@article {pmid42815260,
year = {2026},
author = {Zhao, Y and Zhao, X and Lian, J and Wang, S and Ning, Q and Xu, Q and Zhang, Z and Zong, J and Wang, S},
title = {Microbiome-guided prioritization of Corynebacterium striatum in diabetic foot ulcers and preclinical evaluation of tanshinone IIA.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158803},
doi = {10.1016/j.phymed.2026.158803},
pmid = {42815260},
issn = {1618-095X},
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by impaired healing and infection, but microbial signatures linked to glycemic status and their therapeutic relevance remain unclear.

PURPOSE: To identify DFU taxa associated with glycemic status and test whether microbiome-guided prioritization can inform evaluation of Tanshinone IIA (Tan IIA).

STUDY DESIGN: Clinical metagenomic discovery followed by in vitro functional and multi-omics analyses, biophysical studies, and in vivo evaluation.

METHODS: Wound samples from 54 DFU patients underwent HbA1c-stratified shotgun metagenomics. A prioritized patient-derived Corynebacterium striatum isolate was assessed for Tan IIA antibacterial and antibiofilm activity, multi-omics responses, and candidate-protein binding. Topical Tan IIA was tested in non-inoculated and C. striatum-inoculated diabetic wounds.

RESULTS: C. striatum was enriched in higher-HbA1c wounds and positively associated with continuous HbA1c (β = 0.422, 95% CI 0.095-0.748; P = 0.011; q = 0.064). Tan IIA inhibited the isolate (MIC = 64 μ g/ml), reduced biofilm biomass, and induced stress, redox, cell-envelope, and metabolic responses. SPR supported binding to MurD and TrxB. On day 14, wound closure was significantly greater in inoculated wounds (93.40% vs. 78.80%; adjusted P = 0.0187). In inoculated wounds, Tan IIA reduced EUB338-positive bacterial signal and viable counts versus vehicle (8.587 vs. 8.847 log10 CFU/g; adjusted P =  0.0480).

CONCLUSION: HbA1c-stratified metagenomics prioritized C. striatum as a glycemic-status-associated candidate. These findings support microbiome-guided preclinical evaluation of plant-derived Tan IIA as a topical candidate for infected DFUs.},
}

@article {pmid42815267,
year = {2026},
author = {Liu, L and Li, Y and Pan, X and Zhang, K and Yang, F and Liu, D and Sun, W and Li, P and Du, B},
title = {Fermented Polygonatum kingianum polysaccharide exerts enhanced anti-obesity effects by modulating the gut microbiota-GDCA-TGR5 axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158824},
doi = {10.1016/j.phymed.2026.158824},
pmid = {42815267},
issn = {1618-095X},
abstract = {Probiotic-fermented Polygonatum kingianum polysaccharide (FPKP0) was previously confirmed to exhibit enhanced anti-adipogenic activity in 3T3-L1 cells in vitro owing to altered structural, prompting an examination of whether this modified FPKP0 exerts superior anti-obesity effects in vivo via related mechanism in high-fat diet-fed mice. Physiological results showed that FPKP0 outperformed unfermented PKP0 accounting for reducing body weight, improving blood lipids, alongside alleviating hepatic steatosis and colonic damage. Correspondingly, FPKP0 reshaped the gut microbiota by boosting beneficial genera (especially Akkermansia muciniphila) and suppressing harmful bacteria (e.g., Dubosiella, Helicobacter). Integrated metagenomic and metabolomic analyses identified A. muciniphila and Glycodeoxycholic acid (GDCA) as the key microbial and metabolic factors with the in vivo effects of FPKP0. A strong positive correlation (ρ = 0.83) between A. muciniphila abundance and GDCA levels suggests a potential relationship between microbial remodeling and bile acid metabolism following FPKP0 intervention. Further mechanistic exploration suggested that TGR5 may serve as a downstream receptor associated with FPKP0-related changes in GDCA. Molecular docking and immunoblotting indicated a GDCA-TGR5 interaction and activation of the Gsα-PKA-CREB-UCP1 cascade to stimulate energy expenditure. This enhanced in vivo anti-obesity effect of FPKP0 may involve modulation of the gut microbiota (AKK)-bile acid (GDCA)-TGR5 axis, supporting the potential of FPKP0 as a functional food additive to combat obesity and related disorders.},
}

@article {pmid42815303,
year = {2026},
author = {Qiu, J and Yan, J and Cao, L and Xu, Y and Zhang, X and Zhai, Y and Bai, J},
title = {Temporal shifts in the dominance of tolerant taxa reshape microbial functional potentials from substrate utilization to stress resistance in sediments contaminated with sulfonated methyl phenolic resin.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {126985},
doi = {10.1016/j.watres.2026.126985},
pmid = {42815303},
issn = {1879-2448},
abstract = {Sulfonated methyl phenolic resin (SMP), a widely used additive in water-based drilling fluids, accumulates in sediments due to its low degradability. Bioremediation is a promising strategy for SMP removal, but the microbial responses to SMP remain unclear. Here, we conducted microcosm experiments to compare microbial composition and functional potentials between early and late exposure stages across a SMP concentration gradient. The results showed that SMP exposure reduced microbial diversity and increased the relative dominance of putatively tolerant taxa. Microbial response asynchrony increased and was positively correlated with resistance potential. Life-history proxies indicated contrasting patterns between exposure stages, with lower 16S rRNA gene copy number and longer predicted minimum doubling time at the early stage and the opposite pattern at the late stage. Additionally, degradation- and resistance-related functional genes were enriched at the early and late stages, respectively. At the metagenome-assembled genome (MAG) level, abundant MAGs at the late exposure stage exhibited high resistance potential. Overall, our results showed that SMP could exert a double-edged sword effect on microorganisms, acting as both a stressor and a carbon source, thereby inducing stage-specific microbial functional transitions.},
}

@article {pmid42815610,
year = {2026},
author = {Dong, H and Li, Y and Aziz, P and Song, M and Yan, L and Chen, Z and Fohrer, N and Messyasz, B and Li, Y},
title = {Physicochemical and microbial regulators of contrasting diffusive greenhouse gas fluxes in Danjiangkou Reservoir.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125819},
doi = {10.1016/j.envres.2026.125819},
pmid = {42815610},
issn = {1096-0953},
abstract = {Reservoirs play a key role in the global greenhouse gas (GHG) balance through carbon and nitrogen cycling, yet the spatiotemporal variation in GHG fluxes from large drinking-water reservoirs and the underlying regulatory mechanisms remain unclear. This study investigated the seasonal dynamics of CO2, CH4, and N2O diffusive fluxes in Danjiangkou Reservoir and examined their physicochemical and microbial associations. In August, when water levels were low and water temperatures were high, the mean CO2 flux was close to zero (5.59 ± 10.74 mg·m[-2]·h[-1]), with both source and sink fluxes observed among sites; the reservoir showed net CO2 emission during the other sampling periods (40.89 ± 8.88 mg·m[-2]·h[-1]). CH4 and N2O exhibited both source and sink fluxes without consistent seasonal patterns. Mixed-effects models and random-forest analyses consistently identified total dissolved solids (TDS) as a major predictor of all three GHG fluxes, whereas pH, dissolved oxygen, and inorganic nitrogen showed gas-specific associations. Metagenomic analyses indicated a reorganization of microbial functional potential with changing water levels: under high-water conditions, the relative contributions of nitrogen-transformation markers, including nitrate reduction, NO-to-N2O conversion, and dissimilatory nitrate reduction to ammonium, were higher; under low-water conditions, carbon-fixation markers, including those associated with the Calvin cycle and the 3-hydroxypropionate cycle, accounted for larger proportions of the target functional profile. Genus-level annotations identified Polynucleobacter as a prominent CO2-associated taxon, Methylibium and Methylocystis as prominent CH4-associated taxa, and Nitrospira and Haliscomenobacter as candidate N2O-associated taxa. Together, these findings describe spatiotemporal GHG flux patterns and their physicochemical and microbial associations, providing a basis for further investigation of reservoir GHG budgets and potential mitigation strategies.},
}

@article {pmid42815804,
year = {2026},
author = {Chang, K and Xie, H and Wang, Y and Na, W and Liu, C and Liu, Y},
title = {Ozone disinfection effectively reduces pathogenic microbial nucleic acid background in mNGS laboratories.},
journal = {Journal of microbiological methods},
volume = {250},
number = {},
pages = {107728},
doi = {10.1016/j.mimet.2026.107728},
pmid = {42815804},
issn = {1872-8359},
abstract = {For the first time, this report confirmed under real-laboratory-contamination scenarios that ozone disinfection effectively reduces microbial nucleic acid background in mNGS laboratories, with consistent and efficient disinfection performance. With the global advancement of standardized clinical application of mNGS technology, the results provide a practical strategy to control laboratory contamination, reduce false-positive risks, and maintain a low nucleic acid baseline. This method addresses the difficulty of eliminating persistent contamination in mNGS laboratories and offers a direct reference for environmental decontamination of metagenomic sequencing laboratories worldwide.},
}

@article {pmid42816384,
year = {2026},
author = {Kondo, S and Kumar, N and Hamahata, N},
title = {Aseptic Meningitis Unmasking Coccidioidomycosis of the Central Nervous System Outside an Endemic Region.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
doi = {10.2169/internalmedicine.7538-26},
pmid = {42816384},
issn = {1349-7235},
abstract = {A 20-year-old male presented with persistent aseptic meningitis. Cerebrospinal fluid (CSF) showed neutrophil-dominant pleocytosis, high protein, low glucose, and an opening pressure >55 cmH2O. Fluid metagenomic next-generation sequencing detected Coccidioides immitis/posadasii and subsequent culture confirmed the diagnosis. The retrospective history revealed residence in Arizona approximately six months prior to hospitalization. Antifungal therapy was escalated, and the patient was transferred to a tertiary neurocritical care center for advanced neurocritical care. This case demonstrates that geographic bias can delay the recognition of coccidioidal meningitis outside endemic regions. Clinicians should therefore obtain a patient's travel history even if the patients have only a remote travel history.},
}

@article {pmid42816497,
year = {2026},
author = {Zhou, F and Pan, S and Ma, C and Sun, W and Ye, Y and Zhu, DZ and Xiong, J and Li, C and Zhang, J and Gan, J and Sun, X and Lu, D and Gan, H},
title = {Humic acid's sheltering effect paradoxically promotes antibiotic resistance gene dissemination during peroxymonosulfate water treatment.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42816497},
issn = {2041-1723},
support = {52070103//National Natural Science Foundation of China (National Science Foundation of China)/ ; LMS26E090008//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; },
mesh = {*Peroxides/pharmacology/chemistry ; Animals ; *Humic Substances/analysis ; *Water Purification/methods ; Caenorhabditis elegans/microbiology ; Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Microbial/genetics ; Oxidative Stress/drug effects ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Advanced oxidation processes (AOPs) utilizing peroxymonosulfate (PMS) are increasingly deployed for water disinfection, yet their impact on the dissemination of antibiotic resistance genes (ARGs) remains poorly understood. Here, we conducted field surveys in three aquaculture ponds in eastern China and employed a Transwell-based horizontal gene transfer (HRT) sorting assay, metagenomics, and transcriptomics to investigate the underlying mechanisms. We found that PMS-treated waters harbored significantly higher intracellular ARG burdens compared to untreated or chlorinated systems. Mechanistically, the ubiquitous humic acid (HA) acts as a selective radical scavenger, protecting bacteria from lethal oxidative damage while stimulating type IV pilus-mediated uptake of extracellular ARGs. This interaction redirects HGT from conjugation toward natural transformation. Crucially, this protective effect is oxidant-specific: HA effectively quenches PMS-derived radicals but provides no defense against direct electrophilic attack by chlorine. Furthermore, predation experiments using Caenorhabditis elegans demonstrate that this "sheltering effect" facilitates the accumulation of ARGs in nematodes, decoupling resistance acquisition from oxidative stress intensity. These findings highlight a critical risk pathway in which some water treatment chemicals can promote the spread of resistance, necessitating a reassessment of oxidant selection based on their specific chemical mechanisms.},
}

*Peroxides/pharmacology/chemistry
Animals
*Humic Substances/analysis
*Water Purification/methods
Caenorhabditis elegans/microbiology
Gene Transfer, Horizontal/drug effects
*Drug Resistance, Microbial/genetics
Oxidative Stress/drug effects
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid42817081,
year = {2026},
author = {Pushp, and Paliwal, A},
title = {Fungal Keratitis: A Narrative Review with a Focus on Antifungal Resistance and Emerging Therapies.},
journal = {Infectious disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715265490828260921074616},
pmid = {42817081},
issn = {2212-3989},
abstract = {Corneal infection that can cause blindness, fungal keratitis has shown an increasing prevalence worldwide, especially in tropical and subtropical areas, where it significantly increases the risk of unilateral corneal blindness. The epidemiology, molecular etiology, diagnosis, antifungal resistance, and changing treatment of fungal keratitis are all reviewed in this article. Geographic diversity is evident in epidemiological patterns, with filamentous fungi such as Aspergillus and Fusarium predominating in warm climes, and an increasing number of reports of Candida species in temperate and healthcare-associated settings. Disease incidence and outcomes have been further affected by post-COVID-19 changes in ophthalmic treatment, extensive corticosteroid exposure, delayed presentations, and environmental factors, including climate fluctuations and increased airborne spore loads. Rapid stromal invasion, enzyme-mediated tissue damage, biofilm development, and host immune dysregulation are key factors determining severity, according to molecular findings. For improved detection, including in culture-negative and polymicrobial cases, diagnostic advancements focus on combining traditional microscopy and culture with in vivo confocal microscopy, MALDI-TOF MS, targeted PCR, and metagenomic next-generation sequencing. Time to treatment is being reduced by rapid point-of-care techniques like tear β-D-glucan tests, LAMP, CRISPR/Cas platforms, and AI-based image analysis. The necessity for systematic susceptibility testing and antifungal management is supported by rising antifungal resistance, particularly rising MIC trends in Fusarium and Aspergillus species, which exhibit variable susceptibility to azoles and amphotericin B, highlighting the need for species-specific antifungal susceptibility testing. The evolving epidemiology, molecular etiology, and new developments in fungal keratitis diagnosis are covered in this article. Additionally, it emphasizes new therapeutic approaches, including advanced drug delivery systems, advances in antifungal resistance management, and potential avenues for improved management. The article presents a narrative review focusing on recent developments in the epidemiology, molecular mechanisms, diagnosis, antifungal resistance, and treatment options for fungal keratitis.},
}

@article {pmid42817572,
year = {2026},
author = {Kundral, S and Giang, PD and Kirk, AM and Buczynski, JB and Arachchige, KSA and Khare, SK and Bernhardt, PV and Evans, PN and Guddat, LW and Bell, SG and De Voss, JJ},
title = {Structural and Functional Characterisation of a Metagenome-Derived CYP108D18 Reveals an Unusual Dioxygen-Bound State and Selective Hydrocarbon Hydroxylation.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70451},
pmid = {42817572},
issn = {1751-7915},
support = {DP210103970//Australian Research Council/ ; },
mesh = {*Cytochrome P-450 Enzyme System/metabolism/chemistry/genetics/isolation & purification ; Hydroxylation ; *Metagenome ; *Oxygen/metabolism ; *Sphingomonadaceae/enzymology/genetics ; Escherichia coli/genetics/metabolism ; Enzyme Stability ; Hot Springs/microbiology ; Protein Binding ; Monoterpenes/metabolism ; Australia ; Gene Expression ; Molecular Docking Simulation ; Cloning, Molecular ; Substrate Specificity ; Recombinant Proteins/genetics/metabolism/isolation & purification/chemistry ; Temperature ; },
abstract = {Cytochrome P450 enzymes form a large superfamily of monooxygenases capable of oxidising diverse substrates. Among them, members of the CYP108 family are recognised for their role in monoterpenoid oxidation. In this study, we report the identification and characterisation of a new CYP108 family member, CYP108D18, from a metagenome-assembled genome derived from microbial communities in a geothermal hot spring located in northern Queensland, Australia. Taxonomic binning associated CYP108D18 with a Novosphingobium species, a genus well-known for its bioremediation potential. CYP108D18 was heterologously expressed in Escherichia coli, yielding 640 nmol L[-1] of culture, and purified to homogeneity. The enzyme exhibited moderate thermostability, with a [15]T50 value of 47°C ± 1°C. Spectroscopic substrate binding assays revealed that while CYP108D18 bound monoterpenoids similarly to other CYP108 enzymes, it showed higher affinity and pronounced larger heme spin-state shifts with aromatic hydrocarbons such as phenylcyclohexane and phenanthrene. Subsequent in silico docking and spectral-binding studies also suggested that CYP108D18 may accommodate larger plant-derived sesquiterpenes, indicating a potential role in their metabolism. Reconstitution of CYP108D18 with spinach ferredoxin and ferredoxin reductase resulted in the oxidation of phenylcyclohexane to trans-4-phenylcyclohexanol. Molecular dynamics simulations and ONIOM (QM/MM) calculations supported selective hydrogen abstraction at the cyclohexane C4 position, rationalising trans-4-phenylcyclohexanol as the predominant product. The high-resolution crystal structure of substrate-free CYP108D18 revealed a bound dioxygen ligand positioned above the heme iron, an unusual feature among P450 structures. Both substrate-free and phenylcyclohexane-bound structures revealed a persistent open conformation, suggesting the absence of a canonical open-to-closed transition upon ligand binding. Spectroelectrochemical analysis showed a heme redox potential of -451 mV versus NHE for the substrate-free CYP108D18, shifting subtly to -409 mV upon phenylcyclohexane binding, which contributes to reduced activity with non-native [2Fe-2S] ferredoxins.},
}

*Cytochrome P-450 Enzyme System/metabolism/chemistry/genetics/isolation & purification
Hydroxylation
*Metagenome
*Oxygen/metabolism
*Sphingomonadaceae/enzymology/genetics
Escherichia coli/genetics/metabolism
Enzyme Stability
Hot Springs/microbiology
Protein Binding
Monoterpenes/metabolism
Australia
Gene Expression
Molecular Docking Simulation
Cloning, Molecular
Substrate Specificity
Recombinant Proteins/genetics/metabolism/isolation & purification/chemistry
Temperature

@article {pmid42817813,
year = {2026},
author = {Wang, L and Yu, S and Huang, J and Meng, Y and Zhao, C and Gan, Y and Hu, W and Yang, Y},
title = {Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70579},
doi = {10.1111/mec.70579},
pmid = {42817813},
issn = {1365-294X},
support = {2023YFD1801900//National Key Research and Development Program of China/ ; 2025KYPT0066//National Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock/ ; 32460897//National Natural Science Foundation of China/ ; Q2022002//'Grassland Talents' Youth Innovation and Entrepreneurship Talent Project of Inner Mongolia Autonomous Region/ ; 2025-Gui-Yan-1-36//Hohhot R&D Investment Incentive Program/ ; },
mesh = {Animals ; *Microbiota/genetics ; Birds/microbiology/virology ; *Ecosystem ; Bacteria/genetics/classification ; *Biodiversity ; Arthropod Vectors/microbiology/virology ; Fungi/genetics/classification ; Phylogeny ; Grassland ; Sequence Analysis, DNA ; Virome ; Viruses/classification/genetics ; },
abstract = {Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito- and bird-associated communities. Ecological network analyses revealed substantial cross-host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system-wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host-associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.},
}

Animals
*Microbiota/genetics
Birds/microbiology/virology
*Ecosystem
Bacteria/genetics/classification
*Biodiversity
Arthropod Vectors/microbiology/virology
Fungi/genetics/classification
Phylogeny
Grassland
Sequence Analysis, DNA
Virome
Viruses/classification/genetics

@article {pmid42817903,
year = {2026},
author = {Olasupo, OA and Olaniyan, OP and Akinde, SB and Adesoye, AA and Ajadi, FA and Obire, O and Oladipo, EK and Sule, WF and Oyinloye, OE and Salami, AA and Fajoyegbe, ES and Ajani, AJ and Ojo, O},
title = {Metagenomic Characterisation of Antibiotic Resistance in Anaerobic Digesters and Their Implications for Environmental Health.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70400},
pmid = {42817903},
issn = {1758-2229},
mesh = {*Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Metagenome ; },
abstract = {Antimicrobial resistance (AMR) in environmental systems represents an emerging One Health challenge, with anaerobic digesters potentially serving as reservoirs of resistance-associated genetic features. This study analysed four publicly available anaerobic digester shotgun metagenomic datasets (M2, M3, M12 and M17) retrieved from the NCBI Sequence Read Archive to characterise microbial functions, resistance-associated annotations and antibiotic target loci. The datasets were generated using Illumina HiSeq 2000 sequencing and analysed through quality assessment, assembly, functional annotation and resistome profiling. A total of 1082 resistance-associated annotations were identified, with the highest abundance detected in M2 (348), followed by M12 (276), M17 (259) and M3 (205). Detected annotations were associated with diverse antimicrobial categories, including aminoglycosides, quinolones, beta-lactams, tetracyclines, glycopeptides, macrolides and sulfonamides. Several frequently detected loci, including rpoB, rpoC, gyrA, gyrB, EF-Tu, EF-G, Ddl and KasA, were interpreted as antibiotic target or housekeeping loci rather than confirmed acquired resistance genes. Exploratory co-abundance analysis identified strong associations among functionally linked loci, including rpoB-rpoC and gyrA-gyrB, likely reflecting shared genomic occurrence or functional relationships. These findings highlight the resistome potential of anaerobic digesters while emphasising the need for host-resolved metagenomics, mobile genetic element analysis and mutation-level characterisation to clarify environmental AMR risks.},
}

*Metagenomics
*Anti-Bacterial Agents/pharmacology
Anaerobiosis
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects/isolation & purification/classification
*Metagenome

@article {pmid42818131,
year = {2026},
author = {Parker, E and Oladipo, F and Levy, JI and Ope-Ewe, OO and Soumare, H and Andersen, K and Happi, AN and Happi, CT},
title = {Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.22.26363641},
pmid = {42818131},
abstract = {Population-scale pathogen surveillance is limited worldwide, particularly in resource-constrained settings, where clinical systems only monitor select priority pathogens and reach only those who can access healthcare. Wastewater-based epidemiology addresses many of these gaps, offering cost-effective surveillance that is adaptable across diverse implementation contexts. In Lagos, Nigeria, a high enteric pathogen burden coincides with a complex sanitation landscape. However, circulating pathogen diversity in Lagos is largely uncharacterised outside of outbreak contexts. Here we characterize human-associated pathogen diversity in Lagos with virus-enriched metagenomic and metatranscriptomic sequencing of untreated wastewater sampled from open drainage canals from July-August 2024. We detected a diverse human-associated virome dominated by enteric adenoviruses, astroviruses and caliciviruses. We recovered numerous partial and near-complete genomes from pathogens of public health concern, including noroviruses, enteroviruses and sapoviruses. Although our enrichment targeted viruses, we detected diverse bacterial pathogens, including recurrent detection of Vibrio cholerae , other enteric bacteria, and zoonotic pathogens such as Streptococcus suis. We also detected antimicrobial resistance genes, including aminoglycoside, beta-lactam and fluoroquinolone resistance and clinically important genes such as mcr . Together, these results establish a regional baseline of pathogen diversity and demonstrate the utility of virus-enriched sequencing for integrated wastewater surveillance.},
}

@article {pmid42818146,
year = {2026},
author = {Song, L},
title = {Lossless compression of protein databases for efficient and accurate metagenomic sequence classification with Centrifuger.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752512},
pmid = {42818146},
issn = {2692-8205},
abstract = {We present a lossless compression algorithm for indexing a protein database while supporting fast taxonomic classification in the method Centrifuger. The algorithm is a new scheme of the previously proposed run-block compression algorithm to reduce the size of the Ferragina-Manzini (FM) index, and it scales better with alphabet size than the original. On the RefSeq prokaryotic and viral protein sequences, Centrifuger reduces the memory footprint by over a third compared to the method Kaiju that builds on a plain FM-index, while having comparable running time. Furthermore, the compressed FM-index is lossless and can locate matches of arbitrary length, which helps Centrifuger achieve greater accuracy than Kraken2, a k-mer-based taxonomic classification method. We leverage the computational efficiency of Centrifuger to create an index of size 182 GB for classifying the reads against the full nr database that contains about 250 billion amino acid characters. Using this index, Centrifuger reveals different SARS-CoV-2 infection states and viral transcriptome profiles across human cell types from single-cell RNA-seq data.},
}

@article {pmid42818234,
year = {2026},
author = {Oliver, A and Podell, S and Allen, EE},
title = {Diverse genome organization strategies for polysaccharide utilization in the oceans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.21.753266},
pmid = {42818234},
issn = {2692-8205},
abstract = {Carbohydrate-active enzymes (CAZymes) drive the turnover of polysaccharides in the oceans. However, the scale of diversity in polysaccharide utilization and genome organization strategies has yet to be characterized, particularly in marine ecosystems. In this paper, we introduce mpcgcdb.com as an interactive web catalog for marine CAZyme gene clusters, their associated metagenome-assembled genomes, and relevant enzyme families found in marine metagenomic samples. This database contains nearly 290,000 marine CAZyme gene clusters from more than 22,000 genomes, enabling user-initiated exploratory visualizations for genome organization networks and enzyme phylogeny. This tool will assist researchers in developing hypotheses about gene function, connecting species to metabolic niches, and identifying gaps where future work is needed to understand different pathways in marine glycan cycling.},
}

@article {pmid42818264,
year = {2026},
author = {Ge, Y and Li, E and Mustafa, H and Varabyou, A and Salzberg, SL},
title = {Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.22.753623},
pmid = {42818264},
issn = {2692-8205},
abstract = {Accurate taxonomic classification in metagenomics is often compromised by low-complexity sequences, which lead to chance matches that in turn cause sequences to be misclassified. Here we present Kmask, an entropy-based masking tool implemented for use either standalone or as part of Kraken [1,2] database construction, which replaces low-entropy regions with Ns. Using a sliding window size aligned with Kraken's default k-mer length and parameters optimized across 12 control bacterial genomes spanning a broad range of GC content, Kmask efficiently removes low-complexity sequences while retaining high-complexity regions. To benchmark performance, we applied Kmask to a newly constructed database, Microbial2025, that contains over 71,000 bacterial, archaeal, viral, and fungal genomes, and we then classified human reads against both masked and unmasked versions of the database using KrakenUniq [2]. We found that Kmask substantially reduced misclassifications, driving down the false positive rate to 5.78% from 7.52%. Notably, Kmask performed comparably to an SDUST-masked [3] database, achieving a similar false positive rate (5.78% vs. 5.17%) while masking out fewer bases (1.33% vs. 1.85%). We also tested Kmask on a database of human cancer sequences, where we found that it eliminated many false positives caused by low-complexity matches between bacterial genomes and human DNA. These results demonstrate that Kmask is an effective method for masking low-complexity sequences in large microbial databases, thus improving the accuracy of metagenomic classification.},
}

@article {pmid42818341,
year = {2026},
author = {Li, T and Yang, Y and Cho, SH and Howell, BR and Wu, Z and Yin, W and Elison, JT and Huynh, KM and Ahmad, S and Yap, PT and Li, G and Wang, L and Zhu, H and Lin, W and , },
title = {Microbes on the Mind: Multi-modal Neuroimaging Reveals Gut-Brain Axes in Infants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.23.753825},
pmid = {42818341},
issn = {2692-8205},
abstract = {The gut microbiome undergoes rapid maturation after birth and has been associated with cognition and mental health, yet its relation to early brain development remains poorly defined. We analyzed 223 typically developing children aged 0-3 years with multimodal MRI and paired fecal shotgun metagenomics. Microbiome-wide association analyses identified associations with cortical morphology, white-matter microstructure, and functional connectivity. Ridge-regularized canonical correlation analysis identified two principal covariance patterns: a structural-metabolic mode and a functional-taxonomic mode. Sparse canonical partial least squares recovered the principal CCA score and phenotype patterns within the same sample. Longitudinal canonical-score slopes were not significantly correlated; in autoregressive cross-lag models, however, neuroimaging CCA1 scores predicted microbiome CCA1 scores 1-6 months later. These results indicate cross-domain covariance and temporal ordering within the measured windows but do not establish causality.},
}

@article {pmid42818393,
year = {2026},
author = {Falahati Khanaman, S and Shrestha Gurung, BD and Aryal, S and Geza Nisrania, M and Gadhamshetty, V and Gnimpieba, E},
title = {Predictors Recover Most of the Metagenomic Signal for Antibiotic Resistance Gene Occurrence: A Cross-City Test of Geographic Transferability in Urban Wastewater.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.24.753270},
pmid = {42818393},
issn = {2692-8205},
abstract = {Antibiotic resistance genes (ARGs) travel from cities into rivers and coastal waters through wastewater treatment plants. Monitoring them normally requires metagenomic sequencing, which is sufficiently costly that most utilities can sample only occasionally. Weather and location data are freely available on a daily basis for virtually any location worldwide, making them attractive predictors for identifying where limited sequencing resources should be prioritized. However, whether such models generalize to previously unseen cities remains largely untested, as most published studies train and evaluate models within the same catchments, thereby assessing interpolation rather than geographic transferability. To address this gap, we paired 235 wastewater metagenomes collected from five European cities with 23 abiotic predictors spanning geospatial, meteorological, hydrological, radiative, and temporal domains. Model performance was evaluated using leave-one-group-out (LOGO) cross-validation, in which all samples from one city were withheld for testing while the remaining cities were used for training. CatBoost achieved a median LOGO ROC-AUC of 0.929 and a median F1-score of 0.750. Using freely available environmental reanalysis predictors (meteorological, hydrological, radiative, geospatial, and temporal) - without any metagenomic sequencing - CatBoost achieved a mean ROC-AUC of 0.722, recovering 78% of the predictive performance of the full omics-integrated model. Removing latitude and longitude reduced ROC-AUC by only 0.003, whereas replacing random cross-validation with city-wise validation reduced ROC-AUC by 0.052. Predictive performance varied across ARG classes, ranging from a ROC-AUC of 0.981 for β-lactam resistance genes to 0.762 for glycopeptide resistance genes. These findings demonstrate that freely available environmental reanalysis predictors - spanning meteorological, hydrological, radiative, geospatial, and temporal domains - recover 78% of the predictive signal for antibiotic resistance gene occurrence in urban wastewater, allowing scarce sequencing capacity to be directed to the catchments where it changes a decision.},
}

@article {pmid42818437,
year = {2026},
author = {Wang, L and Zhang, Y and Nguyen, SM and Peters, BA and Qi, Q and Burk, RD and Kaplan, R and Thyagarajan, B and Daviglus, M and Shu, XO and Ma, S and Dai, Q and Shrubsole, MJ and Zheng, W and Yu, D},
title = {Discovery and Validation of Gut Microbiome Features Associated with Dietary Patterns in U.S. Black/African and Hispanic/Latino Populations.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.04.26362286},
pmid = {42818437},
abstract = {BACKGROUND: Large-scale studies examining dietary patterns and gut microbiome have focused predominantly on European ancestry populations; evidence from other ancestry groups remains limited.

OBJECTIVES: We conducted a two-stage study to evaluate associations of multiple dietary patterns with gut microbiome diversity and composition among Black/African American adults and validate significant findings in a Hispanic/Latino population in the US.

METHODS: Included were 514 Black participants from the Southern Community Cohort Study (SCCS) and 2,133 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Diet was collected by food frequency questionnaires or 24-h dietary recalls at cohort enrollment. Gut microbiome profiling was performed by shotgun metagenomic sequencing of stool samples collected during cohort follow-up. Five dietary patterns - Healthy Eating Index (HEI), Dietary Approaches to Stop Hypertension (DASH), Empirical Dietary Inflammatory Potential (EDIP), Empirical Dietary Index for Hyperinsulinemia (EDIH), and Ultra-Processed Foods (UPF) - were examined for associations with microbiome diversity and composition by linear regression after data transformation and confounders adjustment. Microbial taxa with FDR<0.1 and their constituent lower-level features identified in SCCS were targeted for validation in HCHS/SOL.

RESULTS: In SCCS, HEI, DASH, EDIP, or EDIH were associated with the relative abundances of 14 microbial taxa, primarily members of families Coriobacteriaceae and unclassified Firmicutes, as well as species Lactococcus lactis and Clostridium sp. AF20-17LB . Among these, the inverse associations of genus Collinsella and its species C. aerofaciens with HEI or DASH were validated in HCHS/SOL (all P <0.05). Additionally, Collinsella and C. aerofaciens were associated with higher odds of obesity in SCCS (BMI≥ 30 kg/m2; OR [95%CI]:1.24 [1.01, 1.53] and 1.32 [1.07, 1.63], respectively).

CONCLUSIONS: Healthier dietary patterns were consistently associated with lower abundances of Collinsella and C. aerofaciens in Black/African and Hispanic/Latino Americans. Further research should clarify causal pathway linking diet, gut microbiome, and health outcomes across diverse populations.},
}

@article {pmid42818523,
year = {2026},
author = {Chen, D and Wang, Y and Portik, DM and Nearing, J and Nickols, WA and Wilkinson, JE and Christiani, DC and Nguyen, LH and Franzosa, EA and Spengler, JD and Huttenhower, C and Thompson, KN},
title = {Microbial transmission and ecology of human and environmental microbial communities in childcare centers.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10207669/v1},
pmid = {42818523},
issn = {2693-5015},
abstract = {Background Early-life microbial exposures profoundly impact lifelong health trajectories by shaping immune maturation and modulating disease risk, e.g. as described by the "hygiene hypothesis." Childcare facilities represent a critical yet understudied source of microbial exposures where preschool-aged children spend 7-10 hours daily during key developmental periods. This study presents the first multi-omic and multi-kingdom investigation of microbial transmission and community ecology across childcare environments, integrating microbiome samples from both high-touch and low-touch surfaces with children's nasal and oral microbiomes, using full-length 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing paired with short-read (SR) and long-read (LR) metagenomic sequencing. This combination provides enhanced species-level taxonomic resolution and improved recovery of genomes and genomic elements compared to conventional short-read approaches. Results Our findings revealed distinct microbial signatures across environments, with human-associated microorganisms predominating in high-touch areas, while greater taxonomic diversity characterizes low-touch areas. Specifically, on high-touch surfaces, several bacterial and fungal species were shared between host and environmental communities, such as food-associated Lactococcus lactis and Streptococcus thermophilus , suggesting defined transmission routes via host shedding, environmental exposures, and food consumption. With improved genomic resolution and reconstruction from paired SR and LR metagenomics, we identified novel lateral gene transfer (LGT) events enriched for mobile elements, DNA-interacting domains, and adaptive elements such as antibiotic resistance and virulence factors. These methods also shed light on viral ecology, such as Caudoviricetes bacteriophages ubiquitous across host and environmental communities with phylogenetically-differentiated niche- and bacterial host-specific lineages. The positive relationship between the host prediction frequency and its community relative abundance suggested host abundance (availability)-driven phage-bacteria population dynamics. Conclusions This work highlights previously understudied components of early-life microbial exposures in childcare environments with enhanced resolution and provides methods for identifying potential pathogen reservoirs, tracking transmission routes, and developing targeted interventions.},
}

@article {pmid42818648,
year = {2026},
author = {Xia, H and Wen, Y and Li, X and Hu, L and Yuan, Y and Tian, J and Li, S and Zhan, Y and Dang, X and Lin, Y and Li, L and Chen, Y and Zhang, Y and Guan, Y and Wang, J},
title = {A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1938149},
pmid = {42818648},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; *Databases, Genetic ; *Bacteria/genetics/classification/isolation & purification ; *Genome, Microbial ; Computational Biology/methods ; Cohort Studies ; Biocuration ; },
abstract = {INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) enables broad, untargeted pathogen detection, but its analytical performance depends on host depletion strategy, reference database composition, and alignment methodology. We developed the Clinical Microbial Genomic Database (CMGD), a clinically focused reference resource prioritizing medically relevant taxa.

METHODS: CMGD was manually curated, clinically stratified, and included more than 18,000 microbial species. We evaluated host-depletion references, alignment and classification strategies, six published clinical cohorts, and 30 retrospective mNGS-positive clinical samples.

RESULTS: The combined GRCh38-T2T reference achieved the highest human-read depletion rate while minimizing microbial-read loss. CMGD provided broader target-species coverage than the standard Kraken2 database, and BWA-CMGD showed lower erroneous assignment rates overall, although Kraken2 yielded higher unique species-level assignment rates for many shared taxa. Across six published clinical cohorts, CMGD achieved 91.0% detection concordance with BLAST-NT and a strong read-count correlation (R[2] = 0.97). In 30 retrospective samples, CMGD and NT showed strong correlations for total mapped reads (R[2] = 0.99) and uniquely mapped reads (R[2] = 0.89), with concordance correlation coefficients of 0.99 and 0.92, respectively. High sequence-mapping accuracy did not ensure reliable species-level discrimination for highly homologous taxa such as Escherichia coli and Shigella flexneri.

DISCUSSION: Clinically stratified database curation improves the analytical performance, computational efficiency, and interpretability of mNGS-based pathogen detection. Species-complex-level reporting may be more appropriate when species-level discriminatory evidence is insufficient. Prospective multicenter validation is required to establish clinical diagnostic utility.},
}

Humans
*Metagenomics/methods
High-Throughput Nucleotide Sequencing
*Databases, Genetic
*Bacteria/genetics/classification/isolation & purification
*Genome, Microbial
Computational Biology/methods
Cohort Studies
Biocuration

@article {pmid42818693,
year = {2026},
author = {Landsittel, JA and Howe, A and Kuehn, S and Lee, KK and Mani, M},
title = {The ecological context of enzymatic variation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.09.750510},
pmid = {42818693},
issn = {2692-8205},
abstract = {Among the challenges in understanding microbial ecosystems is the presence of physics at vastly different scales. Reactions, catalyzed by enzymes but regulated at the level of the cell, propel the flux of carbon and nitrogen through our atmosphere. Compounding this is the presence of pervasive enzyme sequence variation; this variation has been shown to contain coevolving modes of amino acids which encode the enzyme's evolutionary history. In this work, we take steps towards bridging the gap between the enzymatic variation present in an ecosystem and its subsequent activity. We employ the reduction of nitrate by NarG as a model system, which acts as an essential step in the nitrogen cycle by mediating both the return of di-nitrogen to the atmosphere and the assimilation of nitrate into biomass. Considering both metagenomic reconstructions as well as functional data from soil nitrate reducers, we find that sequence variants of enzymes obey predictable responses to environmental fluctuations. That is, while prior community-level metagenomic studies have characterized the response of bacterial strains to the environment, our study provides an enzyme variant level sequence-to-response map. Further, we demonstrate that a simple statistical model can predict the organismal phenotype from variant sequence; in soil samples not originally seen by that model, the prediction of a variant's reduction rate correlates with how much cells with that variant grow in abundance.},
}

@article {pmid42818746,
year = {2026},
author = {Qihong, L and Juan, W and Xue, T and Zhiheng, D and Dongyan, C and Lili, Y and Feiqiu, W and Sixi, L and Shilin, L},
title = {Scrub typhus triggers hemophagocytic lymphohistiocytosis in children: metagenomic next-generation sequencing enables rapid diagnosis.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1888645},
pmid = {42818746},
issn = {2296-2565},
mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology ; Male ; *Scrub Typhus/complications/diagnosis ; Female ; Child, Preschool ; Child ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; Adolescent ; Metagenomics ; },
abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome. Rapid identification of the underlying trigger is critical for effective clinical management. This study describes the clinical features and diagnostic approach for scrub typhus-associated HLH in children, emphasizing the role of metagenomic next-generation sequencing (mNGS).

METHODS: We retrospectively analyzed 12 pediatric patients diagnosed with scrub typhus-associated HLH at Shenzhen Children's Hospital between July 2023 and July 2025. Demographic, clinical, laboratory, and treatment data were analyzed. The diagnostic timeline was systematically evaluated, including patient's delay, doctor's delay, and mNGS turnaround time.

RESULTS: The median age was 7.5 years (range: 3-13.7), with a male-to-female ratio of 1:2. All patients presented with prolonged fever (median duration: 9 days). Common clinical findings included eschar (66.7%), lymphadenopathy (100%), hepatomegaly (58.3%), and splenomegaly (66.7%). Notably, four patients (33.3%) were initially misdiagnosed as having Kawasaki disease. All patients met the HLH-2004 criteria, with prominent hyperferritinemia (median: 5,355 ng/mL) and elevated sCD25 (median: 5,065 U/mL). Peripheral blood mNGS confirmed the diagnosis of scrub typhus in all patients (median sequence reads: 333). Cerebrospinal fluid (CSF) mNGS was positive for Orientia tsutsugamushi in four out of five patients tested, and cytokine profiling revealed elevated levels of IL-6, IL-10, and IFN-γ. Basic CSF parameters, including white blood cell count, protein, and glucose, are reported for all patients who underwent lumbar puncture. Severe complications included pulmonary hemorrhage (n = 3) and shock (n = 3). All patients survived following targeted antibiotic and immunomodulatory therapy.

CONCLUSION: Scrub typhus is a significant trigger for secondary HLH in children from endemic areas. mNGS may facilitate rapid etiological diagnosis and timely targeted therapy. CSF mNGS and cytokine analysis may be considered in severe cases, though further validation is warranted. We also acknowledge that our study demonstrates feasibility rather than superiority of mNGS over conventional diagnostic methods.},
}

Humans
*Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology
Male
*Scrub Typhus/complications/diagnosis
Female
Child, Preschool
Child
Retrospective Studies
High-Throughput Nucleotide Sequencing
Adolescent
Metagenomics

@article {pmid42818833,
year = {2026},
author = {Perez, RK and Prakash, H and Jaynes, D and Huang, P and Deegan, J and Hopkins, L and Ross, M and Minor, M and Payne, K and Ayvaz, T and Clark, JR and Boerwinkle, E and Tisza, MJ and Maresso, AW},
title = {Wastewater Metagenomic Virome Analysis of the 2026 World Cup in Texas.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.04.26362178},
pmid = {42818833},
abstract = {Mass gatherings are thought to create conditions for pathogen introduction and spread, yet whether such events measurably alter the viral community of a city has rarely been tested against an extensive historical baseline. We analyzed 5,137 hybrid-capture metagenomic wastewater samples collected from 55 sites across 17 Texas cities between June 2022 and July 2026, spanning the 2026 FIFA World Cup. We asked (1) whether host-city viral community composition during the tournament departed from its established summer-to-summer range, (2) whether targeted respiratory viruses rose above their characteristic summer trend, and (3) whether the load of rare and novel taxa was elevated in host cities relative to non-host cities. Despite the plausibility of these hypotheses, we detected no tournament-associated perturbations. Although based on a single event, these findings favor continuous wastewater surveillance over event-triggered deployment, both for detecting introductions that arrive unpredictably and for supplying the baseline against which any event should be judged.},
}

@article {pmid42818860,
year = {2026},
author = {Zhang, R and Chen, Y and Hou, D},
title = {Functional organization outweighs spatial separation in structuring microbial communities across a petroleum-hydrocarbon groundwater plume.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938677},
pmid = {42818860},
issn = {1664-302X},
abstract = {OBJECTIVE: Petroleum-hydrocarbon plumes in groundwater are shaped by hydrological transport, redox conditions, and indigenous microbial activity. However, it remains unclear whether spatial differences among groundwater microbiomes primarily reflect physical separation among wells or ecological reorganization associated with distinct attenuation states within a plume.

METHODS: We integrated hydrogeological context, petroleum-hydrocarbon concentrations, hydrochemical variables, and shotgun-metagenomic profiles from 15 groundwater monitoring wells at a petroleum-hydrocarbon-impacted site. Community beta diversity, spatial and functional distance relationships, permutation-based group tests, and exploratory composite indices of natural attenuation potential and taxonomic-functional diversity were evaluated.

RESULTS: Genus-level community dissimilarity increased with estimated spatial distance (Mantel r = 0.240, p = 0.034), but was more strongly associated with functional-module dissimilarity (r = 0.670, p = 0.001). Biodegradation potential remained associated with community dissimilarity after controlling for spatial distance (partial Mantel r = 0.428, p = 0.001). Operational attenuation states explained 35.4% of genus-level compositional variation (PERMANOVA p = 0.008). High natural attenuation potential and high taxonomic-functional diversity occurred in partly distinct wells.

CONCLUSION: The results indicate that groundwater microbiome turnover within the plume is spatially structured but is more closely coupled to functional reorganization than to distance alone. Joint consideration of hydrological setting, microbial degradation potential, and functional diversity may improve groundwater natural-attenuation assessment.},
}

@article {pmid42819055,
year = {2026},
author = {Jingjing, T and Nannan, Y and Jingjie, Z and Ping, C and Yankun, Z},
title = {Presumed Candida tropicalis endogenous endophthalmitis with multifocal systemic Candida albicans abscesses: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1951092},
pmid = {42819055},
issn = {2296-858X},
abstract = {BACKGROUND: Endophthalmitis is a kind of infectious diseases that seriously threatens vision; Endogenous fungal endophthalmitis (EFE) accounts for 2% to 8% of all endophthalmitis, and is rare and often misdiagnosed in clinical practice. Different strains of Candida may have organ orientation differences, and mixed infections have also been reported in literature.

CASE REPORT: A 72 year old male patient was admitted to the hospital due to fever for 5 months and decreased vision in both eyes. The patient's left vitreous fluid underwent metagenomic next-generation sequencing (mNGS), which revealed the presence of Candida tropicalis (1 sequence detected); The fungal culture of vitreous humor and the blood culture sent for testing at the same time was negative. Candida albicans was detected in the culture of surgical specimens for renal and lumbar lesions. The core clinical feature of this case is the inconsistency of pathogen detection between the whole body and the eyes. Due to mNGS only detected one Candida tropicalis sequence and the vitreous fungal culture was negative, this case should be considered as a suspected Candida tropicalis endophthalmitis clinically diagnosed. It may be a mixed invasive infection of Candida albicans and Candida tropicalis, and there may be differences in organ orientation between the two strains (Candida albicans prefers kidney and bone tissues, while Candida tropicalis is invasive to intraocular tissues), forming a zoning colonization pattern. However, this explanation still lacks conclusive microbiological evidence. The patient received local and systemic antifungal treatment in both eyes, and underwent bilateral vitrectomy. The systemic infection was controlled, and the left eye vision improved from near blindness to 0.25 (8 months) with some recovery in visual function.

CONCLUSION: EFE is prone to misdiagnosis, and high-risk individuals should undergo pathogen testing as soon as possible. mNGS is a rapid identification tool, but caution should be exercised when single sequence detection and negative culture occur. When the pathogens are inconsistent, alternative explanations such as contamination and sequential infection should be excluded. The combination of comprehensive antifungal therapy and surgical treatment is effective,Clinical physicians need to establish a global mindset and pay attention to the intrinsic relationship between systemic lesions and eye damage.},
}

@article {pmid42819200,
year = {2026},
author = {Wu, L and Bao, Y and Pu, J and Zhang, L and Huang, J and Xi, X and Luo, L},
title = {Post-vertebroplasty lumbar spondylodiscitis due to Cutibacterium modestum.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1905143},
pmid = {42819200},
issn = {2296-858X},
abstract = {Percutaneous vertebroplasty-associated spinal infection is uncommon but may cause progressive vertebral destruction and can mimic tuberculous spondylitis on imaging. The detection of low-virulence skin commensals such as Cutibacterium species in deep specimens also creates a diagnostic challenge because contamination and true infection must be distinguished. We report a 78-year-old man who developed recurrent progressive low back pain shortly after percutaneous vertebroplasty for an L2 compression fracture. Baseline computed tomography (CT) and contrast-enhanced magnetic resonance imaging (MRI) showed destructive spondylodiscitis centered at L2/3, with adjacent vertebral body and disc-space involvement, paravertebral inflammatory extension, and bilateral psoas abscess-like collections, initially suggesting tuberculous spondylitis. However, molecular testing for the Mycobacterium tuberculosis complex and targeted sequencing for mycobacterial drug-resistance genes were negative, and histopathology demonstrated acute and chronic inflammatory necrotic changes without typical tuberculous granulomas. Metagenomic next-generation sequencing of aspirated fluid identified a high abundance of Cutibacterium modestum, which was subsequently detected again in lesion tissue and peripheral blood by targeted high-throughput sequencing. Given the repeated detection in deep-site specimens, exclusion of tuberculosis and other competing diagnoses, compatible clinical and imaging findings, and improvement after targeted antimicrobial therapy and percutaneous stabilization, C. modestum was considered the most probable causative pathogen. These findings suggest that pathogen attribution in post-vertebroplasty spinal infection should rely on integrated clinical, microbiological, pathological, and therapeutic evidence rather than on imaging findings alone. Integrated clinico-microbiological assessment may improve pathogen attribution for rare low-virulence organisms in postoperative spinal infection.},
}

@article {pmid42819311,
year = {2026},
author = {Shen, R and Liu, S and Yu, P and Xie, S and Xie, Q and Wang, Q and Pan, Y and Zhang, Z and Wang, Z and Zhao, W},
title = {Integrative hologenomic analysis reveals apolipoprotein D-associated host-microbe metabolic crosstalk linked to fat deposition in Jinhua pigs.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1915318},
pmid = {42819311},
issn = {1664-302X},
abstract = {BACKGROUND: Adipose deposition is a complex trait shaped by both host genetics and environmental factors, including the gut microbiota. While quantitative trait loci (QTLs) and candidate genes underlying fat accumulation have been extensively identified in diverse pig breeds, the hologenomic regulatory networks integrating host genetic variation and microbial signals remain to be fully deciphered.

METHODS: In this study, we utilized a strictly controlled dietary cross-fostering model involving Jinhua and Landrace×Yorkshire pigs across developmental stages (day60, day90 and day180). We integrated population genetics, eQTL analysis, transcriptomics, metagenomics and metabolomics to elucidate the host-metabolite-microbe axis.

RESULTS: Phenotypic analysis revealed a robust genetic trait for high backfat thickness in Jinhua pigs, independent of dietary intervention. Through F ST analysis and eQTL mapping, we pinpointed a strongly differentiated locus (13_133481393_A_G) that was nearly fixed in JH pigs (allele frequency 0.95) and was associated with upregulation of APOD. In our multi-omics dataset, this locus was linked to shifts in cecal gene expression that were consistent with a pro-adipogenic program, which coincided with an intestinal metabolic profile marked by elevated oleic acid and reduced oleoylethanolamide. This metabolic niche, in turn, directionally recruited synergistic microbes, specifically Eubacterium sp. AM28-29 and Blautia, which functioned as biochemical amplifiers to further accelerate lipid accumulation.

CONCLUSION: Our study establishes a hologenomic framework demonstrating how foundational genetic selection (APOD) shapes the host-microbe metabolic interplay to drive complex production traits. This study offers novel molecular targets and a theoretical framework for precision breeding and nutritional modulation of meat quality in livestock.},
}

@article {pmid42819442,
year = {2026},
author = {Li, Y and Yu, Z and Shen, M and Cui, S and Yang, X},
title = {Adult Epstein-Barr virus encephalitis: a retrospective case report series with metagenomic next-generation sequencing-based diagnosis.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1861146},
pmid = {42819442},
issn = {1664-2295},
mesh = {Humans ; Female ; *Encephalitis, Viral/diagnosis/cerebrospinal fluid/drug therapy ; Middle Aged ; Retrospective Studies ; Male ; High-Throughput Nucleotide Sequencing ; *Epstein-Barr Virus Infections/diagnosis/cerebrospinal fluid/drug therapy/complications ; Aged ; Metagenomics ; Adult ; Magnetic Resonance Imaging ; Herpesvirus 4, Human/genetics ; Antiviral Agents/therapeutic use ; },
abstract = {BACKGROUND: EBV encephalitis is uncommon in adults, and its diagnosis and management remain challenging, particularly in patients with underlying medical conditions.

METHODS: We retrospectively analyzed seven adult patients with EBV encephalitis confirmed through cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) between December 2021 and January 2024.

RESULTS: Six patients (86%) were female, with a median age of 59 years. Five patients had significant underlying conditions, including malignancies (n = 2), systemic lupus erythematosus (n = 1), and EBV-associated hemophagocytic lymphohistiocytosis (HLH, n = 2). Common clinical presentations included fever (86%), impaired consciousness (86%), neck stiffness (57%), headache (43%), and decreased muscle strength (43%). CSF analysis revealed elevated protein levels (57%) and leukocytosis (71%). Magnetic resonance imaging (MRI) identified encephalitis-associated lesions in three of six patients (50%), whereas computed tomography (CT) was largely unremarkable. All patients received antiviral therapy, and five additionally received corticosteroids. Three patients recovered, whereas four died, with all deaths occurring in patients with concurrent malignancies or HLH.

CONCLUSION: MRI is the preferred imaging modality for suspected encephalitis, and CSF-mNGS is an essential pathogen detection assay. Underlying conditions such as malignancies and HLH are associated with poor clinical outcomes.},
}

Humans
Female
*Encephalitis, Viral/diagnosis/cerebrospinal fluid/drug therapy
Middle Aged
Retrospective Studies
Male
High-Throughput Nucleotide Sequencing
*Epstein-Barr Virus Infections/diagnosis/cerebrospinal fluid/drug therapy/complications
Aged
Metagenomics
Adult
Magnetic Resonance Imaging
Herpesvirus 4, Human/genetics
Antiviral Agents/therapeutic use

@article {pmid42819443,
year = {2026},
author = {Lutsiv, T and Thompson, HJ and Fiehn, O and Gareau, MG and Borowsky, AD and Chen, BH and Hussan, H},
title = {A Distinct Host-Microbiome Signature Underlies the Accelerated Malignant Potential of Colorectal Laterally Spreading Tumors.},
journal = {Gastro hep advances},
volume = {5},
number = {12},
pages = {101102},
pmid = {42819443},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Laterally spreading tumors (LST) are flat colorectal neoplasms with an accelerated risk of malignant transformation and interval colorectal cancer. Despite their clinical importance, the molecular and microbial mechanisms underlying LST's aggressive biology remain poorly understood. Thus, we aimed to characterize the transcriptomic and microbial landscape of LST in comparison with paired protruding lesions and the adjacent normal colonic tissue.

METHODS: Formalin-fixed, paraffin-embedded tissues from 36 samples were obtained from 15 adults and analyzed using RNA sequencing and 16S rRNA gene amplicon sequencing. Patterns of the differential gene expression were assessed using Gene Set Enrichment Analysis and Ingenuity Pathway Analysis. Microbial community composition and its predicted functional capacity were evaluated with analysis of compositions of microbiomes with bias correction in QIIME 2 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, respectively.

RESULTS: Compared with paired protruding lesions and normal tissue, LST exhibited a distinct protumorigenic transcriptomic profile marked by the activation of MYC, E2F, mTOR, DNA damage, and senescence-associated secretory phenotype pathways, as well as robust proinflammatory signaling driven by TNF, NF-κB, IL-1, and IL-17. LST tissue also demonstrated a permissive environment for genomic instability. Microbiome analysis revealed enrichment of Fusobacterium and depletion of beneficial taxa, including Lactococcus, accompanied by predicted suppression of carbohydrate fermentation and short-chain fatty acid production, as well as altered sulfur metabolism. Fusobacterium abundance correlated with increased TNF expression, supporting a microbiota-driven inflammatory niche in LST.

CONCLUSION: LST are characterized by a unique inflammatory/metabolic/senescence axis that distinguishes them from other paired colorectal tissue samples. This procarcinogenic signature is driven by a Fusobacterium-enriched and carbohydrate-fermentation-depleted microbial ecosystem. These findings highlight the gut microbial ecosystem as a critical cofactor in LST pathogenesis and further support that combined host/microbiota-targeted strategies may improve colorectal cancer prevention in this population. Given the exploratory nature and limited cohort size, these findings require validation in larger prospective cohorts with metagenomic and metabolomic integration.},
}

@article {pmid42819542,
year = {2026},
author = {Feng, B and Chen, Y and Chen, Y and Feng, J and Yu, Z and Guo, F and Ruan, J},
title = {Case Report: Coinfection of influenza A and Chlamydia psittaci pneumonia.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1895006},
pmid = {42819542},
issn = {2296-858X},
abstract = {The coinfection of influenza A and Chlamydia psittaci pneumoniae is rarely described in China. However, the clinical features of these diseases pose a significant diagnostic challenge. Therefore, it is necessary to report and review such a potentially fatal case. We report an 89-year-old male patient requiring admission to the intensive care unit with acute hypoxemic respiratory failure, shock and MODS. He presented with fever, fatigue, anorexia and dyspnea. The patient exhibited severe hypoxemia, shock, hepatic dysfunction (elevated liver enzymes and serum bilirubin), acute kidney injury and a SOFA score of 17. Mechanical ventilation (MV) and venous-venous extracorporeal membrane oxygenation (VV-ECMO) were established for respiratory support. The initial diagnosis focused on influenza A for his positive influenza A nucleic acid. However, the patient's imaging presentation was not coupled with viral pneumonia, which raised suspicion for other pathogens. Metagenomic next-generation sequencing (mNGS) detected coinfection of C psittaci, influenza A H3N2 virus, and Klebsiella pneumoniae in bronchoalveolar lavage fluid. Concurrent targeted NGS (tNGS) detected C. psittaci in blood. Omadacycline and baloxavir marboxil were prescribed. The patient's condition improved, and he was successfully weaned from VV-ECMO and MV. He was discharged and recovered on day 60 of the follow-up. This case underscores the diagnostic complexity of coinfection and the use of NGS testing in this severe condition and the role of omadacycline in psittacosis.},
}

@article {pmid42819899,
year = {2026},
author = {, },
title = {Correction: Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1981765},
doi = {10.3389/fmicb.2026.1981765},
pmid = {42819899},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1924993.].},
}

@article {pmid42820078,
year = {2026},
author = {Cao, Z and Luo, J and Zhuang, H and Li, X and Ban, Y and Ouyang, Y and Hu, J and You, P and Liu, X and Liang, Q and Zhang, Z},
title = {Severe Vibrio vulnificus Sepsis without Typical Wound Exposure in a Patient with Chronic Liver Disease and Diabetes: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {644649},
pmid = {42820078},
issn = {1178-6973},
abstract = {BACKGROUND: Vibrio vulnificus, a Gram-negative bacillus, is frequently present in warm estuarine and coastal waters and is a notable pathogen responsible for seafood-related fatalities globally. Infection typically arises from ingesting contaminated seafood or exposure of skin wounds to tainted seawater, resulting in primary or secondary sepsis, as well as severe skin and soft tissue infections.

CASE PRESENTATION: Upon hospital admission, a 51-year-old man with chronic gastritis, long-term alcohol use, type 2 diabetes, thrombocytopenia, and active hepatitis B and C presented with acute right upper quadrant abdominal pain, high fever, and a history of consuming raw fish (sashimi) before symptom onset, suggesting a foodborne infection. Despite denial of recent seawater exposure or seafood handling, his condition rapidly deteriorated, resulting in septic shock, moderate acute respiratory distress syndrome, and necrotizing fasciitis of the left lower extremity within 72 hours. Laboratory findings revealed severe thrombocytopenia, hyperlactatemia, multiple organ dysfunction, and metabolic acidosis. Vibrio vulnificus was identified via peripheral blood metagenomic next-generation sequencing. Whole-exome sequencing incidentally detected a heterozygous missense variant in the DOCK2 gene (c.4511C>T, p. Thr1504Met), classified as a variant of uncertain significance. In silico analyses suggested a benign effect, leaving any potential link to disease severity undetermined without functional confirmation.

CONCLUSION: Severe V. vulnificus sepsis may develop through foodborne transmission, even in the absence of typical exposure to seawater or seafood handling. Disease severity in this patient was primarily influenced by chronic liver disease, alcohol abuse, and diabetes. Clinicians should watch for V. vulnificus infection in patients with these risk factors who present with septic shock or rapidly progressive soft tissue infections, regardless of exposure history.},
}

@article {pmid42820214,
year = {2026},
author = {Sola, M and Paravel, A and Auger, S and Chatel, JM and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Veiga, P and Frioux, C and Mariadassou, M and Berland, M},
title = {NeighborFinder: an R package inferring local microbial network around a species of interest.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag201},
pmid = {42820214},
issn = {2635-0041},
abstract = {MOTIVATION: Understanding interactions from microbiome data is a central aspect in microbial ecology, as it provides insights into ecosystem stability, disease mechanisms, and can be used to design synthetic communities. Current network inference tools reconstruct global networks from co-abundance data, which means they capture the overall correlation structure for the entire set of taxa considered. These approaches are computationally intensive and suboptimal when the focus is on the local neighborhood of one or a few taxa of interest.

RESULTS: We introduce NeighborFinder, a local network inference method that enables the targeted discovery of direct neighbors around a species of interest. Using cross-validated multiple linear regression with ℓ 1 penalty and microbiome-specific filters, our approach infers interpretable species-centered interactions, with F1 score ≥ 0.95 on simulated cohorts ranging from 250 to 1000 samples. This method is well-suited for large metagenomic datasets and is particularly valuable for exploratory studies where the targeted hypotheses outweigh the need for global community structure. The approach complements existing methods by being biologically intuitive and computationally efficient.

The R package is available on CRAN https://CRAN.R-project.org/package=NeighborFinder. The data and source code used to calculate performances and produce the use case example can be found respectively at: https://doi.org/10.57745/UPITJ0 and https://doi.org/10.57745/HJLWW4.

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

@article {pmid42820688,
year = {2026},
author = {Yang, X and Wu, J and Wang, T and Li, Z and Xi, Y and Zhao, L and Luo, M and Xie, X and Zhao, G and Zhou, H and Zhang, L},
title = {GCF-anchored and target-oriented mining of metagenomic BGC space for bioactive product discovery.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0109826},
doi = {10.1128/spectrum.01098-26},
pmid = {42820688},
issn = {2165-0497},
abstract = {Microbial natural products are vital for drug discovery, yet pervasive genomic fragmentation and data volume hinder the translation of metagenomic biosynthetic gene clusters (BGCs) into therapeutic leads. We present metasynBGC, a target-oriented framework that employs a "function-first" logic using experimentally validated gene cluster families (GCFs) as evolutionary templates and functional beacons. This dual-path strategy enables (i) template-guided reconstruction of fragmented BGCs via conserved biosynthetic synteny, and (ii) high-resolution prioritization of complete BGCs based on therapeutic potential. Applying metasynBGC to large-scale public metagenome-assembled genome (MAG) data sets, we uncovered hidden biosynthetic potential, including BGC0001089_plus, a novel bacillaene-like variant containing an additional functional pksF gene. Simultaneously, bioactivity-prioritized mining of nonribosomal peptide synthetase (NRPS) BGCs, coupled with deep learning and chemical synthesis, yielded six novel compounds. These molecules exhibited diverse in vitro cytotoxic profiles across seven cancer cell lines, with [Formula: see text] values as low as 38.04 µM. Compounds D and E showed potent activity and pronounced cell-line selectivity. By transforming microbial "dark matter" into an actionable reservoir of therapeutic leads, metasynBGC provides a practical target-oriented strategy for linking metagenomic BGC mining with downstream experimental validation. The scripts used in this study are publicly available at https://github.com/Shirly-Yang/metasynBGC.IMPORTANCEThe vast chemical diversity hidden within metagenomic data remains largely inaccessible because biosynthetic gene clusters (BGCs) are often highly fragmented. Our study introduces metasynBGC, a target-oriented framework designed to bridge these gaps by using well-characterized BGCs within gene cluster families (GCFs) as templates to reconstruct incomplete biosynthetic pathways. Unlike traditional methods, metasynBGC integrates a dual-path discovery engine: it performs priority-driven mining to precisely locate naturally intact clusters while reconstructing fragmented ones using representative BGC members as guides. We demonstrate its efficacy by identifying and synthesizing novel compounds with notable cytotoxic activity, providing a validated "sequence-to-molecule" pipeline. This work offers a scalable framework for the systematic discovery of therapeutic candidates from uncultivated microbes and expands our capacity to interpret genomic "dark matter." By enabling the functional validation of complex molecules from fragmented data, metasynBGC facilitates the translation of metagenomic data sets into promising leads for therapeutic development.},
}

@article {pmid42820708,
year = {2026},
author = {Islam, MR and Sarkar, R and Dey, SS and Ahmed, I and Patwary, MRH and Hasan, Z and Mishu, MA and Ahmed, MM and Chowdhury, A},
title = {Metagenomic profiling and temporal dynamics of antimicrobial resistance genes across hospital wastewaters in Dhaka, Bangladesh.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0075526},
doi = {10.1128/spectrum.00755-26},
pmid = {42820708},
issn = {2165-0497},
abstract = {UNLABELLED: Hospital wastewater (HWW) in Bangladesh is often discharged into municipal sewage and water bodies without adequate treatment. It raises concern that hospitals may act as reservoirs and amplification points for clinically important antimicrobial resistance genes (ARGs). However, culture-independent data on the composition, mobility, and seasonal behavior of these genes in Bangladeshi hospital wastewater remain limited. Here, we combined single monsoon time-point baseline shotgun metagenomic sequencing with longitudinal qPCR to characterize wastewater from three tertiary hospitals in Dhaka and a nearby community wastewater line across three seasonal sampling points. Across sites based on baseline metagenomic profiling, the putative resistome was dominated by aminoglycoside, sulfonamide, macrolide-lincosamide-streptogramin (MLS), tetracycline, and β-lactam resistance, primarily associated with Actinomycetota and Pseudomonadota. Hospital effluents contain putative clinically important genes, including the vanA cluster, blaVIM, blaOXA-232, blaIMP, and blaKPC. Metagenomic analysis linked many putative ARGs to plasmid-predicted contigs, transposition, or integration modules, while virulence profiling showed enrichment of putative genes related to adhesion, motility, iron acquisition, and secretion, particularly in MHWW-2. Exploratory network co-occurrence from baseline metagenomics primarily suggested fecal-derived gut commensals, alongside pathogens, as reservoirs and putative vectors for ARG input into the wastewater system. Longitudinal qPCR showed higher absolute loads of selected ARGs at the pre-winter sampling point, and the class 1 integron gene (intI1LC) tracked total ARG burden across seasonal transitions. These findings identify hospital wastewater in Dhaka primarily as a dynamic reservoir of clinically important and potentially mobile resistance determinants, and support its use as a target for wastewater-based AMR surveillance.

IMPORTANCE: Wastewater surveillance can provide early warning of AMR, but in Bangladesh, it is rarely applied beyond culture or single-gene PCR, limiting detection of emerging, mobile, and facility-specific threats. This study integrates metagenomics with longitudinal qPCR to connect which resistance genes are present with who carries them and how they change seasonally across multiple hospitals. We show that hospital effluents contain a shared background resistome yet disproportionately concentrate last-line resistance in taxa that include clinically important lineages, with signals rising toward pre-winter. By placing high-risk putative ARGs in putative plasmid, integron, and transposase contexts and alongside virulence repertoires from baseline metagenomic profiling, our results identify plausible genomic mechanisms that may contribute to spread beyond hospitals. These findings position hospital effluents in Dhaka preliminarily as dynamic reservoirs of clinically important, mobile AMR and support wastewater-based epidemiology for sustained surveillance and risk mitigation.},
}

@article {pmid42820737,
year = {2026},
author = {Liu, T and Smeds, J and Nilsson, M and Öquist, M and Bertilsson, S},
title = {Depth-stratified boreal peatland microbiomes reveal recurring community organization and methane-cycling potential.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag111},
pmid = {42820737},
issn = {1574-6941},
abstract = {Microbial communities in peatlands vary with depth, but most studies have been limited in spatial extent or replication, constraining assessment of general community patterns. We characterized microbial community structure and metabolic potential across replicated depth profiles in seven boreal peatlands in Sweden. Combining 16S rRNA gene sequencing and shotgun metagenomics, we identified recurring vertical stratification across sites. Microbial richness declined with depth, and core taxa including Rice Cluster II, Terriglobales, Subgroup 2, Roseiarcus, Methylocystis, and Candidatus Solibacter were shared across locations. Functional gene profiles revealed depth-related reorganization of carbon-cycling potential, with hydrolytic and fermentative functions relatively more abundant near the surface and acetogenic and methanogenic pathways more prominent in deeper anoxic horizons. Gene-centric analyses indicated an important contribution of Rice Cluster II-related methanogens to hydrogenotrophic methanogenesis, while co-occurrence networks identified a depth-conserved syntrophic module centered on this lineage. Environmental variables showed depth-specific associations with microbial communities. Despite geographic separation and site-specific variation among peatlands, recurring depth-resolved microbial assemblages and functional profiles were observed, suggesting that common environmental constraints associated with peat development contribute to broad patterns of microbial community organization and carbon-cycling potential.},
}

@article {pmid42820741,
year = {2026},
author = {Napier, BA and Merrill, BD and Krieger, M and Gevers, D and Reid, G},
title = {Formulations containing co-biotic compounds mediate microbiome function and composition without increased gas production in an ex vivo gastrointestinal model.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131126},
doi = {10.1128/aem.01311-26},
pmid = {42820741},
issn = {1098-5336},
abstract = {UNLABELLED: Dietary supplement formulations that contain co-biotics or compounds that modulate biological processes in both the host and microbiome to confer a health benefit are an emerging strategy to fine-tune both host physiology and gut microbiome function. Here, we evaluated three novel formulations containing co-biotic compounds (DM-02, a multivitamin; AM-02, formulated for energy and focus; and PM-02, formulated to promote sleep) for their effects on human gut microbiome composition and function. The three formulations and untreated control (Unt-Ctrl) were subjected to upper gastrointestinal digestion, after which the digesta were exposed to 24-h simulated colonic fermentation in the validated ex vivo systemic intestinal fermentation research (SIFR) technology (n = 6 healthy adults). Outcomes included pH, short-chain fatty acid (SCFA) and gas production, ultra-deep metagenomic profiling, and untargeted metabolomics of post-colonic supernatants, each compared to Unt-Ctrl. All three formulations significantly reduced pH (3%-4%) and increased total SCFAs (9%-11%) and acetate (9%-12%), with AM-02 and PM-02 also increasing butyrate by 20% and propionate by 7%-8%, without increasing gas production. Each formulation significantly enriched specific SCFA- and B-vitamin-producing taxa. AM-02 significantly increased the abundance of two pyruvate fermentation to acetate/lactate pathways. PM-02 significantly increased the abundance of two tryptophan biosynthesis pathways, accompanied by an increase in available tryptophan and the abundance of tryptophan-producing microbes. All three formulations increased the availability of microbiome-derived metabolites, indicating microbiome functional modulation by the treatments. These findings support clinical evaluation of these novel formulations as a strategy to enhance microbiome composition and function.

IMPORTANCE: The gut microbiome produces metabolites, including short-chain fatty acids, B vitamins, and tryptophan derivatives, that are critical regulators of host physiology, from energy metabolism and gut barrier integrity to sleep and immune function. While probiotics introduce live microorganisms, and prebiotics selectively feed existing microbes, co-biotics represent a distinct category of compounds that simultaneously modulate host cell biology and microbiome activity. Despite growing interest in co-biotic supplementation, the impact of complete co-biotic-containing formulations on gut microbiome composition and functional output has not been evaluated. Using a validated ex vivo gastrointestinal model inoculated with fecal microbiota from six healthy adults, we demonstrate that three supplement formulations containing co-biotic compounds consistently increased production of health-associated metabolites, selectively enriched beneficial microbial taxa, and modulated functional metabolic pathways, all without increasing gas production. These findings establish a mechanistic foundation for the clinical investigation of co-biotic formulations as targeted, tolerable interventions for optimizing gut microbiome function across diverse human populations.},
}

@article {pmid42820871,
year = {2026},
author = {Zhang, J and Liang, C and Jiang, F and Zhao, X and Zhang, T},
title = {Seasonal and Regional Dietary Heterogeneity Is Associated With Gut Microbiota Differentiation in Przewalski's Gazelle (Procapra przewalskii).},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70215},
pmid = {42820871},
issn = {1749-4877},
support = {2025-ZJ-J09//Innovation Platform Construction Project of Qinghai Province/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University/ ; },
abstract = {Wild ungulates on the Qinghai-Tibet Plateau experience seasonal shifts in food resources, yet integrated evidence linking diets with gut microbiota and metabolic profiles remains limited. We combined fecal DNA metabarcoding, 16S rRNA sequencing, metagenomics, and untargeted metabolomics to analyze diet, gut microbiota composition, functional pathways, and fecal metabolic profiles in 82 fecal samples of Przewalski's gazelle (Procapra przewalskii) from three regions. Seasonal comparisons were conducted within each region and regional comparisons within each season. Winter diets showed regional specificity, with Poaceae and Cyperaceae enriched in the N region, Poaceae and Fabaceae in the S region, and Iridaceae in the W region, whereas summer diets shifted toward forb families including Asteraceae, Apiaceae, Brassicaceae, and Polygonaceae. Gut microbiota composition and KEGG Level 3 functions differed between seasons. Representative taxa enriched in winter included UCG-007 within Oscillospiraceae, Akkermansia, Mailhella, and Papillibacter, whereas taxa enriched in summer included Candidatus Saccharimonas, [Eubacterium]_brachy_group, and Colidextribacter. Representative pathways included Biosynthesis of cofactors, Biosynthesis of nucleotide sugars, Biosynthesis of various nucleotide sugars, and Glyoxylate and dicarboxylate metabolism in winter, whereas representative pathways in summer included the Phosphotransferase system (PTS), Ribosome, Aminoacyl-tRNA biosynthesis, and Peptidoglycan biosynthesis. Fecal metabolomic profiles differed among regions within both seasons, and dietary dissimilarity was significantly correlated with metabolomic, genus-level microbial, and KEGG Level 3 functional dissimilarities. Correlation analyses linked LEfSe-identified plant families to dominant genus-level taxa and KEGG Level 3 pathways. Together, these results support a close link between dietary variation and changes in gut microbiota composition, functional potential, and fecal metabolic profiles.},
}

@article {pmid42822169,
year = {2026},
author = {Zhou, Y and Zhang, M and Zhai, Y and Zhang, Y and Zhang, A and Wang, B and Song, J and Wang, M and Zheng, Y},
title = {Microbial functional differentiation and flavor formation across layer exchange in cereal vinegar fermentation: Multi-omics insights and targeted bioaugmentation.},
journal = {International journal of food microbiology},
volume = {463},
number = {},
pages = {112088},
doi = {10.1016/j.ijfoodmicro.2026.112088},
pmid = {42822169},
issn = {1879-3460},
abstract = {Spatial heterogeneity is common in cereal vinegar fermentation, but microbial and metabolic changes across the layer-exchange process remain unclear. We combined metagenomics and metatranscriptomics with physicochemical, organic-acid, and volatile profiling to investigate layer-associated changes during Tianjin Duliu mature vinegar (TDMV) fermentation and guide bioaugmentation. Before exchange, the frequently turned upper layer consumed ethanol at 1.14 times the lower-layer rate, rapidly accumulated acetic acid, and was enriched in Acetobacter and Komagataeibacter. The lower layer retained more ethanol and lactic acid, was enriched in lactic acid bacteria and yeasts, and contained more ethyl esters. After upward transfer, the original lower-layer Cupei rapidly accumulated acetic acid as several ethyl esters decreased; after downward transfer, the original upper-layer Cupei acidified more slowly while phenethyl alcohol, phenethyl acetate, ethyl lactate, and 2,3-butanediol increased. Genus-level transcript profiles showed that Acetobacter-affiliated transcripts related to acetaldehyde oxidation and the acetolactate/acetoin branch were more pronounced in upper-positioned Cupei, whereas LAB-affiliated lactate-forming transcripts were prominent in the lower layer. At the 100-kg scale, a targeted two-strain treatment using Lactobacillus helveticus and Acetobacter pasteurianus increased substrate conversion efficiency from 47.35 ± 1.36% to 51.19 ± 0.32% and final total acid by approximately 9.7% in both portions. In a → A, day-17 acetic acid was 43.8% higher than in the control, but the difference was not significant at the endpoint. The bioaugmentation samples showed changes in aroma-related volatile composition. These findings support complementary microbial functional differentiation across Cupei positions and inform position-targeted regulation of TDMV fermentation.},
}

@article {pmid42822223,
year = {2026},
author = {Liao, M and Qiu, Y and Wu, Z and Zhao, S and Ji, Y and Lin, N and Ma, J and Abraham, EN and Liu, G and Feng, Y},
title = {Nature-based solution-inspired electroactive ecological floating bed: a technology for carbon-nitrogen removal and ecological performance assessment in aquaculture Tailwater.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127010},
doi = {10.1016/j.watres.2026.127010},
pmid = {42822223},
issn = {1879-2448},
abstract = {The remediation of polluted aquaculture water and sediment, which severely threatens aquatic ecosystems, is of paramount importance. In this study, a Nature-based Solution (NbS) of electroactive ecological floating bed coupled with an oxygen-producing submerged plants system (EEFB-PS) was designed, where a conductive floating-bed matrix functioned as an integrated biocathode embedded within the rhizosphere and was coupled to the anode in the sediment. Under a 12 h light/dark condition, submerged plants induced diel DO oscillations that enabled nitrification in the daytime and electroautotrophic denitrification at night, as supported by distinct nitrate-reduction signals in cyclic voltammetry (CV) and differential cyclic voltammetry (DCV). Compared with the control system, EEFB-PS achieved a low effluent concentration of COD (7.2 mg/L), TN (1.3 mg/L), NH4[+]-N (0.1 mg/L), and NO3[-]-N (1.1 mg/L), and enhanced nitrogen removal dominated by microbially mediated pathways. 16S rRNA and metagenomics revealed enrichment of electroactive and nitrogen-cycling bacteria (e.g., Geobacter and Nitrospira) and functional shifts toward intensified denitrification/DNRA. Notably, the abundance of nosZ gene, which encodes nitrous oxide reductase, was significantly up-regulated (by 13.8-fold), demonstrating the system's high potential to mitigate N2O emissions. Meanwhile, EEFB-PS significantly mitigated the Global Warming Potential (GWP) to 4.6 mg CO2-eq m[-2]h[-1] by suppressing methanogenesis and promoting methane oxidation modules. Moreover, EEFB-PS rebalanced the aquatic food web by shifting phytoplankton dominance from Chlorophyta to Bacillariophyta, reducing phytoplankton density while increasing zooplankton abundance, thereby mitigating eutrophication risk. In summary, EEFB-PS demonstrates a rhizosphere-integrated, low carbon emission ecotechnology that couples with electron supply, plant-driven process, and microbial functional succession for aquaculture tailwater treatment and ecological restoration.},
}

@article {pmid42822226,
year = {2026},
author = {Chen, J and Lv, X and Li, L and Liu, T and Zhang, J and Luo, L and Wang, Z and Tian, Y},
title = {Threshold-dependent sulfamethoxazole biodegradation in activated sludge: linking extracellular interfacial reorganization to intracellular metabolic activation.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127033},
doi = {10.1016/j.watres.2026.127033},
pmid = {42822226},
issn = {1879-2448},
abstract = {Antibiotic removal in activated sludge is highly variable, yet the mechanisms governing activation of effective biodegradation remain poorly understood. Here, we combined interpretable machine learning trained on 176 literature-derived cases with controlled microcosm experiments, extracellular polymeric substance characterization, metagenomics, and transformation-product profiling to investigate threshold behavior in sulfamethoxazole (SMX) biodegradation. A threshold-dependent transition from persistent discharge to effective biodegradation emerged at an influent SMX concentration of approximately 0.2 mg/L, with sufficient acclimation (∼15 d) required for degradative capacity to develop, whereas removal remained limited below this concentration. Microcosm experiments showed that SMX removal remained below 20% at 0.2 mg/L throughout acclimation, whereas removal at 2.5 mg/L increased rapidly after day 15 and reached 99.70% by day 18. Allylthiourea inhibition further showed that SMX removal at 2.5 mg/L decreased from 97.38% to 19.35%, accompanied by a 93% reduction in the apparent degradation rate constant, indicating a major contribution from nitrifier-linked co-metabolism under threshold-exceeding conditions. Threshold exceedance was further associated with extracellular interfacial reorganization, enrichment of oxidative metabolic functions and SMX-relevant catabolic potential, and broader shifts in transformation-product profiles. These findings reveal that effective SMX biodegradation is governed by an activation-limited response, providing a mechanistic explanation for the persistent discharge of antibiotics under low-exposure conditions and offering a new conceptual framework for understanding and improving micropollutant attenuation in biological wastewater treatment.},
}

@article {pmid42822283,
year = {2026},
author = {Li, Y and Li, YA and Dong, S and Luo, J and Yu, S and Xie, W and Shi, B and Zhao, R},
title = {Zinc differentially modulates resistome responses to ciprofloxacin and sulfamethazine in activated sludge.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143785},
doi = {10.1016/j.jhazmat.2026.143785},
pmid = {42822283},
issn = {1873-3336},
abstract = {Antibiotics and metals frequently coexist in wastewater, but whether metals uniformly intensify antibiotic-driven resistome selection remains unclear. Here, activated sludge reactors were exposed to zinc (Zn), ciprofloxacin (CIP), sulfamethazine (SMZ), and their combinations across four stepwise exposure stages. Read-based, assembly-based, and genome-resolved metagenomics were integrated to characterize antibiotic resistance gene (ARG) abundance, composition, mobility-associated genetic contexts, and putative hosts. Antibiotics primarily drove resistome restructuring, whereas Zn alone had limited effects. CIP strongly enriched ARGs, while Zn co-exposure attenuated this response and caused late-stage declines in total ARG abundance and the relative abundance of ARG-hosting metagenome-assembled genomes (MAGs). In contrast, ARG abundance remained comparatively stable under SMZ but increased progressively under Zn+SMZ. Because antibiotic concentrations increased sequentially over time, these patterns represent stage-dependent responses rather than independent concentration effects. Antibiotic-related treatments showed higher contributions of ARGs on predicted plasmid-like contigs and more frequent ARG-mobile genetic element co-localization. Pseudomonadota dominated putative ARG hosts, and CIP showed broader ARG-host profiles. Approximately 67% of ARG-hosting MAGs carried virulence factor genes, indicating co-occurring resistance and virulence-associated genomic potential. These findings demonstrate that Zn altered activated sludge resistome in an antibiotic-dependent manner, highlighting that mixture effects cannot be inferred from single-contaminant responses alone.},
}

@article {pmid42822627,
year = {2026},
author = {Zhou, L and Sha, H and Han, H and Wang, S and Li, S and Peng, X},
title = {Oxygen-associated differentiation of TBBPA-transforming activated sludge consortia and characterization of a cultivable Klebsiella degrader.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125834},
doi = {10.1016/j.envres.2026.125834},
pmid = {42822627},
issn = {1096-0953},
abstract = {Tetrabromobisphenol A (TBBPA), a widely used brominated flame retardant, poses increasing environmental and health concerns, yet how oxygen availability is associated with the assembly and degradation potential of TBBPA-transforming microbiomes remains poorly resolved. Here, ten enrichment consortia (six aerobic and four anaerobic) were established from activated sludge collected at six municipal wastewater treatment plants, achieving up to 63.46% TBBPA removal at an initial concentration of 5 mg/L. Metagenomic analysis revealed marked community divergence between the aerobic and anaerobic enrichment conditions, with Burkholderia predominating in the aerobic consortia and Klebsiella predominating in the anaerobic consortia. Read-mapping-based abundance profiling detected the HY4.102-affiliated Klebsiella pneumoniae population under both oxygen conditions, with higher relative abundance in the anaerobic consortia. Strain NCHT, isolated from the aerobic consortium NC_H, shared >99% ANI and AAI with HY4.102 and transformed TBBPA under both aerobic and anaerobic batch conditions. During aerobic incubation, strain NCHT transformed 51.0-68.4% of TBBPA across the tested concentrations, and UHPLC-MS/MS analysis yielded 17 putatively identified transformation intermediates consistent with an interconnected network involving debromination, hydroxylation, O-methylation, and β-scission. Molecular docking further prioritized DhmA, GSTs, CbdA/B, and PobB as candidate enzymes for debromination and downstream aromatic transformation, broadly consistent with the dehalogenation-related genes annotated in MAG HY4.102. Together, these findings provide an integrated community-to-strain framework for investigating TBBPA transformation.},
}

@article {pmid42810054,
year = {2026},
author = {Ghorbani, Y and Schwenger, KJP and Maughan, H and Teterina, A and Lou, W and Comelli, EM and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP},
title = {Multi-omic profiling and pathways related to changes in liver histology after Roux-en-Y gastric bypass: a longitudinal study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106498},
doi = {10.1016/j.ebiom.2026.106498},
pmid = {42810054},
issn = {2352-3964},
abstract = {BACKGROUND: Roux-en-Y gastric bypass (RYGB) improves metabolic dysfunction-associated steatotic liver disease (MASLD). However, the impact of RYGB on hepatic transcriptome, faecal microbiome and serum/faecal metabolome remain understudied. Our objective was to investigate the change in these omics and their relationships with changes in liver histology.

METHODS: In this prospective cohort study, patients undergoing RYGB were recruited between 2013 and 2020 and followed for 12 months. Anthropometrics, biochemistry, hepatic transcriptome, faecal microbiome (shotgun metagenomics) and serum/faecal metabolomes were measured. Liver histology and NAFLD Score (NAS) were assessed.

FINDINGS: Thirty-eight patients completed the study. Anthropometrics, biochemical and histological parameters improved post-RYGB (p < 0.05). Hepatic transcriptome analysis revealed a co-expression module enriched in fatty acid metabolism which correlated with changes in NAS post-RYGB (ρ = 0.38, p = 0.019). The core enrichment genes in this pathway were involved in mitochondrial and peroxisomal β-oxidation (ACADVL, ACOX1, and EHHADH) and the tricarboxylic acid (TCA) cycle (SUCLG2, SDHC, and SERINC1). There was an increase in TCA cycle gene expression associated with the resolution of ballooning, while upregulation of β-oxidation genes correlated with less reduction in NAS, ballooning, and inflammation. Metabolomic changes related to the identified co-expression module and pathways reveal a significant increase in faecal acylcarnitines, likely due to malabsorption from RYGB, with a significant reduction in circulating acylcarnitines which correlated positively with SUCLG2 expression and resolution of ballooning. Additionally, the increase in faecal acylcarnitines positively correlated with the bacterial species utilising acylcarnitines. In network analysis, ballooning of hepatocytes was associated with faecal/serum acylcarnitines and TCA metabolites while SUCLG2 was the hub gene associated with these changes.

INTERPRETATION: These findings provide insight on how post-RYGB changes in the transcriptome, metabolome, and microbiome could be associated with improvement in liver histology and may inform the development of future strategies for MASLD management.

FUNDING: Canadian Institutes of Health Research and American College of Gastroenterology.},
}

@article {pmid42810079,
year = {2026},
author = {Chen, F and Zhao, N and Fan, Q and Tao, W and Du, E and Wei, J},
title = {Integrative metabolic and lipidomic analysis reveals microbiota-associated mechanisms of thigh meat quality variation in spent laying hens from different rearing systems.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107848},
doi = {10.1016/j.psj.2026.107848},
pmid = {42810079},
issn = {1525-3171},
abstract = {This study aims to elucidate the differences in poultry meat quality between cage-rearing (CR) and free-range (FR) rearing systems and to dissect the underlying microbiota-mediated mechanisms. A total of 200 Jianghan laying hens (50-week-old) were equally assigned to either FR or CR group. At 56 w, 10 hens from each group were selected and underwent integrated analyses of gut microbial metagenomes, muscle nutrient composition, amino acid, and lipid profiles. The results showed that the FR group had lower abdominal fat yield but higher leg muscle yield (P < 0.01). Leg muscle of FR hens exhibited lower crude fat content, drip loss, malondialdehyde levels, but higher pH24h, glutathione peroxidase (GSH-Px) activity and DPPH radical-scavenging rate (P < 0.05). Additionally, the FR group showed significant increases in glutamic acid, alanine, isoleucine, tyrosine, phenylalanine, histidine, arginine and total flavor amino acids (FAA, P < 0.05). Lipidomic profiling identified 38 differentially abundant lipids and an elevation in total fatty acyls in FR muscles. Subsequent fatty acids composition analysis revealed higher proportions of C20:4 and total polyunsaturated fatty acids (PUFA) in the FR group (P < 0.05). Cecal microbiota analysis indicated FR rearing increased the relative abundances of Ligilactobacillus aviarius, Enterococcus faecium, Corynebacterium stationis, C.glutamicum, and C.casei (P < 0.05). Correlation analyses demonstrated that L. aviarius was positively correlated with FAA content, while the three Corynebacterium species were positively correlated with GSH-Px activity, pH24h, FAA, and PUFA, and negatively with drip loss (|r| > 0.6, P < 0.05). Collectively, free-range rearing improves meat quality and nutritional traits, which may be linked to changes in the gut microbial community.},
}

@article {pmid42810185,
year = {2026},
author = {Yan, J and Lei, Z and Li, K and Zheng, M and Zhang, A and Sun, Z and Liu, Y},
title = {Far-UVC-activated calcium peroxide facilitates simultaneous antibiotic removal and carbon recovery from waste activated sludge.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {126990},
doi = {10.1016/j.watres.2026.126990},
pmid = {42810185},
issn = {1879-2448},
abstract = {Antibiotic residues in waste activated sludge (WAS) require effective removal to reduce ecological risks and improve the safety of sludge resource recovery. This study evaluated 222 nm far-UVC-activated calcium peroxide (CaO2) pretreatment for simultaneous antibiotic removal and carbon recovery from WAS, using sulfamethoxazole (SMX) as a model antibiotic. Far-UVC and CaO2 exhibited a synergistic effect, achieving 80% apparent SMX removal within 240 min at a CaO2 dosage of 0.1 g/g TS. Mechanistically, continuous CaO2 hydrolysis induced sludge disintegration and alkalization (pH = 9.55). This dual-action not only co-released the entrapped SMX and endogenous dissolved organic matter (DOM) into the aqueous phase but also shifted SMX toward its highly photo- and radical-susceptible deprotonated state. Consequently, efficient far-UVC photolysis of slowly released H2O2 and DOM-mediated sensitization unlocked an abundant reactive species cascade (dominated by HO• and [1]O2), which efficiently degraded SMX and its intermediates to minimize potential ecological risks. From a practical standpoint, the process effectively buffered complex matrix interferences, degrading 13 indigenous multi-class antibiotics in real sludge (with removal efficiencies of up to 89%) while yielding a 1.4-fold increase in energy efficiency compared to far-UVC alone. Furthermore, far-UVC/CaO2 enhanced WAS solubilization and subsequent anaerobic fermentation, increasing volatile fatty acids (VFAs) production to 3.8 times that of the control. Metagenomic profiling indicated enrichment of hydrolytic and acidogenic microbial populations and functional genes related to substrate hydrolysis and VFA formation, supporting enhanced carbon recovery from antibiotic-containing WAS.},
}

@article {pmid42810338,
year = {2026},
author = {Yang, L and Singh, V and Gawey, BJ and Sinnwell, JP and Johnson, S and Billings, EC and Van Gorp, TM and Harrington, JJ and Slama, MQ and Till, LM and Singh, M and Samineni, TR and Zhu, M and Kalari, KR and Farrugia, G and Chen, J and Mars, RAT and Kashyap, PC},
title = {Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.009},
pmid = {42810338},
issn = {1097-4172},
abstract = {The gut microbiome has emerged as a key contributor to cancer biology. Prior studies have focused on individual cancers and often overlook comorbidities, obscuring whether reported associations are specific to a cancer type. Here, we present findings from a real-world mixed-cancer cohort (Mayo Clinic Cancer Microbiome), comprising 1,364 cancer patients and 287 healthy controls. By applying a framework to account for non-specific microbiome associations with cancer, comorbidities, and demographic and clinical variables, we identified 341 cancer-associated species across five cancer classes that represent the most plausible contributors to cancer pathogenesis. Within cancer classes, we found lower levels of fecal bile acids and C. scindens in early-onset breast cancer and elevated lactate and Veillonella parvula in early-onset colorectal cancer. Additionally, Anaerostipes hadrus encoding dihydropyrimidine dehydrogenase was protective against 5-fluorouracil-induced diarrhea. These findings demonstrate the strength of our cohort and provide a foundational resource for the discovery of cancer-specific microbiome signatures and predictive biomarkers.},
}

@article {pmid42810659,
year = {2026},
author = {Yue, Y and Liu, H and Ma, Z and Cai, L and Liu, Z and Liu, G and Cui, X},
title = {Chlorite-Mediated Regulation of Nitrite Accumulation and Nitrogen Removal in Integrated Partial Denitrification/Anammox Biofilter.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125786},
doi = {10.1016/j.envres.2026.125786},
pmid = {42810659},
issn = {1096-0953},
abstract = {Achieving stable and efficient nitrite accumulation in integrated partial denitrification/anammox (PD/A) processes is typically constrained by substrate competition among microorganisms, posing a significant challenge for large-scale engineering applications. This study proposes a novel strategy for regulating nitrogen transformation pathways using chlorite (ClO2[-]) as a bioregulator, by inducing denitrification to remain at the nitrite stage and thereby providing a stable substrate supply for the anammox process. In the continuous-flow PD/A biofilter, the increase of ClO2[-] concentration from 0 to 1.0 mg/L was associated with an increase in total nitrogen removal efficiency (Re.TN) from 62.74% to a peak value of 85.27%, accompanied by an increase in effluent nitrite accumulation rate (NAR) from 62.24% to 81.77%. [15]N stable isotope tracing further confirmed that the anammox pathway dominated the system, contributing up to 98.9% of the total N2 production and serving as the primary functional support for deep nitrogen removal. The system demonstrated exceptional process robustness across a wide hydraulic retention time (HRT) range of 5-12 h, with Re.TN consistently maintained above 80%. In addition, the system exhibited good conversion capacity for ClO2[-], with the residual concentration in the effluent maintained within the safety limits, thereby reducing the potential risk of secondary pollution. Microbial community analysis indicated that ClO2[-] regulation was associated with changes in the functional microbial community structure, accompanied by increased relative abundances of the core autotrophic anammox bacteria (Candidatus Brocadia and Candidatus Jettenia) and the succession of heterotrophic Thauera populations toward nitrite-producing subgroups. Metagenomic functional profiling revealed that the functional potential of core nitrogen metabolism changed under ClO2[-] regulation, with increased relative abundances of nitrate reduction-related genes (narG/H/I) and decreased relative abundance of the nitrite reduction-related gene (nirS), while the relative abundance of the Anammox-related marker gene hdh increased by 27.5%. This study provides new insights into optimizing the stability of the PD/A system and offers new perspectives for the further engineering application of efficient nitrogen removal processes.},
}

@article {pmid42810665,
year = {2026},
author = {Zhou, X and Chen, W and Zhao, K and Han, X and Fu, J and Chen, S and Yang, S and Yu, X and Zou, L},
title = {Thermophilic Parageobacillus toebii G12 suppresses ARG enrichment during chicken manure composting even with multidrug-resistant plasmid-harboring bacteria as a stressor.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125810},
doi = {10.1016/j.envres.2026.125810},
pmid = {42810665},
issn = {1096-0953},
abstract = {The enrichment of antibiotic resistance genes (ARGs) during composting poses a substantial risk to the safe utilization of chicken manure. However, the role of multidrug-resistant plasmid (MRP)-harboring bacteria in ARG dissemination and microbial succession during composting remains poorly understood. In this study, we investigated the regulatory effects of thermophilic Parageobacillus toebii G12 (G12) on ARG dynamics, as well as its performance under interference from MRP-harboring bacteria. Our results showed that G12 inoculation elevated compost temperature, extended the thermophilic phase, and accelerated maturation. It increased overall ARG removal to 60.9 % and 55.6 % in the conventional and MRP-contaminated systems, respectively, and reduced persistent ARG enrichment by 71.4 % and 66.3 %, respectively. Although MRP-associated stress shifted the suppression preference of G12 from protection-type to alteration/replacement-type persistent ARGs, the strain consistently suppressed efflux- and inactivation-type persistent ARGs. Moreover, G12 markedly reduced the coverage depth of MRPs after composting, thereby alleviating MRP-associated stress. Integrated analyses, including co-occurrence network, Mantel test, partial least squares path modeling, and metagenome-assembled genome approaches, revealed that G12 reshaped the microbial community by suppressing the dominant host Pseudomonadota, thereby reducing its efflux-type persistent ARGs, while directly diminishing integration/excision-type mobile genetic elements to curtail horizontal gene transfer potential. This study elucidates the core mechanisms by which G12 counteracts ARG enrichment and demonstrates its efficacy even under MRP-associated stress, providing a theoretical foundation for mitigating antimicrobial resistance risks in manure composting.},
}

@article {pmid42811263,
year = {2026},
author = {Li, L and DU, L},
title = {[Clinical value of cerebrospinal fluid metagenomic next-generation sequencing in the diagnosis of neonatal intracranial infection].},
journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences},
volume = {55},
number = {7},
pages = {675-682},
doi = {10.3724/zdxbyxb-2025-0965},
pmid = {42811263},
issn = {1008-9292},
mesh = {Humans ; Infant, Newborn ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Female ; Sensitivity and Specificity ; Male ; *Cerebrospinal Fluid/microbiology ; },
abstract = {OBJECTIVES: To investigate the diagnostic performance of cerebrospinal fluid metagenomic next-generation sequencing (mNGS) for neonatal intracranial infections and its value in clinical decision-making.

METHODS: A retrospective observational study was conducted, enrolling neonates admitted to the Children's Hospital, Zhejiang University School of Medicine from 2020 to 2025 with suspected intracranial infection who underwent cerebrospinal fluid mNGS. The sensitivity of mNGS and its concordance with cerebrospinal fluid culture-quantitative polymerase chain reaction (qPCR) were calculated. Clinical impact was evaluated using predefined criteria, and samples were categorized accordingly into positive-impact and no-impact groups to explore independent factors influencing the positive impact of mNGS on clinical decision-making.

RESULTS: Among 61 neonates with suspected intracranial infection, 48 were confirmed. Pathogens were identified in 18 cases, of which 9 were detected exclusively by mNGS, accounting for 50% of etiological diagnoses. The sensitivity of mNGS was 31.3% (95%CI: 18.7%-46.3%), higher than that of cerebrospinal fluid culture-qPCR at 18.8% (95%CI: 8.9%-32.6%), though the difference was not statistically significant (P=0.15). The positive and negative concordance rates between mNGS and cerebrospinal fluid culture-qPCR were 66.7% (95%CI: 29.9%-92.5%) and 76.9% (95%CI: 60.7%-88.9%), respectively. mNGS positively influenced clinical decisions in 23 patients: 12 cases with positive results guided etiological diagnosis and treatment adjustment, while 11 cases with negative results led to antibiotic de-escalation or discontinuation. Multivariate analysis identified a positive mNGS result as an independent factor associated with positive clinical impact (OR=22.127, P<0.01).

CONCLUSIONS: Cerebrospinal fluid mNGS provides positive support in etiological diagnosis and clinical decision-making for neonatal intracranial infection.},
}

Humans
Infant, Newborn
Retrospective Studies
*High-Throughput Nucleotide Sequencing
*Metagenomics
Female
Sensitivity and Specificity
Male
*Cerebrospinal Fluid/microbiology

@article {pmid42811337,
year = {2026},
author = {Detman-Ignatowska, A and Schiro, G and Filip, R and Samborowska, E and Karczmarski, J and Jarmakiewicz-Czaja, S and Jakubowska, K and Williams, A and Hickman, NR and Laubitz, D and Sikora, A},
title = {Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42811337},
issn = {1475-2859},
support = {MG-2/21-18//Institute of Biochemistry and Biophysics Polish Academy of Sciences/ ; },
mesh = {Humans ; *Feces/microbiology ; Fermentation ; *Crohn Disease/microbiology/diagnosis ; Lactic Acid/metabolism ; Butyrates/metabolism ; *Gastrointestinal Microbiome ; Acetates/metabolism ; Bacteria/metabolism/classification ; Glucose/metabolism ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.

RESULTS: HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.

CONCLUSIONS: Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.},
}

Humans
*Feces/microbiology
Fermentation
*Crohn Disease/microbiology/diagnosis
Lactic Acid/metabolism
Butyrates/metabolism
*Gastrointestinal Microbiome
Acetates/metabolism
Bacteria/metabolism/classification
Glucose/metabolism

@article {pmid42811560,
year = {2026},
author = {Wei, CJ and Cheng, ZS},
title = {[Advances in early bedside etiological diagnosis of severe pneumonia].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {10},
pages = {1046-1049},
doi = {10.3760/cma.j.cn112147-20260519-00286},
pmid = {42811560},
issn = {1001-0939},
support = {2026AFC0828//Joint Fund Project of Hubei Provincial Natural Science Foundation for Innovation and Development/ ; },
mesh = {Humans ; *Pneumonia/diagnosis/microbiology ; Early Diagnosis ; *Pneumonia, Bacterial/diagnosis/microbiology ; Point-of-Care Systems ; },
abstract = {The case fatality rate of severe pneumonia remains high, early and accurate etiological diagnosis is a prerequisite for precision antimicrobial therapy. Conventional culture techniques are limited by long turnaround times and low positivity rates. In recent years, novel detection systems such as microbiological rapid on-site evaluation(M-ROSE), point-of-care immunoloassays, multiplex PCR, and metagenomic sequencing have advanced rapidly, markedly shortening the time to pathogen identification. The integration of rapid detection assays for antimicrobial resistance genes has further facilitated precision antimicrobial therapy. Multi-omics analysis integrating the pathogen spectrum with host immune response status helps distinguish colonization from infection, thereby helping prevent antibiotic overuse. This article reviews techniques for pathogen and antimicrobial resistance gene detection together with strategies to distinguish colonization from infection to inform rapid bedside etiological diagnosis in severe pneumonia.},
}

Humans
*Pneumonia/diagnosis/microbiology
Early Diagnosis
*Pneumonia, Bacterial/diagnosis/microbiology
Point-of-Care Systems

@article {pmid42811876,
year = {2026},
author = {Bo, T and Liu, X and Liu, M and Shen, W and Zhang, X and Guo, H and Wen, J},
title = {Winter Caching of Artemisia frigida Is Associated With Host Physiological and Gut Microbial Variation in Brandt's Voles.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70576},
doi = {10.1111/mec.70576},
pmid = {42811876},
issn = {1365-294X},
support = {32470487//National Natural Science Foundation of China/ ; 32201278//National Natural Science Foundation of China/ ; 2023FY100305//Science & Technology Fundamental Resources Investigation Program/ ; 5242016//Natural Science Foundation of Beijing Municipality/ ; },
mesh = {Animals ; *Arvicolinae/physiology/microbiology/genetics ; Seasons ; *Artemisia ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Hypothalamus/metabolism ; Cold Temperature ; Transcriptome ; Lipid Metabolism/genetics ; },
abstract = {Seasonal variation in food resources represents a major ecological challenge for wild herbivores, yet how naturally selected dietary resources become associated with host and microbial responses remains poorly understood. During winter, Brandt's voles (Lasiopodomys brandtii) cache large amounts of Artemisia frigida, suggesting that this plant may have ecological significance beyond its nutritional value. However, the biological basis underlying this seasonal food preference remains unclear. Here, using Brandt's voles as a model system, we investigated whether the naturally selected winter food A. frigida was associated with coordinated variation in host physiology and gut microbial organization under cold conditions. By integrating physiological phenotyping, hypothalamic neuroendocrine analyses, adipose tissue transcriptomics, shotgun metagenomics and metagenomic binning, we characterized host and microbial responses across multiple biological levels. Dietary A. frigida was associated with altered hypothalamic AgRP expression, increased UCP1 expression in BAT and transcriptional changes related to lipid metabolism and thermogenic pathways during cold exposure. Supplement of A. frigida was associated with changes in gut microbial community structure, enrichment of specific bacterial taxa and shifts in predicted microbial functional potential. Genome-resolved analyses further reconstructed 277 non-redundant metagenome-assembled genomes, enabling assessment of microbial ecological variation associated with seasonal food conditions. Together, our findings provide molecular ecological evidence linking winter caching of A. frigida with coordinated variation in host physiology and gut microbial organization, highlighting seasonal dietary resources as an overlooked component of ecological variation in wildlife.},
}

Animals
*Arvicolinae/physiology/microbiology/genetics
Seasons
*Artemisia
*Gastrointestinal Microbiome/genetics
Metagenomics
Hypothalamus/metabolism
Cold Temperature
Transcriptome
Lipid Metabolism/genetics

@article {pmid42812340,
year = {2026},
author = {Nakajima, Y and Kato-Kogoe, N and Yasuda, T and Sakaguchi, S and Kamiya, K and Inubushi, J and Hamada, W and Horiuchi, M and Kudo, A and Tsuda, K and Nakano, T and Tamaki, J and Ueno, T},
title = {Serum antibody titers against Porphyromonas gingivalis are associated with oral and gut microbiota.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1956003},
pmid = {42812340},
issn = {2673-4842},
abstract = {INTRODUCTION: Porphyromonas gingivalis (P. gingivalis) is a keystone pathogen in the oral microbiota and has attracted attention for its association with periodontal as well as systemic diseases. While animal studies have suggested that P. gingivalis affects the gut microbiota and may trigger related pathologies, evidence from human studies remains insufficient. In this study, we aimed to identify characteristics of the oral and gut microbiota associated with serum antibody titers against P. gingivalis, which serve as an indicator of P. gingivalis infection.

METHODS: Serum antibody titers against P. gingivalis were measured in 149 community-dwelling older adults, who were classified by their quartile into high (PgAb_H), medium (PgAb_M), and low (PgAb_L). Simultaneously collected saliva and stool samples were subjected to 16S rRNA metagenomic analysis to compare the bacterial composition of the oral and gut microbiota between the PgAb_H and PgAb_L groups. Using Linear Discriminant Analysis Effect Size (LEfSe), we identified the bacteria whose abundance differed significantly between the groups. The prevalence of bacterial genera commonly present in both the oral and gut microbiota of the same individual was compared between the groups.

RESULTS: Significant differences were observed between the PgAb_H and PgAb_L groups regarding the bacterial composition of the oral microbiota (unweighted UniFrac distance, p = 0.001; weighted UniFrac distance, p = 0.041) and that of the gut microbiota (weighted UniFrac distance, p = 0.045). LEfSe analysis identified several bacterial genera in the oral and gut microbiota whose abundances differed between the two groups. Although the two groups did not differ in the number of bacterial genera shared between the oral and gut microbiota in the same individual, the proportion of individuals possessing Haemophilus in both the oral and gut microbiota was significantly lower in the PgAb_H group than in the PgAb_L group (p = 0.003).

CONCLUSION: This study characterized the oral and gut microbiota profiles associated with serum antibody titers against P. gingivalis. These findings deepen our understanding of how P. gingivalis infection affects the human body beyond the oral cavity, and suggest that serum antibody titers against P. gingivalis could serve as a potentially meaningful indicator for health management.},
}

@article {pmid42813064,
year = {2026},
author = {Lei, X and Zhao, L and Zhong, Z and Lin, H and Xie, Z and Guo, Y and Zhang, S and Zhang, C and Gong, T},
title = {Clinical Characteristics and Machine Learning-Based Severity Classification of Chlamydia psittaci Pneumonia: A Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {622689},
pmid = {42813064},
issn = {1178-6973},
abstract = {BACKGROUND: Chlamydia psittaci infection can cause severe community-acquired pneumonia with significant mortality. Distinguishing severe from non-severe disease remains challenging. This study used clinical data from patients with C. psittaci pneumonia and multiple machine-learning methods to develop a model for severity classification.

METHODS: We retrospectively analyzed 231 hospitalized patients with C. psittaci pneumonia, including 84 severe cases, between January 2022 and April 2025 in Jiangxi Province, China. Severe pneumonia was defined according to the IDSA/ATS and Chinese adult community-acquired pneumonia criteria. The model outcome was the composite clinical label of severe versus non-severe pneumonia rather than mortality. A comprehensive machine-learning framework incorporating 11 algorithms and six feature-selection strategies was used to develop the severity-classification model.

RESULTS: C. psittaci pneumonia cases were sporadic and widely distributed across Jiangxi Province. Elderly patients, especially those with cardiovascular disease or diabetes, had an increased risk of severe illness. Laboratory tests in severe cases showed higher neutrophils, D-dimer, CRP, PCT, IL-6, IL-8, and IL-10, with lower lymphocytes, NK cells, albumin, and serum calcium. CT commonly showed large patchy opacities in the lower lung lobes. Additional microorganisms were co-detected by mNGS in 74.03% of patients. In the internal hold-out test set (n = 69), the RF+SVM model achieved an area under the receiver operating characteristic curve (AUC) of 0.845 (95% CI, 0.754-0.935) for distinguishing severe from non-severe pneumonia. The final RF+SVM severity-classification model incorporated nine laboratory predictors.

CONCLUSION: This study identified key clinical and laboratory differences between non-severe and severe C. psittaci pneumonia and developed a predictive model using comprehensive machine learning approaches. The model may support admission-based severity stratification and identify patients who may warrant closer monitoring. This is a single-center retrospective study, and the model needs further validation in prospective multicenter cohorts.},
}

@article {pmid42813505,
year = {2026},
author = {Huang, S and Sun, S and Zhao, Z and Gao, D and Zhang, W and Zhou, N and Jin, Y and Jin, B and Sun, D},
title = {Associations of Gut Microbiota Composition and Fecal Metabolomic Profiles in Patients With Acquired Premature Ejaculation: A Cross-Sectional Pilot Study.},
journal = {American journal of men's health},
volume = {20},
number = {5},
pages = {15579883261493263},
doi = {10.1177/15579883261493263},
pmid = {42813505},
issn = {1557-9891},
mesh = {Humans ; Male ; Pilot Projects ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Premature Ejaculation/microbiology/metabolism ; Metabolomics ; Case-Control Studies ; *Metabolome ; },
abstract = {Premature ejaculation (PE) is a prevalent male sexual disorder with an incompletely understood pathogenesis and limited effective therapeutic strategies. Although the gut microbiota has been implicated in several diseases, its association with PE remains unclear. Metabolomic analyses and metagenomic sequencing were performed to compare the intestinal microbiota profiles between 20 patients with PE and 20 healthy controls, investigating the association between PE and gut microbiota. Comprehensive analysis revealed distinct microbial signatures between PE and control groups. The PE group exhibited significantly reduced relative abundances of Bifidobacteriaceae bacterium, Blautia, Coprobacillus, Ruminococcus sp. ctHOG1, Siphoviridae, and Alistipes. Metabolomic profiling identified 150 upregulated and 73 downregulated metabolites between the two groups. Kyoto encyclopedia of genes and genomes pathway enrichment analysis indicated significant enrichment of several potential signaling pathways in the PE group. This study characterized distinct gut microbiota features in patients with PE compared with healthy controls and investigated microbiota-associated pathways potentially related to PE through integrated metabolomics analysis. The findings provide preliminary insights into microbiome-associated alterations in PE.},
}

Humans
Male
Pilot Projects
Adult
*Feces/microbiology/chemistry
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Premature Ejaculation/microbiology/metabolism
Metabolomics
Case-Control Studies
*Metabolome

@article {pmid42813801,
year = {2026},
author = {Xu, J and Fan, Y and Qu, G and Li, J and Peng, Y and Wang, M and Zhang, J and Feng, Y and Liu, X and Hu, Y and Kan, B and Li, Z and Zeng, M and Lu, X},
title = {Comparative gut microbiome in diarrheal and non-diarrheal children: an individually matched case-control study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019826},
doi = {10.1128/msystems.00198-26},
pmid = {42813801},
issn = {2379-5077},
abstract = {Diarrhea, a leading cause of under-five mortality in developing countries, drives therapeutic challenges amid global antibiotic resistance. This study aimed to compare gut microbiota, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) in diarrheal and non-diarrheal children, explore reasons for asymptomatic pathogen carriage, and develop a microbiome-based model to predict the potential etiology of diarrhea. This individually matched case-control study analyzed 42 paired fecal samples (selected from 716 diarrhea/non-diarrhea cases) to compare gut microbiome profiles, ARGs, MGEs, and VFs using metagenomic sequencing and pathogen-specific PCR. Diarrheal children showed reduced alpha diversity, increased Proteobacteria, and elevated VFs and MGEs. Surprisingly, ARGs were more abundant in non-diarrheal children, suggesting ARG colonization in healthy hosts. Actinomyces was enriched in non-diarrheal pathogen carriers and may be associated with asymptomatic bacterial pathogen carriage. A random forest (RF) model incorporating non-pathogenic bacteria achieved high accuracy in predicting diarrheal status and pathogen carriage. This study reveals distinct microbial ecologies between diarrheal and healthy children. The enrichment of specific bacterial taxa in asymptomatic carriers may be associated with pathogen tolerance. The unexpected ARG abundance in healthy children highlights a hidden antimicrobial resistance reservoir. These findings inform microbiome-based diagnostics and antibiotic stewardship in pediatric diarrhea.IMPORTANCEThis study is significant because it provides robust, individually matched case-control evidence linking childhood diarrhea to gut microbiome dysbiosis and the distribution of pathogenic and resistance-related genetic elements. By integrating metagenomic sequencing with pathogen-specific polymerase chain reaction (PCR), it offers a comprehensive comparison of microbial composition, virulence factors (VFs), mobile genetic elements (MHEs), and antibiotic resistance genes (ARGs) between diarrheal and non-diarrheal children. The findings demonstrate reduced microbial diversity and enrichment of Proteobacteria, virulence factors, and mobile genetic elements in diarrheal cases, highlighting microbiome instability during infection. Importantly, the unexpectedly higher abundance of antibiotic resistance genes in non-diarrheal children underscores the underestimated role of healthy populations as reservoirs of resistance. Furthermore, the establishment of predictive models for diarrhea status and pathogen carriage enhances the translational value of the study. Overall, this work advances the understanding of pediatric diarrheal disease and informs prevention, surveillance, and treatment strategies in the context of global antimicrobial resistance.},
}

@article {pmid42813975,
year = {2026},
author = {Aitolo, GL and Rambo, IM and Weisend, RE and Mullis, MM and Tringe, S and Kosmopoulos, JC and Anantharaman, K and Kiel Reese, B and Baker, BJ and De Anda, V},
title = {Shifts in vegetation impact estuary microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107126},
doi = {10.1128/msystems.01071-26},
pmid = {42813975},
issn = {2379-5077},
abstract = {Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth's most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe-virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by Sporobolus alterniflorus), black mangrove (Avicennia germinans), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus-host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems.IMPORTANCECoastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerable ecosystems are undergoing rapid transformation. Yet, little is known about the microbes that regulate carbon storage and nutrient cycling. Here, we characterized microbial and viral communities associated with coastal wetland sediments along the Texas Gulf Coast. We identified key microbial groups responsible for key carbon, sulfur, nitrogen, and iron cycling and showed that vegetation type influences their distribution and ecological roles. We also found that viruses interact with dominant microbial groups and carry genes linked to carbon processing, suggesting an important role in shaping ecosystem function. These findings provide insights into the mechanisms that sustain coastal wetlands and help predict how shifts in vegetation may affect nutrient cycling and ecosystem resilience in the future.},
}

@article {pmid42814154,
year = {2026},
author = {Sivarajan, D and Pothayi, V and Devasia, SC and Ramachandran, B},
title = {Photoperiod driven modulation of behavior, gut microbiota, and brain transcriptomics in zebrafish.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {478},
number = {10},
pages = {},
pmid = {42814154},
issn = {1432-2013},
support = {CSIR-UGC-JRF-905/2018//CSIR-UGC/ ; ECR/2018/002479//DST-SERB/ ; },
mesh = {Animals ; *Zebrafish/physiology ; *Brain/metabolism/physiology ; *Photoperiod ; *Gastrointestinal Microbiome/physiology ; *Transcriptome ; Circadian Rhythm/physiology ; *Behavior, Animal/physiology ; },
abstract = {Circadian rhythms regulate physiological and behavioural processes, with the light-dark cycle acting as the principal environmental cue synchronising the biological clock; disruption of this cue can affect brain function and behaviour. Using zebrafish (Danio rerio) as a translational model, we examined how chronic photoperiod alteration, applied from the larval stage to adulthood, affects exploratory activity, anxiety-like behaviour, aggression, and social preference, and whether these changes are paralleled by shifts in gut microbiota composition and brain transcriptomic profile. Zebrafish were reared under three photoperiod regimes: 14L/10D (control), 20L/4D (extended light), and 4L/20D (extended dark), followed by behavioural, gut metagenomic, and brain transcriptomic analyses. Extended darkness (4L/20D) reduced anxiety-like behaviour, whereas extended light (20L/4D) increased aggression both extended photoperiods altered social behaviour, but with distinct behavioural profiles. Gut microbiota in the 20L/4D group showed phylum-level co-dominance of Actinomycetota and Pseudomonadota, including a greater presence of potentially pathogenic taxa, while the 4L/20D group was dominated by Bacillota. Brain transcriptome profiling, based on a single pooled sample per condition, identified transcripts showing the largest expression differences in each group: in 20L/4D, transcripts linked to phototransduction (gnat1, saga, pde6ga, exorh), ribosomal function (rpl13a, rpl9, knop1), melatonin synthesis (asmt), calcium signalling (plcb4a), and glycolysis (eno1a) were elevated; in 4L/20D, transcripts linked to neuroprotection (nr4a1), DNA repair and chromatin remodelling (fance, uimc1, histh1l), synaptic plasticity (serpina10a), neurodevelopment (six6a), and cell-cycle regulation (btg2) were elevated. These findings indicate that photoperiod shapes zebrafish behaviour, gut microbial composition, and brain gene expression, providing a hypothesis-generating basis for future studies incorporating biological replication.},
}

Animals
*Zebrafish/physiology
*Brain/metabolism/physiology
*Photoperiod
*Gastrointestinal Microbiome/physiology
*Transcriptome
Circadian Rhythm/physiology
*Behavior, Animal/physiology

@article {pmid42814861,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {},
number = {},
pages = {OF1-OF17},
doi = {10.1158/0008-5472.CAN-25-5143},
pmid = {42814861},
issn = {1538-7445},
support = {1R37CA237384//National Cancer Institute (NCI)/ ; 1R01CA282786//National Cancer Institute (NCI)/ ; RP190256//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200173//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; 13723124//U.S. Department of War (DOW)/ ; P30CA125123//National Cancer Institute (NCI)/ ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

@article {pmid42815123,
year = {2026},
author = {Sun, Y and He, W and Yin, G and Wan, J and Yi, C and Ke, J and Shen, W and Zhang, M and Guo, R and Liu, Y and Shang, J and Chen, J and Liao, Q},
title = {Effects and mechanisms of sustained-release embedded composite biochar in carbon enhancement and acid reduction of acidified black soil.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131051},
doi = {10.1016/j.jenvman.2026.131051},
pmid = {42815123},
issn = {1095-8630},
abstract = {Black soils in Northeast China are undergoing acidification and organic matter degradation, and are in urgent need of efficient and environmentally sustainable improvement technologies. In this study, a novel sustained-release embedded composite biochar material was fabricated through a ball-milling integration process, in which biochar, reduced iron powder, and polymer materials were combined. A systematic screening process was established through the optimization of biochar substrate preparation conditions, the selection of functional loading components, and the development of a sustained-release carrier process. Through physicochemical characterization and evaluation of environmental effects, Chitosan-Fe-Biochar(CS-Fe-BC) and Polyacrylamide-Fe-Biochar(PAM-Fe-BC) were ultimately identified as the optimal materials. A 180-day incubation experiment was conducted under simulated climate conditions representative of Northeast China. Within 180 days, the application of 5‰ CS-Fe-BC[5] increased soil pH by approximately 0.5 units and enhanced SOC content by about 26.88%.The application of different material treatments effectively improved the structural integrity of the soil carbon pool, leading to significant increases in POC, ROC, andMOC contents. The metagenomic sequencing results revealed that, while maintaining overall abundance stability, the composite material reshaped the soil microbial community structure, facilitated the enrichment of functional bacteria involved in carbon fixation and acid mitigation, and achieved carbon enhancement and acid reduction through differentiated metabolic pathways. These findings suggest that the material plays a pivotal role in driving the processes of carbon accumulation and acid mitigation.The research findings may offer novel materialand theoretical support for the sustainable management of black soil acidification in Northeast China.},
}

@article {pmid42815128,
year = {2026},
author = {Wang, W and Sun, J and Wang, Z and Su, Y and Zhan, M and Hong, S and Xie, B},
title = {Enzymatic valorization of food waste leachate into volatile fatty acid-rich carbon source for enhanced denitrification.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131041},
doi = {10.1016/j.jenvman.2026.131041},
pmid = {42815128},
issn = {1095-8630},
abstract = {Food waste leachate (FWL) is a high-strength organic waste stream that poses increasing disposal and resource recovery challenges. This study developed an integrated enzymatic fermentation strategy to convert FWL into a volatile fatty acid (VFA)-rich carbon source for wastewater denitrification. Screening of ultrasonic, alkaline, alkaline-thermal, and enzymatic pretreatments identified the combined amylase-protease treatment as the most effective for FWL solubilization, increasing SCOD by 23.4% and promoting the release of biodegradable organic matter. During semi-continuous thermophilic anaerobic fermentation (55 ± 2°C, HRT 3 d), the enzymatically pretreated FWL showed enhanced VFAs production compared with the untreated system, with acetate and butyrate as the dominant products. The fermentation broth derived from enzyme-pretreated FWL achieved 99.5% NO3[-]-N removal within 8 h and showed nitrate-removal performance comparable to commercial sodium acetate. Metagenomic analysis indicated that enzymatic pretreatment enriched hydrolytic and acidogenic microorganisms associated with VFAs production, particularly Sporanaerobacteraceae and Tepidanaerobacter, while the VFA-rich fermentation broth promoted the enrichment of denitrifying bacteria such as Thauera and Paracoccus. Moreover, economic analysis shows that using FWL-derived fermentation carbon sources can reduce the estimated annual external carbon source cost by 34.4% compared to sodium acetate. These findings demonstrate a feasible waste-to-resource pathway for recovering intrinsic organic carbon from FWL as an alternative carbon source for wastewater denitrification.},
}

@article {pmid42815131,
year = {2026},
author = {Mu, X and Bi, J and Yu, Q and Han, Q and Wang, X and Li, H},
title = {Urban parks as potential hotspots for pathogenic determinants: A One Health perspective on environmental-human transmission risks.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131067},
doi = {10.1016/j.jenvman.2026.131067},
pmid = {42815131},
issn = {1095-8630},
abstract = {Urban parks are vital public spaces, yet their role as potential reservoirs and transmission pathways for pathogenic bacteria under the "One Health" framework remains poorly understood. We gathered paired soil, water, and human fecal samples from nine parks in Lanzhou, China. Metagenomic and 16S rRNA sequencing revealed abundant pathogenic bacteria, virulence factor (VF) genes, and pathogen-host interaction (PHI) genes. Pathogenic bacteria were significantly more abundant in water than in soil, and their presence was positively correlated with key environmental nutrients (TC, TN, TP, TS). Immune modulation and motility genes dominated the VF repertoire, while PHI genes primarily mediated virulence attenuation, maintenance, or enhancement. Crucially, the profile of these virulence genes was significantly shaped by the native bacterial community and mobile genetic elements (MGEs). Metagenomic binning provided direct genomic evidence that MGEs frequently co-localize with VF and PHI genes, demonstrating a high potential for horizontal gene transfer from park environments to humans. Our findings highlight urban parks as significant environmental reservoirs for pathogenic determinants and delineate the ecological and genetic drivers of their dissemination, providing a critical basis for targeted environmental management and public health protection.},
}

@article {pmid42410522,
year = {2026},
author = {Wu, S and Wang, K and Ge, X and Yuan, S and Wu, DD and Ge, C and Jia, J and Su, Z and Dou, T},
title = {Comparative and population genomics analyses of eared pheasants inhabiting highly varying altitudes.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42410522},
issn = {1471-2164},
mesh = {Animals ; *Altitude ; *Galliformes/genetics ; *Genetics, Population ; *Genomics ; Selection, Genetic ; Adaptation, Physiological/genetics ; Genetic Variation ; *Metagenomics ; },
abstract = {BACKGROUND: Oxygen pressure varies dramatically with altitudes on Earth; however, humans and animals thrive at almost all altitudes.

RESULTS: To better understand genetic basis underlying adaptation of closely related species to varying altitudes, we annotated and compared the genome of a white eared pheasant (WT) (Crossoptilon crossoptilon) inhabiting high altitudes and the genome of a brown eared pheasant (BR) (C. mantchuricum) inhabiting low altitudes. Moreover, we compared genetic variations in populations of WT and BR as well as of blue eared pheasants (BL) (C. auritum) inhabiting intermediate altitudes, and identified thousands of selective sweeps in each species.

CONCLUSIONS: Intriguingly, the unique genes and pseudogenes in the genomes of WT and BR converge on the same set of altitude adaptation-related pathways of four functional categories as genes in selective sweeps in each species. Thus, these species appear to adapt to highly varying altitudes by diverging selection on the same traits via loss-of-function mutations and fine-tuning genes in common pathways.},
}

Animals
*Altitude
*Galliformes/genetics
*Genetics, Population
*Genomics
Selection, Genetic
Adaptation, Physiological/genetics
Genetic Variation
*Metagenomics

@article {pmid42805094,
year = {2026},
author = {Schoier, AF and de Castro, ÍMS and Dorn, M},
title = {Foundation models and taxonomy inference for metagenomics: A practical review.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 1},
pages = {109409},
doi = {10.1016/j.compbiolchem.2026.109409},
pmid = {42805094},
issn = {1476-928X},
abstract = {Taxonomic classification in metagenomics remains anchored in alignment-based methods and exact k-mer indexers, which provide calibrated, traceable species-level assignments at scale when reference coverage is comprehensive. This review synthesizes the progression of the field toward self-supervised, DNA-specific foundation models, clarifying where they add value and how they should be evaluated. We report a structured literature search with explicit inclusion and exclusion criteria, and then critically compare families of approaches along two axes of practical relevance: reference coverage (in-index versus open-set) and read context and quality (short and accurate versus long and noisy). Across the evidence base, classical k-mer pipelines remain preferable for routine, high-throughput species-level assignment on well-covered clades, whereas the gains reported for foundation models at the read level are mixed and highly sensitive to evaluation design. The most plausible benefits arise under conditions of novelty, for long or noisy sequences, or when a calibrated back-off to higher taxonomic ranks is acceptable; embeddings can also support sample-level augmentation and quality control. Because pretraining and long-context inference impose substantial GPU and memory requirements, practical deployments favor hybrid designs: fast, reference-based classification for the bulk of reads, combined with compact, parameter-efficient adapters or selective embedding to rescore ambiguous cases and flag off-index content. We conclude with a roadmap that emphasizes standardized open-set benchmarks, joint reporting of accuracy and computational cost, and lightweight adaptation techniques that bring foundation-model components within reach of resource-constrained laboratories.},
}

@article {pmid42805174,
year = {2026},
author = {Perl, M and Guetter, S and Shah, D and Holzinger, S and Becker, L and Tariq, M and Menauer, P and Delahais, S and Lutzny-Geier, G and Scherer, JN and Göttert, S and Herfeld, K and Heinrich, P and Kreitmeier, KG and Gebhard, C and Herr, W and Trefny, MP and Doerr, J and Sameri, S and Harrer, DC and Ziegler-Martin, K and Staudt, S and Hansmann, L and Edinger, M and Wolff, D and Weber, D and Meedt, E and Denk, A and Gessner, A and Holler, E and Wertheimer, T and Neuhaus, K and Zheng, T and Cordas Dos Santos, DM and Theurich, S and Schirmer, M and Kleigrewe, K and Schluter, J and van den Brink, M and Schmitt, M and Feuerer, M and Heuser-Loy, C and Baldwin, J and Gattinoni, L and Rehli, M and Hudecek, M and Bigenwald, C and Zitvogel, L and Subklewe, M and Blumenberg, V and Schubert, ML and Stein-Thoeringer, C and Luu, M and Kobold, S and Fante, MA and Thiele Orberg, E and Poeck, H},
title = {Opposing functions of gut immunomodulatory metabolites on CAR-T therapy.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.004},
pmid = {42805174},
issn = {1097-4172},
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has transformed hematological cancer treatment, yet nearly half of patients still relapse or progress. Increasing evidence implicates the gut microbiome and antibiotic exposure as key modulators of clinical outcomes. In a cohort of 129 patients across three German centers, shotgun metagenomics and targeted mass spectrometry revealed that reduced short-chain fatty acids, particularly valeric acid, prior to CAR-T cell therapy correlated with increased risk of disease progression. Conversely, high levels of indole metabolites, including indole-3-carboxaldehyde and indole-3-acetic acid as well as the branched-chain fatty acid isovaleric acid, were linked to adverse outcomes. Functional validation in human and murine CAR-T cell models demonstrated that valeric acid supplementation enhanced, while indole-3-carboxaldehyde and isovaleric acid impaired, CAR-T cell efficacy. These findings reveal the opposing roles of immunomodulatory metabolites on CAR-T cell therapy, carrying significant implications for the design of metabolite-guided, microbiome-based therapeutics.},
}

@article {pmid42805386,
year = {2026},
author = {Hang, G and Sun, J and Kwok, LY and Gao, G and Li, W},
title = {An exploratory dual-platform metabolomics reveals region- and milk source-associated signatures in commercial cheeses.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-29087},
pmid = {42805386},
issn = {1525-3198},
abstract = {Commercial cheeses exhibit distinct compositional profiles shaped by milk substrate, production practices, and geographical terroir. However, the relative contribution of geographic origin versus milk source to cheese metabolomes remains poorly quantified, particularly in unstandardized commercial products. This exploratory study investigated region-associated metabolic signatures in commercially available cheeses, with a focus on comparing the relative contributions of geographic origin and milk source to metabolomic variance. We applied complementary volatile (HS-SPME-GC-MS) and non-volatile (UHPLC-MS/MS) metabolomic profiling to 32 commercial cheeses from Hungary (n = 11) and 3 Australian regions (Queensland, New South Wales, Victoria; n = 21), representing cow (n = 24) and goat/sheep (n = 8) milk sources. Multivariate ANOVA and random forest analyses revealed pronounced metabolic separation by geographic origin, which accounted for a substantially larger proportion of variance than milk source. Hungarian cheeses were enriched in citrate-derived flavor compounds (e.g., 2,3-butanedione, 2,3-butanediol), while Australian samples exhibited elevated lipid oxidation and branched-chain amino acid catabolites. Non-volatile profiles further highlighted regional differences in fatty acid composition and dipeptide abundance, with phenylalanine metabolism emerging as a consistent discriminant pathway. Correlation-based association networks revealed interconnected volatile and non-volatile metabolic modules. Since cheese variety, ripening protocols, and starter cultures were uncontrolled, observed patterns reflect region-associated metabolic signatures rather than causal terroir effects. These findings provide a preliminary metabolomic landscape for authenticity tracing and hypothesis-driven fermentation research. Future controlled trials integrating metagenomics and standardized production parameters are needed to isolate the specific contributions of geography, milk substrate, and processing technology.},
}

@article {pmid42805416,
year = {2026},
author = {Jiang, L and Li, J and Wang, H and Xie, R and Zhang, L},
title = {Single-stage autotrophic removal of thiocyanate and nitrogen from high-strength thiocyanate wastewater: start-up, performance, and metabolic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135971},
doi = {10.1016/j.biortech.2026.135971},
pmid = {42805416},
issn = {1873-2976},
abstract = {A single-stage partial nitrification and thiocyanate-driven denitrification (SPN-TDN) process offers a promising and resource-efficient route for simultaneous thiocyanate and nitrogen removal from high-strength thiocyanate (SCN[-]) wastewater. However, reliable start-up remains challenging because the establishment of this process requires coordination under contrasting oxygen and substrate conditions. Here, a sequencing batch reactor was operated for 384 cycles using a staged enrichment-optimization strategy to investigate how the synergistic process became established under increasing SCN[-] loading. During enrichment, SCN[-] removal remained above 98 %, partial nitrification was established, but total nitrogen (TN) removal stayed limited. In the optimization phase, TN removal progressively increased to 40 %, accompanied by biogenic elemental sulfur accumulation. Ex-situ batch tests confirmed SCN[-]-driven autotrophic denitrification, achieving 49 % TN removal with a nitrite/SCN[-] consumption ratio of 0.38. Community profiling showed that phase I established the dominant Thiobacillus (0.2 % to 23.0 %) and Nitrosomonas (0.99 % to 2.46 %), with the normalized stochasticity ratio indicating a greater deterministic contribution at both genus and species levels. Phase II largely retained this genus-level framework while exhibiting taxonomic-scale-dependent assembly and lineage-level turnover. Genome-resolved metagenomics further showed increased representation of cyanate-pathway lineages, a corresponding decline in the carbonyl sulfide-pathway lineages, and lineage-level turnover within ammonia-oxidizing bacteria. Collectively, successful process establishment involved multiple functional pathways during enrichment and subsequent pathway- and lineage-level reorganization under intensified constraints. These findings provide a mechanistic basis for understanding and further optimizing staged start-up of single-stage SPN-TDN for high-strength SCN[-] wastewater treatment.},
}

@article {pmid42805474,
year = {2026},
author = {Du, S and Shi, Y and Tong, C and Qi, X and Wen, H and Ji, B},
title = {Ferric iron enhances granule densification and pollutant removal in microalgal-bacterial granular sludge via iron-homeostatic microbial rewiring.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125791},
doi = {10.1016/j.envres.2026.125791},
pmid = {42805474},
issn = {1096-0953},
abstract = {Microalgal-bacterial granular sludge (MBGS) is a promising low-energy wastewater treatment technology, but the role of Fe[3+] concentration in regulating its structure and function remains unclear. MBGS was cultivated under four Fe[3+] concentrations (0.1, 1, 3, and 5 mg/L). At 5 mg/L Fe[3+], granules became more compact, with SVI5 decreasing from 80.0 to 60.1 mL/g and average size increasing from 1.72 to 1.90 mm. These changes were accompanied by enhanced extracellular polymeric substances (EPS) hydrophobicity despite reduced EPS production. The 5 mg/L treatment also increased dark-cycle COD and PO4[3-]-P removal, while NH4[+]-N removal remained unchanged. At 5 mg/L Fe[3+], Thauera and iron-associated Rubrivivax formed a synergistic consortium, supporting the superior dark-cycle pollutant removal. Metagenomic analysis revealed limited variation in C/N/P metabolic genes but strong iron-related regulation, with fur decreasing by 40.4% at 5 mg/L relative to the initial inoculum, suggesting a community shift toward iron-homeostatic configuration rather than a stress response. Four MAGs (Thauera mechernichensis MAG43, Rubrivivax sp. MAG118 and MAG36, and Microcoleus sp. MAG30) showed distinct C/N/P/Fe gene distributions, reflecting functional differentiation among community members. These findings provide a mechanistic basis for optimizing iron supplementation strategies to enhance the stability and performance of MBGS in practical applications.},
}

@article {pmid42805588,
year = {2026},
author = {Metris, A and Guan, R and Ampatzoglou, A and Murphy, B},
title = {Methods to Address Compositional Data Challenges in Clinical Studies for the Safety Assessment of Human Microbiome Perturbations.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100933},
doi = {10.1016/j.jfp.2026.100933},
pmid = {42805588},
issn = {1944-9097},
abstract = {Advances in sequencing technologies have enabled increasingly detailed characterisation of the human microbiome in clinical studies, but interpretation of microbiome modulation which has relevance to health and disease characterisation or safety assessments remains methodologically challenging. Taxonomic profiles generated by amplicon or shotgun sequencing are inherently compositional, sparse, and limited by detection, which complicates differential abundance analysis and may lead to unstable or misleading conclusions, especially in low-biomass settings where contamination and under-detection are concerns. Here, we review strategies used to analyse and complement sequencing-derived taxonomic count data, with the aim of obtaining more quantitative information on microbial differential abundance and viability. These include transformations for relative-abundance-based analyses and bias corrections between samples based on mathematical assumptions or additional experimental measurements such as spike-ins, broad-range qPCR and flow cytometry. We find that there is no consensus on which method best addresses compositionality and that detection level and significance of low-level microbes in health and diseases are overlooked. We discuss the limitations of sequence-based methods, such as the biases induced by the experimental and analytical process, as well as viability measurements for meaningful differential abundance assessment. We illustrate the need to integrate prevalence as well as abundance and the importance of covariates in models in the case of bacterial vaginosis. Overall, meaningful assessment of microbiome perturbations requires not only statistical correctness of differential abundance analysis, but also careful study design, appropriate measurement choices, quantitative context, and explicit recognition of the biological and analytical limits of sequencing-derived data.},
}

@article {pmid42805970,
year = {2026},
author = {Wu, Y and Su, Z and Zhang, B and Zhou, F and Xi, R and Peng, X and Li, Y and Yue, L and Wang, X and Chen, F and Lu, Y and Zhou, X and Ren, B and Li, J},
title = {Spatially resolved single cell atlas deciphers SAA1 inflammatory epithelial cells.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {},
pmid = {42805970},
issn = {2049-3169},
support = {81991501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170949//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024NSFSC1584//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2025ZNSFSC1910//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; },
mesh = {Humans ; *Epithelial Cells/metabolism ; *Serum Amyloid A Protein/metabolism ; Porphyromonas gingivalis ; *Inflammation/metabolism ; Transcription Factors/metabolism ; Cell Differentiation ; Periodontitis ; Single-Cell Analysis ; Gingiva/metabolism ; },
abstract = {Disruption of epithelial integrity is a pivotal event in inflammation, disease pathogenesis, and tissue homeostasis. To investigate these processes in chronic inflammatory disease, we performed spatial transcriptomics integrated with single-cell RNA sequencing (scRNA-seq) on human gingival tissue, coupled with metagenomic analysis of matched subgingival plaque. This approach allowed in situ characterization of epithelial heterogeneity and microbiome-epithelium-connective tissue crosstalk. We identified a distinct inflammatory epithelial subpopulation (SAA1+Epi), situated within the junctional epithelium, that becomes activated through the TLR2-PITX2 axis by Porphyromonas gingivalis lipopolysaccharide. These SAA1+Epi cells secrete TGFβ, which induces an inflammatory program in the connective tissue by driving the differentiation of inflammation-associated fibroblasts (C3+FB) via the PI3K/Akt pathway. Concurrently, SAA1+Epi cells express chemotactic factors such as CXCL6 to recruit NK cells, thereby sustaining the inflammatory niche. The transcription factor PITX2 emerged as a critical regulator of SAA1+Epi differentiation; targeting PITX2 suppressed C3+FB induction and natural killer (NK) cells recruitment, ultimately attenuating periodontitis progression. Our findings position SAA1+Epi as a frontline responder to dysbiotic bacteria at the inflammatory interface and underscore its essential role in regulating epithelial-connective tissue homeostasis during inflammation.},
}

Humans
*Epithelial Cells/metabolism
*Serum Amyloid A Protein/metabolism
Porphyromonas gingivalis
*Inflammation/metabolism
Transcription Factors/metabolism
Cell Differentiation
Periodontitis
Single-Cell Analysis
Gingiva/metabolism

@article {pmid42805991,
year = {2026},
author = {Minch, B and Moniruzzaman, M},
title = {Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42805991},
issn = {2041-1723},
support = {OCE-2346438//National Science Foundation (NSF)/ ; },
mesh = {*Genomic Islands/genetics ; *Genome, Viral/genetics ; *Giant Viruses/genetics ; *Mosaicism ; *Genetic Variation ; Evolution, Molecular ; Phylogeny ; Metagenome ; },
abstract = {Giant viruses in the phylum Nucleocytoviricota possess exceptionally large and mosaic genomes, yet the mechanisms underlying their remarkable plasticity remain poorly understood. Genomic islands are dynamic genomic regions that are major drivers of diversification and adaptation in bacteria. However, their contribution to giant virus evolution remains largely unexplored. Here, we characterize the genomic island landscape of giant viruses using 369 high-quality genomes spanning cultured isolates and long-read metagenome-assembled genomes. We identify 307 genomic islands across >50% of the genomes, demonstrating that these regions are pervasive across Nucleocytoviricota. These genomic islands are frequently associated with genomic hypervariability and enriched in genes involved in host interaction, particularly surface adhesion proteins, suggesting roles in host adaptation during the virus-host arms race. Comparative analyses further reveal these islands as hotspots of genome diversification, exhibiting frequent gain/loss and rearrangement even among highly similar genomes. Notably, many genomic islands are enriched in bacterial homologs, and several exhibit striking synteny with genomic regions recovered from co-occurring bacterial genomes, supporting large-scale genetic exchange between bacteria and giant viruses. Together, these findings identify genomic islands as pervasive and dynamic drivers of giant virus genome evolution, providing a framework for genome plasticity, mosaicism, and adaptive potential of giant viruses.},
}

*Genomic Islands/genetics
*Genome, Viral/genetics
*Giant Viruses/genetics
*Mosaicism
*Genetic Variation
Evolution, Molecular
Phylogeny
Metagenome

@article {pmid42806173,
year = {2026},
author = {Balasubramaniyan, M and Karthik, PA and Veeran, Y},
title = {Predicted shifts in microbial functional potential across the late glacial to holocene transition: a 16S rRNA-based inference from southeastern Arabian Sea sediments.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {10},
pages = {},
pmid = {42806173},
issn = {1572-9699},
mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; Phylogeny ; Seawater/microbiology ; *Archaea/genetics/classification/metabolism ; },
abstract = {Marine sediments preserve valuable records of ancient microbial communities. In this exploratory study, direct environmental amplicon sequencing reconstruction is often constrained by DNA degradation. In this exploratory study, we applied predictive functional profiling (PICRUSt2) to 16S rRNA gene amplicon data from five discrete sediment horizons spanning ~14.400 years (Bølling-Allerød, Younger Dryas, Early Holocene, Mid-Holocene, and Late Holocene) in the southeastern Arabian Sea. Inferred functional profiles based on Clusters of Orthologous Groups (COGs) pointed to variations in the predicted abundance of genes associated with carbon metabolism-specifically COG0183 (Acetyl-CoA acetyltransferase) and COG1024 (Enoyl-CoA hydratase/carnitine racemase)-and transport systems. Notably, the predicted potential for carbon metabolism reached its peak during the early Holocene, suggesting possible changes in carbon cycling dynamics during this warming phase. Principal component analysis accounted for 68.7% of the variance in predicted functions across time periods. While these findings are predictive and rely on amplicon-based inference, they provide a preliminary model of microbial functional reorganisation during major climate transitions, offering hypotheses for future high-resolution metagenomic validation.},
}

*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
*Microbiota/genetics
Phylogeny
Seawater/microbiology
*Archaea/genetics/classification/metabolism

@article {pmid42806489,
year = {2026},
author = {Song, K and Qin, Y and Luo, J and Liu, L and Luo, C and Qiu, Y and Zhong, Y and Zhong, H and Wu, K and Ni, M and Wu, D and Dai, M and Zhu, S and Chen, H},
title = {Gut Microbial Topology and Metabolic Signatures Associated With Colorectal Neoplasia.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77991},
doi = {10.1002/advs.77991},
pmid = {42806489},
issn = {2198-3844},
support = {2024YFA0918500//National Key Research and Development Project of China/ ; 2022-I2M-1-003//CAMS Innovation Fund for Medical Sciences/ ; 2025ZD0551704//National Science and Technology Major Program of China/ ; BRWEP2024W034010101//Beijing Research Ward Excellence Program/ ; 82273726//National Natural Science Foundation of China/ ; 82473705//National Natural Science Foundation of China/ ; XZ202501JD0021//Science and Technology Projects of Xizang Autonomous Region, China/ ; UGG06641//PUMCH Talent Development Program (Category B Project)/ ; 2025-LYZX-C-B03//National High Level Hospital Clinical Research/ ; 2025-PUMCH-C-048//National High Level Hospital Clinical Research/ ; },
abstract = {Alterations of gut microbial communities impact health. However, the structure and function of community-level topologies related to colorectal neoplasia (CRN) remain unclear. We analyzed 3807 newly sequenced stool metagenomes from participants (2725 healthy controls, 759 non-advanced adenomas, 297 advanced adenomas, and 26 colorectal cancers) in a multicenter TARGET-C screening trial and validated our findings in multiple independent cohorts. We identified a CRN-associated network (14 species, including Clostridium symbiosum) and a negatively associated network (37 species, including Roseburia and Lachnospira), forming a "seesaw-like" microbial association pattern characterized by within-group co-occurrence and between-group co-exclusion. The structures were stable across the independent datasets. A composite score derived from the microbial topology stratified CRN risk, and diagnostic models based solely on the presence/absence status of the topological species achieved moderate accuracy across the cohorts (area under the curve ranging from 0.66 to 0.87). Functionally, changes in CRN-related microbial association patterns were associated with microbe-derived metabolites. Our findings provide novel insights into the microbial topology associated with CRN and support its potential application in non-invasive risk stratification. However, the utility of these topological features in colorectal cancer remains exploratory and requires further validation in larger colorectal cancer cohorts.},
}

@article {pmid42806510,
year = {2026},
author = {Singh, S and Sharma, VK and Shrivastav, D and Kushwaha, JM and Mishra, MK and Beg, MMA},
title = {From Rhizosphere to Resistance: Microbe-Plant Interactions in Eco-Smart Biocontrol.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70398},
doi = {10.1002/mbo3.70398},
pmid = {42806510},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Plant Diseases/prevention & control/microbiology ; Pest Control, Biological/methods ; Soil Microbiology ; Plant Roots/microbiology ; *Biological Control Agents ; Microbiota ; Multiomics ; Crops, Agricultural/microbiology ; Fungi ; *Plants/microbiology ; },
abstract = {The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain biocontrol, eco-smart biocontrol integrates multi-omics discovery, artificial intelligence-assisted predictive microbiome design, and dynamic rhizosphere ecology. This review brings together ecological, molecular, and technological dimensions of eco-smart biocontrol, focusing on the rhizosphere as a dynamic hotspot for plant-microbe interactions. We investigate rhizosphere microbiome assembly and demonstrate the preferential recruitment of beneficial bacteria, fungi, actinomycetes, and mycorrhizal symbionts by plant root exudates. Moreover, the review highlights the impact of innovations in multi-omics techniques (metagenomics, transcriptomics, proteomics, and metabolomics), systems biology, and artificial intelligence on microbial biocontrol agent discovery, functional validation, and predictive design. Examples from cereal crops, legumes, and horticulture crops indicate that the application of beneficial microbial inoculants can significantly lower the burden of pests and diseases, enhance crop productivity, and fit perfectly within an integrated pest management system. Lastly, we critically analyze the main challenges preventing large-scale adoption, such as inconsistent field performance, limited microbial survival and competitiveness, and comparative regulatory frameworks across global markets. Ultimately, eco-smart microbial biocontrol combines mechanistic insights with omics-driven discovery, artificial intelligence (AI)- assisted prediction, advanced formulation strategies, and field-level validation, creating a strong, scalable, and environmentally friendly framework for resilient, low-input agricultural systems.},
}

*Rhizosphere
*Plant Diseases/prevention & control/microbiology
Pest Control, Biological/methods
Soil Microbiology
Plant Roots/microbiology
*Biological Control Agents
Microbiota
Multiomics
Crops, Agricultural/microbiology
Fungi
*Plants/microbiology

@article {pmid42806854,
year = {2026},
author = {Min, J and Niu, Z and Yin, J and Xu, S and Zhang, S and Mao, J and Liu, M and Li, L and Li, R and Zhang, H and Wu, X},
title = {Diagnostic value of metagenomic next-generation sequencing for bacterial and fungal detection and its role in antimicrobial therapy adjustment in critically ill patients with non-resolving pneumonia.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2740261},
doi = {10.1080/07853890.2026.2740261},
pmid = {42806854},
issn = {1365-2060},
mesh = {Humans ; Female ; Retrospective Studies ; Critical Illness ; Male ; Aged ; *Metagenomics/methods ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Intensive Care Units ; Bronchoalveolar Lavage Fluid/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Fungi/isolation & purification/genetics ; Bacteria/isolation & purification/genetics ; *Pneumonia/drug therapy/microbiology/diagnosis ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; },
abstract = {INTRODUCTION: Early targeted antibiotic therapy is critical for improving outcomes in ICU patients with pneumonia unresponsive to initial treatment. Metagenomic next-generation sequencing (mNGS) is a unique diagnostic tool; however, its effectiveness for high-risk populations remains unclear.

METHODS: This retrospective study included 642 ICU patients with pneumonia unresponsive to initial treatment, categorized into single- or repeat-test groups based on mNGS testing frequency. We analyzed the results of mNGS and conventional microbiological tests (CMTs), compared microbial detection characteristics between patients with different immune statuses, assessed the impact of repeat testing on microbial detection and treatment adjustments and evaluated its association with patient prognosis using multivariable logistic regression and propensity score matching.

RESULTS: Among 642 patients, patient-level agreement between mNGS and CMTs was low (κ = 0.180, p < 0.001). First bronchoalveolar lavage fluid (BALF)-mNGS results showed a higher microbial detection rate in immunocompromised than immunocompetent patients. Among patients undergoing repeat BALF-mNGS testing, partial concordance between first and second tests was most common pattern. Antibiotic treatments were modified in 67.6% of cases based on mNGS results, with a higher adjustment rate in the repeat-test group. Although ICU mortality was higher in the repeat-test group, multivariate logistic regression analysis revealed no significant association between repeat testing and mortality risk (adjusted odds ratio = 1.15, 95% CI: 0.64-2.06, p = 0.630). After propensity score matching, no significant difference was observed between two groups (absolute risk difference: 1.12%, 95% CI: -7.43% to 9.67%, p = 0.798).

CONCLUSION: mNGS is a valuable microbial detection tool for ICU patients with pneumonia unresponsive to initial treatment and can support early antimicrobial adjustment. Repeat testing can provide information on dynamic changes in the microbial spectrum during disease but was not associated with improved patient outcomes, suggesting that repeat testing frequency should be carefully considered to avoid unnecessary testing. mNGS results should be interpreted in conjunction with CMTs, host immune status and inflammatory biomarkers to optimise its clinical value in ICU pneumonia.},
}

Humans
Female
Retrospective Studies
Critical Illness
Male
Aged
*Metagenomics/methods
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Intensive Care Units
Bronchoalveolar Lavage Fluid/microbiology
*Anti-Bacterial Agents/therapeutic use
Fungi/isolation & purification/genetics
Bacteria/isolation & purification/genetics
*Pneumonia/drug therapy/microbiology/diagnosis
*Pneumonia, Bacterial/drug therapy/diagnosis/microbiology

@article {pmid42807009,
year = {2026},
author = {Li, J and Li, X and Zhong, H and Wang, L and Yue, L},
title = {Case Report: Sequential mNGS captures fatal HSV-1 reactivation after intestinal obstruction-associated ARDS in a 91-year-old.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1910309},
pmid = {42807009},
issn = {2296-858X},
abstract = {Herpes simplex virus type 1 (HSV-1) is a ubiquitous pathogen. Nevertheless, disseminated HSV-1 infection with confirmed viremia and fatal acute respiratory distress syndrome (ARDS) following intestinal obstruction in very old individuals is exceedingly rare. Here we report a 91-year-old patient with previously intact immunity who developed ARDS after incomplete intestinal obstruction, followed by HSV-1 reactivation. Although routine microbiological tests remained negative, five consecutive metagenomic next-generation sequencing (mNGS) assays dynamically tracked the evolving pathogens throughout the disease course. Despite broad-spectrum antibiotics, antifungals, antivirals, corticosteroids, IVIG, and mechanical ventilation, the patient's refractory hypoxemia remained uncorrected, leading to multiple organ dysfunction and death. This case highlights a rare clinical scenario and provides valuable insights for the diagnosis and management of critically ill elderly patients, offering a comprehensive, longitudinal perspective on the clinical application of mNGS.},
}

@article {pmid42807220,
year = {2026},
author = {Liu, Y and Liu, Y and Huang, S and Zhao, Y and Zhu, L and Wang, T and Liang, H and Liu, M and Geng, W},
title = {Systemic lupus erythematosus complicated by refractory Mycobacterium avium complex infection involving bilateral lower extremities: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1936197},
pmid = {42807220},
issn = {2296-858X},
abstract = {BACKGROUND: Patients with systemic lupus erythematosus (SLE) receiving long-term glucocorticoids and immunosuppressants are at markedly increased risk of opportunistic infections. Mycobacterium avium complex (MAC) is a common nontuberculous mycobacterial pathogen, but MAC osteomyelitis is extremely rare in non-HIV SLE patients, posing diagnostic and therapeutic challenges.

CASE PRESENTATION: We report a 52-year-old female with SLE on long-term prednisone, azathioprine, leflunomide, and hydroxychloroquine, who developed bilateral tibial and femoral osteomyelitis complicated by soft tissue abscesses, drug-induced dermatitis, and severe malnutrition. Conventional microbiological tests remained negative. Metagenomic next-generation sequencing (mNGS) of lower-extremity secretions and pus identified MAC. She underwent five surgical debridements and prolonged multidrug antimycobacterial therapy (azithromycin, rifampicin, ethambutol, amikacin), along with nutritional support and immunosuppressant adjustment. The infection was controlled with no SLE flare, and she recovered favorably.

CONCLUSION: Disseminated MAC osteomyelitis can occur in SLE patients under sustained immunosuppression even during disease remission. mNGS enables rapid pathogen identification and is crucial for diagnosing complicated infections. Management requires combined surgical debridement, prolonged antimycobacterial therapy, and multidisciplinary care.},
}

@article {pmid42807267,
year = {2026},
author = {Xu, N and Guo, T and Yang, Z and Zheng, Y and Wang, Y and Sha, W and Yin, B and Dong, W},
title = {Effects of dietary supplementation with bacteriocin-like inhibitory substance-producing Weissella cibaria XN-2a on growth performance, immune responses, and gut microbiota in crucian carp (Carassius auratus).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953174},
pmid = {42807267},
issn = {1664-302X},
abstract = {INTRODUCTION: The intensive farming of crucian carp (Carassius auratus) often compromises fish health and increases disease susceptibility, driving interest in probiotic interventions as sustainable alternatives to antibiotics. However, the in vivo efficacy and mechanistic basis of Weissella cibaria strains in freshwater fish remain poorly understood.

METHODS: A bacteriocin-producing strain, Weissella cibaria XN-2a, was isolated from fish viscera and supplemented in the diet of crucian carp at an initial viable dose of 2.74 × 10[10] CFU/g feed (freshly prepared and replaced every 3 days) for 30 days, followed by a challenge with Aeromonas hydrophila. Growth performance, immune parameters, intestinal histology, and gut metagenomic profiles were compared between the probiotic-fed group (XS) and the control group (XD).

RESULTS: Probiotic supplementation significantly improved weight gain (28.17% vs. 13.98%), feed conversion ratio (1.88 ± 0.32 vs. 2.58 ± 0.27, p < 0.05), and post-challenge survival (50% vs. 0%) (p < 0.001). The XS group exhibited enhanced intestinal morphology (higher mucosal fold height and FH/IFD ratio, lower inter-fold distance), elevated IgM and SOD activities, and reduced post-challenge IL-6 and MDA levels. Metagenomic analysis revealed that the probiotic reshaped the gut microbiota from a pathogen-associated virulence profile (LPS, flagella, enterobactin) toward a commensal profile enriched in T6SS/T2SS and alternative siderophores, without increasing the overall antibiotic resistance burden. The butanoate metabolism pathway showed differences consistent with increased butyrate synthesis potential, with enrichment of butyrate-synthetic enzymes (e.g., enoyl-CoA hydratase, acetolactate decarboxylase) in XS and butyrate-diverting enzymes in XD. CAZy profiling further showed enrichment of antibacterial (GH25/GH73) and antioxidant (AA4) gene families in XS, with Weissella as a major contributor.

DISCUSSION: These findings suggest that dietary Weissella cibaria XN-2a enhances growth performance, intestinal health, and disease resistance in crucian carp, potentially through a dual mechanism involving bacteriocin-mediated microbiota modulation and enhanced butyrate synthesis potential. Further investigations, including direct metabolite quantification, are warranted to validate these mechanistic inferences.},
}

@article {pmid42807290,
year = {2026},
author = {Huang, J and Xu, R and Liu, B and Liao, Q and Wang, M and Shan, Z and Zhong, H and Liao, F and Liang, H and Wang, H and Li, S and Fu, Y and Liang, H and Rong, X},
title = {Molecular confirmation of transfusion-transmitted dengue virus infection following platelet transfusion in the Chinese mainland.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1920581},
pmid = {42807290},
issn = {2235-2988},
mesh = {Humans ; *Dengue/transmission/virology/diagnosis ; *Dengue Virus/genetics/isolation & purification/immunology/classification ; *Platelet Transfusion/adverse effects ; RNA, Viral/blood/genetics ; Antibodies, Viral/blood ; China ; Immunoglobulin M/blood ; Retrospective Studies ; Immunoglobulin G/blood ; Viral Nonstructural Proteins/genetics ; Male ; Female ; Adult ; *Transfusion Reaction ; High-Throughput Nucleotide Sequencing ; Blood Donors ; Blood Donation ; East Asian People ; },
abstract = {BACKGROUND: Dengue virus (DENV) is considered an emerging threat to blood safety. While transfusion-transmitted DENV (TT-DENV) cases have been documented, TT-DENV has never been reported in Chinese mainland. In this study, a retrospective investigation was conducted after two patients developed dengue fever (DF) following apheresis platelet (PLT) transfusion from the same healthy donor.

METHODS: Blood samples from the recipients and the donor were tested for DENV RNA by nucleic acid testing (NAT). Nonstructural protein 1 (NS1) antigen and anti-DENV immunoglobulin M/G (IgM/IgG) antibodies were detected by ELISA. To confirm transmission, DENV E gene fragments were amplified, and whole-genome sequences were obtained by metagenomic next-generation sequencing (mNGS).

RESULTS: Our results revealed that the PLT donor was asymptomatic, tested positive for DENV RNA, and negative for anti-DENV IgM/IgG antibodies at donation. After donation, no dengue-like symptoms was developed. Seroconversion was observed at day 21 postdonation. After receiving the DENV-positive PLT unit, recipient 1 had DF only, while recipient 2 developed DF together with headache, joint/muscle pain, and rash. After transfusion, both recipients were positive for DENV RNA and NS1 while negative for anti-DENV IgM/IgG antibodies. Viral sequences from the donor and recipients were identical and belonged to DENV-2.

CONCLUSIONS: To our knowledge, this is the first TT-DENV case reported in the Chinese mainland, revealing the necessity of revising current donor deferral policies and testing strategies that predominantly rely on symptoms and travel history.},
}

Humans
*Dengue/transmission/virology/diagnosis
*Dengue Virus/genetics/isolation & purification/immunology/classification
*Platelet Transfusion/adverse effects
RNA, Viral/blood/genetics
Antibodies, Viral/blood
China
Immunoglobulin M/blood
Retrospective Studies
Immunoglobulin G/blood
Viral Nonstructural Proteins/genetics
Male
Female
Adult
*Transfusion Reaction
High-Throughput Nucleotide Sequencing
Blood Donors
Blood Donation
East Asian People

@article {pmid42807808,
year = {2026},
author = {Struillou, A and Deschamps, P and Moreira, D and López-García, P},
title = {Phylogeny-guided curation reveals widespread misannotation of Asgard archaeal 16S rRNA gene sequences in public databases.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag253},
pmid = {42807808},
issn = {2730-6151},
abstract = {Accurate taxonomic assignment of 16S rRNA gene sequences is essential for the reliable interpretation of microbial community studies based on amplicon sequence data. Yet, it critically depends on the reliability of reference databases such as the Genome Taxonomy Database (GTDB) and the SILVA ribosomal RNA database. Here, we evaluate the consistency of taxonomic annotations within the Asgardarchaeota phylum, a lineage of major evolutionary and ecological interest. Using a phylogenetically curated set of GTDB-derived 16S rRNA gene sequences, we show that most of the affiliations of these sequences were consistent with the phylogenomic placement of their corresponding metagenome-assembled genomes (MAGs), although a small fraction of them exhibited clear inconsistencies likely resulting from erroneous binning to MAGs. In contrast, phylogenetic analyses of SILVA-derived 16S rRNA gene sequences including curated reference sequences revealed widespread taxonomic misannotation and/or limited resolution of taxon assignment. Specifically, many sequences annotated as Odinarchaeales robustly clustered within Lokiarchaeia, Heimdallarchaeia, Hermodarchaeia, or Sifarchaeia, leading to an artificial inflation of Odinarchaeales assignments and potentially biased ecological interpretations. To mitigate these issues, we constructed a curated reference dataset of Asgardarchaeota 16S rRNA gene sequences and generated phylogenetically validated taxonomic assignments across clustered entries, providing a resource for improved classification of environmental sequences. Our results demonstrate that widely used reference databases can contain systematic annotation errors that propagate across studies and distort ecological inference. Although illustrated using Asgard archaea, these limitations are likely pervasive across understudied microbial diversity, highlighting the need for routine phylogenetic validation and systematic curation of reference datasets.},
}

@article {pmid42808285,
year = {2026},
author = {Wang, X and Patel, RH and Li, Q and Ching, CB and Schwartz, L and Rosado, JDR and Spencer, JD and Becknell, B},
title = {Leveraging Bioinformatic Strategies to Advance Care of Children With Urinary Tract Infections.},
journal = {Journal of paediatrics and child health},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpc.70607},
pmid = {42808285},
issn = {1440-1754},
support = {1R03DK140423-01A1/DK/NIDDK NIH HHS/United States ; LRP 2L40DK130152-02//NIH/ ; },
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections and pose a significant global health challenge in children. UTIs can cause a range of conditions from cystitis and pyelonephritis to bacteraemia. Current methods for diagnosing UTI lack adequate sensitivity and specificity and are time-consuming, driving demand for improved approaches. Although most UTIs resolve with antibiotic therapy, some children develop recurrent UTIs due to multidrug-resistant organisms and progressive chronic kidney disease. Currently, there are no reliable methods to identify which children are at risk for adverse outcomes, representing a critical gap in paediatric UTI management. This review explores how bioinformatic approaches can offer a comprehensive framework to harness scientific discoveries and meet clinical challenges posed by paediatric UTI. Recent advances in high-throughput sequencing and proteomics have generated extensive datasets, enabling detailed analysis of microbial and host responses during UTI. We summarize how computational and multi-omics approaches, including metagenomics, bulk and single-cell transcriptomics, proteomics, epigenetics and integrative frameworks, have deepened our understanding of UTI pathogenesis and the foundational determinants of a successful host response. We consider the collective potential of these discoveries and technologies to transform future UTI management.},
}

@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42809384,
year = {2026},
author = {Shen, Q and Shi, W and Liu, C and Cao, Z and Fu, Y and Ndjekadom, A and Wang, X and Liu, Y and Yang, S and Ji, L and Li, H and Zhou, C and Liu, J and Zhang, W},
title = {AI-Empowered Viral Metagenomics for Clinical Diagnosis: Advances, Bottlenecks, and Translational Pathways.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag239},
pmid = {42809384},
issn = {1365-2672},
abstract = {Viral metagenomics, leveraging high-throughput sequencing technologies, provides comprehensive, hypothesis-free characterization of viral communities in clinical specimens, establishing itself as a pivotal tool for clinical diagnosis, pathogen discovery, and epidemiological surveillance of viral infectious diseases. The integration of artificial intelligence (AI) has demonstrated transformative potential in viral metagenomic data analysis, significantly enhancing sequence classification, feature extraction, pattern recognition, and result interpretation, thereby improving analytical efficiency, accuracy, and automation. Machine-learning and deep-learning approaches have shown potential for detecting low-abundance viral signals and mitigating background noise in complex clinical samples, and facilitating pathogen identification in complex clinical samples, substantially augmenting the clinical utility of viral metagenomics. Nevertheless, routine clinical implementation faces persistent challenges, including high host nucleic acid background, low viral titers, contamination control, limited reference databases, absence of standardized analytical pipelines, and limited interpretability and generalizability of some predictive models. Furthermore, clinical validation, result reproducibility, ethical compliance, and data security represent critical translational barriers that impede widespread adoption. This review comprehensively summarizes recent advances and clinical applications of AI-empowered viral metagenomics, highlighting its transformative potential in pathogen detection, diagnosis of challenging infections, infectious disease surveillance, and precision medicine. We comprehensively address major technical bottlenecks and translational barriers that must be overcome to facilitate standardized development and clinical implementation of this emerging paradigm.},
}

@article {pmid42809394,
year = {2026},
author = {Chen, M and Liu, J and Tsai, HY and Li, CY and Batucan, JD and Eckhardt, CW and Pham, THD and Ellis, EK and Ratnayake, R and Paul, VJ and Bruner, SD and Donia, MS and Luesch, H and Ding, Y},
title = {Biosynthetic origin of anticancer dolastatin 15 reveals a noncanonical NRPS architecture enabling 2-keto acid activation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {40},
pages = {e2615454123},
doi = {10.1073/pnas.2615454123},
pmid = {42809394},
issn = {1091-6490},
support = {RM1GM145426//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM128742//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; AWD13127-2236414//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Depsipeptides/biosynthesis/chemistry/genetics ; *Peptide Synthases/metabolism/genetics/chemistry ; Multigene Family ; *Antineoplastic Agents/metabolism/chemistry ; *Cyanobacteria/genetics/metabolism ; Biosynthetic Pathways ; Phylogeny ; Genome, Bacterial ; },
abstract = {Elucidating the biological origins and biosynthetic pathways of marine natural products remains a major challenge, particularly for compounds derived from microbial consortia. Here, we identify the marine cyanobacterial genus Dapis as the source of the potent anticancer natural product dolastatin 15 using genome-resolved metagenomics. Reconstruction of two complete and two near-complete genomes provides genome-resolved characterization of the genus Dapis, revealing extensive biosynthetic potential. Genome mining identified the dolastatin 15 biosynthetic gene cluster. Subsequent analyses reconstructed its pathway and uncovered a noncanonical five-domain nonribosomal peptide synthetase module containing an embedded 2-keto acid-activating domain, revealing an unexpected architectural solution for incorporating 2-keto acid-derived hydroxy acid building blocks. Comparative and evolutionary analyses support a model in which this architecture may have arisen through recruitment of keto acid-activating domains and reduction of canonical adenylation domain features. We further biochemically and structurally characterize an O-methyltransferase that catalyzes formation of the characteristic methoxy pyrrolinone moiety, thereby validating a key terminal tailoring step in the proposed biosynthetic pathway. Together, these findings define the biosynthetic logic of dolastatin 15 and expand understanding of substrate activation and assembly-line diversification in nonribosomal peptide biosynthesis.},
}

*Depsipeptides/biosynthesis/chemistry/genetics
*Peptide Synthases/metabolism/genetics/chemistry
Multigene Family
*Antineoplastic Agents/metabolism/chemistry
*Cyanobacteria/genetics/metabolism
Biosynthetic Pathways
Phylogeny
Genome, Bacterial

@article {pmid42801164,
year = {2026},
author = {Ye, Q and Liu, Y and Zhang, K and Tian, M and Zhang, Z and Lin, M and Zheng, Y},
title = {Recent Advances and Future Perspectives in the Detection of Carbapenem-Resistant Acinetobacter Baumannii.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {612634},
pmid = {42801164},
issn = {1178-6973},
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major global public health threat. The World Health Organization (WHO) has classified CRAB as a critical priority pathogen. This threat is mainly attributed to its multidrug resistance, efficient nosocomial transmission, and limited therapeutic options. Timely and accurate detection is essential for early diagnosis, targeted antimicrobial therapy, and effective infection control. This review summarizes recent advances in CRAB detection technologies, including conventional phenotypic methods, nucleic acid amplification-based assays, genomic and AI-assisted diagnostics, mass spectrometry-based methods, and biosensor platforms. Conventional antimicrobial susceptibility testing (AST) remains the reference standard. However, it requires bacterial culture and isolation before testing, and the process usually takes 18-24 h after bacterial colony growth. This delay may limit its value for early therapeutic decision-making. Phenotypic carbapenemase assays provide complementary information on carbapenemase activity and resistance mechanisms, but their sensitivity, specificity, and clinical applicability vary across methods. Molecular methods substantially shorten turnaround times, with PCR and qPCR generally producing results within approximately 2-3 h. Isothermal amplification platforms further accelerate detection. LAMP-based assays report turnaround times of approximately 21-60 min, whereas RPA-based assays complete detection within approximately 40-90 min, supporting their potential application in point-of-care testing (POCT). Emerging genomic approaches, including whole-genome sequencing, nanopore sequencing, and metagenomic sequencing, enable comprehensive resistance profiling, outbreak investigation, and surveillance, while AI-assisted diagnostics may enhance resistance prediction and clinical interpretation. Mass spectrometry-based methods enable high-throughput species identification and can support resistance profiling in selected assay formats, with some assays detecting resistance-associated features within 15-90 min. Biosensor-based and CRISPR-integrated platforms offer highly sensitive, rapid, and portable detection, although challenges remain in multiplexing, standardization, cost, and clinical validation. Overall, this review highlights the transition of CRAB diagnostics from culture-based susceptibility testing toward integrated, automated, and clinically adaptable platforms, emphasizing the need to balance analytical performance, turnaround time, cost, and suitability for POCT.},
}

@article {pmid42801199,
year = {2026},
author = {Zhou, F and Cao, L and He, Y and Bai, J and Wang, Y},
title = {ViTax-RAG: a retrieval-augmented language modeling tool for viral contig taxonomic classification.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag247},
pmid = {42801199},
issn = {2635-0041},
abstract = {MOTIVATION: Taxonomic classification of viral metagenomic contigs remains difficult for short or divergent sequences. Reference-based methods are precise when close homologs exist, whereas representation-based models can generalize beyond direct matches but lack explicit biological evidence.

RESULTS: Here, we present ViTax-RAG, a retrieval-augmented framework that integrates alignment-derived evidence with learned sequence representations for robust viral classification. ViTax-RAG reformulates BLAST as a domain-specific retrieval module and integrates retrieved homology information into a sequence modeling framework, thereby enabling the complementary use of alignment-based and representation-based signals. We evaluated ViTax-RAG on in-distribution (ID) and within-genus out-of-distribution (OOD) datasets, where it consistently outperformed current viral taxonomy methods at comparable taxonomic endpoints and supported fragment lengths. The pipeline processed all 195 728 GOV 2.0 contigs; 87.2% of predictions terminated at class, demonstrating hierarchical backoff rather than fine-rank accuracy on data without ground truth.

ViTax-RAG is implemented in Python and is freely available at GitHub (https://github.com/Ying-Lab/ViTax-Rag) under an open-source license. Documentation and example workflows are provided to facilitate integration into metagenomic analysis pipelines.},
}

@article {pmid42801217,
year = {2026},
author = {Shen, F and Hu, L and Xin, C and Du, F and Zhang, S},
title = {Gut Microbiota and SCFA Changes After Alendronate-Calcitriol Therapy in Postmenopausal Osteoporosis.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {636595},
pmid = {42801217},
issn = {1179-1411},
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO) is driven primarily by estrogen deficiency, and gut microbiota-derived metabolites may participate in bone remodeling. The intestinal effects of conventional anti-osteoporosis therapy remain unclear. We investigated gut microbial and short-chain fatty acid (SCFA) changes associated with alendronate-calcitriol therapy in PMO.

METHODS: Forty-one postmenopausal women were enrolled, including 21 healthy controls and 20 patients with PMO. PMO patients received oral alendronate plus calcitriol for six months, with paired fecal samples collected before and after treatment. Shotgun metagenomic sequencing was used to assess microbial taxonomy, KEGG pathways, and CAZy profiles. Fecal SCFAs were quantified by gas chromatography-mass spectrometry.

RESULTS: After treatment, lumbar spine BMD T-score improved from -2.98 to -2.65, and femoral neck BMD T-score increased from -2.40 to -2.12, and all measured bone turnover markers (BALP, TRACP-5b, PINP and osteocalcin) decreased significantly (P < 0.05). Global microbial diversity did not differ significantly among groups, but treatment was accompanied by shifts in specific taxa. Roseburia, Megamonas, Dialister, and unclassified Lactobacillaceae increased, whereas Enterobacter, Salmonella, Raoultella, Serratia, and Rahnella decreased. Functional profiles showed treatment-associated shifts in propanoate metabolism, pyruvate metabolism, the TCA cycle, and selected carbohydrate-active enzyme patterns. Overall fecal SCFA composition remained relatively stable; however, propionic acid concentration increased significantly after treatment (FDR-adjusted P = 0.021). Correlation analyses linked selected commensal taxa and SCFAs with BMD and bone turnover markers.

CONCLUSION: Alendronate-calcitriol therapy was associated with improved bone metabolism and treatment-associated shifts in gut microbial composition, microbial functional potential, and propionate-related SCFA profiles. These findings provide preliminary evidence for microecological changes accompanying conventional PMO therapy.},
}

@article {pmid42801568,
year = {2026},
author = {Zhu, H and Chen, X and Li, Q and Sun, C and Xia, H and Huang, Y and Wang, C and Chen, P and Gao, C},
title = {Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77591},
pmid = {42801568},
issn = {2198-3844},
support = {XDA28030401//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2025YFF0512900//National Key R&D Program of China/ ; 32322053//National Natural Science Foundation of China/ ; },
abstract = {Community-level average genome size (AGS) is a key trait linking microbial diversity, functional potential, and eco-evolutionary strategy, yet estimates of AGS diverge markedly among common methods. Here, we introduce and validate a framework that adjudicates conflicting AGS estimates by testing which estimate yields a gap between scaled functional diversity and scaled taxonomic diversity that is consistent with the expected positive association between genome size and gene functional breadth. Across independent environmental gradients, metagenomic AGS estimates align with this framework and expectations from metagenome-assembled genome (MAG) dynamics and gene co-occurrence network module sizes, whereas 16S rRNA metabarcoding-based AGS estimates deviate, particularly in extreme environments with sparse reference coverage. Applying this validated framework, we reveal a U-shaped relationship between soil pH and AGS across a broad pH range, unifying prior findings of decreasing AGS from acidic to neutral soils with a newly observed increase along an alkaline gradient. Applying the same framework to a saline-gradient dataset, we further suggest that conclusions of a recent study regarding eco-evolutionary trade-offs under salt stress may stem from method biases. This work identifies a potentially pervasive conflict in AGS estimation, provides a framework to resolve it, and clarifies and expands relationships between AGS and the environment.},
}

@article {pmid42802002,
year = {2026},
author = {Li, H and Wang, J and Li, Y and Chen, X and Chen, L and Jin, X and Jin, P},
title = {Enriched multifunctional microbes coupling antibiotic resistance risk and nitrogen metabolic potential in eutrophic lakes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125764},
doi = {10.1016/j.envres.2026.125764},
pmid = {42802002},
issn = {1096-0953},
abstract = {Lakes are facing increasing threats from the dual challenges of eutrophication and antibiotic contamination, yet how microorganisms respond to these concurrent threats remains poorly understood. Here, we conducted a metagenomic binning investigation into the co-occurrence patterns of antibiotic resistance genes (ARGs) and nitrogen cycling functional genes (NFGs) within resistant microbes across three lakes with distinct eutrophic levels. We found a significant increase in the abundance and diversity of ARGs along the trophic gradient. Meanwhile, ARG hosts tended to show a transition pattern from carrying combinations of ARGs, virulence factor genes (VFGs), and NFGs to possessing highly integrated complexes encompassing ARGs, mobile genetic elements (MGEs), VFGs, and NFGs. This reflected the coupling between antibiotic resistance and nitrogen metabolism, and contributed to the survival of resistant microbes that cope with environmental stress. Furthermore, multifunctional hosts (accounting for 57.55%), dominated by Limnohabitans_A, CAISIP01, and RFTU01, could play important roles in linking ecological functions and biosafety risks under highly eutrophic conditions. These findings present a framework centered on multifunctional microbes for elucidating resistome evolution across varying trophic levels, thus guiding host-based strategies to inform ARG risk assessment and eutrophication management in lakes.},
}

@article {pmid42802107,
year = {2026},
author = {Beeby, N and Rasoanarimalala, C and Rasoavolandrainy, MF and Rothman, JM and Higham, JP and Sardaro, MLS and Amato, KR and Webster, TH and Baden, AL},
title = {Microbial and Metabolic Flexibility in Response to Habitat Disturbance in an Ecologically Specialist Primate.},
journal = {Molecular ecology},
volume = {35},
number = {18},
pages = {e70562},
doi = {10.1111/mec.70562},
pmid = {42802107},
issn = {1365-294X},
mesh = {Animals ; *Ecosystem ; Diet ; Forests ; *Gastrointestinal Microbiome/genetics ; *Strepsirhini/microbiology/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; Energy Metabolism ; Lemuridae ; },
abstract = {In the Anthropocene, understanding what renders a species prone to extinction is critical to wildlife management. Ecological specialists are hypothesised to be at particular risk, given that morphological, physiological, and/or behavioural constraints are expected to impede their responses to rapid habitat degradation. Nevertheless, studies have found mixed support for this hypothesis, raising the question, 'how resilient are specialists to environmental change?' Here, we test the hypothesis that ecological specialists, limited by behavioural and physiological constraints, may be at an energetic disadvantage in degraded habitats. Specifically, we tested whether Critically Endangered dietary specialist primates, black-and-white ruffed lemurs (Varecia variegata), living in secondary forests suffered nutritional and energetic deficits compared to those in primary forest habitats over a 12-month period. To do this, we used mixed modelling approaches to examine relationships among behaviour, nutritional chemistry, 16S sequencing, metagenome functional predictions, metabolite profiles, and energetic outcomes. Compared to primary forest-living conspecifics, we found that animals in the degraded forest consumed slightly fewer calories from less diverse diets. These animals exhibited less diverse gut microbiota, reduced microbial functional potential, and altered metabolomic profiles. Nevertheless, despite apparent nutritional constraints, energetic outcomes were broadly similar across habitats. These findings suggest that an organism's gut microbiome may be able to regulate microbial metabolic potential to facilitate resilience under suboptimal conditions. These findings highlight host-microbiome interactions as an important component of resilience in ecological specialists, with broad implications for predicting species persistence amid ongoing environmental change.},
}

Animals
*Ecosystem
Diet
Forests
*Gastrointestinal Microbiome/genetics
*Strepsirhini/microbiology/metabolism/physiology
RNA, Ribosomal, 16S/genetics
Energy Metabolism
Lemuridae

@article {pmid42802256,
year = {2026},
author = {Wang, Y and Huang, S and Pei, Y and Ma, H and Ji, L and Guo, S and Wei, B and Cai, S and Xue, Y and Lv, Z and Zhang, W and Yang, S},
title = {Identification and characterization of a novel Taupapillomavirus strain in lymphoid tissue of a stray dog.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {42802256},
issn = {1572-994X},
support = {2023YFD1801300//the National Key Research and Development Programs of China/ ; },
abstract = {In this study, viral metagenomic approach was employed to identify a novel canine papillomavirus (CPV) strain in the lymphoid tissue of a stray dog. The complete circular genome (8,297 bp) of a novel papillomavirus strain, designated canpapil01, was characterized and taxonomically assigned to the genus Taupapillomavirus. The genome encodes five early genes (E1, E2, E4, E6, E7) and two late genes (L1 and L2), lacking the E5 gene. Conserved motifs essential for viral replication and host interaction were identified, including ATP-binding and cyclin interaction sites in E1, DNA-binding domains in E2, and zinc-binding domains in E6 and E7. Notably, the pRb-binding motif (LXCXE) was absent in E7. The long control region (LCR) contained predicted E1 and E2-binding sites, indicating regulatory functions. Phylogenetic analysis based on the L1 gene revealed that canpapil01 clustered with Taupapillomavirus 2 strains, which were isolated from nasal swab or blood samples of dogs and wolves in the Switzerland and the USA, forming a separate branch. Genome-wide comparisons showed 71.4% amino acid identity with the Taupapillomavirus 2 reference strain (NC_040578), confirming it as a novel strain within this species. These findings expand the known genetic diversity of canine papillomaviruses and provide valuable genomic data for future research into CPV-associated diseases.},
}

@article {pmid42803159,
year = {2026},
author = {Merkesvik, J and Langa, J and Pietroni, C and Alberdi, A and Poulsen, LL and Bojesen, AM and Meuronen, T and Turunen, S and Kärkkäinen, O and Westereng, B and Pope, PB and Hvidsten, TR},
title = {Integrative holo-omic data analysis predicts interactions across the host-microbiome axis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0026326},
doi = {10.1128/spectrum.00263-26},
pmid = {42803159},
issn = {2165-0497},
abstract = {Understanding the interplay between host organisms and their microbiomes is central to the development of sustainable food systems. However, high dimensionality and spurious associations remain major obstacles to extracting meaningful biological insight from multi-omic host-associated microbiome data; a challenge further exacerbated when "holo-omic" analyses across the host-microbiome boundary are considered. Here, we show that a computational method designed for multi-omic analysis in eukaryotes can be leveraged to integrate and analyze five layers of holo-omic data from porcine hosts and their gut microbiomes. We collected caecal tissue and digesta samples during a feeding trial that tested the impact of microbiota-directed fibers (acetylated galactoglucomannan) at critical developmental stages. From 800,000 features including microbial and host genes, metagenome-assembled genomes, and metabolites from caecal tissue and digesta, we used multiset correlation and factor analysis to select the most relevant features for capturing coordinated patterns across omic layers. From these features, we predicted over 2,000 putative host-microbiome interactions based on co-occurrence. Some interactions reflected previously known relationships between animal and microbiome features, such as microbial genes for carbohydrate metabolism being linked to glycoside abundances in host tissue. Other predicted co-occurrences included features that were not detected in single-omic analysis and offer new hypotheses of host-microbiome interactions that warrant future investigation. Hence, we showcase an application of holo-omic analysis that avoids common pitfalls in high-dimensional data analysis, identifies known interactions as a form of validation, and most importantly, predicts new leads for understanding host-microbiome symbiosis.IMPORTANCEWhile study systems involving mammalian hosts and their microbiomes are inherently complex, multi- and holo-omic analyses promise to provide interpretable results with translational value for the animal production industry. Unfortunately, computational methods capable of this kind of integration are currently scarce, as most existing multi-omics approaches have been developed for analysis of data layers within a single multicellular organism. We propose to adapt existing multi-omic methods for holo-omics by combining feature selection and interaction inference. This two-step analysis approach addresses common challenges in data-driven studies and can be implemented with a variety of tools for feature selection and interaction modeling. Through this holistic approach, we show that both known and novel relationships across the holobiont axis can be identified in a data-driven manner, offering new targets for the continued study and experimental validation of host-microbiome interactions and the effect of dietary interventions on production animals.},
}

@article {pmid42803189,
year = {2026},
author = {Aplakidou, E and Baltoumas, FA and Chasapi, MN and Lamari, E and Chasapi, IN and Georgakopoulos-Soares, I and Karatzas, E and Iliopoulos, I and Aydin Buluç, and Finn, RD and Camargo, AP and Kyrpides, NC and Pavlopoulos, GA},
title = {"Quadrupling" the protein family space with global metagenomics.},
journal = {Nucleic acids research},
volume = {54},
number = {18},
pages = {},
doi = {10.1093/nar/gkag938},
pmid = {42803189},
issn = {1362-4962},
support = {23592-EMISSION//Foundation for Research and Innovation/ ; //Hellenic Foundation for Research and Innovation/ ; 28787-VIROMINE//Research Project to support Postdoctoral Researchers'/ ; 945405//Marie Skłodowska-Curie Grant agreement/ ; DE-AC02-05CH11231//University of Texas at Austin/ ; DE-AC02-05CH11231//Advanced Scientific Computing Research/ ; //US Department of Energy/ ; DE-AC02-05CH11231//US Department of Energy Office of Science/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; *Proteins/genetics/classification/chemistry ; Open Reading Frames ; Multigene Family ; },
abstract = {The known universe of protein families represents only a small fraction of nature's molecular diversity. From 40.3 billion predicted open reading frames across 40 446 metagenomes, 9540 metatranscriptomes, and 539 million proteins from 167 415 reference genomes, we identified 608 258 previously uncharacterized putative protein families with ≥100 members and 6.5 million families with ≥25 members, none matching known Pfam domains or reference proteins. This effort doubles the known repertoire of large families and quadruples that of smaller families. Integration of AlphaFold2-based structural predictions with gene-neighborhood and taxonomic analyses enables the characterization of these previously unannotated proteins, revealing candidates for both novel and known biological functions in understudied microbial lineages and biomes. This expanded repertoire provides insights into microbial adaptation and broadens the molecular toolkit available for biotechnology, highlighting the power of global metagenomics to uncover hidden protein diversity.},
}

*Metagenomics/methods
*Metagenome
*Proteins/genetics/classification/chemistry
Open Reading Frames
Multigene Family

@article {pmid42803406,
year = {2026},
author = {Saeed, M and Huang, X and Mustafa, G and Li, M and Yang, P},
title = {Rhizosphere Microbiome-Mediated Drought Resilience in Cereals: Implications for Grain Nutrition, Yield, and Tolerance.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70901},
pmid = {42803406},
issn = {1365-3040},
support = {2024BBB001//Hubei Provincial Key Research and Development Projects/ ; 2023AFB614//Hubei Provincial Natural Science Foundation/ ; 2023AFA016//Hubei Provincial Natural Science Foundation/ ; },
abstract = {Drought-mediated declines in grain nutritional quality and cereal yield put global food security at risk, yet the rhizosphere microbiome provides an alternative solution for improving crop tolerance. Our review synthesised existing knowledge on how soil microbiomes, particularly arbuscular mycorrhizal fungi (AMF) and plant-growth-promoting rhizobacteria (PGPR), simultaneously regulate three interlinked pillars of crop performance (stress tolerance, grain nutrient uptake, and yield) under drought. Our in-depth analysis showed that such relationships were governed by synergies (improved root architecture improves all three traits) and trade-offs (i.e., ABA-induced stomatal closure improves water efficiency but restricts carbon assimilation). Furthermore, these relationships were governed at different biological layers through multi-omics (metagenomics, transcriptomics, proteomics, and metabolomics) to identify biomarkers and pathways. With the application of an integrated framework through bioinformatics, it is now possible to reveal the hidden molecular layout between cereals and their underground partners, identify drought-responsive pathways, and discover biomarkers (nutrient transporter gene, microbial abundance, osmolyte accumulation, and root exudates). Despite advancements, critical technical gaps hinder data integration and standardised pipelines to identify complex traits through heterogeneous databases of omics. Our review proposes an integrated framework linking multi-omics tools, microbiome traits, and crop outcomes. Furthermore, we provide a research roadmap prioritising drought biofortification, synthetic communities (SynComs), microbial consortia, and spatial omics. Such research directly supports hidden hunger and food security agendas, while progressing climate-resilient agriculture.},
}

@article {pmid42803537,
year = {2026},
author = {Watts, TD and Jirapanjawat, T and Perlaza-Jiménez, L and Ricci, F and Tudor-Matthew, E and Chiri, E and Bay, SK and Grinter, R and Lappan, R and Lithgow, T and Woods, LC and Greening, C},
title = {Integrated cross-sectoral surveillance of antimicrobial resistance genotypes and phenotypes across disparate reservoirs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0074126},
doi = {10.1128/msystems.00741-26},
pmid = {42803537},
issn = {2379-5077},
abstract = {Antimicrobial-resistant (AMR) bacteria and genes are continually exchanged among humans, animals, and environmental reservoirs. Disparate and siloed surveillance methods present a major challenge for tracing and disrupting AMR transmission, with clinical monitoring focusing on detecting specific pathogens or specific genes of interest, and environmental surveys often relying on inferences drawn from indicator organisms. Here, we demonstrate that, following sample-specific pre-processing, common surveillance approaches can be applied consistently to profile AMR abundance, distribution, and phenotypes across diverse reservoirs in both urban and agricultural settings. Across all sample types, three core methods provided complementary insights: (i) quantitative PCR (qPCR) arrays to measure multiple AMR genes, (ii) gene- and genome-centric metagenomics for comprehensive resistome profiling, and (iii) culture-based genomics with susceptibility testing to link genotypes to phenotypes. We applied this approach to profile 1,032 metagenome-assembled genomes, 66 bacterial isolate genomes, and 78 and 6,642 AMR genes/reference sequences via qPCR and metagenomics, respectively. This integrated framework revealed the prevalence and diversity of resistance mechanisms in both putative pathogens and non-pathogenic bacteria with potentially transmissible genes, with wastewater especially enriched in AMR genes. We detected mismatches between genotype and phenotype predictions and a prevalence of intermediate resistance phenotypes, highlighting how many mechanisms of environmental resistance remain poorly understood. Overall, this study demonstrates that unified, field-leading surveillance methods can be used in diverse environmental and animal samples while highlighting that multiple methods are needed to capture the diverse AMR genotypes and phenotypes in these settings to enable comprehensive monitoring and adaptive solutions to restrict transmission.IMPORTANCEAntimicrobial resistance (AMR) is driven by the exchange of resistant bacteria and genes across interconnected human, animal, and environmental reservoirs, yet fragmented surveillance limits our ability to track transmission and intervene effectively. We demonstrate that widely used surveillance methods can be applied cohesively across diverse sample types, including wastewater, soil, water, agricultural environments, and fecal samples, to generate comparable insights into AMR abundance, diversity, and phenotype. By integrating qPCR, metagenomics, and culture-based genomics, we reveal resistance in both pathogenic and non-pathogenic bacteria, reaffirm wastewater as a major AMR reservoir, and uncover frequent mismatches between genetic predictions and observed susceptibility. The prevalence of intermediate resistance further suggests that many environmental resistance mechanisms remain poorly understood. These findings show that no single method captures AMR complexity and highlight the need for unified, multi-method surveillance to support comprehensive monitoring and strategies to control the spread of resistance.},
}

@article {pmid42803564,
year = {2026},
author = {Wolfe, MK and North, D and Jaffe, AL and Zulli, A and Duong, D and Shelden, B and Goldman, M and Richardson, M and Thana, P and Chan-Herur, V and Kheradpour, P and Bidwell, AL and Hilton, SP and Conforti, S and Paulos, AP and Boehm, AB},
title = {Prospective metagenomic sequencing of wastewater across the United States yields robust viral enrichment and concordance with digital PCR measurements.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0102026},
doi = {10.1128/aem.01020-26},
pmid = {42803564},
issn = {1098-5336},
abstract = {Metagenomic sequencing is increasingly applied to wastewater to characterize the diversity, dynamics, and relative abundance of human and animal viruses. Among these sequencing approaches are those that enrich viral nucleic acids from the wastewater matrix, aiming to increase the viral read fraction for analysis. However, the feasibility of scaling targeted viral sequencing to diverse sewersheds across large geographic scales is currently unknown. In this study, we apply hybrid capture metagenomic sequencing to nearly 450 weekly wastewater samples collected during the respiratory virus season in the United States and evaluate sequencing performance for generating public health-relevant data. Analysis of data from 15 wastewater treatment plants demonstrates that our approach enabled efficient capture of pathogens of interest, achieving a median viral read fraction over 19%. Importantly, relative abundance estimates of common pathogens correlated with direct quantification of viral targets using reverse transcription digital droplet PCR. Together, our results demonstrate that hybrid capture sequencing of wastewater is a viable tool to monitor both common and rare pathogens across geographically diverse sewersheds.IMPORTANCEWastewater testing is commonly used to identify and quantify human pathogens at a community scale. However, the most commonly used approaches rely on targeted, PCR-based methods that are highly specific to a single virus. Metagenomic sequencing provides an opportunity to detect and quantify the relative abundance of a wide range of viruses that are important for human health from wastewater, and hybrid capture approaches work by first enriching samples for these extremely rare targets to increase sensitivity. We demonstrate that hybrid capture metagenomic sequencing successfully enriches wastewater samples from diverse locations across the United States and that data derived from sequences are associated with detections of 11 key viruses using standard RT-ddPCR methods. This work suggests that scaling hybrid capture metagenomics for viruses in wastewater is a feasible way to generate data critical for public health to support infectious disease outbreak response.},
}

@article {pmid42803581,
year = {2026},
author = {Lim, S and Murali, R and Speth, DR and Szabo, RE and Cordero, OX and Orphan, VJ},
title = {Activity and diversity of sulfate- and methane-based pathways of anaerobic chitin and N-acetylglucosamine degradation in marine sediments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0128026},
doi = {10.1128/aem.01280-26},
pmid = {42803581},
issn = {1098-5336},
abstract = {UNLABELLED: Sulfate reduction is estimated to account for half of the organic carbon respiration in anoxic, organic-rich ocean sediments. Sulfate-reducing microorganisms (SRMs) typically oxidize simple carbon compounds, such as primary alcohols, or small fatty acids. However, much of the organic input to the seafloor is complex, driving interactions between terminal respirers, such as SRMs and methanogens, and primary degraders that initiate the breakdown of complex organic carbon. To explore how these interactions shape sediment microbiomes, we conducted multi-month microcosm experiments using serially diluted sediments in deep 96-well plates. Sediments from a former deep-sea whalefall site were amended with either the insoluble polymer chitin or its soluble monomer N-acetylglucosamine. The high replication in these experiments allowed us to evaluate the effects of complex versus labile carbon on degradation activity, microbial diversity, community structure, and functional redundancy over time. Geochemical analysis, combined with 16S rRNA gene sequencing and metagenomics, revealed that chitin addition preserved higher microbial diversity and increased predicted interactions among microorganisms. Despite anaerobic chitin degradation producing N-acetylglucosamine, microbial communities enriched by these substrates showed low nestedness over the 7-month experiment. Complex carbon inputs fostered unique microbial assemblages and functional interactions, including the emergence of diverse methanogenic lineages at medium to high dilutions-less apparent in monomer treatments. In microoxic sediments, methanogens and other rare biosphere members co-exist with SRM and dynamically respond to complex carbon inputs. Our results highlight the contribution of carbon complexity and recalcitrance in stimulating metabolically diverse community members in sediments, driving the assembly of functional microbial networks.

IMPORTANCE: Deep-sea sediments cover over 60% of the planet's surface and harbor diverse microbial communities that are important contributors to the carbon and nitrogen budget of the ocean. Despite their importance, the mechanisms by which these communities maintain diversity are poorly understood. In this work, we discuss the contribution of complex carbon to the community structure of marine sediment microbial consortia through the establishment of highly replicated anaerobic incubations provided with either the complex cosmopolitan carbon source chitin or its monomer N-acetylglucosamine.},
}

@article {pmid42803773,
year = {2026},
author = {Ettinger, CL and Eisen, JA and Stajich, JE},
title = {Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001845},
pmid = {42803773},
issn = {2057-5858},
mesh = {*Zosteraceae/microbiology/genetics ; *Metagenome ; Phylogeny ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Chytridiomycota/genetics/classification ; Genome, Fungal ; Diatoms/genetics/classification ; },
abstract = {Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, Zostera marina, have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with Z. marina leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Lobulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte alga in the genus Prymnesium (40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent undersequenced and possibly novel eukaryotic lineages. Of particular interest, the chytrid MAG was placed within the order Lobulomycetales, consistent with the identity of the dominant chytrid from previous Z. marina amplicon survey results. Annotation of this MAG yielded 5,650 gene models, of which 77% shared homology with current databases. Within these gene models, we predicted 121 carbohydrate-active enzymes (CAZymes) and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes has revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on CAZyme composition classified this MAG's CAZyme profile as most consistent with a symbiotic lifestyle. Overall, these five eukaryotic MAGs represent substantial genomic novelty and valuable community resources, contributing to a deeper understanding of the roles of fungi and other microbial eukaryotes in the larger seagrass ecosystem.},
}

*Zosteraceae/microbiology/genetics
*Metagenome
Phylogeny
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Chytridiomycota/genetics/classification
Genome, Fungal
Diatoms/genetics/classification

@article {pmid42803857,
year = {2026},
author = {Ali, S and Ali, B and Shaukat, A and Alghamdi, S and Kabrah, A and Ahmed, MA and Zhang, L},
title = {From dysbiosis to disease: the role of gut microbial communities in Toxoplasma gondii pathogenesis, zoonotic transmission, diagnostic innovation, and therapeutic outcomes.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42803857},
issn = {1573-7446},
mesh = {Animals ; *Dysbiosis/veterinary/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Toxoplasma/physiology ; *Zoonoses/transmission/parasitology/microbiology ; Humans ; *Toxoplasmosis, Animal/transmission/microbiology/diagnosis ; *Toxoplasmosis/transmission/therapy/microbiology/diagnosis/parasitology ; },
abstract = {Toxoplasma gondii, an obligate intracellular protozoan infecting approximately one-third of the global human population, causes substantial morbidity in immunocompromised individuals, congenital complications, neuropsychiatric sequelae, and considerable economic losses in livestock production. Gut microbial communities critically modulate T. gondii infection susceptibility, disease progression, and clinical outcomes, positioning the microbiome as a central axis in toxoplasmosis pathogenesis. This review examines the bidirectional relationship between gut microbiota and T. gondii, wherein dysbiosis functions simultaneously as a consequence and driver of disease severity. Protective commensal taxa reinforce intestinal barrier integrity, produce short-chain fatty acids, and stimulate anti-parasitic immunity through IFN-γ, IL-12, and tryptophan-aryl hydrocarbon receptor signaling, while pathobionts exacerbate immunopathology via TLR4 and inflammasome activation. Conversely, acute infection drives rapid microbial community collapse with persistent Proteobacteria expansion, butyrate-producing taxa depletion, neuroinflammation, and cognitive impairment in chronic infection. Across the One Health spectrum, host-specific microbiome signatures in felids, livestock, wildlife, and environmental reservoirs modulate zoonotic transmission dynamics and population-level susceptibility. Diagnostically, emerging microbiome-based approaches including metagenomics and multi-omics platforms offer promising biomarker discovery opportunities, though validated clinical signatures remain absent. Microbiome-targeted therapeutic strategies including probiotics, prebiotics, fecal microbiota transplantation, and postbiotics show preclinical promise, although human clinical trial validation is critically lacking. Critical research gaps and interdisciplinary One Health priorities are identified to advance microbiome-informed surveillance, diagnosis, and treatment of toxoplasmosis.},
}

Animals
*Dysbiosis/veterinary/parasitology/microbiology
*Gastrointestinal Microbiome
*Toxoplasma/physiology
*Zoonoses/transmission/parasitology/microbiology
Humans
*Toxoplasmosis, Animal/transmission/microbiology/diagnosis
*Toxoplasmosis/transmission/therapy/microbiology/diagnosis/parasitology