune interplay, AB4 is a promising therapeutic strategy for UC.},
}

@article {pmid42861600,
year = {2026},
author = {Liu, Y and Ning, X and Liu, Y and Yu, Z and Liu, J and Xu, X and Zhao, J and Sun, S},
title = {Potential Roles of Escherichia coli in IgA Nephropathy: Evidence, Mechanistic Hypotheses and Microbiota-Targeted Strategies.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70455},
doi = {10.1111/1751-7915.70455},
pmid = {42861600},
issn = {1751-7915},
support = {82470735//National Natural Science Foundation of China/ ; 2023TD-02//Shaanxi Provincial Health Commission/ ; 2023-ZDLSF-15//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLSF03-12//Key Research and Development Projects of Shaanxi Province/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/therapy/pathology ; *Escherichia coli/pathogenicity ; Animals ; *Gastrointestinal Microbiome ; Immunoglobulin A/metabolism ; },
abstract = {IgA nephropathy (IgAN), the most common primary glomerular disease, involves mucosa-kidney axis dysregulation, with gut dysbiosis increasingly implicated in its pathogenesis. Certain Escherichia coli (E. coli) strains harbour virulence-associated features that promote intestinal colonization, barrier disruption and immune activation. Recent microbiome and metagenomic studies have reported an enrichment of E. coli in patients with IgAN, suggesting a potential link to the mucosa-kidney axis. Nevertheless, E. coli may contribute to IgAN through two major pathways. First, sustained LPS exposure may induce aberrant production of galactose-deficient IgA1 (Gd-IgA1) by stimulating B cells and activate the NLR family pyrin domain containing 3 (NLRP3) inflammasome in macrophages, thereby amplifying systemic and renal inflammation. Second, metabolic reprogramming is associated with increased circulating sphingosine-1-phosphate (S1P) and altered production of indole and trimethylamine (TMA); S1P may promote mesangial proliferation and fibrosis, whereas indole- and TMA-related pathways may contribute to tubulointerstitial injury and chronic kidney disease (CKD) progression. Beyond conventional gut microbiota-targeted interventions, emerging precision therapeutic strategies offer promising new directions for the etiological treatment of IgAN. This review summarizes E. coli virulence factors, pathogenesis, and host, environmental, and ecological factors driving its gut expansion in IgAN patients and outlines corresponding therapeutic strategies.},
}

Humans
*Glomerulonephritis, IGA/microbiology/therapy/pathology
*Escherichia coli/pathogenicity
Animals
*Gastrointestinal Microbiome
Immunoglobulin A/metabolism

@article {pmid42861963,
year = {2026},
author = {Xie, P and Luo, M and Fan, J and Xiong, L},
title = {A global atlas of the gut virome reveals subtype-specific and functional alterations in irritable bowel syndrome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0090126},
doi = {10.1128/msystems.00901-26},
pmid = {42861963},
issn = {2379-5077},
abstract = {The gut virome is a critical component of the microbiome-gut-brain axis; however, its role in irritable bowel syndrome (IBS) remains poorly understood due to limited sample sizes and geographic bias. We aimed to construct a comprehensive global atlas of the IBS gut virome to elucidate its composition, functional potential, and clinical relevance across diverse populations and IBS subtypes. We integrated multi-cohort data comprising 1,104 samples (790 IBS patients and 314 healthy controls) from 11 cohorts across 10 geographic regions. A standardized bioinformatic pipeline was employed to perform viral mining from metagenomic and virus-like particle-enriched metaviromic data. The IBS virome exhibited significant taxonomic alterations, with specific viral signatures distinguishing IBS-D, IBS-C, and IBS-M subtypes. Geographic region was identified as a significant factor influencing the viral community structure. Functionally, the IBS virome was enriched in auxiliary metabolic genes involved in carbon metabolism and neurotransmitter precursor synthesis (histidine and tryptophan metabolism), as well as a distinct profile of virulence factors and antibiotic resistance genes. Furthermore, in a specific cohort, certain viral taxa were significantly correlated with the severity of anxiety and depression. Machine learning models based on viral signatures achieved robust performance for IBS subtyping (area under the curve = 0.92). This study establishes a global baseline for the IBS gut virome, demonstrating that viral communities are dynamically shaped by geography and disease subtypes while encoding gene repertoires with the potential to influence host physiology, thereby providing a foundational resource for precision medicine.IMPORTANCEResearch on the human gut microbiome in IBS has focused primarily on bacteria, leaving the viral component as a vast and poorly understood reservoir. By profiling over 1,000 human samples globally, this study characterizes the taxonomic and functional features of the IBS gut virome. We demonstrate that these viral communities vary across geographic populations and IBS subtypes and are enriched in specific auxiliary metabolic genes, virulence factors, and antibiotic resistance genes. In addition, certain viral profiles show significant correlations with patient psychological symptoms such as anxiety and depression. This study also evaluates the potential of virome-based diagnostic biomarkers. Consequently, our findings provide a valuable reference for future in-depth research into the specific roles and mechanistic contributions of the gut virome in the pathogenesis of IBS.},
}

@article {pmid42861989,
year = {2026},
author = {Wang, G and Zhang, N and Peng, Y and Wen, X and Chen, X and Zou, M and Gao, S and Min, C and Min, X and Huang, J},
title = {Association of quantitative sputum Candida load with respiratory dysbiosis and airway inflammation in suspected invasive pulmonary candidiasis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0083726},
doi = {10.1128/msystems.00837-26},
pmid = {42861989},
issn = {2379-5077},
abstract = {UNLABELLED: The clinical significance of Candida species isolation from sputum remains ambiguous due to the colonization-infection dilemma. Integrating quantitative culture with microbiome profiling may clarify its role, yet systematic evidence is scarce. In this exploratory study (June 2023-June 2026), we enrolled 140 hospitalized patients suspected of invasive pulmonary candidiasis (IPC) and stratified them into possible IPC (n = 36), probable IPC (n = 71), and negative control (n = 33) groups based on clinical criteria. All underwent quantitative fungal culture of sputum and metagenomic next-generation sequencing (mNGS). Patients were stratified by sputum Candida species load into low (<10[5] CFU/mL), high (≥10[5] CFU/mL), and negative control (0 CFU/mL) groups. We investigated associations between Candida species burden, respiratory microbiota, local inflammation (IL-8), and clinical outcomes. Higher Candida species load was significantly associated with prolonged hospitalization, elevated sputum IL-8, an increased microbial dysbiosis index, and depletion of key commensals (e.g., Neisseria, Prevotella, Rothia, Streptococcus, and Veillonella). Counterintuitively, it correlated negatively with several classic bacterial pathogens (such as Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Pseudomonas aeruginosa). A random forest model identified a nine-species microbiome signature that effectively discriminated probable from possible IPC (AUC, 0.877; 95% CI, 0.662-0.944). In patients with suspected IPC, higher sputum Candida species load is associated with exacerbated respiratory dysbiosis and airway inflammation. Quantitative Candida species assessment combined with microbiome signatures may serve as a complementary tool for stratifying disease severity and ecological disruption, meriting further validation in larger, multicenter cohorts.

IMPORTANCE: Respiratory specimens dominate clinical fungal cultures, yet interpreting the role of Candida spp. in sputum remains a diagnostic dilemma. Here, by integrating quantitative culture with metagenomic sequencing, we show that a high sputum Candida species load is a marker of profound ecological disruption. High Candida species burden was associated with significant depletion of key commensals, an elevated dysbiosis index, and heightened local inflammation. Counterintuitively, it correlated negatively with several classic bacterial pathogens, revealing a distinct dysbiotic signature. Moreover, a microbiome-based model accurately discriminated patients with probable invasive pulmonary candidiasis. Our findings suggest that quantitative sputum Candida species load, interpreted within the context of the microbial community, may be a practical biomarker for identifying patients with significant respiratory dysbiosis and inflammation, offering a path toward more refined, ecology-informed therapeutic strategies.},
}

@article {pmid42862002,
year = {2026},
author = {Zhang, M and Ge, L and Liu, K and Liu, Y and Zhao, G and Kwok, LY and Sun, Z and Sun, Z and Zhang, W},
title = {Sex- and Time-Resolved Physiological and Gut Ecosystem Responses to a Food-Grade Microbiome-Targeted Intervention in Collegiate Endurance Athletes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77664},
doi = {10.1002/advs.77664},
pmid = {42862002},
issn = {2198-3844},
support = {NMGLLY2025-02//Inner Mongolia Autonomous Region Special Project for Scientific and Technological Innovation Research in Key Fields of the "Two Barriers," "Two Bases," and "One Bridgehead" Initiative/ ; 32325040//National Natural Science Foundation of China/ ; 32502149//National Natural Science Foundation of China/ ; U25A20733//National Natural Science Foundation of China/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; },
abstract = {Endurance athletes experience sustained physiological demands during high-volume training, yet evidence for microbiome-targeted interventions in real-world settings remains limited. We conducted a two-stage, randomized, double-blind, placebo-controlled trial in 150 athletes allocated 2:1 to combined probiotics-yeast extract (CPYE) or placebo for 6 weeks; 44 completers confirmed for the 12th Inner Mongolia Autonomous Region University Games entered an exploratory 6-week extension with intensified training. Integrating wearable-derived phenotyping, field-based cardiorespiratory indices, clinical assessments, fecal metagenomics, and metabolomics, we found that during the randomized short-term phase, CPYE was associated with changes in device-estimated maximal oxygen uptake, exercise heart-rate indices, lactate, and redox biomarkers versus placebo. Exploratory sex-stratified analyses suggested heterogeneous response patterns, while the selected long-term extension indicated time-dependent changes requiring confirmation. Multi-omics identified sex- and phase-associated differences in microbial taxa, functions, metabolites, and network topology. Indirect-effect models nominated candidate features (rmlD, PISD-linked phosphatidylethanolamine pathways, Bacteroides ovatus, and folate-related functions) as potential indirect correlates of host outcomes. These findings support further evaluation of CPYE-associated responses in collegiate endurance athletes; subgroup, long-term, network, and indirect-effect results are hypothesis-generating.},
}

@article {pmid42854592,
year = {2026},
author = {Giannis, D and Gianni, P},
title = {Herpesvirus reactivation in critical illness: Pathogenesis, clinical consequences, and diagnostic challenges.},
journal = {Virology},
volume = {625},
number = {},
pages = {111097},
doi = {10.1016/j.virol.2026.111097},
pmid = {42854592},
issn = {1096-0341},
abstract = {Human herpesviruses (HHV) remain latent after primary infection and may reactivate during critical illness. HHV reactivation has been associated with adverse clinical outcomes, yet its pathogenic significance and optimal management remain unclear. This review summarizes the dysregulated immune mechanisms and risk factors for HHV reactivation in critical illness, treatment options, outcomes, current diagnostic challenges, and emerging precision medicine approaches. Critical illness induces profound immune dysregulation characterized by an initial hyperinflammatory response followed by immunosuppression, T-cell exhaustion, impaired natural killer cell function, and disrupted antiviral surveillance. These changes facilitate reactivation of latent HHV, including herpes simplex virus type 1 (HSV-1), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus 6 (HHV-6). HSV and CMV reactivation in mechanically ventilated and septic patients have been associated with prolonged mechanical ventilation, longer intensive care unit (ICU) stay, secondary infections, and increased mortality. However, the distinction between clinically significant disease from asymptomatic reactivation remains challenging. Current evidence does not support routine antiviral prophylaxis in immunocompetent ICU patients. Emerging approaches including metagenomic next-generation sequencing, host transcriptomics, immune phenotyping, and multi-omics integration may improve risk stratification and identify patient subgroups that are most likely to benefit from targeted intervention. HHV reactivation may serve as a biomarker and potential mediator of adverse outcomes. Improved understanding of host-virus interactions, coupled with precision medicine that integrates virological and immunological data, is required to differentiate clinically relevant reactivation from epiphenomena and to guide individualized therapeutic strategies.},
}

@article {pmid42854651,
year = {2026},
author = {Molendijk, MM and Prasad, DK and Worp, N and Schapendonk, CME and Nieuwenhuijse, D and Aarestrup, FM and Verbon, A and van Wamel, WJB and Koopmans, MPG and de Graaf, M},
title = {Metagenomic insights into the global occurrence of ESKAPE-targeting bacteriophages in urban wastewater.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127032},
doi = {10.1016/j.watres.2026.127032},
pmid = {42854651},
issn = {1879-2448},
abstract = {Antimicrobial resistance (AMR) poses a serious threat to global public health, with Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species - collectively known as ESKAPE pathogens - as high priority threats. Bacteriophages represent a potential alternative therapy for AMR infections. While many of the bacteriophages that target ESKAPE pathogens have been isolated from environmental sources, such as wastewater, the global distribution of these bacteriophages remains poorly understood. In this study, metagenomic sequencing of wastewater was used to assess the presence and distribution of known bacteriophages in urban wastewater collected from 62 sites worldwide. Focusing specifically on lytic bacteriophages known to target ESKAPE pathogens, a literature review was conducted to curate a collection of bacteriophages with known therapeutic properties and publicly available genomes. The presence and distribution of these therapeutic bacteriophages in wastewater were examined, both geographically and temporally. Our analysis revealed a high abundance of bacteriophage families associated with the human gastrointestinal tract, as well as those infecting bacteria native to aquatic environments. Bacteriophages similar to those targeting ESKAPE pathogens were detected across the wastewater samples, except for bacteriophages targeting Staphylococcus aureus. Both the presence and abundance of these putative ESKAPE-phages varied considerably across regions, with African sample sites exhibiting the highest diversity and European sample sites the lowest. No clear temporal trends were observed for these bacteriophages. This study provides the use of wastewater to provide insights into the global diversity and distribution of bacteriophages, with a specific focus on species with therapeutic potential against ESKAPE pathogens, while further offering a valuable dataset for future bacteriophage research.},
}

@article {pmid42854696,
year = {2026},
author = {Cabello-Yeves, E and Samarra, A and Summers, K and Comas, I and Wellington, E and Millard, A and Collado, MC and Marina, A},
title = {Breastfeeding and maternal microbial reservoirs are associated with infant gut phageome development during the first year of life.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103107},
doi = {10.1016/j.xcrm.2026.103107},
pmid = {42854696},
issn = {2666-3791},
abstract = {The early-life assembly of the gut microbiome is a critical determinant of long-term health, yet the role of bacteriophages in this process remains poorly understood. Here we longitudinally profile the gut phageome of 34 mother-infant dyads during the first year of life with metagenomics and a phage-centered computational workflow. Phage diversity increases with age, paralleling bacterial diversification but following distinct ecological trajectories. Shared viral populations across maternal and infant samples are consistent with potential maternal contribution, although not indicative of direct transmission. Feeding-related variables are consistently associated with phageome composition at specific developmental stages. No single factor fully explains phageome variation, supporting a multifactorial model involving maternal, environmental, and dietary inputs. Together, these findings provide a framework for understanding early-life phage ecology, positioning phages as active participants in early microbiome assembly and supporting the inclusion of viral components in microbiome-based strategies aimed at promoting healthy ecosystem development in infancy.},
}

@article {pmid42854797,
year = {2026},
author = {Huang, Y and Yang, S and Wei, P and Zhou, H and Zhang, F and Li, X and Zhang, S},
title = {Ca/Fe-modified drinking water treatment residue with Vallisneria natans controls algal blooms via phosphorus transformation and smicrobial network shifts.},
journal = {Bioresource technology},
volume = {464},
number = {Pt C},
pages = {136025},
doi = {10.1016/j.biortech.2026.136025},
pmid = {42854797},
issn = {1873-2976},
abstract = {Internal phosphorus (P) loading is a key driver of algal blooms in shallow lakes, yet submerged macrophyte (SM) restoration alone often fails because clear water also favors epiphytic filamentous algae and regime shifts. We constructed a co-remediation system combining Ca/Fe-modified drinking water treatment residue (Ca/Fe-DWTR) with Vallisneria natans and ran a 183-day microcosm experiment to reveal how sediment P transformation coupled with macrophyte restoration controls water quality and suppresses two different algal blooms. Co-remediation markedly reduced sediment total-P and mobile-P while increasing stable-P forms, and no bloom occurred throughout cultivation, with chlorophyll a below 1.5 μg/L. The nitrogen (N) release risk associated with Ca/Fe-DWTR alone was also eliminated. Conversely, unremediated-sediment sustained planktonic blooms through sulfide-driven Fe bound P release coupled with nitrogen fixation, whereas the SM-only treatment stayed clear early but later developed massive epiphytic filamentous algae once photosynthetic pH rise mobilized Al bound P, confirming that success depends on P-stabilization rather than transient clarity. Metagenomics showed that co-remediation created low-P and oxidative niches that restructured microbial communities, enhancing nitrogen cycling potential in the phyllosphere while suppressing sulfate-reducing bacteria in sediment, thereby achieving coupled N and P removal within a resilient functional gene network. Mantel tests and PLS-SEM revealed that pH elevation by V. natans enhanced microbial P fixation and stable-P formation, while Ca/Fe-DWTR most strongly drove nitrogen transformation, and thus sediment P transformation indirectly governed water quality through microbial functional gene networks. Overall, the co-remediation showed potential for mitigating internal P loading and algal proliferation in shallow eutrophic lakes.},
}

@article {pmid42854799,
year = {2026},
author = {Wei, D and Zhai, FS and Zhao, CF and Zhang, YF and Wei, Q and Ni, SQ},
title = {Dissolved organic nitrogen molecular transformation and microbial mechanisms in a completely autotrophic nitrogen removal over nitrite (CANON)-based algal-bacterial symbiotic system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136037},
doi = {10.1016/j.biortech.2026.136037},
pmid = {42854799},
issn = {1873-2976},
abstract = {Sunlight-driven CANON-based algal-bacterial symbiotic system (CANON-AB) achieves efficient nitrogen removal through algal oxygen production and assimilation. However, dissolved organic nitrogen (DON), as a major fraction of residual total dissolved nitrogen, remains poorly understood in CANON-AB. This study investigated DON transformation and microbial mechanisms in CANON-AB compared with conventional CANON. After 140 days operation, CANON-AB increased average dissolved inorganic nitrogen (DIN) removal efficiency from 83.6 % to 98 %, reducing effluent nitrate from 27.4 ± 8.3 to 0.7 ± 0.8 mg/L. Meanwhile, DON concentration decreased by 54.8 % in CANON-AB (1.4 ± 0.2 mg/L) compared with CANON (3.1 ± 0.2 mg/L). FT-ICR MS revealed that algae integration reduced DON molecular diversity from 1396 to 723 formulas, with preferential removal of carbohydrates, condensed aromatics, tannins, and sulfur-containing DON molecules. Metagenomic analysis demonstrated enhanced DON mineralization potential in CANON-AB, with DON transformation genes enriched by 1.1-2.4 times higher compared with CANON. These results reveal a coupled mineralization-assimilation mechanism driving DON removal in CANON-AB, providing new insights into nitrogen cycling in sustainable wastewater treatment.},
}

@article {pmid42854800,
year = {2026},
author = {Peng, Y and Yu, H and Sun, F and Huang, X and Wei, L and Chen, C},
title = {Molecular transformation of dissolved organic matter during landfill leachate treatment by microbial electrolysis cell-anaerobic digestion system.},
journal = {Bioresource technology},
volume = {464},
number = {Pt C},
pages = {136038},
doi = {10.1016/j.biortech.2026.136038},
pmid = {42854800},
issn = {1873-2976},
abstract = {The complex dissolved organic matter (DOM) in landfill leachate posed significant challenges for conventional biological treatment. In this study, a microbial electrolysis cell-anaerobic digestion (MEC-AD) system was constructed to explore DOM transformation pathways. An orthogonal experimental design was employed to evaluate the effects of applied voltage, anode-to-cathode area ratio, and stainless-steel cathode mesh size. Under an applied voltage of 1.2 V, an anode-to-cathode area ratio of 1:1, and a cathode mesh size of 200 mesh, the highest overall COD removal efficiency of 60.2% was observed. Spectroscopic analysis showed a reduction in biodegradable soluble microbial byproducts during treatment. GC-MS showed changes in the profiles of representative aliphatic and aromatic compounds. FT-ICR MS analysis revealed compositional reorganization of DOM, characterized by the disappearance of a fraction of protein- and lipid-like DOM and the persistence or relative enrichment of more unsaturated and aromatic constituents. Microbial community analysis revealed the relative enrichment of hydrolytic and fermentative bacteria (e.g., norank_f__Anaerolineaceae) as well as bacteria potentially involved in electron transfer (e.g., Thiobacillus). Metagenomic analysis suggested functional potential for amino acid metabolism, fatty acid degradation, glycolysis, and pyruvate metabolism. In contrast, the relatively low abundance of aromatic compound degradation functions was consistent with the persistence of refractory aromatic DOM. This study revealed that MEC-AD treatment was associated with differential transformation and molecular reorganization of landfill leachate DOM, and provided molecular-level insights beyond conventional bulk organic matter removal.},
}

@article {pmid42854825,
year = {2026},
author = {Zhang, Y and Lu, R},
title = {Characteristics of metagenome and metabolomics of biliary flora in biliary acute pancreatitis for severity prediction.},
journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract},
volume = {},
number = {},
pages = {102625},
doi = {10.1016/j.gassur.2026.102625},
pmid = {42854825},
issn = {1873-4626},
abstract = {OBJECTIVE: To investigate the characteristics of the metagenome and metabolomics of biliary flora in patients with acute biliary pancreatitis and its predictive value for the severity of the disease.

METHODS: This study included 80 ABP patients (Jan 2022 - Dec 2024) and 30 healthy controls. ABP patients were divided into mild (n = 50) and moderate-severe (n = 30) groups using the revised Atlanta criteria. Chao1 index, Shannon index, relative abundances of Klebsiella, Enterococcus, and Escherichia coli, serum amylase, and C-reactive protein (CRP) were compared. ROC analysis assessed predictive value of Shannon index, Klebsiella abundance, and CRP for severity. Correlations between these parameters and severity were examined.

RESULTS: Significant differences were observed among the three groups in Chao1 and Shannon indices, relative abundances of the three bacterial genera, and serum amylase and CRP levels (all P < 0.05). ROC analysis showed that Shannon index, Klebsiella relative abundance, and CRP level predicted disease severity with AUCs of 0.804, 0.804, and 0.850, respectively (P < 0.05). Shannon index was negatively correlated with ABP severity, while Klebsiella abundance and CRP level were positively correlated with severity (P < 0.05).

CONCLUSION: In this cohort, biliary microbiome characteristics and serum inflammatory markers were associated with the severity of biliary acute pancreatitis. The Shannon index, Klebsiella relative abundance, and CRP showed exploratory discriminatory performance. These findings provide a basis for further prospective validation; they do not establish a causal driving factor, a clinically validated early-warning system, or an individualized treatment strategy.},
}

@article {pmid42854947,
year = {2026},
author = {Yang, Y and Yu, H and Wang, J and Yang, S and Han, J and Jin, W and Luo, D and Zhou, S and Ma, C},
title = {Species-associated toxicological trajectories in social bees exposed to sublethal metribuzin: A multi-omics perspective on host-microbiome interactions.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {411},
number = {Pt A},
pages = {129320},
doi = {10.1016/j.envpol.2026.129320},
pmid = {42854947},
issn = {1873-6424},
abstract = {The divergent sensitivities of honeybees (Apis mellifera) and bumblebees (Bombus terrestris) to agrochemicals challenge the one-species-fits-all framework of ecological risk assessment, yet the mechanistic basis for this variation remains underexplored. Here, we used an integrated multi-omic approach, combining transcriptomics, metabolomics, and gut metagenomics, to map the species-associated responses of these pollinators under sublethal metribuzin (MET) exposure (30 mg/kg). Honeybees, exhibited broad transcriptional activation accompanied by suppressed P450 and glutathione S-transferase (GST) activities, metabolically associated with a disruption in cellular cofactor (NADPH/FAD) biosynthesis pathways, coincided with midgut tissue pathology and microbial structural dysbiosis. Conversely, bumblebees showed targeted cytochrome P450 (CYP) induction and elevated P450/GST activities, linked to an energy-intensive rewiring of carbohydrate metabolism that supported both xenobiotic clearance and antioxidant defense. While the bumblebee gut microbiota remained structurally stable, it displayed functional shifts toward xenobiotic efflux and cellular cytoprotection. Collectively, our multi-omic landscapes delineate two divergent correlative models: metabolic impairment coupled with microbial dysbiosis in honeybees, versus physiological resilience associated with microbiome functional plasticity in bumblebees. These findings propose a testable framework wherein baseline metabolic capacity shapes species-associated trajectories of host-microbiome interactions under herbicide stress, highlighting the critical need to incorporate mechanistic insights from multi-species comparisons into future ecological risk assessments.},
}

@article {pmid42856459,
year = {2026},
author = {Takeuchi, T and Reddy, A and Robinson, EK and Kotaka, KM and Higginbottom, SK and Sonnenburg, ED and Sonnenburg, JL},
title = {Functional Divergence in Gut Clostridia from Hadza Hunter-Gatherers Reveals Diet-Adapted Metabolic Machinery That Shapes Gut Ecology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.29.755216},
pmid = {42856459},
issn = {2692-8205},
abstract = {Lifestyle changes associated with industrialization, including shifts in diet, are linked to extensive remodeling of the human gut microbiome. Investigating the gut microbiomes of traditional populations living non-industrialized lifestyles, such as the Hadza hunter-gatherers of Tanzania, therefore offers insight into bacterial taxa and functions depleted in industrialized microbiomes. Despite pronounced compositional differences that correspond to lifestyle, many commensal gut species are shared between industrialized and non-industrialized populations, raising a fundamental question of whether and how their functional repertoires diverge across contrasting gut environments. Here, by integrating strain-resolved metagenomics with culturomics and in vivo models, we identify phylogenetic and functional divergence within prevalent gut species shared between Hadza and industrialized populations, particularly among members of the Clostridia class. Dorea longicatena , prevalent across diverse human populations independent of lifestyle, is a poorly characterized member of Clostridia. Using strains of this D. longicatena isolated from either Hadza or industrialized human stool samples, we uncover metabolic pathways selectively enriched in Hadza strains, including machinery for utilizing plant-derived pectic polysaccharides. We further demonstrate that this Hadza-enriched polysaccharide-utilization machinery can be leveraged with its cognate dietary substrate to promote D. longicatena colonization within a model industrialized microbiota, reshaping intestinal and portal-vein metabolite profiles. Together, our findings reveal substantial functional divergence within gut bacterial species shared across lifestyles, providing a framework for identifying diet-responsive strains and pathways that may complement ecological and metabolic functions underrepresented in industrialized microbiotas.},
}

@article {pmid42856497,
year = {2026},
author = {Tisza, MJ and Simar, SR and Zorz, JK and Javornik Cregeen, SJ and Maresso, AW},
title = {EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.29.755457},
pmid = {42856497},
issn = {2692-8205},
abstract = {Metagenomic sequencing allows for detection of any number of pathogenic viruses from a single sample without a priori knowledge of its contents. This has created a substantial opportunity to characterize pathogens in humans and their environment, but the field is held back by a lack of bioinformatics tools for taxonomic profiling and reconstructing virus genomes. The ideal profiler would simultaneously do two things: report viruses at single-read sensitivity so that ultra-low-abundance pathogens are not missed and hold near-perfect specificity so that a pathogen is never falsely reported. Here we present EsViritu , a taxonomic profiler that pairs an iterative greedy clustering algorithm and lowest-common-ancestor taxonomic refinement with a curated Virus Pathogen Database to reconstruct virus genomes and generate virome profiles directly from reads. We benchmarked EsViritu against four leading metagenomic profilers (Kraken2, Centrifuger, Metabuli , and Sylph), running each program across a full parameter sweep and against the same Virus Pathogen Database for an apples-to-apples comparison. Across synthetic positive controls, pathogen-free negative controls, and mutated mock communities, EsViritu was the most accurate tool at reconstructing community composition: it led or tied every tool on relative abundance accuracy at all taxonomic ranks and led or tied on detection across ranks. Importantly, other tools frequently report the presence of multiple related taxa when only reads for a single genome are present, but EsViritu faithfully records the correct, single taxon and genome. EsViritu achieves read-level sensitivity for sequences as low as 85% average nucleotide identity to the nearest reference and reports essentially no false positives in pathogen-free host and synthetic samples. EsViritu also returns reconstructed consensus genomes whose nucleotide identity to the nearest reference closely tracks ground truth, yielding both a profile and genomes from a single run.},
}

@article {pmid42856507,
year = {2026},
author = {Din, MO and Brennan, C and Zhao, J and Oles, R and Patel, L and Birmingham, A and Sevilir, DM and Hansen, L and Wright, GM and Ambre, M and Tomita, M and Boyer, T and Gonzalez, A and Ackermann, G and McDonald, D and Kralicek, S and Hecht, G and Hasty, J and Smarr, L and Knight, R},
title = {Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.28.754546},
pmid = {42856507},
issn = {2692-8205},
abstract = {Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.},
}

@article {pmid42856590,
year = {2026},
author = {Zhang, J and Zhang, L and Li, SG and Li, J and Zou, Y and Long, T and Yu, R and Zhang, Y},
title = {Case Report: Sequencing-supported probable osteoarticular Mycobacterium avium complex infection in rheumatoid arthritis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1954797},
pmid = {42856590},
issn = {2296-858X},
abstract = {BACKGROUND: Osteoarticular Mycobacterium avium complex (MAC) infection is uncommon and can resemble inflammatory arthritis during immunosuppression.

CASE DESCRIPTION: A 52-year-old woman with an erosive seronegative rheumatoid arthritis phenotype and overlap autoimmune features developed progressive polyarticular swelling, wrist tenosynovitis, hip effusions, and low-back pain after cumulative immunosuppression. Investigations showed macrocytic anemia, lymphopenia, pan-hypogammaglobulinemia, marked B-cell depletion without anti-CD20 exposure, and cytomegalovirus DNAemia. Pre-treatment mNGS reported MAC-spectrum signals in hip, wrist, and elbow aspirates, including 355 right-hip reads. A separate pathogen-targeted joint-fluid sequencing report, with no anatomical site stated, detected MAC complex (116,330 normalized sequences; assay-estimated 10⁵ copies/mL). Neither result was interpreted as organism burden. No tissue histopathology, dedicated mycobacterial culture, or phenotypic susceptibility testing was performed. The working diagnosis was multisite sequencing-supported probable multifocal osteoarticular MAC infection without culture confirmation. Several interventions began concurrently. Selected follow-up MR images showed persistent destructive wrist disease and residual joint or periarticular fluid, but no standardized imaging or microbiological response endpoint was available.

CONCLUSION: In atypical arthritis progressing during immunosuppression, infection-focused sampling should precede further escalation. mNGS can provide an etiologic clue, but culture, histopathology, targeted testing, and longitudinal reassessment remain essential.},
}

@article {pmid42856639,
year = {2026},
author = {Strength, RE and Angelova, A and Robbins, E and Levy, S and McCauley, KE and Lloyd, KM and Margolis, EB and Burns, AS and Mistry, S and Subramanian, P and Dassner, A and Zerbe, C and Band, VI and Namasivayam, S and Chen, Q and Esadah, E and Rees, K and Bacorn, M and Prasad, R and LaPoint, P and Romero-Soto, HN and Dekker, JP and Sears, CL and Shapiro, C and Hamdy, RF and Campos, JM and Hourigan, SK},
title = {Coming Into Resistance: Clinically Important Antibiotic Resistance Genes in NICU vs. Healthy Infants.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.23.26363796},
pmid = {42856639},
abstract = {IMPORTANCE: Antibiotic-resistant infections in neonates often arise from the infant's own colonizing bacteria harboring antibiotic resistance genes (ARG). This study evaluates ARG that impact antibiotic selection and drive resistance-related mortality, termed clinically important antibiotic resistance genes (CI-ARG).

OBJECTIVE: To determine differences in gut CI-ARG abundance in children from birth through 3 years old, stratified by neonatal intensive care unit (NICU) admission and antibiotic (abx) exposure in the first two months.

DESIGN: Cohort study (sequencing, analysis completed 2025-2026) using shotgun metagenomic sequencing of stool samples from infants in two studies: "Neonatal Intestinal Microbiome" (+NICU groups, 2015-2022), "The First 1000 Days of Life and Beyond" (-NICU groups, 2018-2021). Infants grouped into four cohorts: +NICU/+abx, +NICU/-abx, -NICU/-abx, and -NICU/+abx. Prespecified CI-ARG abundance compared longitudinally among groups.

SETTING: NICU, well-baby nursery, Inova Fairfax Hospital, Virginia.

PARTICIPANTS: +NICU criteria: admission to the NICU, anticipated length of stay (LOS) of at least five days, maternal age ≥18 years. -NICU: parents with good general health and age ≥18 years enrolled prior to infant birth. Stool samples: adequate stool processing volume, at least one stool sample from before one month and after one year of age, 7-day minimum between serial samples.

EXPOSURES: NICU versus well-baby nursery; antibiotics versus none in first two months of corrected age.

MAIN OUTCOMES AND MEASURES: Predefined primary outcome-longitudinal CI-ARG abundance by group, compared using linear mixed effects models with adjustment for multiple comparisons (Benjamini-Hochberg procedure). Predefined secondary outcomes-differences in overall microbiota and resistome composition.

RESULTS: 1000 serial stool samples, 179 infants (birth-39 months). Longitudinal abundance significantly differed among cohorts for 11 CI-ARG (p<0.05); often higher in the +NICU groups in early life, with or without antibiotic exposure. Abundance of ARG conferring resistance to aminoglycosides, macrolides, and fluoroquinolones later decreased below -NICU levels. mecA , which often drives methicillin resistance in Staphylococcus , was detected only in +NICU infants during premature period.

CONCLUSIONS: This longitudinal study demonstrates significant longitudinal CI-ARG differences in children grouped by early-life NICU status and/or antibiotic exposure. Future studies should explore the mechanisms driving these CI-ARG changes and evaluate their impact on infection risk and community spread.

KEY POINTS: Question: How do clinically important antibiotic resistance genes (CI-ARG) differ longitudinally among infants up to 3 years old based on NICU admission and antibiotic exposure in the first two months of life?Findings: In this cohort study of 179 infants through 39 months of age, longitudinal abundance was significantly different for 11 prespecified CI-ARG, often higher in the NICU groups in early life, with or without antibiotic exposure.Meaning: Children with a history of NICU hospitalization, whether due to the NICU environment itself, prematurity, or other factors, may have increased CI-ARG burden early in life, irrespective of direct antibiotic exposure.},
}

@article {pmid42856694,
year = {2026},
author = {Soveral, LF and Holanda, LRL and Assunção, IBF and Gomes, LG and de Souza, IB and Rodrigues, GS and Vanny, PA and Bruna-Romero, O and Palmeiro, JK and Scheffer, MC and Sincero, TCM and Zárate-Bladés, CR},
title = {Identification of antibiotic resistance genes in fecal microbiota selected donors during the establishment of a biobank in the south of Brazil.},
journal = {Frontiers in antibiotics},
volume = {5},
number = {},
pages = {1905540},
pmid = {42856694},
issn = {2813-2467},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is increasingly explored for other dysbiosis-related disorders. However, its implementation as a regulated therapeutic strategy requires robust donor screening, biosafety frameworks, and standardized processing workflows. Here, we describe the establishment of the first fecal microbiota biobank in southern Brazil and evaluate the incorporation of metagenomic sequencing as a complementary layer of donor characterization and safety assessment. A structured donor selection pipeline based on international guidelines was implemented, integrating clinical screening, biochemical and serological testing, and microbiological analyses. Of 100 screened candidates, only four donors met all eligibility criteria and were included in the biobank, highlighting the stringency of the selection process. Shotgun metagenomic sequencing revealed a diverse resistome across all donors, including a shared core set of resistance genes alongside marked interindividual variability. Dominant resistance determinants included tetracycline-associated genes, ermF, CfxA-type β-lactamases, and aminoglycoside-modifying enzymes, which were associated with specific gut taxa. Genomic context analysis further identified four ARG-containing contigs with features compatible with potential mobility, although active horizontal gene transfer was beyond the scope of this study. Notably, tet(Q) and ermF were predominantly associated with Bacteroides fragilis, supporting its role as a reservoir of resistance determinants in the gut microbiota. These findings support the use of metagenomic profiling as a complementary approach to donor characterization and risk assessment rather than as a standalone criterion for donor exclusion. Overall, this study provides a framework for microbiota biobank implementation and highlights the potential of metagenomic analysis to complement conventional biosafety screening in FMT.},
}

@article {pmid42856732,
year = {2026},
author = {Wallace, BA and Baker, L and Papke, E and Ushijima, B and Rosales, SM and Silveira, CB},
title = {Temperate and filamentous bacteriophages as reservoirs of bacterial virulence in stony coral tissue loss disease.},
journal = {Coral reefs (Online)},
volume = {45},
number = {5},
pages = {2211-2230},
pmid = {42856732},
issn = {1432-0975},
abstract = {UNLABELLED: Lysogenic conversion, in which bacteriophages (viruses that infect bacteria) integrate into bacterial genomes and confer new phenotypic traits on their hosts, is a well-established mechanism for the emergence of pathogens. While this process underpins many bacterial diseases in humans and other animals, its role in coral disease remains largely unexplored. Here, we investigate the potential role of lysogenic conversion in stony coral tissue loss disease (SCTLD), which has caused unprecedented mortality of Caribbean corals since 2014 and for which the etiological agent remains unknown. Across 27 original coral samples and 174 publicly available metagenomes from the Florida Reef Tract spanning seven coral species, we detected a greater number of unique viral genomes harboring genomic features associated with lysogeny in diseased corals or visually healthy portions of diseased corals (DD and HD, respectively) compared to visually healthy (VH) corals. SCTLD-associated bacteriophages were primarily predicted to infect bacterial taxa previously implicated in the disease, such as Vibrionales, Rhodobacterales, and Flavobacteriia, and carried abundant and widespread virulence factors with the potential to enhance bacterial colonization, competition, or direct host damage, including homologs of Tse2, Zot, RTX, pneumolysin, and cytolytic delta-endotoxin. Although causal relationships remain unresolved, our findings indicate that phages have the genomic capacity to laterally transfer bacterial virulence genes in SCTLD-affected corals. The acquisition of genes via lysogenic conversion could contribute to bacterial virulence while maintaining community taxonomic profiles, helping to explain previous community profiling observations and providing a mechanistic framework for disease pathogenesis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s00338-026-02902-2.},
}

@article {pmid42856881,
year = {2026},
author = {Ding, L and Wang, H and Li, F},
title = {Case Report: Streptococcus suis-associated meningoencephalitis with profound bilateral labyrinthine deafness and intra-operative cochlear fibrosis treated by cochlear implantation.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1941314},
pmid = {42856881},
issn = {2296-858X},
abstract = {Streptococcus suis is a common zoonotic pathogen that usually causes monomicrobial meningitis. Occult bloodstream detection of Klebsiella pneumoniae, together with proven central-nervous-system S. suis infection, followed by irreversible cochlear fibrotic changes requiring cochlear implantation, appears exceptionally rare. We report a 52-year-old male with chronic heavy alcohol intake and occupational swine-exposure history who developed severe sepsis, recurrent suppurative meningoencephalitis caused by S. suis, and permanent bilateral labyrinthine-related deafness. Combined blood and cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) identified suspected additional bloodstream infection by K. pneumoniae, although K. pneumoniae was not detected in CSF. Multimodal antimicrobial, anti-inflammatory, and immunomodulatory therapy cleared intracranial infection but failed to restore hearing. Preoperative imaging suggested cochlear fibrotic changes; left-sided cochlear implantation achieved full electrode insertion with stable intraoperative neural responses despite abundant intracochlear fibrous tissue observed intraoperatively. This case raises three important considerations: occupational swine exposure together with chronic alcoholism may plausibly contribute to suspected polymicrobial sepsis; in selected patients, peripheral-blood mNGS may help identify occult Gram-negative bacteremia when CSF assays remain negative during recurrent meningitis; and cochlear fibrosis may not absolutely preclude technically-successful cochlear implantation.},
}

@article {pmid42857043,
year = {2026},
author = {Fang, C and Wang, C and Wang, R and Lu, YF and Ma, L},
title = {Gut microbial characteristics and kynurenine-related metabolism across sarcopenia groups: associations with neuromuscular and physical function.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1883616},
pmid = {42857043},
issn = {1663-4365},
abstract = {BACKGROUND: Sarcopenia is characterized by heterogeneous alterations in muscle mass, strength, and physical performance and may involve interactions among the gut microbiota, tryptophan metabolism, and neuromuscular function. However, these biological characteristics across different sarcopenia stages remain incompletely understood. This study investigated gut microbial characteristics, kynurenine-related metabolism, circulating biomarkers, and physical function in older adults with different sarcopenia status.

METHODS: In this cross-sectional study, 67 older adults were classified according to the Asian Working Group for Sarcopenia 2019 criteria as non-sarcopenia (NSG, n = 17), possible sarcopenia (PSG, n = 20), or sarcopenia (SG, n = 30). Muscle mass, handgrip strength, and multidimensional physical performance were assessed. Serum C-terminal agrin fragment (CAF), tumor necrosis factor-α (TNF-α), amino acids, kynurenine (KYN), and tryptophan (Trp) were measured, and the KYN/Trp ratio was calculated. Gut microbiome composition was characterized by shotgun metagenomic sequencing. Differential abundance was evaluated using MaAsLin2 with adjustment for age and body mass index (BMI), and exploratory correlations among microbial genera, metabolites, circulating biomarkers, and physical function were examined with false discovery rate correction.

RESULTS: ASMI was significantly lower in the SG group than in the NSG and PSG groups, whereas several measures of physical performance differed among groups without a uniform stepwise pattern. No significant differences were observed in alpha diversity, beta diversity, or the Firmicutes/Bacteroidetes ratio, and sarcopenia group explained only 3% of the variation in overall microbial community composition (PERMANOVA, R [2] = 0.03, p = 0.226). Several genus-level associations were nominally significant after adjustment for age and BMI, but none remained significant after BH-FDR correction. After adjustment for age and BMI, serum KYN concentrations and the KYN/Trp ratio were significantly higher in the SG group than in the NSG group (p = 0.011 and p = 0.043, respectively), whereas Trp and the measured amino acids showed no significant pairwise differences. The unadjusted increase in CAF across sarcopenia groups was attenuated after covariate adjustment, and TNF-α did not differ significantly among groups. Exploratory correlation analyses identified several FDR-significant associations across microbial, metabolic, and functional domains, including negative associations of KYN and KYN/Trp with handgrip strength and a positive association between CAF and 6-m gait speed(GS).

CONCLUSION: Established sarcopenia was associated with altered circulating kynurenine-related metabolism despite the absence of pronounced differences in overall gut microbial community structure. Exploratory cross-domain associations further suggest potential interactions among gut microbial characteristics, tryptophan metabolism, and neuromuscular and physical function. These findings support further investigation of host-microbial tryptophan metabolism in sarcopenia but do not establish a causal microbiota-kynurenine-NMJ pathway.},
}

@article {pmid42857110,
year = {2026},
author = {Zou, X and Chen, Q and Pu, W and Gao, J and Yang, Y and Long, X},
title = {Dietary American Cockroach (Periplaneta americana) Chitin Influences Growth Performance, Nutrient Utilization, Gut Microbiota, and Riboflavin-Related Metabolism in Juvenile Grass Carp (Ctenopharyngodon idella).},
journal = {Aquaculture nutrition},
volume = {2026},
number = {},
pages = {3097646},
pmid = {42857110},
issn = {1365-2095},
abstract = {The American cockroach (Periplaneta americana) is an emerging sustainable source of insect-based chitin, yet its physiological effects and optimal inclusion levels in herbivorous fish diets remain undefined. This study evaluated the dose-dependent effects of dietary P. americana chitin (0%, 2.5%, 5%, 10%, and 20%) on juvenile grass carp (Ctenopharyngodon idella) over a 63-day trial. Results revealed a distinct biphasic response in growth and nutrient utilization. Fish fed the 5% chitin diet exhibited the highest weight gain and specific growth rate (SGR), coinciding with the highest apparent digestibility coefficient (ADC) of crude protein (74.34%) compared with the control (72.01%). Conversely, higher inclusion levels (10% and 20%) significantly suppressed growth and reduced protein digestibility. Metagenomic reanalysis showed that the riboflavin-biosynthesis gene ribA (K01497) was significantly reduced at 2.5%-10% dietary chitin (F (4,10) = 7.78, FDR p = 0.041), while the overall riboflavin metabolism pathway, the M00125 biosynthesis module, and intestinal riboflavin levels did not differ significantly among diets. Among the inclusion levels tested, 5% produced the most favorable overall response under the present experimental conditions, balancing improved growth and protein digestibility with the negative responses observed at higher inclusion levels.},
}

@article {pmid42857159,
year = {2026},
author = {Galetović, A and Ortiz, J and Peña, G and Arros, P and Guerra-Leal, N and Berríos-Pastén, C and Silva, M and Acosta, J and Varas, MA and Allende, ML and Marcoleta, AE},
title = {A genome-resolved cyanobacterial consortium from the Atacama Desert reveals novel bacterial diversity, stress-resilience potential, chromatic flexibility, and photoprotection.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1939861},
pmid = {42857159},
issn = {2296-4185},
abstract = {The Atacama Desert is one of the most extreme terrestrial environments on Earth, characterized by hyper-aridity, intense solar and ultraviolet radiation, oxidative stress, and metal-rich substrates. Here, we characterized an enriched cyanobacteria-associated consortium obtained from a high-altitude, river-influenced site in Quebrada Talabre, Atacama Desert. Deep shotgun metagenomic sequencing, achieving 99.7% estimated community coverage, enabled the reconstruction of 14 high-quality metagenome-assembled genomes representing five bacterial phyla. Genome-resolved analyses revealed multiple putative novel bacterial lineages, including a potential novel family-level lineage within Thermomicrobiales, putative novel species of Allosphingosinicella, Flavobacterium, and Caulobacter, and a distinct Nostocaceae lineage corresponding to the dominant cyanobacterium, tentatively named Talabrenema galetoviciae TAL-12. Functional annotation revealed marked differentiation among consortium members. Heterotrophic bacteria encoded predicted functions associated with aromatic compound degradation, nitrogen and sulfur turnover, iron acquisition, metal-biocide resistance, and oxidative-stress responses, whereas the TAL-12 cyanobacterial metagenome-assembled genome encoded the core machinery for oxygenic photosynthesis, carbon fixation, and pigment biosynthesis. Phylogenomic analyses supported T. galetoviciae TAL-12 as a novel species and likely novel genus within Nostocaceae. Comparative genomic and structural analyses revealed a diversified phycobiliprotein repertoire comprising phycocyanin, allophycocyanin, and phycoerythrocyanin components, together with divergent but structurally conserved paralogs and variable accessory pigment modules across related Nostocaceae genomes, consistent with enhanced light-harvesting flexibility. Pigment fractionation supported the absence of canonical phycoerythrin production and confirmed phycocyanin enrichment. Purified TAL-12 phycocyanin displayed moderate thermal stability, while the cyanobacterial component of TAL-12 consortium cultures retained chlorophyll during prolonged exposure to elevated temperature. In addition, the TAL-12 cyanobacterial genome encoded a Nostocales-like scytonemin biosynthetic gene cluster consistent with UV photoprotection, while lacking canonical cyanotoxin biosynthetic gene clusters. Together, these findings reveal previously underexplored bacterial diversity and predicted functional complementarity within an Atacama cyanobacteria-associated consortium, while identifying T. galetoviciae TAL-12 as a distinctive Nostocaceae lineage with light-harvesting, thermal-resilience, and photoprotective traits relevant to extremophile-based bioinnovation.},
}

@article {pmid42857378,
year = {2026},
author = {Zhang, Y and Cidan, Y and Xu, J and Li, B},
title = {CRC-TrustBench: benchmarking cross-study and cross-country generalization in gut metagenomic colorectal cancer prediction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1971707},
pmid = {42857378},
issn = {1664-302X},
abstract = {BACKGROUND: Gut metagenomic classifiers for colorectal cancer (CRC) are often evaluated with random splits that place samples from the same studies, countries, or processing workflows in both training and test sets, potentially inflating apparent performance. We developed CRC-TrustBench, a leakage-aware framework for evaluating cross-study and cross-country generalization and probability reliability.

METHODS: From 2,340 MetaGenoPolis V16 source samples, we curated 1,953 CRC or healthy samples from 15 studies and 10 countries; 185 adenoma samples were retained outside binary model development as a challenge population. Subject-aware random, leave-one-study-out (LOSO), and leave-one-country-out (LOCO) protocols were applied to taxonomic profiles with 2,543 features and functional profiles with 378 features. We compared Elastic Net, LightGBM, cohort-balanced Elastic Net, and pre-specified neural domain-robust methods using fold-specific pre-processing. The Microbiome Leakage and Confounding Audit (MiLCA) quantified study and country shortcuts, while Platt calibration, conformal-style sets, and selective abstention were evaluated without outer-test labels.

RESULTS: For taxonomic profiles, LightGBM achieved an area under the receiver operating characteristic curve (AUROC) of 0.874 under random splitting, 0.827 under LOSO, and 0.821 under LOCO; the single pre-specified RANDOM estimate was numerically higher than the held-out-domain summaries. Microbiome profiles predicted study and country identity, and a descriptive feature-level audit indicated pervasive study-associated structure. Cohort balancing yielded limited gains, and neural domain-robust methods did not consistently outperform LightGBM. Platt scaling reduced the mean LOCO Brier score from 0.180 to 0.169 and log loss from 0.630 to 0.521. LightGBM conformal-style coverage fell below the pre-specified 90 and 95% targets, while uncertainty-based abstention reduced error relative to matched-random rejection in most recorded repeats. Functional profiles were less predictive, although more functional features met the pre-specified high-stability tiers.

DISCUSSION: The tiered features remain stable candidate hypotheses, and raw counts are not directly comparable across the differently sized feature spaces. Adenoma predictions were heterogeneous, and no reviewed external resource met all criteria for formal independent evaluation. CRC-TrustBench separates in-distribution discrimination from cohort generalization and probability reliability without implying clinical deployment or independent external validation.},
}

@article {pmid42857515,
year = {2026},
author = {Karthick, V and Thamarai, R and Amalraj, S and Narayanasamy, K},
title = {Cytopathology of the microbiome-immune interface: Emerging applications of cytology in infectious, inflammatory, and neoplastic conditions.},
journal = {CytoJournal},
volume = {23},
number = {},
pages = {57},
pmid = {42857515},
issn = {0974-5963},
abstract = {OBJECTIVES: The objective of the study is to synthesize current evidence on the microbiome-immune interface as reflected in cytopathologic specimens and to explore the emerging diagnostic, prognostic, and translational applications of cytology in infectious, inflammatory, and neoplastic diseases.

MATERIAL AND METHODS: This narrative review integrates published literature on cytopathology, microbiome research, and immune profiling. Relevant studies examining cytologic specimens, including fine-needle aspiration, effusion cytology, liquid-based cytology, and lavage samples, were evaluated for their contributions to understanding host-microbe interactions. Emphasis was placed on studies incorporating molecular microbiome analysis (16S ribosomal ribonucleic acid sequencing, metagenomics), immunocytochemistry, cytokine profiling, and digital image analysis.

RESULTS: Cytologic specimens provide a minimally invasive platform that captures dynamic interactions between epithelial cells, immune infiltrates, and microbial communities. In infectious diseases, cytology enables direct pathogen visualization while reflecting immune activation patterns such as granuloma formation and neutrophilic inflammation. In chronic inflammatory disorders, cytologic features including lymphoid infiltrates and macrophage activation may correspond with microbiome-driven immune dysregulation. In oncology, tumor-associated microbiota detectable in cytology samples influence immune checkpoint expression, macrophage polarization, and tumor microenvironment remodeling. Integration of molecular assays, single-cell technologies, and artificial intelligence further enhances the ability of cytology to characterize microbiome-immune signatures within limited specimens.

CONCLUSION: Cytopathology is evolving from a purely morphologic discipline into an integrative platform that bridges microbial ecology and immune dynamics. Incorporating microbiome profiling and immune phenotyping into routine cytologic evaluation holds promise for improved disease stratification, early detection, and personalized therapeutic decision-making. Recognizing cytology as a window into the microbiome-immune interface may redefine its role in precision medicine across infectious, inflammatory, and neoplastic conditions.},
}

@article {pmid42857638,
year = {2026},
author = {Chen, J and Jiang, J and Zhou, X and Fan, L and Wu, F and Liang, P and Song, H and Wang, J and Luo, J and Zhu, G},
title = {Characteristics of Microbiota in Different Segments of the Digestive Tract of Orange-Collared Keelback (Rhabdophis himalayanus).},
journal = {Ecology and evolution},
volume = {16},
number = {10},
pages = {e74508},
pmid = {42857638},
issn = {2045-7758},
abstract = {The gastrointestinal tract of animals plays an essential role in digestion and nutrient absorption. The diversity of gut microbiota is critical for maintaining the physiological functions of animals. However, current research has focused primarily on mammals; research on the gut microbiota of reptiles, particularly snakes, remains limited. This study utilized metagenomic sequencing and untargeted metabolomics to investigate the microbial community composition and functional potential in the stomach, large intestine, and small intestine of the Orange-collared Keelback (Rhabdophis himalayanus). The results demonstrate that the three most dominant phyla in the R. himalayanus gut microbiota are Pseudomonadota, Actinomycetota, and Bacillota. Moreover, analysis of microbial communities across the stomach, small intestine, and large intestine shows no significant differences in α-diversity and β-diversity among the three regions. Linear Discriminant Analysis Effect Size (LEfSe) reveals significant differences in the gut microbiota abundance. MetaStats analysis further reveals significant differences in the abundance of both microbial taxa and CAZymes. Although overall metabolite profiles did not differ significantly among gastrointestinal regions, pairwise analyses identified differentially abundant metabolites associated with amino acid, lipid, nucleotide, and cofactor metabolism. Gut microbiota from different parts of the digestive tract may reveal a unique characteristic of the gut microbiome of R. himalayanus and the impact of microbial community structure on function. Collectively, these findings expand our understanding of gastrointestinal microbial communities and associated functional potential in an understudied snake species.},
}

@article {pmid42858079,
year = {2026},
author = {Yang, X and Ye, T and He, Y and Zhao, J and Wang, J and Cheng, X},
title = {Qi-Fu-Yin Attenuates Frailty by Regulating Gut Microbiota and Neuroendocrine Hormones in 5xFamilial Alzheimer's Disease Transgenic Mice.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/73003},
pmid = {42858079},
issn = {1940-087X},
mesh = {Animals ; *Alzheimer Disease/drug therapy/microbiology/blood/metabolism ; Mice, Transgenic ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; *Frailty/drug therapy/microbiology ; Female ; Male ; Disease Models, Animal ; },
abstract = {Frailty is a common and debilitating feature of Alzheimer's disease (AD), yet effective therapeutic strategies targeting both cognitive decline and physical frailty remain limited. Qi-Fu-Yin (QFY), a traditional Chinese herbal formulation, has been used to treat aging-related disorders, but its effects on frailty in AD and the underlying mechanisms are unclear. This study aimed to evaluate whether QFY alleviates frailty in 5xFamilial Alzheimer's Disease (FAD) transgenic mice and to explore the potential involvement of gut microbiota and neuroendocrine hormones. Mice were treated with QFY at low (2.8 g/kg), medium (5.6 g/kg), or high (11.2 g/kg) doses, or with donepezil as a positive control, for 194 days. Frailty-related behaviors were assessed using CatWalk gait analysis, grip strength, rotarod, nest-building, and aging scoring. Plasma hormone levels were measured, and fecal gut microbiota composition and function were analyzed by 16S rRNA sequencing and metagenomic analysis. QFY treatment significantly improved gait parameters, grip strength, motor coordination, nesting ability, and reduced aging scores in 5xFAD mice, with effects comparable to or superior to those of donepezil. QFY also restored aberrant levels of estradiol, testosterone, and corticosterone, and reshaped gut microbiota composition, particularly by increasing the abundance of Adlercreutzia, which negatively correlated with senescence and testosterone levels. Functional metagenomics revealed that QFY partially restored disease-associated microbial pathways, including those involved in carbohydrate metabolism and virulence. These findings suggest that QFY alleviates frailty in 5xFAD mice, with effects associated with concurrent modulation of gut microbiota and neuroendocrine function, though causal relationships require further validation. These findings support further investigation of QFY as a potential intervention for AD-associated frailty.},
}

Animals
*Alzheimer Disease/drug therapy/microbiology/blood/metabolism
Mice, Transgenic
Mice
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/administration & dosage
*Frailty/drug therapy/microbiology
Female
Male
Disease Models, Animal

@article {pmid42858083,
year = {2026},
author = {Zheng, Y and Yang, Y and Mei, X and Guo, T and Gu, L and Liu, X and Yu, J and Yang, X and Yang, M and Li, Y and Zhang, X and Zhou, Y and Zheng, J and Hu, X},
title = {Paired Exploratory Metagenomic Analysis of Gut Microbiota Before and After Ceftizoxime Treatment in College Students with Acute Enteritis.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/71529},
pmid = {42858083},
issn = {1940-087X},
mesh = {Humans ; *Ceftizoxime/therapeutic use/pharmacology/administration & dosage ; Female ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Metagenomics/methods ; Young Adult ; Adolescent ; *Enteritis/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/microbiology ; Students ; Acute Disease ; Metagenome/drug effects ; },
abstract = {This study explored the short-term changes in gut microbiota concurrent with ceftizoxime sodium therapy and clinical recovery in college students with acute enteritis. A retrospective, self-controlled before-and-after design was adopted, enrolling 10 college students (5 males, 5 females; aged 18-24 years) with acute enteritis admitted to Southwest University Hospital. Fecal samples were collected before intravenous antibiotic treatment and at the time of clinical recovery (5-7 days later). All patients received intravenous ceftizoxime sodium (1.0 g every 12 h). Metagenomic sequencing was performed to analyze microbiota composition and diversity. We hypothesized that short-term ceftizoxime therapy would induce detectable species-level restructuring without substantially altering higher-level diversity. Phylum-level analyses showed no statistically significant differences between the two groups. Also, α-diversity analysis at the genus level revealed that the Shannon, Simpson, and Chao1 showed no differences between the two groups (q = 0.054, 0.054 and 0.084, respectively). PERMANOVA based on Bray-Curtis distances at the genus level demonstrated a statistically significant difference in overall microbial community structure between the two groups before and after treatment (F = 1.81, P = 0.043), but no significant difference after adjustment (P = 0.054). ANOSIM performed on the raw full-species abundance table at the species level further detected significant separation between the two groups (R = 0.114, P = 0.016). No species remained statistically significant after false-discovery-rate correction. These exploratory, descriptive findings indicate that species-level temporal changes in the gut microbiota occurred concurrently with ceftizoxime exposure and clinical recovery, but cannot be attributed specifically to the antibiotic. The study provides hypothesis-generating data for future controlled investigations of antibiotic-microbiota interactions in young adults.},
}

Humans
*Ceftizoxime/therapeutic use/pharmacology/administration & dosage
Female
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Metagenomics/methods
Young Adult
Adolescent
*Enteritis/drug therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects/genetics
Feces/microbiology
Students
Acute Disease
Metagenome/drug effects

@article {pmid42858216,
year = {2026},
author = {Khan, A and Ullah, Z and Siraj, M and Younas, S and Wahab, S and Waris, A and Hong, ST},
title = {The Gut Microbiota-Epilepsy Axis: Bibliometric Trends, Mechanistic Insights, and Microbiota-Targeted Next-Generation Therapeutic Opportunities.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42858216},
issn = {1559-1182},
mesh = {Humans ; *Epilepsy/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; Brain ; },
abstract = {Epilepsy is a complex neurological disorder with diverse underlying causes. Growing evidence suggests that gut dysbiosis may promote epileptogenesis by disrupting short-chain fatty acids, tryptophan-kynurenine metabolism, immune signaling, and neuronal excitability. In this review, we combine findings from human and animal studies to explain how gut dysbiosis may influence seizures through the gut-brain axis. We highlight emerging and less-discussed mechanisms, including vagus nerve signaling, microbial amyloids, bacterial extracellular vesicles (BEVs), the queuosine salvage pathway, and multi-kingdom microbiota interactions. We also summarize microbiota profiling studies and describe dysbiosis patterns linked to seizure. To support translation, we propose a peri-ictal multi-omics strategy for biomarker discovery. This includes standardized sampling and integration of metagenomics, metabolomics, and host transcriptomics. In addition, our bibliometric analysis further shows rapidly growing global interest in this topic. Recent studies increasingly focus on the gut-brain axis, ketogenic diet, and inflammation-driven mechanisms. Finally, we outline both established approaches and emerging next-generation microbiome-based therapeutic strategies, including SCFA-restoring synbiotics, engineered psychobiotics, bacteriophage therapy, and AI-guided personalization. These advances highlight the microbiota as modifiable target for adjunctive epilepsy management and provide a translational roadmap for future mechanistically informed research and clinical interventions.},
}

Humans
*Epilepsy/therapy/microbiology
Animals
*Gastrointestinal Microbiome/physiology
Dysbiosis
Brain

@article {pmid42858339,
year = {2026},
author = {Song, S and Guo, T and You, T and Wang, P},
title = {Diagnosis and treatment of four cases of pulmonary cryptococcosis: case report and literature review.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {9},
pages = {1408-1414},
doi = {10.3855/jidc.20737},
pmid = {42858339},
issn = {1972-2680},
mesh = {Humans ; *Cryptococcosis/diagnosis/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology ; Male ; Antifungal Agents/therapeutic use ; Fluconazole/therapeutic use ; Middle Aged ; *Lung Diseases, Fungal/diagnosis/drug therapy/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Adult ; Tomography, X-Ray Computed ; Aged ; Metagenomics ; Immunocompromised Host ; },
abstract = {INTRODUCTION: Cryptococcosis has attracted global attention due to its high mortality rate, unique geographical distribution, and tendency to cause severe and rapid disease progression. Metagenomic next-generation sequencing (mNGS) is a novel detection technology that provides diagnostic insights for identifying pathogens, particularly rare ones. The present article describes 4 individuals diagnosed with pulmonary cryptococcosis (PC) using mNGS of bronchoalveolar lavage fluid (BALF).

CASE PRESENTATION: Among these patients, 3 had cancer, 1 had sarcoidosis and diabetes, and 2 were exposed to pigeons and/or pigeon droppings. These patients experienced symptoms, including fever, cough, and chest pain. They were diagnosed with PC after mNGS of BALF. The patient was diagnosed based on mNGS test results. Subsequently, the patient was treated with fluconazole, and the patient's chest computed tomography scan showed significant absorption of the lung lesions.

CONCLUSIONS: mNGS of BALF can quickly diagnose PC. This diagnostic method has minimal trauma to the body and is worthy of clinical promotion. Fluconazole remains the preferred and best therapeutic drug for PC treatment.},
}

Humans
*Cryptococcosis/diagnosis/drug therapy
Bronchoalveolar Lavage Fluid/microbiology
Male
Antifungal Agents/therapeutic use
Fluconazole/therapeutic use
Middle Aged
*Lung Diseases, Fungal/diagnosis/drug therapy/microbiology
Female
High-Throughput Nucleotide Sequencing
Adult
Tomography, X-Ray Computed
Aged
Metagenomics
Immunocompromised Host

@article {pmid42858532,
year = {2026},
author = {Paladsing, Y and Linsuwanon, P and Jittmittraphap, A and Leaungwutiwong, P and Morand, S and Chaisiri, K},
title = {Rodent-associated viruses in Asia: ecological drivers, host-virus associations and insights from a systematic review.},
journal = {Research in veterinary science},
volume = {213},
number = {},
pages = {106394},
doi = {10.1016/j.rvsc.2026.106394},
pmid = {42858532},
issn = {1532-2661},
abstract = {Rodent-associated viruses are important zoonotic agents of increasing relevance to public and veterinary health. Muroid rodents occupy diverse natural and human-modified environments, facilitating interactions with humans, livestock and wildlife. However, knowledge of rodent-associated viral diversity and the ecological processes influencing viral maintenance and transmission remains fragmented. This review synthesizes published literature on viral diversity, host-virus associations, research trends, and ecological drivers of viral occurrence in Asian muroid rodents. PubMed and Scopus were systematically searched using terms related to rodents, viruses, and Asian regions. Extracted data included publication characteristics, diagnostic methods, host and virus taxonomy, geography, and ecological metadata. Descriptive analyses, geospatial mapping, and network approaches were applied to identify patterns and knowledge gaps. Of 1,049 records retrieved, 165 studies published between 1968-2025 from 30 Asian countries met the inclusion criteria. These studies documented 106 viral taxa representing 74 genera and 35 families. Research activity increased markedly after 2000 alongside advances in molecular diagnostics and metagenomic sequencing. Studies were concentrated in East and mainland Southeast Asia. Orthohantavirus spp. were the most studied viral group, whereas many other viruses remained poorly characterized. Network analyses identified core murine genera, particularly Rattus, Apodemus, Niviventer, Bandicota and Mus, sharing extensive viral associations. Host age, sex, population density, habitat disturbance, climate, and biodiversity were commonly linked with viral prevalence and dynamics. Despite substantial progress, gaps remain in ecological integration, longitudinal surveillance, and comparative study design. Future research should prioritize standardized, ecologically informed surveillance within an integrated One Health framework to improve zoonotic risk assessment and prevention.},
}

@article {pmid42858585,
year = {2026},
author = {Guo, Y and Xu, T and Yang, Q and Guo, S and Sun, P and Zhou, Y and Wu, X and Chen, Y},
title = {Mechanisms of acid generation and reduction during Jiangxiangxing Baijiu fermentation: insights from practices of raw materials saccharification regulation.},
journal = {Food chemistry},
volume = {532},
number = {Pt 1},
pages = {151434},
doi = {10.1016/j.foodchem.2026.151434},
pmid = {42858585},
issn = {1873-7072},
abstract = {Elevated total acidity in the first round base liquor is a major challenge in Jiangxiangxing Baijiu production. Production practice has shown that enhanced raw material saccharification effectively reduces total acidity. This study investigated the underlying regulatory mechanism. Enhanced saccharification reduced total acidity, predominantly attributable to acetic acid, to 0.059 mol/L, representing a 14.47% reduction, without altering overall microbial succession. Multi-omics and culture-dependent analyses identified Limosilactobacillus panis, Lactobacillus acetotolerans, and Limosilactobacillus avium as core acetic acid-producing microorganisms, with their relative abundances reduced by 48.43%, 43.01%, and 32.67%, respectively. The acetate kinase-mediated pathway was the dominant route of acetic acid biosynthesis, and enhanced saccharification reduced transcription of the acetate kinase-encoding gene. Fermentation validation showed that elevated reducing sugar promoted yeast growth and ethanol production, thereby suppressing acetic acid formation. Overall, enhanced saccharification reduces total acidity in base liquor by modulating reducing sugar-driven microbial dynamics and suppressing acetic acid biosynthesis.},
}

@article {pmid42858690,
year = {2026},
author = {Guler Cekic, S and Vatansever, C and Akpinar, A and Belge, S and Shahrokhi, G and Unal, C and Altintas, A and Aydin, S and Can, F},
title = {Interactions between vaginal, periurethral and urinary microbiota in genitourinary syndrome of menopause and the effects of local estrogen therapy.},
journal = {Maturitas},
volume = {214},
number = {},
pages = {109146},
doi = {10.1016/j.maturitas.2026.109146},
pmid = {42858690},
issn = {1873-4111},
abstract = {OBJECTIVES: Alterations to the vaginal microbiota have been investigated in genitourinary syndrome of menopause but data regarding periurethral and urinary microbiota remain limited. We aimed to characterize vaginal, periurethral, and urinary microbiota in clinically stratified postmenopausal women and to evaluate the effects of estrogen therapy.

STUDY DESIGN: In this prospective study, postmenopausal women were categorized as controls without atrophy or symptoms, women with clinical atrophy without symptoms, symptomatic women, and symptomatic women receiving 12 weeks of vaginal estriol. Vaginal, periurethral, and bladder samples were collected.

MAIN OUTCOME MEASURES: Microbiota composition and diversity (alpha diversity - Shannon index; and beta diversity - Bray-Curtis dissimilarity) across urogenital niches and changes in these following estrogen therapy.

RESULTS: Vaginal and periurethral alpha diversity was higher in women with asymptomatic atrophy and symptomatic women at baseline than in controls and estrogen-treated women. Beta diversity analyses demonstrated separation of controls and estrogen-treated women from the atrophy groups at baseline. Controls exhibited Lactobacillus-enriched periurethral communities and Klebsiella-dominant urinary profiles. Women with asymptomatic atrophy and symptomatic women showed reduced Lactobacillus and increased anaerobic taxa in vaginal and periurethral niches, while urinary samples were characterized by Escherichia predominance. Notably, in women with asymptomatic atrophy, Lactobacillus abundance was higher in periurethral than vaginal samples. Estrogen therapy increased Lactobacillus abundance in vaginal and periurethral compartments and shifted urinary microbiota toward a control-like composition. Periurethral Streptococcus abundance correlated with sexual symptom scores.

CONCLUSIONS: Microbial alterations in genitourinary syndrome of menopause are compartment-specific and extend beyond the vagina. Periurethral microbiota may contribute to symptom expression, while local estrogen therapy promotes restoration of Lactobacillus-dominant urogenital microbiota.

CLINICALTRIALS: gov registration: NCT06633705.},
}

@article {pmid42858715,
year = {2026},
author = {Zhang, X and Zhang, C and Ji, B and Zhang, Z and Xu, C and Cui, T and Chen, L},
title = {Plant litter promotes nitrate-sulfate co-removal in constructed wetlands: DOM dynamics and metagenomic insights into carbon, nitrogen, and sulfur transformations.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131111},
doi = {10.1016/j.jenvman.2026.131111},
pmid = {42858715},
issn = {1095-8630},
abstract = {Plant litter is a low-cost carbon source for constructed wetlands (CWs), but its effectiveness and associated microbial mechanisms in nitrate-sulfate co-contaminated wastewater remains insufficiently understood. This study evaluated cattail and reed litters as in situ carbon sources by integrating substrate characterization, dissolved organic matter (DOM) spectroscopy, microbial community analysis, and metagenomic annotation. Both litter-amended systems effectively promoted simultaneous nitrogen and sulfate removal. The cattail-amended system achieved total nitrogen (TN) removal efficiencies of 73.48%-93.82% and a maximum SO4[2-] removal efficiency of 58.27%, while the reed-amended system achieved 61.10%-91.73% TN removal and 52.90% maximum SO4[2-] removal. DOM optical indices and PARAFAC analysis showed a gradual shift from protein-like to microbial humic-like fluorescence in the cattail-amended system, whereas microbial humic-like fluorescence dominated earlier in the reed-amended system. Metagenomic analysis revealed differences in carbon, nitrogen, and sulfur metabolic potentials. The cattail-amended system showed higher abundances of PPP-related genes associated with NADPH-generating reactions and several denitrification- and sulfur-oxidation-related genes, including narGHI, nirS/K, nosZ, sox, sqr, and fccA/B. The reed-amended system showed higher abundances of selected EMP- and TCA-associated genes and several reductive sulfur genes, including dsr, phs, and ttrABC. The detection of doxD and ttrABC further suggested potential thiosulfate-tetrathionate transformation. Overall, plant litter amendment effectively supported nitrate-sulfate co-removal, while integrated DOM, microbial, and metagenomic analyses revealed different metabolic potentials under cattail and reed amendment.},
}

@article {pmid42858760,
year = {2026},
author = {Yu, C and Wang, Z and Wu, L and Meng, L and Liu, L and Sha, L and Tuo, J and Wang, J and Li, J and Peng, Z and Zhang, Y and Liu, Z and Jin, Z},
title = {Global phylogeography, genomic characteristics and transmission of antibiotic resistance of multi-drug resistant ORN-1-producing Raoultella ornithinolytica B1645-1B.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {106038},
doi = {10.1016/j.meegid.2026.106038},
pmid = {42858760},
issn = {1567-7257},
abstract = {OBJECTIVE: To characterize the genomic phylogeny and antimicrobial resistance (AMR) genotypes of the ORN-1-producing R. ornithinolytica B16451B, and to elucidate the transfer mechanisms of resistance genes at the genomic level.

METHODS: The genome of R. ornithinolytica B16451B was sequenced using the Illumina HiSeq 4000 and PacBio RSII sequencing platforms. A global phylogenetic analysis of the genomic data was conducted by the Center for Genomic Epidemiology (CGE), incorporating information on geographical distribution, isolation sources, and host associations. A comparative phylogenomic analysis was performed using the BLAST Ring Image Generator (BRIG). Genome annotation was performed using Glimmer and the Rapid Annotation using Subsystem Technology (RAST) server. Mobile genetic elements were predicted using TnCentral, ISFinder, and PHASTER. The antibiotic resistance genes (ARGs) were analyzed using the Comprehensive Antibiotic Resistance Database (CARD), while the virulence factors genes (VFGs) were analyzed using the Virulence Factor Database (VFDB). Gene transfer experiments were conducted in the intestinal tract of mice. Transconjugants were identified using 16S rRNA metagenomic sequencing, and drug-resistance genes were amplified by PCR.

RESULTS: A chromosome (designated chromosome 01) was first identified in strain B16451B. A carrying IS4 insertion sequence distinct resistance region within this chromosome, designated B1645-1B-RG, harbors the β-lactamase gene blaORN-1. Three intact prophages, designated prophage YC1, YC2, and YC3, were also first identified. The blaORN-1 gene was successfully transferred from strain B16451B to Escherichia coli (designated B1645-1BLMY1) and Klebsiella pneumoniae (designated B1645-1BYCF2) in the intestines of mice. The strain B16451B harbored 25 antimicrobial resistance genes and 8 classes of virulence factor genes. Based on comparative genomic analysis of strains retrieved from the NCBI Genome Database, 98 antimicrobial resistance genes (ARGs) (e.g., sul1, blaKPC-2, blaNDM-1) among 234 R. ornithinolytica strains were identified to exhibit significantly higher prevalence in human isolates than in non-human host sources (e.g., water, animals, plants).

CONCLUSIONS: The chromosome 01 was identified in a multi-drug resistant ORN-1-producing the strain B16451B isolated from China. The genome of strain B16451B harbors three integrated prophages: YC1 (42.2 kb), YC2 (60.5 kb), and YC3 (23.8 kb) was identified. The IS4 insertion might promote blaORN-1 gene transfer within the intestinal flora of mice. Among these 234 R. ornithinolytica strains analyzed in this study, most virulence factor genes (e.g., ompa, yagx/ecpc) and resistance genes (e.g., blaKPC, blaNDM) exhibited higher prevalence in Homo sapiens isolates than in strains from non-human sources including water, animals and plants. These findings provide valuable references for clinicians optimize the management of R. ornithinolytica infections and guide clinical treatment.},
}

@article {pmid42858812,
year = {2026},
author = {Shi, M and Yao, S and Zhou, X and Zhang, J and Pei, Y and Xie, J and Yang, S},
title = {Mitigating NH3 emissions via synergistic regulation of ammonification and ammonia assimilation during black soldier fly larvae mediated chicken manure bioconversion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136044},
doi = {10.1016/j.biortech.2026.136044},
pmid = {42858812},
issn = {1873-2976},
abstract = {Bioconversion with black soldier fly larvae (BSFL) is an efficient method for disposing of chicken manure. However, large amounts of ammonia (NH3) are released during bioconversion, resulting in significant nitrogen loss. Previous studies generally neglected the synergistic regulation of ammonification and ammonia assimilation for mitigating NH3 emissions. In this study, a novel biotechnological strategy combining propionic acid, probiotics, and glucose (PPG) was established. Specifically, acidification combined with Bacillus was applied to inhibit ammonification, while glucose was added to regulate substrate carbon to nitrogen ratio (C/N) and promote ammonia assimilation during BSFL mediated chicken manure bioconversion. The results showed that PPG significantly reduced NH3 emissions by 70.98 % compared to the control (CK) (p < 0.05). Metagenomics was used to analyze microbial regulatory mechanisms. PPG treatment resulted in a significantly higher relative abundance of ammonia assimilation gene (glnA) and lower abundance of ammonification associated genes (ureC, glsA, gcvT, gudB) (p < 0.05). These observations could be attributed to microbial community perturbations. Genera including Proteiniphilum and Petrimonas were primary contributors to ammonification and ammonia assimilation in CK, whereas genera such as Limosilactobacillus and Romboutsia dominated these two nitrogen metabolic functions in PPG. Further, the applicability of PPG strategy was effectively verified in high-density BSFL cultivation system. Finally, application of cost-optimized biotechnological strategy using calcium propionate and industrial carbon sources achieved a net profit of 10.81 USD/t. In summary, this study provided a promising biotechnological strategy for NH3 mitigation and elucidated the microbial response mechanism underlying the synergistic regulation of ammonification and ammonia assimilation.},
}

@article {pmid42858840,
year = {2026},
author = {Li, Z and Qin, Y and Cai, J and Luo, X and Yao, Y and Wang, Y and Liang, Q and Xie, L and Bai, M and Liang, X and Liang, C and He, J and Wu, H},
title = {Rhizosphere Penicillium and phosphorus availability drive bioactive compound accumulation in Amomum villosum.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.10.030},
pmid = {42858840},
issn = {2090-1224},
abstract = {INTRODUCTION: Amomum villosum (A. villosum) , a medicinal herb rich in bioactive metabolites (borneol, bornyl acetate), exhibits superior quality in its core production region Yangchun (YC). However, the key habitat factors influencing the quality of A. villosum, as well as the underlying mechanisms, remain unclear.

METHODS: This study employed an integrated multi-omics approach, incorporating metabolomics, transcriptomics, soil physicochemical property analysis, and metagenomics, to systematically compare the core production region with non-core regions. By identifying potential factors influencing regional disparities and validating the functional roles of key biotic and abiotic soil components through multi-level experimental designs, this research aimed to elucidate the primary determinants of product quality and their underlying regulatory mechanisms.

RESULTS: The accumulation of major bioactive components, such as borneol and bornyl acetate, was significantly enhanced in YC A. villosum. Transcriptomic analyses showed that YC A. villosum exhibited preferential gene expression patterns, and further identified a functional gene (WvBAHD3) associated with bornyl acetate synthesis. Furthermore, we analyzed the physicochemical properties of soils from the four regions and revealed that available phosphorus (AP) were more abundant in YC soils than the other three non-core regions. Metagenomic analysis revealed that Penicillium, Limnoraphis, and Alcaligenes species were the dominant rhizosphere microorganisms, showing significant enrichment in YC soils compared to other regions. Correlation analysis indicated significant associations among the three dominant microorganisms, soil AP, and the accumulation of major bioactive components in A. villosum. We further isolated a fungus strain, Penicillium citrinum, and demonstrated its role in promoting the release of soil AP by secreting organic acids. Additionally, soil AP was confirmed to enhance the accumulation of bornyl acetate in A. villosum by upregulating the expression of regulatory genes.

CONCLUSION: This study demonstrates that the recruitment of Penicillium species modulates bioactive compound accumulation in A. villosum via improved phosphorus availability, providing key guidance for high-quality cultivation of A. villosum.},
}

@article {pmid42858843,
year = {2026},
author = {Cheng, Y and Ye, M and Yu, J and Guo, S and Xu, D and Yang, J and Li, T and Li, J and Wang, J and Xing, B and Shan, L and Liu, C and Xu, H and Wang, J and Du, B},
title = {Multi-omics reveals a host-microbe metabolic synergy underlying brown planthopper biotype divergence.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.10.005},
pmid = {42858843},
issn = {2090-1224},
abstract = {INTRODUCTION: The brown planthopper (BPH) is a highly destructive pest in rice production. The widespread cultivation of resistant rice varieties drives BPH populations to evolve new biotypes, posing a continuous challenge to crop protection. Understanding the adaptation mechanisms of these biotypes is therefore critical.

OBJECTIVES: This study aimed to investigate the potential mechanisms underlying the adaptation of a new BPH biotype to resistant rice varieties.

METHODS: We compared the host adaptability of Biotype 1 and Biotype Y on a resistant rice variety (carring Bph15). An integrative multi-omics approach (transcriptomic and metabolomic) was employed, alongside metagenomic analysis of symbiotic microbiota.

RESULTS: Biotype Y exhibited superior adaptation to the resistant variety. Multi-omics analysis revealed that the adaptation was associated with upregulation of carbohydrate, detoxification, and energy metabolism pathways, downregulation of vitamin pathways, and a distinct symbiotic microbiota enriched in Wolbachia. Functional experiments provided evidence suggesting that Wolbachia may contribute to this enhanced adaptation, possibly through riboflavin supplementation.

CONCLUSION: The adaptation of BPH to resistant rice appears to be associated with coordinated transcriptional and metabolic reprogramming, potentially involving symbiont-mediated nutritional support. These findings may provide new insights into tripartite host-pest-microbiota interactions and offer potential targets for sustainable pest management strategies.},
}

@article {pmid42858898,
year = {2026},
author = {Xu, X and Yan, Z and Hu, Y and Jiang, H and Sun, L and Yi, R and Yan, X},
title = {Multi-omics analysis reveals Oscillibacter valericigenes gavage increases fetal and placental weights and is associated with altered estrogen-related metabolism and valerate production in mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101878},
doi = {10.1016/j.tjnut.2026.101878},
pmid = {42858898},
issn = {1541-6100},
abstract = {BACKGROUND: Our prior work associated Oscillibacter valericigenes and valerate-related features with offspring birth weight in Landrace × Yorkshire sows, but functional evidence was limited.

OBJECTIVES: To test whether O. valericigenes or valerate increases late-gestation fetal weight and characterize maternal metabolic and placental responses.

METHODS: Pregnant mice received 200 μL of sterile culture medium (Control), O. valericigenes bacterial suspension (OV_B; 10[8] CFU/mL), or sterile-filtered culture supernatant (OV_M) by oral gavage every other day from embryonic day (E) 7.5 to E17.5 (n = 7/group). Another cohort received sodium valerate (SV; 0-1.20 mg/mL) in drinking water from E7.5 to E17.5 (n = 8/group). At E18.5, fetal and placental weights, serum hormone concentrations, colonic and serum short-chain fatty acid concentrations, and placental gene expression were measured and analyzed using one-way ANOVA followed by Dunnett's test. Multi-omics profiling was performed in the Control and OV_B groups.

RESULTS: Compared with control, maternal gavage with O. valericigenes or its culture supernatant increased fetal weight by 4.56% and 6.81%, respectively (both P < 0.01), and placental weight by 8.57% and 8.25%, respectively (both P < 0.05). Multi-omics analyses revealed that O. valericigenes gavage was associated with altered estrogen-related metabolism and placental proteomic and transcriptional responses related to nutrient transport, angiogenesis, and tight junctions. Compared with the control group, OV_B increased colonic valerate concentration by 53.64% (P < 0.05) and tended to increase serum estradiol concentration by 34.58% (P = 0.054). SV supplementation at 0.60 mg/mL increased fetal weight by 6.44% (P < 0.01), placental weight by 7.30% (P < 0.05), and serum valerate concentration by 125.25% (P < 0.05) compared with its respective control. SV supplementation did not significantly alter serum estradiol or progesterone concentrations.

CONCLUSIONS: O. valericigenes increases placental and fetal weights and is associated with altered estrogen-related metabolism and colonic valerate production in mice.},
}

@article {pmid42858945,
year = {2026},
author = {Yang, J and Gao, Y and Han, L and Guo, Y and Zhang, Q and Miao, H and Li, T},
title = {NOD1 contributes to reduced postoperative memory performance induced by preoperative sleep deprivation and anesthesia/surgery in mice.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {106277},
doi = {10.1016/j.neuint.2026.106277},
pmid = {42858945},
issn = {1872-9754},
abstract = {BACKGROUND: Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) recognizes bacterial peptidoglycan fragments and regulates inflammatory responses. However, its role in perioperative memory performance remains unclear. This study investigated the involvement of NOD1 in the hippocampal CA1 region and gut-related alterations in postoperative memory performance.

METHODS: Mice underwent preoperative acute sleep deprivation, anesthesia/surgery, or both. Behavioral testing, hippocampal transcriptomics, fecal metagenomic sequencing, western blotting and immunofluorescence were performed. Iba1 promoter-driven NOD1 knockdown in the hippocampal CA1 region and Lyz1[-/-] mice were used to investigate the involvement of NOD1 in the hippocampal CA1 region and intestinal lysozyme, respectively.

RESULTS: No statistically significant synergistic or facilitating interaction between sleep deprivation and anesthesia/surgery was detected. Significant main effects were observed in the object location memory test (OLMT) and novel object recognition test (NORT), whereas the Y-maze showed only a post hoc difference between the SD + Sur and Con groups. The reduced postoperative memory performance was accompanied by increased NOD1 expression, an elevated p-p65/p65 ratio and Iba1-related changes in the hippocampal CA1 region, together with gut microbiota dysbiosis and increased ileal expression of lysozyme. Both Iba1 promoter-driven NOD1 knockdown and Lyz1 deficiency reduced NOD1 expression, p65 phosphorylation and Iba1-related changes. Iba1 promoter-driven NOD1 knockdown improved memory performance, whereas Lyz1 deficiency improved OLMT and Y-maze performance and showed a trend toward improved NORT performance.

CONCLUSIONS: Hippocampal CA1 NOD1, gut microbiota dysbiosis and ileal lysozyme may contribute to reduced postoperative memory performance associated with preoperative acute sleep deprivation and anesthesia/surgery.},
}

@article {pmid42858969,
year = {2026},
author = {Liu, X and Feng, C and Fan, Q and Li, F and Liu, J and Yi, S and Lu, H and Wu, Y and Liu, Y and Tian, J},
title = {Temporal dynamics of the antibiotic resistome in pepper fruits: The trade-off between phytochemical defenses and heavy metal-induced co-selection.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120411},
doi = {10.1016/j.foodres.2026.120411},
pmid = {42858969},
issn = {1873-7145},
mesh = {*Metals, Heavy/analysis ; *Capsicum/microbiology/chemistry/genetics ; *Fruit/chemistry/microbiology ; Capsaicin/analysis ; *Phytochemicals/analysis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Pepper fruits are globally consumed vegetables and spices that may serve as potential vectors for the dissemination of antibiotic resistance genes (ARGs) into the human food chain. This study investigated the associations of endogenous capsaicin and exogenous heavy metals with the resistome dynamics of peppers across successive harvest stages. Metagenomic analyses revealed temporal variations in the pepper resistome within the agroecosystem. High capsaicin levels during early harvest stages were negatively associated with ARG abundance, whereas the gradual decline of phytochemical defenses during later stages coincided with increased heavy metal accumulation and ARG enrichment. Analysis of large-scale field samples further supported the inverse relationship between capsaicin content and ARG abundance. RT-qPCR assays conducted under controlled laboratory conditions indicated that, unlike capsaicin, heavy metals (such as Cu and Cd) directly promoted the expression of metal resistance and efflux-related genes in a dose-dependent and synergistic manner. Exposure to 50 mg/L of Cu[2+] increased the abundance of CopR by 11.63-fold, while 0.6 mg/L Cd[2+] exposure increased the abundances of baeR and mdtB by 8.51- and 7.89-fold, respectively. Furthermore, heavy metal stress substantially enhanced horizontal gene transfer, with Cd exposure increasing conjugation frequencies by 2.57-fold. These findings demonstrate that the pepper microenvironment represents a dynamic ecological niche in which plant-derived chemical defenses and abiotic contaminants jointly influence ARG dissemination. This study provides new insights into the multifactorial mechanisms driving ARG migration in soil-pepper systems and offers a scientific basis for reducing antibiotic resistance risks in agricultural production.},
}

*Metals, Heavy/analysis
*Capsicum/microbiology/chemistry/genetics
*Fruit/chemistry/microbiology
Capsaicin/analysis
*Phytochemicals/analysis
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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