@article {pmid42580113,
year = {2026},
author = {Zhang, Y and Xu, Z and Chu, W and He, H and Ma, L and Zhang, J and Ye, C},
title = {Underappreciated role of polluted storm sewer discharge in the accumulation of antibiotic resistance genes in downstream sediments.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143253},
doi = {10.1016/j.jhazmat.2026.143253},
pmid = {42580113},
issn = {1873-3336},
abstract = {Polluted storm sewers (PSSs) are important pathways for contaminant transport to receiving waters, yet the association between PSS discharge and antimicrobial resistance in downstream sediments remains poorly understood. We investigated antibiotic resistance gene (ARG) distributions in paired upstream-downstream stream water and sediments around six PSS outfalls, together with PSS outfall samples, using metagenomic sequencing and binning. Downstream sediments exhibited transitional ARG profiles between upstream and PSS sediments, indicating a compositional linkage with PSS sediments. Acquired ARGs (sulfonamide and tetracycline resistance genes) were enriched in downstream sediments, while the intrinsic chromosomal resistance determinant mexB showed a similar pattern, consistent with their higher abundances in PSS discharges. SourceTracker indicated that sediment sources (87%) from upstream and PSSs contributed more to downstream sediment ARG profiles than water sources. The intermediate suspended solid levels in downstream water between PSS water and upstream water further supported particle-associated transport. Sulfonamide resistance genes were associated with putative plasmid contigs and co-occurred with qacEdelta1 and IS91, suggesting potential mobility. Azonexus was the dominant potential host of sulfonamide and tetracycline resistance genes, whereas Pseudomonas_E was associated with mexB enrichment. Collectively, these findings highlighted PSS discharge as an important anthropogenic pathway associated with ARGs in downstream sediments.},
}

@article {pmid42580122,
year = {2026},
author = {Gao, Z and Xue, L and Ma, Y and Chen, C and Ling, H and Wang, L and Zhang, W and Qian, J and Yang, Z and Hua, M and Pan, B},
title = {Mechanistic insights into low-dose nZVI-enhanced process stability under variable industrial loads in field-scale anaerobic treatment: Interfacial evolution and strain-resolved adaptation.},
journal = {Water research},
volume = {307},
number = {},
pages = {126665},
doi = {10.1016/j.watres.2026.126665},
pmid = {42580122},
issn = {1879-2448},
abstract = {Anaerobic treatment of industrial wastewater is limited by high variability and low biodegradability, which compromise process stability under varying industrial loads. A low-dose nanoscale zero-valent iron (nZVI)-augmented continuous-flow strategy was proposed and evaluated long-term in an on-site 3000 L reactor coupled to a full-scale expanded circulating granular sludge bed (ECSB). nZVI increased the mean chemical oxygen demand (COD) removal efficiency from 12.96% to 25.94% and reduced effluent fluctuation by 49%. Concurrently, sludge aggregation intensified, accompanied by protein enrichment in tightly bound extracellular polymeric substances (T-EPS) and a shift in dissolved organic matter (DOM) fluorescence toward humic-like hydrolytic intermediates. Metagenome-assembled genomes indicated a stable community core without structural replacement, alongside enriched iron-metabolism pathways. Incomplete electron-output pathways in key populations further suggest a possible contribution of nZVI-derived iron phases to conductive-material-mediated direct interspecies electron transfer (cDIET). Nonsynonymous single-nucleotide variant (SNV) trajectories and strain deconvolution further identified population-level selection in genes for iron homeostasis, oxidative stress, and electron transfer. These findings reposition nZVI from a reactive supplement to an interfacial stability regulator. More broadly, they provide field-scale evidence that refined nanomaterial dosing strategies can stabilize anaerobic treatment under real industrial loads by coupling interfacial reorganization with within-population adaptation.},
}

@article {pmid42580131,
year = {2026},
author = {Liu, C and Zhang, H and Guo, Z and Jiang, L and Yu, L and Zhu, C and Zhu, G},
title = {Electron flow boosted highly selective ammonium production from microbial nitrate reduction.},
journal = {Water research},
volume = {307},
number = {},
pages = {126656},
doi = {10.1016/j.watres.2026.126656},
pmid = {42580131},
issn = {1879-2448},
abstract = {Microbial dissimilatory nitrate reduction to ammonium (DNRA) process is considered as a bridge connecting nitrification and denitrification processes, which helps to improve the removal efficiency of nitrate wastewater. However, the competitiveness of DNRA was weaker than the denitrification, resulting in over 60-70% of nitrogen loss each year as N2 or N2O via denitrification. Here, we report a strategy of employing electron flow to rapidly initiate DNRA process (e-DNRA) with no external energy input. This e-DNRA strategy lies in establishing a high carbon-to-nitrogen ratio habitat to create favorable conditions for the growth and reproduction of DNRA bacteria. Subsequently, DNRA functional bacteria are enriched under reducing microenvironment induced by electron flow, ultimately forming a stable biofilm with high DNRA activity. By controlling extracellular electron flow, a nitrate reduction efficiency, conversion efficiency of nitrate to ammonium, and yield rate of 93.2%, 92.7%, and 1.23 µmmol N d[-1] g[-1] (MLSS) m[-3] were achieved, respectively. Transcriptome analysis and [15]N isotope tracing technology demonstrated that electron flow promoted the expression of nrfA gene by an order of magnitude. Genus-level microbial community structure revealed species Lentimicrobium, Geobacter, and Thauera are the primary determinants for the high DNRA efficiency. Moreover, metagenome-assembled genomes found that the electron flow increased the expression of cyt b and cyt c1 subunits in complex III by 1-2 orders of magnitude which sustained the high-rate DNRA. The proposed e-DNRA strategy provides a new solution for the synergistic treatment of nitrate wastewater and ammonium recovery.},
}

@article {pmid42580322,
year = {2026},
author = {Yang, L and Xiang, L and Rilong, J and Yihe, H},
title = {Tuberculous Arthritis Diagnosed by Metagenomic Sequencing after Negative Microbiology Studies and a 4-Year Delay.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.26-0309},
pmid = {42580322},
issn = {1476-1645},
abstract = {Tuberculous arthritis of the knee is a rare form of extrapulmonary tuberculosis that often presents with nonspecific symptoms, leading to delayed or missed diagnosis, particularly in elderly patients with comorbidities. We report the case of a 70-year-old man with a 2-year history of left knee pain and recurrent swelling. The patient was under therapy for lung cancer. He underwent two arthroscopic procedures for both diagnostic and therapeutic purposes. Repeated standard tests for tuberculosis were negative before metagenomic next-generation sequencing (mNGS) identified Mycobacterium tuberculosis nearly 2 years later. After 1-year triple-antituberculous therapy, he remained asymptomatic at the 2-year follow-up. This case highlights a high index of suspicion for indolent infection in culture-negative chronic arthropathy. The use of mNGS-increasingly accessible and cost effective-enables rapid and sensitive diagnosis of paucibacillary extrapulmonary tuberculosis.},
}

@article {pmid42580423,
year = {2026},
author = {Song, W and Shang, H and Yang, H},
title = {Performance stability and adaptability of embedded phosphorus removal biofillers: insights from microbial community responses and regulatory mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135602},
doi = {10.1016/j.biortech.2026.135602},
pmid = {42580423},
issn = {1873-2976},
abstract = {Given the typically low phosphorus (P) concentrations in municipal wastewater, this study established a reactor employing embedded P removal biofillers (EBPAOs). The P removal performance of the system was systematically evaluated under three aerobic-phase operating modes: high-P batch feeding (Experiment S), low-P batch feeding (Experiments T10-T2), and low-P continuous feeding (Phases A-E). The results exhibited that, under the low-P batch feeding mode, the aerobic P uptake rate (Pup-rate) of the EBPAOs followed the Michaelis-Menten equation (R[2] = 0.940). Under the continuous feeding mode, the Pup-rate remained stable throughout the aerobic phase. When the influent PO4[3-]-P concentrations were sequentially adjusted to 10, 8, 6, 4, and 2 mg/L, with corresponding hydraulic retention times (HRTs) of 60, 50, 40, 30, and 25 min, respectively, the aerobic effluent PO4[3-]-P concentration remained below 0.3 mg/L in all cases. The volumes of wastewater treated per cycle were 2.5, 3, 3.75, 5, and 6 times the nominal reactor volume, respectively. Microbial community analysis revealed that Candidatus_Accumulibacter (48.59-58.82%) was the dominant genus in the EBPAOs. Metagenomic analysis further showed that, as the influent PO4[3-]-P concentration decreased, polyphosphate-accumulating organisms (PAOs) consumed more COD to synthesize additional polyhydroxyalkanoates (PHA), thereby providing the energy required for efficient P uptake under aerobic low-P conditions. Concurrently, the abundances of the PstS gene and genes associated with the Embden-Meyerhof-Parnas (EMP) pathway, the tricarboxylic acid (TCA) cycle, and PHA synthesis were significantly upregulated. In conclusion, EBPAOs enable efficient and stable P removal from low-P wastewater.},
}

@article {pmid42580547,
year = {2026},
author = {Wei, Y and Zhu, L and Jin, X and Yao, H and He, S and Feng, P and Yu, F and Xiang, Y and Li, Z and He, S},
title = {Metagenomic indications of potential pathogen-associated and antibiotic resistance risks following UV-chlorine disinfection in sprout production.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128943},
doi = {10.1016/j.envpol.2026.128943},
pmid = {42580547},
issn = {1873-6424},
abstract = {Hydroponic agriculture commonly relies on low-pressure UV combined with chlorination (LPUV-chlorine) disinfection for water reuse, yet its impacts on non-coliform pathogens and associated resistance risks remain insufficiently understood. Here, metagenomic analysis of a commercial sprout production system revealed that LPUV-chlorine treatment did not completely remove pathogen-associated DNA signals and was associated with an increased relative abundance of Pseudomonas aeruginosa, accompanied by increased abundance of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). The relative abundances of VFGs related to biofilm formation and exoenzyme activity increased by 16∼18-fold compared to source water (SW), while β-lactam resistance genes showed marked increases in relative abundance. Network analysis revealed statistical associations between several pathogen-associated taxa and ARG profiles but did not establish their genomic hosts or transfer pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further revealed higher relative representation of genes associated with two-component systems and flagellar assembly, suggesting potential stress-adaptive functions and preferential persistence. In contrast, medium-pressure UV (MPUV) achieved ≥ 4-log reductions of P. aeruginosa, Escherichia coli, and Salmonella enterica within seconds, with 40.24%, 2.29%, and 26.44% lower fluence than LPUV, respectively. Transcriptomic analysis revealed decreased expression of selected virulence-associated genes and increased expression of phage-associated genes, suggesting potential effects on virulence-related functions and prophage responses. These findings highlight a potential pathogen-selection risk under LPUV-chlorine disinfection and indicate MPUV as a promising chlorine-free microbial risk control strategy in hydroponic water reuse systems.},
}

@article {pmid42581103,
year = {2026},
author = {Wang, R and Tabrizian, T and Wang, D and English, J and Ayer, A and Gal, M and Yang, WL and Wu, Z and Mao, K and Novaj, A and Zhang, X and Basu, I and Brodin, NP and Koba, W and Saxena, D and Choi, J and Augenlicht, LH and Ericsson, A and Gavathiotis, E and Guha, C and Huffman, DM},
title = {TNFR1 signaling connects inflammation to impaired fatty acid oxidation to drive intestinal stem cell aging.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {42581103},
issn = {2662-8465},
support = {P30CA013330//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 1210OD023591-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK020541//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; T32AG23475//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R56AG052981//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; P30AG038072//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; T32AG23475//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {Aging is characterized by a decline in function of intestinal stem cells (ISCs), but the extent to which this is shaped by systemic factors is unclear. Here we show that the ISC aging phenotype can be propagated from old to young mice utilizing heterochronic parabiosis, and implicate a role for inflammation in these effects, as anti-inflammatory drugs, including TNF antibodies, restored function. Parabiotic rescue experiments demonstrate that TNFR1 knockout protected young ISCs from the old environment. In young organoids, TNF downregulated crypt budding, while impairing mitochondrial pathways and fatty acid oxidation (FAO). However, aged ISC function was enhanced by boosting mitochondrial fusion, whereas FAO in aged crypts was improved by countering inflammation with salicylate treatment. Thus, these data identify the old environment through the progeronic factor TNF, as a driver of ISC aging phenotypes through intestinal epithelial cell TNF receptor 1 signaling to downregulate FAO, proliferation and regenerative capacity in these cells.},
}

@article {pmid42581991,
year = {2026},
author = {Song, X and Liu, X and Lou, M and Xu, J and Gong, X and Yang, Q and Chen, G and Mei, J},
title = {Atypical cat-scratch disease with acute high-grade fever and neuropsychiatric symptoms: a case report.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1810698},
pmid = {42581991},
issn = {2297-1769},
abstract = {OBJECTIVE: To report an atypical case of neurological cat-scratch disease (NCSD) presenting with acute-onset fever and prominent neuropsychiatric manifestations in an older adult.

PATIENT: An 85-year-old East Asian man with a history of hypertension and coronary artery disease.

RESULTS: Three months after a cat scratch, the patient developed abrupt high-grade fever, followed by nocturnal delirium with visual hallucinations and a witnessed seizure-like episode, and later complained of occipital headache. Physical examination revealed mild bilateral axillary and left supraclavicular lymphadenopathy without focal neurologic deficits. Cerebrospinal fluid cultures and stains were negative for bacteria and fungi. Serum metagenomic next-generation sequencing (mNGS) detected Bartonella henselae. After antibiotic therapy, the fever and headache resolved.

CONCLUSION: Cat-scratch disease should be considered as a rare but important infectious etiology in patients presenting with febrile illness accompanied by delirium or other neuropsychiatric symptoms. Clinicians should carefully inquire about recent cat exposure or scratch history and consider early pathogen-directed empiric antibiotic therapy to minimize diagnostic delay and improve outcomes.},
}

@article {pmid42582033,
year = {2026},
author = {Shi, P and Liu, Z and Wu, X and Zhao, F and Xu, J and Li, Q and Ye, M and Nian, D},
title = {Clinical utility of CSF metagenomic next-generation sequencing in suspected CNS infection: performance against a composite reference standard and read-count stratification.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905481},
pmid = {42582033},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/virology ; Male ; Reference Standards ; Adult ; Middle Aged ; Sensitivity and Specificity ; Aged ; *Cerebrospinal Fluid/virology ; Meningitis/diagnosis/cerebrospinal fluid ; Young Adult ; Adolescent ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is increasingly used to identify pathogens in suspected central nervous system (CNS) infections. However, integrating these results into real-world clinical decision-making remains problematic, particularly given the lack of standardized quantitative metrics beyond raw read counts.

METHODS: We retrospectively analyzed 46 patients with suspected encephalitis, meningitis, or meningoencephalitis who underwent CSF mNGS testing. Etiologic certainty was classified using a composite clinical reference standard as Definite, Probable, or Unlikely. We assessed concordance between mNGS findings and the Likely etiology category (Definite or Probable), calculated diagnostic performance metrics, characterized the detected pathogens, and explored a tiered interpretation framework based on maximum read counts per patient (<10, 10-49, and >=50). Trends across read-count strata were evaluated using the Cochran-Armitage test, and exact binomial 95% confidence intervals (CIs) were calculated.

RESULTS: CSF mNGS detected pathogens in 13 of 46 patients (28.3%). Positivity increased with greater adjudicated diagnostic certainty, from 0% in Unlikely cases to 11.8% in Probable cases and 73.3% in Definite cases. Within the composite reference framework, mNGS showed 40.6% sensitivity, 100% specificity, 100% positive predictive value, and 42.4% negative predictive value, indicating stronger rule-in than rule-out performance. Viral detections predominated, with herpes simplex virus type 1 and varicella-zoster virus as the most frequent pathogens; all findings should be interpreted in the context of DNA-only testing. Among mNGS-positive patients with Likely etiologies, the proportion classified as Definite increased across higher max-read strata, but these tier-specific estimates were imprecise and should be viewed as exploratory.

CONCLUSION: In this real-world cohort, positive CSF mNGS results supported an infectious etiology more strongly than negative results excluded it. Max-read-based stratification may have exploratory interpretive value for positive findings, but it should not be considered a validated clinical decision rule and requires confirmation in larger multicenter studies with standardized reference standards.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Female
*Metagenomics/methods
Retrospective Studies
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/virology
Male
Reference Standards
Adult
Middle Aged
Sensitivity and Specificity
Aged
*Cerebrospinal Fluid/virology
Meningitis/diagnosis/cerebrospinal fluid
Young Adult
Adolescent

@article {pmid42582222,
year = {2026},
author = {Zhang, Q and Zhang, Z and Zhang, Z and Qin, G and Jin, M and Chen, B and Yu, Y and Wang, T and Wang, M and Lu, T and Zhu, D and Cui, L and Qian, H and Rillig, MC and Zhu, YG},
title = {Potential plastic biodegradation in lakes worldwide.},
journal = {Innovation (Cambridge (Mass.))},
volume = {7},
number = {8},
pages = {101338},
pmid = {42582222},
issn = {2666-6758},
abstract = {Plastic pollution is ubiquitous, yet the biodegradation of plastic waste remains poorly understood due to limited knowledge of microbial plastic degradation potential. Here, we demonstrate that plastic waste shapes the global distribution of plastic-degrading potential across 182,661 lakes worldwide using integrated metagenomic and machine learning analyses and identify a tipping point (≥7.44 particles/m[3]) for effective in situ bioremediation. We constructed, for the first time, a catalog of candidate plastic-degrading bacteria, including 15,715 nonredundant enzyme homologs and 4,856 metagenome-assembled genomes. To facilitate future applications, we developed a computational approach to categorizing candidate plastic-degrading bacteria according to their degradation potential, ecological risk, environmental adaptation, and competition capacity. Furthermore, we customized eight template culture media based on the growth factor biosynthesis profiles of high-priority candidate plastic-degrading bacteria. Using these media, we successfully enriched the plastic-degrading microbial communities and isolated a high-priority strain, Serratia ficaria HfyG-1, from Xiazhu Lake, which harbors a wide variety of previously uncharacterized putative degrading enzymes that effectively degrade polylactic acid and polyethylene terephthalate. Our study provides a molecular resource for the bioremediation of plastic-polluted environments worldwide and highlights a proof-of-concept framework for identifying, investigating, and exploiting unknown functional microorganisms for practical applications.},
}

@article {pmid42582600,
year = {2026},
author = {Chen, J and Fan, W and Chen, X and Zhang, H and Feng, M and He, S and Song, C and Wang, J},
title = {Domestication shapes the gut microbial structure and metabolic function in felids: a metagenomic study of wild and domestic cats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1828152},
pmid = {42582600},
issn = {1664-302X},
abstract = {INTRODUCTION: The domestication process has profoundly altered the dietary patterns and living conditions of cats, with corresponding effects on their gut microbiome.

METHODS: This study compared the gut microbiota composition and metabolic functions between wild felids (Otocolobus manul and Felis bieti) and domestic cats using metagenomic sequencing.

RESULTS: Taxonomic analysis revealed significantly higher microbial alpha diversity and distinct community structure in wild felids compared to domestic cats. The gut microbiota of domestic cats was characterized by a higher relative abundance of Bacteroidota (when compared to F. bieti) and of Pseudomonadota, Uroviricota, and Cyanobacteriota, as well as an enrichment of carbohydrate-associated genera such as Segatella. In contrast, wild felids exhibited enrichment of potential pathogens (e.g., Clostridium perfringens, Escherichia coli) and genera including Clostridium and Fusobacterium, alongside a higher abundance of microbial genes linked to protein degradation and fermentation. Functional metagenomic analysis further identified consistent differences in microbial metabolic potential across both wild species comparisons. Wild felids showed higher abundances of genes involved in butyrate production, lysine degradation, and de novo synthesis of vitamins and cofactors. Domestic cats, in contrast, exhibited enrichment of genes for plant polysaccharide hydrolysis, ketone body formation, aromatic amino acid biosynthesis, and salvage of folate derivatives.

DISCUSSION: These results suggest that domestication is associated with a shift in the gut microbial functional repertoire - from a butyrogenic, protein-catabolic, and de novo-synthesizing profile in wild felids toward a more carbohydrate-hydrolyzing, ketogenic, and salvage-oriented profile in domestic cats, reflecting dietary and environmental adaptations.},
}

@article {pmid42582632,
year = {2026},
author = {Tshisekedi, KA and Van Den Bossche, T and Martens, L and De Maayer, P and Botes, A},
title = {Temporal and Functional Profiling of the Microbiome of High and Low Nitrogen Content Barley Seed in Silo Storage.},
journal = {Food science & nutrition},
volume = {14},
number = {8},
pages = {e72179},
pmid = {42582632},
issn = {2048-7177},
abstract = {Barley grain quality is influenced by nitrogen content and storage conditions; however, their impact on the composition and function of the grain microbiome is not well understood. This study combined metataxonomic (16S rRNA and ITS) profiling, metagenome sequencing, and metaproteome analyses to characterize the structure and function of the barley grain microbiome. Grains with high (> 1.5%) and low (< 1.5%) nitrogen content from a single barley cultivar (Kadie) were sampled at harvest and after 3, 6, and 9 months of storage. Amplicon sequencing revealed a community dominated by Proteobacteria, Firmicutes, and Ascomycota, while metagenomics confirmed the abundance of genera such as Erwinia, Pantoea, and Pseudomonas, aligning with previous reports of barley endophytes. While a consistent set of core microbial genera was identified, their relative abundances varied throughout storage. Metagenomic analysis revealed the high-nitrogen grain microbiome had potential for rapid metabolic activity that declined post-harvest, whereas the low nitrogen grain community sustained prolonged metabolic potential. Metaproteomics confirmed that these functional shifts revealed a temporal transition from active growth to stress tolerance. Findings from this work contribute to a better understanding of the barley grain microbiome during prolonged storage, offering insights that could help optimize storage for malting and brewing.},
}

@article {pmid42583033,
year = {2026},
author = {Bi, D and Yu, S and Zhang, M and Huang, Y and Dou, Z and Tian, B and Lu, J},
title = {The gut virome and regulatory T cell axis in health and systemic disease.},
journal = {Microbiome research reports},
volume = {5},
number = {2},
pages = {14},
pmid = {42583033},
issn = {2771-5965},
abstract = {The gut virome, comprising bacteriophages and eukaryotic viruses, represents a complex and dynamic component of the intestinal microbiome whose functional significance has long been underestimated. Emerging evidence highlights the gut virome as a pivotal modulator of the host immune system, particularly in regulating the balance and function of regulatory T cells (Tregs), which are essential for maintaining immune homeostasis. This review distinguishes two mechanistic axes by which the virome influences Tregs: (i) an indirect 'virome-bacteriome-metabolite-Treg axis', and (ii) a direct 'viral pathogen-associated molecular patterns (PAMPs)-pattern recognition receptors (PRRs)-Treg' signaling axis. This review comprehensively examines the dualistic role of the gut virome in preserving intestinal equilibrium and its involvement in the pathogenesis or amelioration of intestinal inflammatory disorders such as inflammatory bowel disease (IBD). Furthermore, the influence of the gut virome extends beyond the gut, potentially impacting systemic immune-related diseases. By integrating recent advances in metagenomics, viromics, and immunology, we elucidate the molecular mechanisms through which the gut virome orchestrates immune regulation. This synthesis aims to provide a comprehensive understanding of the gut virome as a critical immune regulator and to explore its potential as a biomarker for disease diagnosis and a novel target for therapeutic intervention.},
}

@article {pmid42583788,
year = {2026},
author = {Han, L and Wu, X and Gong, B and Li, X and Li, X and Wang, Z},
title = {A Two-Sample Mendelian Randomisation Analysis of the Oral Microbiome and Oral/Oropharyngeal/Tongue Cancers.},
journal = {Oral health & preventive dentistry},
volume = {24},
number = {},
pages = {613-621},
doi = {10.3290/j.ohpd.c_2778},
pmid = {42583788},
issn = {1757-9996},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Tongue Neoplasms/microbiology ; *Oropharyngeal Neoplasms/microbiology ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Mouth Neoplasms/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Tongue/microbiology ; },
abstract = {OBJECTIVE: To assess the potential causal relationships of the oral microbiome with the risks of oral cancer, oropharyngeal cancer, and tongue cancer using two-sample Mendelian randomisation (MR) analysis, while distinguishing these from reverse causal effects of the cancers on microbial abundance.

METHODS AND MATERIALS: Using single-nucleotide polymorphisms as instrumental variables, we applied the MR inverse-variance-weighted approach to evaluate the effects of the dorsal-tongue and salivary microbiomes on oral, oropharyngeal, and tongue cancers. Analyses were conducted with the R package TwoSampleMR, leveraging genome-wide association study (GWAS) summary statistics from CNGBdb, the FinnGen consortium, and other sources. Sensitivity, heterogeneity, and pleiotropy assessments were performed. Additionally, reverse MR sensitivity analyses were conducted to explore the possible causal influence of cancers on the oral microbiota.

RESULTS: Using a single nucleotide polymorphism (SNP) significance threshold of p 5 × 10-6, our large-scale MR study revealed genetically supported causal relationships between microbial taxa derived from saliva and the tongue and the risk of oral, oropharyngeal, and tongue cancers. Integrating these results, we found that both 's Veillonella_rogosae_mgs_2008' and 's unclassified_mgs_1048' conferred a reduced risk of oropharyngeal and tongue cancers. Sensitivity analyses based on heterogeneity tests and pleiotropy evaluations further corroborated the robustness of our findings, lending additional credibility to the conclusions.

CONCLUSION: This study leveraged large-scale publicly available genetic data and identified significant causal relationships between the oral microbiota and cancers of the oral cavity, oropharynx, and tongue. Reverse MR analyses indicated that oral and tongue cancers may in turn alter the abundance of specific oral microbes, suggesting a potential bidirectional causal loop. Future work should integrate metagenomic data to further validate these microbiota-cancer associations.},
}

Humans
*Mendelian Randomization Analysis
*Microbiota/genetics
*Tongue Neoplasms/microbiology
*Oropharyngeal Neoplasms/microbiology
Polymorphism, Single Nucleotide
Genome-Wide Association Study
*Mouth Neoplasms/microbiology
Saliva/microbiology
*Mouth/microbiology
Tongue/microbiology

@article {pmid42583799,
year = {2026},
author = {Lee, I and Suk, KT and Park, JY and Yong, D and Kim, DJ and Kim, BS and Lee, SS},
title = {Fecal microbiota transplantation accelerates clearance of carbapenemase-producing Enterobacterales intestinal carriage: influence of recipient gut microbiome ecology.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag414},
pmid = {42583799},
issn = {1537-6613},
abstract = {BACKGROUND: Persistent intestinal carbapenemase-producing Enterobacterales (CPE) carriage challenges infection prevention and antimicrobial stewardship. We evaluated fecal microbiota transplantation (FMT) for decolonization and response-associated recipient microbiome features.

METHODS: This prospective cohort study assessed intestinal CPE clearance in 131 adult carriers (68 receiving FMT; 63 under observation). Responders achieved clearance, defined as three consecutive negative rectal surveillance cultures for CPE, obtained at 3-day intervals within 1 month after FMT. Following least absolute shrinkage and selection operator (LASSO)-based covariate selection, Cox proportional hazards models estimated associations between FMT and time to successful decolonization within prespecified 0-30-day and 0-90-day windows. A longitudinal metagenomic subcohort of 21 FMT recipients (102 fecal samples) underwent shotgun sequencing to characterize taxonomic composition, microbial network organization, functional pathways, antimicrobial resistance genes (ARGs), and donor engraftment.

RESULTS: After LASSO-based covariate selection, FMT was associated with faster CPE clearance than observation at 1 month (hazard ratio, 4.02; 95% confidence interval, 1.84-8.79), with effects sustained at 3 months. Responders showed relatively preserved baseline microbial network organization and enrichment of taxa annotated with arginine-related pathway features, suggesting metabolic relevance to microbial niche competition. After FMT, responders had greater engraftment of donor-associated taxa and donor-like ecological reassembly, with reduced Klebsiella pneumoniae dominance and ARG abundance.

CONCLUSIONS: FMT may accelerate intestinal decolonization in CPE carriers; response variability was associated with recipient gut-microbiome ecology, suggesting microbiome-guided patient selection could optimize microbiota-based strategies.},
}

@article {pmid42584065,
year = {2026},
author = {Roush, C and Whiteley, M},
title = {Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0182026},
doi = {10.1128/spectrum.01820-26},
pmid = {42584065},
issn = {2165-0497},
abstract = {Bacteriophages (phages) are being explored as alternatives or complements to antibiotics because of their ability to selectively kill bacterial pathogens. However, phages that infect many oral bacteria remain undiscovered. Here, we discovered that dental wastewater harbors previously underexplored phage diversity. Viral particles concentrated from dental wastewater displayed diverse morphologies, including abundant filamentous phage-like particles. Deep long-read metagenomic sequencing of concentrated viral particles generated 7.4 billion bases of sequence data and yielded 255 medium- to high-quality viral operational taxonomic units (vOTUs), including 46 predicted complete genomes. Comparison with large phage databases revealed that 63 of these 255 vOTUs had no detectable match, indicating that extensive sequencing of dental wastewater substantially expands the number of potential bacteriophages associated with the human oral microbiome. Host prediction linked many vOTUs to oral-associated bacterial taxa, including species with few or no previously reported phages, such as Porphyromonas gingivalis, Tannerella forsythia, and Candidatus Saccharibacteria. Functional annotation identified diverse genes associated with antiphage defense systems within a subset of vOTUs, suggesting that oral phages may contribute to the movement of genes encoding bacterial immune functions within the oral microbiome. Together, these findings expand the known oral phageome and show that dental wastewater contains a largely untapped diversity of phages.IMPORTANCEThe human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phages shape oral microbial communities. Here, we show that dental wastewater is an underexplored source of oral phage diversity. Deep long-read metagenomic sequencing revealed 255 medium- to high-quality phage operational taxonomic units, many of which are not present in existing oral phage databases. These genomes include predicted phages of periodontal disease-associated bacteria and other oral taxa with few or no known phages. Dental wastewater therefore expands the known human oral phageome and reveals candidate phages linked to bacteria associated with oral health and disease.},
}

@article {pmid42584072,
year = {2026},
author = {Eiler, A},
title = {Rethinking evolutionary inference in metagenomic time series.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0069326},
doi = {10.1128/msystems.00693-26},
pmid = {42584072},
issn = {2379-5077},
abstract = {As ecologists increasingly use metagenomic time series to track evolution in the wild, there is a risk of misinterpreting ecological dynamics as rapid adaptation. This Perspective identifies methodological limitations that generate misleading signatures of microbial evolution. A primary issue is confusing evolutionary change (driven by de novo mutation or horizontal gene transfer) with ecological lineage turnover, such as seasonal oscillations or the reactivation of dormant lineages. Current metagenome-assembled genomes can collapse micro-diverse lineages and decouple adaptive mobile elements, creating inaccurate genomic signatures of sweeps or stasis. To address these issues, I propose a framework integrating long-read sequencing, pangenome graph theory, and forward-time simulations to model populations as temporal genetic networks and better resolve microbial evolutionary dynamics.},
}

@article {pmid42584101,
year = {2026},
author = {Yu, D and Zhang, L and Agu, D and Gao, N and Xiao, Y and Zhang, M and Zhang, J and Yan, J},
title = {Temporal succession of microbiomes and resistomes during buried rat carcass decomposition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043726},
doi = {10.1128/msphere.00437-26},
pmid = {42584101},
issn = {2379-5042},
abstract = {Burial is a prevalent approach for disposing of human and animal carcass. Carcass decomposition is a key natural disturbance that reshapes microbial communities and modulates biogeochemical cycles. Animal intestines serve as critical natural reservoirs of antibiotic resistance genes (ARGs), and carcass decomposition concurrently remodels intestinal bacterial assemblages and resistome profiles. Most previous studies have characterized microbial succession in surface-exposed carcasses, yet the coordinated temporal shifts of intestinal microbiota, resistomes, and horizontal gene transfer (HGT) signatures within buried carcasses remain underexplored. We established a buried rat carcass model and performed metagenomic sequencing to characterize temporal dynamics of intestinal bacteria, ARGs, mobile genetic elements (MGEs), and HGT events. Bacterial communities underwent directional succession accompanied by reduced α-diversity and stage-specific β-diversity. Proteobacteria gradually outcompeted Firmicutes and Bacteroidetes to become dominant taxa. The resistome followed regular temporal changes: tetracycline and macrolide-lincosamide-streptogramin (MLS) ARGs prevailed in early decomposition, while multidrug, β-lactam, polymyxin, and quinolone ARGs accumulated in mid-late stages, with ARG richness peaking on day 28. Approximately 83% of temporally dynamic ARG subtypes were positively correlated with decomposition duration. Procrustes analysis (R[2] = 0.859) revealed strong correlations between bacterial succession and resistome dynamics, with Proteobacteria as potential multidrug-resistant hosts and major HGT donors. This study identifies a correlative cascade of microbial succession that drives MGE functional shift, which in turn increased HGT potential and ultimately leads to resistome accumulation in buried carcass intestinal habitats. These findings expand the theoretical framework of disturbance-driven microbial-resistome co-succession and offer insights into drivers of antibiotic resistance propagation in terrestrial cadaver systems.IMPORTANCEAnimal carcass burial is a ubiquitous natural terrestrial disturbance, and carcass intestinal contents represent a major endogenous reservoir of environmental antibiotic resistance genes (ARGs). Although extensive research has characterized microbial succession of exposed carcasses, the co-occurrence patterns of gut microbiome and resistome together with associated horizontal gene transfer (HGT) under buried conditions remain underexplored. Using metagenomic profiling of decomposing rat intestinal feces, this study explores a potential correlative cascade spanning bacterial succession, mobile genetic element (MGE) functional shifts, increased HGT potential, and gradual ARG enrichment. Our findings expand the ecological data set focused on subsurface buried carcass habitats and advance mechanistic knowledge of coupled microbiome-resistome succession driven by postmortem decomposition.},
}

@article {pmid42584108,
year = {2026},
author = {Vaziri, GJ and Pritchard, JC and Howard, JI and Stamm, GE and O'Connor, DH and Newman, CM and Aliota, MT and Dzikwi-Emennaa, A},
title = {Metagenomic sequencing detects viruses and bacteria in a cross-sectional clinical cohort of undifferentiated febrile illness in Nigeria.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0015726},
doi = {10.1128/msphere.00157-26},
pmid = {42584108},
issn = {2379-5042},
abstract = {UNLABELLED: Molecular and microscopy-based diagnostic capacity is often insufficient or unavailable in places where infectious disease burdens are highest, such as in West Africa. Rapid diagnostic testing (RDT) can provide quick and affordable diagnoses of common infections but is an imperfect solution due to limitations around detecting and dealing with false-negative and false-positive results. An alternative to RDT is unbiased metagenomic sequencing for pathogen surveillance. Here, we present data from unbiased metagenomic sequencing used to identify causes of undiagnosed febrile illness in Jos, Plateau State, Nigeria. Proof of concept for this approach has been demonstrated by several groups who have identified epidemic and endemic viral diseases like Lassa fever, yellow fever, and chikungunya. We show that unbiased deep sequencing and metagenomic analysis can be used to identify RNA viruses in clinical samples. We sequenced RNA from sera of patients (n = 343), many of whom were acutely febrile (76%), in a survey of clinics in Jos. We detected five human-infecting viruses in 39 (11 %) specimens. Among these were hepatitis B virus, human pegivirus, and several anelloviruses. While most of the viruses identified are unlikely to cause clinical symptoms in the patients we sampled, their presence demonstrates the validity of our approach. Additionally, our sequencing data allowed us to identify genetic material from potentially pathogenic bacteria, another possible etiological agent of febrile illness.

IMPORTANCE: In low-resource areas, fevers due to infectious pathogens are a major source of illness, but tools for detecting and identifying such pathogens are often limited. Unbiased approaches for identifying genetic material from all potentially infectious organisms in a sample represent an opportunity for discovering sources of fever. Metagenomic sequencing can improve insight into pathogen landscapes in low-resource settings, potentially providing early detection of disease outbreaks. However, unbiased metagenomic sequencing (mNGS) is no panacea; it is susceptible to contamination and false positives. We used mNGS to evaluate serum from >300 Nigerian clinic-goers in Jos, Nigeria, most of whom (>70%) had fevers of unknown origin. Our goal was to understand arbovirus prevalence in Jos, Nigeria, and identify the sources of infection not routinely monitored for at clinics. We detected hepatitis B virus, as well as nonpathogenic anelloviruses. Our study provides insight into the utility and limitations of mNGS for pathogen surveillance.},
}

@article {pmid42584675,
year = {2026},
author = {Tozluyurt, A and Acar, A},
title = {Postoperative Nocardia cyriacigeorgica infection after glioblastoma resection: correlating metagenomic next-generation sequencing with conventional microbiology.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42584675},
issn = {1432-1912},
abstract = {Postoperative nocardial infection after cranial surgery is rare and difficult to diagnose because Nocardia spp. grow slowly in conventional culture. Metagenomic next-generation sequencing (mNGS) can shorten the interval to microbial detection, but read abundance is influenced by commensal DNA and by contamination during sampling, laboratory processing, and sequencing. mNGS findings therefore require correlation with conventional microbiology and with the clinical context. An 84-year-old woman developed purulent surgical wound discharge with epidural empyema approximately 2 weeks after resection of a World Health Organization grade 4 glioblastoma and postoperative corticosteroid exposure. Revision surgery comprised extensive debridement, removal of the infected bone flap and fixation screw, and evacuation of the empyemas. Direct Gram and modified acid-fast stains of the operative specimen showed branching, acid-fast filamentous organisms on day 1. mNGS of abscess fluid reported 196,785 reads assigned to Nocardia cyriacigeorgica on day 7, and culture on buffered charcoal yeast extract agar yielded N. cyriacigeorgica on day 18, confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. More than 20 million reads were assigned to Corynebacterium tuberculostearicum, yet no corresponding coryneform predominance was seen microscopically; its significance was therefore interpreted cautiously as a possible skin-derived or background contribution, although a true polymicrobial contribution could not be excluded. Surgical source control with intravenous meropenem and amikacin was followed by resolution of the infection. Additionally, three multimodal artificial intelligence systems were each queried five times with the same prompt. mNGS enabled earlier species-level recognition of N. cyriacigeorgica than culture, but direct microscopy gave the earliest diagnostic clue and culture remained essential for confirmation and isolate recovery. Taxonomic read abundance must not be equated with causality. The artificial intelligence outputs were discordant between systems and, in one system, incorrect in a stable and reproducible way; this illustrates current limitations rather than clinical readiness and supports the need for prespecified, blinded, multi-case validation before clinical deployment.},
}

@article {pmid42584818,
year = {2026},
author = {Sharma, S and Sharma, PK and Gupta, E and Dash, PK and Srivastava, A},
title = {Simplified Inhouse Nanoweb Membrane Enrichment Coupled Viral Whole Genome Shotgun Metagenomics Approach for Waste Water Surveillance.},
journal = {Food and environmental virology},
volume = {18},
number = {3},
pages = {},
pmid = {42584818},
issn = {1867-0342},
mesh = {*Genome, Viral ; *Wastewater/virology ; *Metagenomics/methods ; *Sewage/virology ; SARS-CoV-2/genetics/isolation & purification ; India ; *Viruses/genetics/isolation & purification/classification ; *Environmental Monitoring/methods ; COVID-19/virology ; Shotgun Sequencing ; Animals ; },
abstract = {Wastewater/sewage represents a highly complex environmental matrix and harbors various viruses including viruses of epidemic and pandemic potential like Influenza A and, SARS-CoV-2. The limitations of available methods for sample concentration are cost, efficiency and time. NGS- metagenomics offer sample to virus genomic characterization for even non-cultivable viruses at highest resolution. In this study, we have collected samples from sewage treatment plants located in Gwalior region of Central India (December 2023 to March 2025). In this study a novel in house nanoweb membrane-based sample enrichment followed by magnetic bead based nucleic acid extraction was optimized in conjunction to shotgun whole genome metagenomics on Nanopore and ion torrent NGS. Both the methods were found comparable with commercially available methods by virus specific TaqMan qPCR. Both the methods were found successful in virus recovery at two log through 10[2]GC/50 ml feline calicivirus, Influenza A virus, Zika virus, SARS-CoV-2 spiked in sewage matrix alone or in mixture), suggesting the optimized protocol found working for virus characterization at strain level. Here, we have standardized a simple field amenable waste water sample enrichment followed by nucleic acid extraction protocol, that can easily be integrated with latest onsite downstream molecular diagnostic platforms. The developed method is very simple, cost effective and field deployable. This will help to develop a suitable strategic plan for sewage surveillance towards early warning/microbial forensics and future decisions for prevention and therapeutic interventions.},
}

*Genome, Viral
*Wastewater/virology
*Metagenomics/methods
*Sewage/virology
SARS-CoV-2/genetics/isolation & purification
India
*Viruses/genetics/isolation & purification/classification
*Environmental Monitoring/methods
COVID-19/virology
Shotgun Sequencing
Animals

@article {pmid42584931,
year = {2026},
author = {Kaszecki, E and Azimychetabi, Z and Emery, RJN and Saville, BJ},
title = {Integrated transcriptomic and hormonomic insights into cadmium tolerance of a Euglena mutabilis fungal-algal-bacterial consortium.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
doi = {10.1099/mic.0.001750},
pmid = {42584931},
issn = {1465-2080},
mesh = {*Cadmium/metabolism/toxicity ; *Transcriptome ; *Euglena/genetics/metabolism/drug effects ; *Microbial Consortia/genetics ; *Fungi/genetics/metabolism ; Gene Expression Profiling ; *Bacteria/genetics/metabolism/classification ; Chloroplasts/metabolism ; },
abstract = {Acidic, metal-contaminated environments harbour specialized microbial consortia adapted to extreme stress. We examined an environmental Euglena mutabilis culture naturally associated with Talaromyces and Acidiphilium acidophilum and exposed it to cadmium (Cd). Integrated transcriptomic, hormonal, structural and taxonomic analyses revealed a coordinated Cd-tolerance strategy. RNA sequencing showed differential regulation of metal transporters consistent with a shift from Cd uptake to intracellular sequestration. Transmission electron microscopy confirmed Cd compartmentalization within chloroplasts and increased paramylon granules. Cd exposure suppressed light-harvesting complex genes and formate/nitrite transporters while maintaining core photosynthetic function. Hormone profiling indicated strong repression of bioactive auxin and cytokinin (CK) free bases, alongside accumulation of CK nucleotides and downregulation of CK biosynthetic and activation genes. Metagenomics revealed Cd-driven enrichment of Talaromyces and Acidiphilium, implicating them in detoxification and stress support. Together, these responses highlight early Cd uptake followed by chloroplast-based detoxification, metabolic buffering via paramylon, hormonal downregulation of growth and community-mediated resilience.},
}

*Cadmium/metabolism/toxicity
*Transcriptome
*Euglena/genetics/metabolism/drug effects
*Microbial Consortia/genetics
*Fungi/genetics/metabolism
Gene Expression Profiling
*Bacteria/genetics/metabolism/classification
Chloroplasts/metabolism

@article {pmid42585057,
year = {2026},
author = {de Oliveira, FF and A C Fernandes, M},
title = {BIKE: A Binary $K$-mer Exact Counter with Alphabet-Independent Memory and Deterministic Parallelism.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3723002},
pmid = {42585057},
issn = {2998-4165},
abstract = {K-mer counting is a fundamental computational task in bioinformatics, underpinning genome assembly, metagenomic classification, error correction, and similarity analysis. Existing exact-counting methods rely on hash tables or static allocation strategies whose memory requirements grow exponentially with the alphabet size and substring length, rendering them impractical for amino acid sequences at moderate-to-large values of $k$. We propose BIKE (Binary K-mer Exact Counter), a novel exact k-mer counting algorithm whose memory footprint depends exclusively on the input sequence length $n$, independently of the alphabet size m or the $k$-mer length $k$. BIKE decomposes the counting problem into $n-1$ mutually independent pivot-based comparison blocks operating entirely on binary matrices, requiring only one bit per entry, and employs a union-find aggregation mechanism that guarantees exact counts for $k$-mers of arbitrary multiplicity. This structural regularity yields a fully deterministic degree of parallelism, enabling closed-form analytical models that provide accurate execution-time predictions under ideal parallel execution assumptions. Experimental results on real biological sequences confirm functional correctness and demonstrate memory reductions of up to three orders of magnitude over classical exact methods for amino acid alphabets. Analytical performance projections, derived from the closed-form parallel model, indicate that an FPGA realisation of BIKE would be expected to outperform CPU-based dynamic allocation at moderate sequence lengths; however, these remain theoretical estimates pending hardware implementation. BIKE is therefore presented as a theoretical and data-structural contribution, establishing a new algorithmic foundation for alphabet-independent, exactly-counted, and deterministically parallel $k$-mer analysis.},
}

@article {pmid42585229,
year = {2026},
author = {Fellows Yates, JA and Hübner, A and Borry, M and , and Warinner, C},
title = {De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.},
journal = {PLoS computational biology},
volume = {22},
number = {8},
pages = {e1014591},
doi = {10.1371/journal.pcbi.1014591},
pmid = {42585229},
issn = {1553-7358},
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Humans ; },
abstract = {Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Metagenome/genetics
*Sequence Analysis, DNA/methods
Computational Biology/methods
Software
Humans

@article {pmid42585836,
year = {2026},
author = {Cao, Y and Du, P and Zhai, R and Guo, Y and Lin, M and Wang, Z},
title = {Drought stress adaptation in Ficus carica L.: Modulation of ROS scavenging, nitrogen uptake, and rhizosphere bacterial community assembly and functions.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128678},
doi = {10.1016/j.micres.2026.128678},
pmid = {42585836},
issn = {1618-0623},
abstract = {Rhizosphere microorganisms are crucial for plant drought resistance; however, their response to drought stress in fig plants remains poorly understood. In this study, potted 'BoJi Red' fig plants were utilized to systematically investigate drought-induced changes in the structure, assembly processes, and functional potential of rhizosphere bacterial communities. The results showed that drought significantly inhibited fig growth, photosynthesis, and nitrogen uptake, while increasing reactive oxygen species (ROS) content and antioxidant enzyme activities, although these enzyme activities declined under severe drought conditions. Bacterial community richness and diversity significantly increased under moderate and severe drought, shifting toward drought-resistant groups, notably Actinomycetota and Bacillota. The number of nodes, links, and key species in the microbial co-occurrence network decreased as drought intensified, with stochastic processes dominating community assembly. Moreover, ecological niche breadth and the proportion of generalist species increased with drought severity. Notably, Nocardioidaceae was significantly enriched under drought, and metagenomic profiling indicated this taxon is strongly associated with carbohydrate metabolism pathways, with predicted genetic potential to participate in soil carbon turnover and nutrient transformation. Additionally, drought significantly reduced the abundance of nitrogen-fixing genes (nifD, nifK) and weakened the relative contribution of Rhizobiaceae to nitrogen fixation; correlative functional profiling suggests Nocardioidaceae may possess alternative nitrogen cycling pathways that could partially offset suppressed rhizosphere nitrogen fixation capacity. Overall, these findings indicate that the fig plant response to drought stress involves both physiological adjustments in the host and functional reconfiguration of the rhizosphere microbial community, with Nocardioidaceae playing a key role in maintaining rhizosphere functions and enhancing drought tolerance.},
}

@article {pmid42585873,
year = {2026},
author = {Wang, H and Liang, Z and Guo, W and Ni, L and Lv, X},
title = {Mechanized Qu-making may contribute to lactic acid bacteria overproliferation in Hongqu rice wine brewing: Insights into microbial dysbiosis and flavor quality deterioration.},
journal = {International journal of food microbiology},
volume = {461},
number = {},
pages = {112013},
doi = {10.1016/j.ijfoodmicro.2026.112013},
pmid = {42585873},
issn = {1879-3460},
abstract = {Hongqu (HQ) serves as the core saccharification and fermentation starter (commonly referred to as "Qu") for Hongqu rice wine (HQW), a traditional Chinese fermented alcoholic beverage celebrated for its unique sensory characteristics and potential health-promoting properties. Driven by industrialization, mechanized Qu production has been progressively implemented to enhance process reproducibility, scalability, and operational efficiency. However, the implications of this technological transition on microbial community assembly, metabolic function and flavor formation during HQW brewing remain insufficiently characterized. To address this gap, this study employed an integrated metagenomic and metabolomic approach to comparatively analyze the taxonomic composition and functional metabolic profiles of mechanized Hongqu (MHQ) and traditional Hongqu (THQ), and further monitored their dynamic succession throughout HQW brewing process. Results demonstrated that MHQ exhibited significantly higher saccharification capacity and markedly enriched abundance of Saccharomyces cerevisiae, yet displayed a substantial reduction in Aspergillus niger compared with THQ (1.06% versus 43.41%). Paradoxically, despite these favorable starter attributes, HQW fermentation inoculated with MHQ induced an uncontrollable proliferation of lactic acid bacteria (LAB), predominantly represented by Pediococcus acidilactici, Lactiplantibacillus plantarum and Weissella paramesenteroides. This LAB-dominant consortium proliferated markedly during HQW fermentation, resulting in a community compositional shift toward bacterial dominance, evidenced by a fungi-to-bacteria ratio of 1.00:5.88 in MHQW, whereas THQW retained fungal dominance, with a corresponding ratio of 1.00:0.26. This structural shift coincided with significant declines in the relative abundances of functional fungi, including Saccharomyces cerevisiae and Monascus purpureus, possibly involving changes in niche occupation and acidification. These microbial community changes were associated with a metabolic shift characterized by excessive accumulation of organic acids, dysregulated biogenic amine profiles, depletion of free amino acids, and diminished synthesis of key volatile flavor compounds. Quantitatively, MHQW exhibited significantly higher final titratable acidity (12.67 g/L vs. 5.76 g/L), lower ethanol yield (17.29% v/v vs. 20.39% v/v), elevated total organic acid content (16.62 g/L vs. 6.28 g/L), and reduced total free amino acid concentration (3366.23 mg/L vs. 4303.93 mg/L) relative to THQW. Collectively, these findings indicate that mechanized Qu-making may disrupt the delicate "fungi-bacteria" ecological equilibrium essential for robust and balanced HQW fermentation, potentially favoring LAB proliferation. This study highlights the potential value of rational microbiome design to control LAB proliferation while maintaining functional fungi, which is important for optimizing mechanized Qu-making processes and improving flavor quality and fermentation robustness in HQW production. Collectively, our work provides a mechanism-informed framework for advancing Huangjiu modernization through rational microbiome engineering.},
}

@article {pmid42585927,
year = {2026},
author = {Ma, J and Qin, K and Qiao, Z and Ren, Z and Yang, X and Liu, Y},
title = {Integrative multi-omics reveals comprehensive gut-liver-adipose metabolic changes in peak laying hens with high or low egg production.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107493},
doi = {10.1016/j.psj.2026.107493},
pmid = {42585927},
issn = {1525-3171},
abstract = {Eggs serve as an indispensable global nutritional resource, sustaining the economic foundation of the commercial poultry industry. To meet this continuous demand, egg formation involves an exceptionally energy-intensive biological process requiring continuous yolk precursor synthesis, which imposes a massive metabolic burden on laying hens. However, the comprehensive metabolic differences across the gut-liver-adipose axis between peak laying hens with high or low egg production remain incompletely characterized. A total of 180 healthy Hy-Line Brown laying hens (45-week-old) were continuously fed and monitored for production performance over a 6-week period. Following the exclusion of individuals with extremely low egg production (≤10 eggs during the 6-week monitoring period; n = 5) and candidate hens that repeatedly produced unqualified eggs over multiple weeks (n = 20), the remaining hens were ranked by 6-week average laying rate and allocated into FH (high-production hens at 50 weeks of age, n = 15) and FL (low-production hens at 50 weeks of age, n = 14) groups. Initial body weight did not differ significantly between groups (FH: 1936 ± 29.0 g; FL: 1894 ± 48.2 g; P-value = 0.446). We integrated transcriptomic, untargeted metabolomic, targeted bile acid metabolomics, and microbiome (16S rRNA and metagenomic) profiles to characterize comprehensive metabolic changes across the gut-liver-adipose axis associated with divergent egg-production phenotypes. The results showed that: (1) FH hens exhibited higher serum APOB and lower conjugated bile acids (TCDCA, TCA, and THDCA), with hepatic upregulation of FASN, PPARA, CPT1A, and VTG1 along with downregulation of CYP7A1, CYP7B1, CYP8B1, and CYP27A1; (2) intersecting module hub genes (MHGs) with differentially expressed genes (DEGs) identified 354 upregulated and 299 downregulated core genes, with EEF2 identified as the primary hepatic downregulated hub gene; (3) in abdominal fat, GSEA revealed significant enrichment in fatty acid transport (NES = 1.54), long-chain fatty acid metabolic process (NES = 1.39), and steroid hormone biosynthesis (NES = 1.85), accompanied by significant downregulation of ANGPTL4 and upregulation of HSD3B1, VTG1, VTG2, and VTG3; (4) ileal mucosal transcriptomics identified 619 DEGs (502 upregulated), with GSEA highlighting enrichment in cell junction organization (NES = 1.52) and tube morphogenesis (NES = 1.39), which were further categorized into functional modules including enteric synaptic signaling, epithelial adhesion, mucosal vascularization, and tissue renewal; (5) the functional profile of the ileal microbiota in FH hens showed enrichment of functions related to complex carbohydrate degradation and carbohydrate-binding modules, with keystone taxa including Blautia and Bifidobacterium associated with production and lipid markers. Collectively, these findings suggest that high egg production during the peak laying period is associated with coordinated metabolic differences across the liver, abdominal fat tissue, and intestine. The observed profiles included reduced hepatic translation-related and primary bile acid synthesis-related signatures, adipose endocrine-related changes and microbial functional potential related to carbohydrate utilization and antioxidant-related functional potential. These findings provide candidate multi-omics features for precision nutritional strategies and genetic improvement in commercial poultry.},
}

@article {pmid42585954,
year = {2026},
author = {Yang, S and Zhang, X and Wang, K and Zhao, X and Li, X},
title = {Pyrite fuels electron fluxes to accelerate hydrocarbon removal in coastal wetland soil.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143275},
doi = {10.1016/j.jhazmat.2026.143275},
pmid = {42585954},
issn = {1873-3336},
abstract = {Natural sulfide minerals drive subsurface electron flow, but their role in hydrocarbon turnover is poorly understood. Here, we investigated whether pyrite (FeS2) can sustain electron transfer and accelerate petroleum hydrocarbon degradation in coastal wetland soils using a microbial electrochemical system (MES). High-dose pyrite amendment markedly enhanced long-term voltage output and increased cumulative charge by 34% over 120 days, indicating persistent subsurface electron release. Since pyrite improved soil conductivity and stimulated extracellular electron transfer, as reflected by elevated cytochrome c, extracellular polymeric substances production, and electroactive protein-like components. These electron transfer processes nearly doubled total petroleum hydrocarbon removal and promoted dissolved organic matter transformation from recalcitrant lignin-like compounds toward more bioavailable lipid- and protein-like components. Meanwhile, pyrite oxidation intensified Fe[2 +]/Fe[3+] cycling, secondary iron mineral formation, and coupled carbon-iron-sulfur transformations. Metagenomic analysis further revealed enrichment of hydrocarbon degraders, electroactive microorganisms, sulfate reducers, and methanogens, together with upregulation of genes involved in carbon metabolism, nitrogen cycling, iron-sulfur transformation, conductive pili assembly, and ubiquinone biosynthesis. These findings identify pyrite as a geological energy node that fuels persistent subsurface electron fluxes to enhance hydrocarbon removal in coastal wetland soils, highlighting the potential of activating natural iron-sulfur minerals for in situ bioremediation in anoxic coastal zones.},
}

@article {pmid42585955,
year = {2026},
author = {Han, X and Gao, Y and Chen, J and Yang, P and Liang, X and Wang, L and Ge, Y and Gui, H and He, Y and Zhan, F and Zhang, X and Kuzyakov, Y},
title = {Microplastics disrupt bacterial defense within the plant-AMF-bacteria continuum to amplify Cd bioavailability.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143257},
doi = {10.1016/j.jhazmat.2026.143257},
pmid = {42585955},
issn = {1873-3336},
abstract = {The plant-arbuscular mycorrhizal fungi (AMF)-bacteria continuum provides a critical barrier against heavy-metal toxicity, but how microplastics (MPs) disrupt rhizosphere functions and exacerbate phytotoxicity remains unresolved. Using a maize-AMF-bacteria system in cadmium (Cd)-contaminated soil, we investigated two MP fractions differing in size and morphology added at increasing Cd contents. Although AMF colonization remained resilient, MPs induced fraction-dependent bacterial functional decoupling. Small MPs shifted the microbiome from extracellular Cd-immobilizing taxa (Sphingomonadaceae and Rhizobiaceae) toward intracellular stress-tolerant lineages. Large MPs restricted bacterial contacts, suppressing density-dependent cooperation. Metagenomic profiling and analysis of metagenome-assembled genomes (MAGs) revealed reduced potential for quorum sensing, ABC transporters, and alpha-linolenic acid metabolism under large MP exposure, compromising biofilm formation and extracellular Cd sequestration. Partial least squares path modeling indicated that bulk-soil chemistry did not define Cd uptake by plants. Instead, depletion of available Cd in soil reflected a biological sink associated with enhanced plant uptake. Enhanced Cd accumulation was associated with loss of rhizosphere defense mechanisms: potential root-barrier disruption by large MPs and weakened microbial buffering. Consequently, large MPs increased the Cd bioconcentration factor by 57.5%, compared with 32.1% for small MPs. These findings show that MPs amplify legacy Cd risks without increasing bulk-soil Cd availability, through disruption of root-interface integrity and microbial protection.},
}

@article {pmid42585962,
year = {2026},
author = {Xian, ZN and Hu, J and Wang, Z and Gong, H and Dai, X and Zhu, N},
title = {Process-resolved effects of dibutyl phthalate on sludge anaerobic fermentation: Enzyme inhibition and metabolic disruption underlie the suppression of acidogenesis.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143232},
doi = {10.1016/j.jhazmat.2026.143232},
pmid = {42585962},
issn = {1873-3336},
abstract = {Growing evidence suggests that leaching of plasticizers such as dibutyl phthalate (DBP) from microplastics inhibits methanogenesis in anaerobic digesters treating waste activated sludge. However, how DBP influences upstream anaerobic fermentation (AF) remains unclear. This study evaluated the effects of DBP on overall sludge AF and separately on solubilization, hydrolysis, and acidogenesis processes. Volatile fatty acid (VFA) production showed a V-shaped response to environmentally relevant DBP concentrations. A reduction of 45.3% was observed at 0.5 mg/L DBP, whereas reductions exceeded 95% at 1-2 mg/L. The inhibition then weakened with increasing DBP, with a 60.5% reduction at 200 mg/L, an upper-bound level selected to bracket the maximum concentration reported in sludge. Stage-specific effects intensified with DBP concentration and peaked at 200 mg/L, where solubilization increased by 34.6%, whereas hydrolysis and acidogenesis decreased by 30.8% and 11.2%, respectively. The combined influence of these processes explained the nonmonotonic VFA response. Notably, enzyme assays and molecular simulations indicated that DBP inhibited ACK in a competitive-like manner and reduced its activity. Metagenomic analysis further indicated that DBP reduced genetic potential for downstream pathways converting pyruvate and acetyl-CoA to fermentation products. Collectively, these results reveal a DBP-induced fluctuating AF response and provide mechanistic insights into optimizing anaerobic treatment of plasticizer-laden sludge.},
}

@article {pmid42585964,
year = {2026},
author = {Wang, X and Liao, H and Wang, X and Wang, Y and Li, D and Ma, H and Yang, J and Qian, X and Wang, H and Li, Q and Xiu, Z and Yang, Y},
title = {Cobalamin-autonomous Trichlorobacter facilitates robust In situ bioremediation of halogenated solvents.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143046},
doi = {10.1016/j.jhazmat.2026.143046},
pmid = {42585964},
issn = {1873-3336},
abstract = {Organohalide-respiring bacteria (OHRB) are key mediators of chlorinated solvent detoxification in anoxic groundwater, yet their practical application is often constrained by vitamin B12 (cobalamin) auxotrophy and the requirement for strictly controlled anoxic and nutrient conditions. Here, we report the enrichment and characterization of a Trichlorobacter-dominated consortium (NB-12) that sustains efficient dihaloelimination of halogenated alkanes under minimal nutrient and relaxed anoxic constraints. The NB-12 enrichment completely transformed 1,2-dichloroethane (1,2-DCA) to ethene within 40 h (≥3.3 μmol h[-1]) and also dechlorinated 1,2-dichloropropane and 1,1,2-trichloroethane, as well as debrominated 1,2-dibromoethane and 1,2-dibromopropane. Exogenous vitamin B12 supplementation did not enhance dechlorination kinetics or product yields. Amplicon sequencing and metagenomic analyses identified Trichlorobacter lovleyi as the dominant population (>60% relative abundance) and revealed a complete anaerobic cobalamin biosynthesis pathway in the corresponding metagenome-assembled genome, indicating corrinoid autonomy at the community level. Notably, the NB-12 consortium retained sustained dehalogenation activity in non-sterile, unbuffered, and oxygen-leaky mesocosms prepared using only tap water, trace elements, and lactate-conditions mimicking challenging in situ environments. Field bioaugmentation using this "low-input" inoculant resulted in successful aquifer colonization and a reduction in 1,2-DCA concentrations in contaminated groundwater. Together, these results demonstrate that corrinoid-autonomous, Trichlorobacter-dominated enrichments can relax key physiological and operational constraints of OHR-based remediation, expanding the applicability of low-input, cost-effective strategies for in situ treatment of halogenated alkane-contaminated groundwater.},
}

@article {pmid42586007,
year = {2026},
author = {López-Cañizares, J and Truchado, P and Macrì, M and Cobo-Díaz, JF and Álvarez-Ordóñez, A and Bonetta, S and Allende, A},
title = {Water reuse within a circular economy: Long-read metagenomics reveals distinct residual resistome profiles across full-scale wastewater-reclamation systems in Murcia, Spain.},
journal = {Chemosphere},
volume = {411},
number = {},
pages = {145063},
doi = {10.1016/j.chemosphere.2026.145063},
pmid = {42586007},
issn = {1879-1298},
abstract = {Water reuse is a key pillar of circular economy strategies, particularly in water-scarce regions, by preserving freshwater resources and supporting agricultural production. Current regulations promote the use of reclaimed water for irrigation, placing wastewater treatment plants (WWTPs) at the center of this transition. However, emerging risks related to antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) challenge the safety of reuse as these determinants may persist after treatment. This study evaluated the effectiveness of ozonation, sodium hypochlorite, UV-C irradiation, and membrane bioreactor (MBR) systems in reducing ARGs in effluents from the Region of Murcia (Spain) across five sampling campaigns between 2023 and 2024. Metagenomic sequencing identified ARGs associated with 17 antibiotic classes, with macrolide-, β-lactam-, and tetracycline-ARGs dominating. Total ARG abundance was lower in treated effluents than in influents, with the greatest percentage reduction in MBR system, although based on only two effluent samples. Selected macrolide-, sulfonamide-, tetracycline- and β-lactam-ARGs nevertheless remained detectable after treatment, with distinct gene-specific profiles among the wastewater-reclamation systems. Effluent samples differed in the taxonomic composition of ARG-carrying reads and in the detection of ARGs putatively co-localized on mobilome associated contigs. These findings show that total ARG reduction alone does not fully characterize wastewater-reclamation performance because substantial decreases in total ARG burden were accompanied by different residual resistome profiles. Combining ARG abundance, identity, potential hosts, and genomic context enables a fuller assessment of reclaimed-water treatment. These metagenomic associations indicate potential persistence and mobility but do not constitute direct evidence of horizontal gene transfer or quantitative environmental risk.},
}

@article {pmid42575184,
year = {2026},
author = {Zha, Y and Wang, Z and Sun, W and Meng, J and Liu, Y and Wang, B},
title = {Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125444},
doi = {10.1016/j.envres.2026.125444},
pmid = {42575184},
issn = {1096-0953},
abstract = {Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.},
}

@article {pmid42575312,
year = {2026},
author = {Benmazouz, I and Kövér, L and Laczkó, L and Gyure, P and Kardos, G},
title = {Carriage of ESBL-Producing Enterobacterales in Urban and Rural Hooded Crows in Hungary.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.08.004},
pmid = {42575312},
issn = {2213-7173},
abstract = {BACKGROUND: Considering the increasing reports of antimicrobial resistance (AMR) in wildlife, highlighting its complexity, importance, and spread. We investigated the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in the hooded crow.

METHODS: Faecal samples were collected from 52 rural and 212 urban wild crows in Hungary, caught using ladder traps, and tested for ESBL presence. Bacterial species were identified using MALDI-TOF. Antibiotic susceptibility was tested using the disc diffusion method, and ESBL producers were detected based on double-disc synergy. ESBL-encoding genes were identified using PCR, and WGS was performed on isolated ESBL-producing E. coli (197/221 isolated ESBLs).

RESULTS: Four of the sampled rural hooded crows and 130 urban ones (7.7% vs. 61%, chi-square p < 0.0001) yielded ESBL producers with the overwhelming dominance of E. coli. The blaCTX-M-1 group was predominant in both groups. In addition to CTX-M genes, genes encoding resistance to other antibiotic classes, such as APHs, sul genes, tet genes, etc, various virulence factors, and several incompatible plasmids were also detected. Most isolates belonged to the B1 and A phylogenetic groups. Overall, 22 sequence types (STs) and 33 distinct cgSTs were defined. The most prevalent ST was ST58, followed by ST10, S38, ST155, ST442, and more.

CONCLUSIONS: The much higher carrier frequency among urban crows points to the role of anthropogenic sources in the emergence of ESBL producers. Hooded crows, due to their increasing presence in cities and proximity to humans, likely facilitate the dissemination of ESBL producers between the environment and humans.},
}

@article {pmid42575416,
year = {2026},
author = {Li, W and Yu, Z and Zhang, J and Yang, W and Yang, R and Li, X and Wang, S and Wu, P},
title = {Biodegradable and conventional microplastics differentially affected greenhouse gas emissions from a flooded paddy soil: Insight into metagenomic analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128934},
doi = {10.1016/j.envpol.2026.128934},
pmid = {42575416},
issn = {1873-6424},
abstract = {Paddy soils are important sources of greenhouse gases (GHGs), and microplastics (MPs) are increasingly widespread in paddies. However, the type-dependent effects of biodegradable and conventional MPs on methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) emissions remain unclear. Here, an incubation experiment was conducted to evaluate the effects of polyethylene (PE), polyethylene terephthalate (PET), Polybutylene succinate (PBS), and polylactic acid (PLA) on GHG emissions and the involved mechanism was clarified. PLA significantly increased cumulative CH4 and CO2 emissions by 264% and 27.3%, respectively, whereas PE and PET inhibited CH4 and CO2 emissions. In contrast, PE significantly enhanced N2O emissions by 93.1%, while PLA had no significant effect. Mechanistically, PLA increased dissolved organic carbon (DOC), soil pH, HCl-extractable Fe(II), and soluble/exchangeable Mn contents, but decreased soil redox potential (Eh) and sulfate content, creating favorable conditions for microbial anaerobic metabolism. PLA increased the relative abundances of methanogenic taxa and genes (fwdA, fdhA, acsC, cdhC, mttB, and mtbC), but decreased those associated with anaerobic methane oxidation (mcrA, mtrH, and mer), indicating greater CH4-production potential. PLA also increased fermentation (ldh, pfl, ackA, adhE, and por), sulfate-reduction (sat, aprA, aprB, dsrA, and dsrB), and iron-reduction (feR) gene abundances, suggesting greater anaerobic carbon-transformation potential. PE and PET increased denitrifiers and related genes (narH, narI, nirK, and norB), indicating greater N2O-production potential, whereas increased nosZ abundance under PLA treatment suggested greater N2O-reduction potential. Overall, MPs differentially affected paddy GHG emissions in a type-dependent manner, and biodegradable PLA exacerbated short-term GHG emission risks from paddy soils.},
}

@article {pmid42575708,
year = {2026},
author = {de Oliveira, AFB and Carneiro, BS and de Carvalho, JB and de Oliveira, AR and da Costa da Silva, AL and de Oliveira Veras, AA and Baraúna, RA and das Graças, DA},
title = {Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70396},
doi = {10.1111/1758-2229.70396},
pmid = {42575708},
issn = {1758-2229},
support = {445350/2024-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Metagenomics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism/drug effects ; *Xenobiotics/metabolism ; Brazil ; *Bathing Beaches ; *Drug Resistance, Bacterial ; Biodiversity ; *Drug Resistance, Microbial ; Phylogeny ; Biodegradation, Environmental ; Cities ; },
abstract = {Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.},
}

*Metagenomics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism/drug effects
*Xenobiotics/metabolism
Brazil
*Bathing Beaches
*Drug Resistance, Bacterial
Biodiversity
*Drug Resistance, Microbial
Phylogeny
Biodegradation, Environmental
Cities

@article {pmid42575975,
year = {2026},
author = {Pust, MM and Mohamed, AMT and Stražar, M and Arias-Rojas, A and Cunningham-Oakes, E and Brown, EM and Bumber, A and Pishchany, G and Li, C and Ananthakrishnan, AN and Darby, AC and Vlamakis, H and Plichta, DR and Xavier, RJ},
title = {Antisense transcription reveals disease-associated adaptations in the human gut microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42575975},
issn = {2058-5276},
support = {P30 DK043351//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 DK127171//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI172147//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 530694780//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {The gut microbiome is a dynamic ecosystem in which microorganisms constantly adjust their transcriptional programmes. Here we developed metastrand, a framework that integrates strand-aware metatranscriptomics and metagenomics to quantify mRNAs and antisense RNAs (asRNAs) in complex microbial communities at gene-level resolution. In inflammatory bowel disease (IBD), microbial asRNA programmes converged across patients during active disease, correlated with faecal metabolites and calprotectin levels and remained stable during persistent inflammation, highlighting their potential as biomarkers of inflammatory activity in the gut. These programmes involved antisense-to-sense transcriptional shifts at insertion sequence elements with functionally diverse passenger genes and preceded their detection at new genomic locations, linking asRNA dynamics to structural genome rearrangements and redistribution of adaptive functions under selective pressure. Similar dynamics were observed in a mouse model of colitis, oxidative stress in vitro and in patients with pathogen-confirmed gastroenteritis, establishing asRNAs as an important dimension of microbial adaptation in health and disease.},
}

@article {pmid42576026,
year = {2026},
author = {Shiba, S and Yachida, S and Mizutani, S and Totoki, Y and Nakamura, H and Hama, N and Miyoshi, N and Arai, Y and Saito-Adachi, M and Kimura, H and Hayashi, Y and Takamaru, H and Tanaka, K and Hayashi, R and Rokutan, H and Ikuta, S and Kanemitsu, Y and Doki, Y and Eguchi, H and Hattori, S and Saito, Y and Yamada, T and Shibata, T},
title = {Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {42576026},
issn = {1546-1718},
support = {JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP16H06279, 22K16336//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03662, 23H02892, 25K21771//MEXT | Japan Science and Technology Agency (JST)/ ; },
abstract = {The incidence of colorectal cancer (CRC) has risen in recent decades, with a disproportionate increase observed among younger individuals in Japan and other countries. The etiological contribution of the gut microbiota to CRC pathogenesis is recognized, yet the mechanisms involved remain to be fully clarified. Here we integrated whole-genome sequencing (WGS) and transcriptome profiling of CRC with whole-genome metagenomic sequencing of fecal samples to interrogate host-microbiome interactions at high resolution. Application of interpretable artificial intelligence enabled the stratification of CRC into four distinct microbiome-informed subtypes. WGS analysis identified mutational signatures SBS88 and ID18, linked to colibactin exposure, as early clonal events detected in 44.8% of non-hypermutated patients. Notably, these signatures were significantly more frequent among patients born after the 1960s. Microbiome-based subclassification revealed subtype-specific clinical and molecular features. Collectively, our findings indicate that colibactin exposure constitutes a prevalent and potentially modifiable risk factor for CRC in the Japanese population.},
}

@article {pmid42576510,
year = {2026},
author = {Nio, SA and Mantilen Ludong, DP},
title = {Water Deficit During the Vegetative Stage Alters the Structure of Root-Associated Microbial Communities in Local North Sulawesi Rice.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {29},
number = {5},
pages = {243-250},
doi = {10.3923/pjbs.2026.243.250},
pmid = {42576510},
issn = {1812-5735},
mesh = {*Oryza/microbiology/growth & development/metabolism ; *Plant Roots/microbiology ; Droughts ; Water/metabolism ; *Microbiota/physiology ; Indonesia ; Rhizosphere ; },
abstract = {Background and Objective: Changes in rhizosphere microbial populations have been reported in response to drought, temperature fluctuations, CO2 levels and other environmental factors. However, the structure of the root-associated microbes in local North Sulawesi rice using a metagenomic approach has not yet been investigated. This study examined the microbial community structure in local North Sulawesi rice (cv. Superwin) under drought (water deficit) conditions compared to well-watered conditions at the vegetative phase. Materials and Methods: Rice plants were grown in polybags filled with a 5:1:1 mixture of garden soil, compost and rice husks and were allowed to grow until the four-fully-expanded leaf stage. They were then subjected to two treatments for 14 days: well-watered conditions (irrigated to 100% field capacity) and water deficit conditions (0% field capacity). Root samples were collected for next-generation sequencing analysis to assess molecular response of Superwin rice to water deficit. Results: During drought, several root-associated microbes were more prevalent, including Nitrospirota at the phylum level, Rubrobacteria at the class level, Micrococcales at the order level, Gaiellaceae at the family level, Gaiella at the genus level and Gaiella occulta at the species level. Conclusion: Root-associated microbes, including taxa Nitrospirota, Rubrobacteria, Micrococcales, Gaiellaceae, Gaiella and Gaiella occulta, have a higher relative abundance in rice plants under water deficit. Gaiella occulta serves as sensitive indicator of water deficit in North Sulawesi local rice, i.e. Superwin.},
}

*Oryza/microbiology/growth & development/metabolism
*Plant Roots/microbiology
Droughts
Water/metabolism
*Microbiota/physiology
Indonesia
Rhizosphere

@article {pmid42576818,
year = {2025},
author = {Pearce, DA and Crown, M and Nelson, A and Jabeen, K and Thompson, JR and Argyraki, A and Hursthouse, AS and Bashton, M and Entwistle, JA},
title = {House dust-a Pandora's box of antimicrobial resistance (AMR) activity?.},
journal = {Sustainable microbiology},
volume = {2},
number = {4},
pages = {qvaf022},
pmid = {42576818},
issn = {2755-1970},
abstract = {The presence and spread of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistant Genes (ARGs) in the environment is now recognised as one of the top ten global public health threats to humanity. In a previous study, we used citizen science and MiSeq to target 16S rRNA gene amplicons to investigate house dust microbiomes across diverse households and found a core microbiome. In this study, we used shotgun metagenomics to target antimicrobial resistance (AMR) genes in order to investigate the potential for functional differences and to test the hypothesis that there was a core resistome associated with this core microbiome, including any patterns in a core resistome in terms of likely origin and mechanisms of action. In this study we did not find a core resistome, but found that the predominant and most diverse mechanisms of Anti-Microbial Resistance (AMR) in the dust samples were antibiotic target alteration and antibiotic efflux, accounting for ∼70% of cumulative RPKMs detected, potentially representing a compromise between the certainty of working and energy investment required. Despite the core home microbiome previously detected in diverse house dust samples, there was only limited evidence for a core resistome, with only two AMR genes present in all samples.},
}

@article {pmid42576826,
year = {2025},
author = {Shatara, FJ and Kothari, A and Hou, L and Yokota, K and Majumder, EL},
title = {Microplastic characteristics differentially influence cyanobacterial harmful algal bloom microbial community membership, growth, and toxin production.},
journal = {Sustainable microbiology},
volume = {2},
number = {1},
pages = {qvaf003},
pmid = {42576826},
issn = {2755-1970},
abstract = {Terrestrial runoffs contribute to cyanobacterial harmful algal blooms (cHABs) by providing nutrients and other pollutants that may facilitate cyanobacterial growth. Microplastics (MPs) are being detected at increasing concentrations in various aquatic systems worldwide, including freshwater, yet the MP effects on cHAB formation, toxin production, and transport are largely unknown. We used the statistical design of experiments to elucidate microbe-plastic interactions with freshwater algal bloom communities obtained from a HAB event in the Great Lakes. These experiments measured the impact of differing sizes, concentrations, and UV aging times of polyethylene, polypropylene, and cellulose fibers on the chlorophyll-a content of Trichormus (previously Anabaena variabilis) and Microcystis aeruginosa and microcystin-LR content in M. aeruginosa. Additionally, we conducted metagenomic sequencing on the total community and 16S rRNA microbial community sequencing on members of the total community bound to plastics after 4 weeks of culturing. The results indicate that M. aeruginosa growth rate was inhibited in the presence of polymers, while production of microcystin-LR generally increased in the presence of MPs. Changes to growth of T. variabilis varied with polymer type, size, and UV aging time. These results suggest that specific MP characteristics, not just their presence, may influence the toxicity, growth, and dispersal of cHABs across aquatic systems.},
}

@article {pmid42576858,
year = {2024},
author = {Alfahl, Z and Chueiri, A and Carolan, S and Darcy, G and Hussain, N and Cahill, N and O'Connor, L},
title = {Antimicrobial resistance detection methods in water environments: a scoping review.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae034},
pmid = {42576858},
issn = {2755-1970},
abstract = {Antimicrobial resistance (AMR) in water environments poses a significant threat to public health, ecosystem stability, and the effectiveness of antimicrobial treatments. This review aims to provide a comprehensive overview of the methods used to detect AMR in various water environments. A literature search was conducted following the PRISMA guidelines. Original articles published in English relating to AMR in water environments were included. Reviews, protocols, and abstracts were excluded. A total of 115 publications were selected for full-text evaluation. Overall, river water samples were the most commonly assessed samples across all of the reviewed studies (49/115 studies, 42%). The top 3 countries investigating AMR genes in water samples were the USA (19 studies, 17%), China (11 studies, 10%), and Brazil (10 studies, 9%). The review revealed that polymerase chain reaction and metagenomic methods are increasingly preferred for their high sensitivity, specificity, and comprehensive detection capabilities, appearing in 65/115 (57%) and 31/115 (27%) studies, respectively. Despite higher costs and technical complexity, these methods provide valuable insights into the resistome of water environments. Culture-dependent methods, while most cost effective and straightforward, are limited by their time-consuming nature and inability to detect non-viable resistant organisms, reducing their effectiveness in comprehensive AMR surveillance. The review addresses the challenges and limitations of current detection methods and proposes directions for future research to develop more robust, cost-effective, and user-friendly detection methods. The review highlights the urgent need for integrated approaches to monitor and mitigate AMR in water environments, ensuring better public health and environmental protection.},
}

@article {pmid42576874,
year = {2024},
author = {Cowan, DA and Babenko, D and Bird, R and Botha, A and Breecker, DO and Clarke, CE and Francis, ML and Gallagher, T and Lebre, PH and Nel, T and Potts, AJ and Trindade, M and Van Zyl, L},
title = {Oxalate and oxalotrophy: an environmental perspective.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvad004},
pmid = {42576874},
issn = {2755-1970},
abstract = {Oxalic acid is one of the most abundant organic acids produced by plants. Much of the global production of oxalic acid is deposited on soil surfaces in leaf litter to be oxidized by microorganisms, resulting in a pH increase and shifting the carbonate equilibria. In what is known as the oxalate-carbonate pathway, calcium oxalate metabolism results in CO2 being sequestered into soils as insoluble calcite (CaCO3). There is a growing appreciation that the global scale of this process is sufficiently large to be an important contribution to global carbon turnover budgets. The microbiomics, genetics, and enzymology of oxalotrophy are all soundly established, although a more detailed understanding of the landscape-scale kinetics of the process would be needed to incorporate oxalotrophy as an element of process models informing the relevant Sustainable Development Goals. Here, we review the current state of knowledge of oxalotrophs and oxalotrophy and the role they play in terrestrial ecosystem services and functions in terms of carbon sequestration and nutrient cycling. We emphasize the relevance of these to the Sustainability Development Goals (SDGs) and highlight the importance of recognizing oxalotrophy, when accounting for the natural capital value of an ecosystem.},
}

@article {pmid42576880,
year = {2024},
author = {Provencher, J and George, PBL and Thaler, M and Vincent, WF and Duchaine, C and Culley, AI and Girard, C},
title = {Microbial antibiotic resistance genes across an anthropogenic gradient in a Canadian High Arctic watershed.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae021},
pmid = {42576880},
issn = {2755-1970},
abstract = {Antibiotic resistance is one of the biggest challenges to public health. While the discovery of antibiotics has decreased pathogen-caused mortality, the overuse of these drugs has resulted in the increased transfer and evolution of antibiotic resistance genes (ARGs) in bacteria. ARGs naturally occur in wild bacterial communities, but are also found in increased concentrations in environments contaminated by wastewater effluent. Although such ARGs are relatively well described in temperate environments, little is known about the distribution and dissemination of these genes in the Arctic. We characterized the ARGs in microbial communities from aerosols, lakes and microbial mats around a remote Arctic hamlet using metagenomic approaches. Specific objectives were to (i) compare ARGs across habitats, (ii) to characterize ARG populations along a continuum of anthropogenically influenced environments, and (iii) to identify ARGs of viral origin. We identified ARGs in all habitats throughout the watershed, and found that microbial mats in the most impacted area had the highest diversity of ARGs relative to uncontaminated sites, which may be a remnant signal of wastewater effluent inputs in the area during the 20th century. Although we identified ARGs predominantly in bacterial genomes, our data suggests that mimiviruses may also harbor ARGs.},
}

@article {pmid42577134,
year = {2026},
author = {Wang, H and Jiang, L and Zhong, L and Zhang, H and Li, Y and Zhai, Z and Liu, W and Ma, M and Chen, Q and Tang, X},
title = {Responses of host energy status, intestinal structure and gut microbiota during post-hibernation recovery in high- and low-altitude populations of the plateau frog Rana kukunoris.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1891419},
pmid = {42577134},
issn = {1664-042X},
abstract = {BACKGROUND: Hibernation is an important seasonal strategy that enables amphibians to cope with low temperature and food scarcity. However, how high- and low-altitude amphibian populations differ in host energy status, digestive system structure and gut microbiota during post-hibernation recovery remains insufficiently understood.

OBJECTIVE: This study aimed to evaluate post-hibernation changes in host energy status, intestinal structure and gut microbial composition and functional potential in high- and low-altitude populations of the plateau frog Rana kukunoris.

METHODS: We compared high-altitude and low-altitude populations of R. kukunoris before and after hibernation by integrating morphological traits, whole-animal metabolic rate, digestive tract length, small-intestinal histology and shotgun metagenomic profiles of small-intestinal contents.

RESULTS: After hibernation, both populations showed significant decreases in body mass, liver mass and hepatosomatic index, together with increased whole-animal metabolic rate, indicating a transition from energy reserve depletion to metabolic recovery. The hepatosomatic index showed a significant altitude × stage interaction, suggesting stronger relative liver energy depletion in the low-altitude population. Digestive system analysis showed that the low-altitude population exhibited more pronounced structural remodeling, including shortened digestive tract length, increased muscularis thickness and reduced epithelial thickness after hibernation, whereas the high-altitude population showed a relatively conservative response. Metagenomic analysis showed that alpha diversity remained relatively stable, whereas beta diversity, dominant microbial taxa and functional potential shifted among groups. Microbial functional profiles were mainly associated with metabolism, nutrient transformation and carbohydrate utilization.

CONCLUSION: Post-hibernation recovery in R. kukunoris involves cross-level parallel responses in host energy status, digestive system structure and gut microbiota. High- and low-altitude populations may adopt different physiological recovery strategies after hibernation, providing new evidence for understanding seasonal adaptation in amphibians inhabiting cold environments.},
}

@article {pmid42577254,
year = {2026},
author = {Ouedraogo, FJ and Poulain, AJ and Aris-Brosou, S},
title = {Glacial meltwater is associated with gene-specific diversification of metal resistance genes in high Arctic soil microbiomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903619},
pmid = {42577254},
issn = {1664-302X},
abstract = {Climate warming accelerates glacial meltwater delivery to Arctic lakes, mobilizing metals from thawing catchments and reshaping the selective landscape experienced by resident microbes. Whether these gradients leave detectable signatures of diversification in environmental resistance genes remains unclear. We investigated four metal resistance genes (merA, arsC, cadA, and chrR) in metagenomic datasets from Lake Hazen (Nunavut, Canada), the largest High Arctic freshwater lake, sampled across a natural hydrological gradient of Control, Low-runoff, and High-runoff regimes. Using a space-for-time substitution design, we combined population-genetic and codon-based approaches to quantify diversity and candidate selection signals, including nucleotide diversity, Tajima's D, non-synonymous-to-synonymous diversity ratios, McDonald-Kreitman tests with outgroup-sensitivity analysis, site-level episodic selection (MEME with false-discovery-rate correction), and gene-wide tests (BUSTED and BUSTED-E) and complemented these with ortholog clustering, within-clade re-analysis, taxonomic profiling, rarefaction, and phylogenetic beta-diversity. Marked heterogeneity emerged among genes: merA showed increasing diversity and patterns consistent with diversification along the runoff gradient, and these signals were preserved within the largest orthologous cluster (90% of haplotypes), supporting an interpretation of within-orthogroup diversification; cadA displayed the strongest McDonald-Kreitman signal under low and high runoff, but its gene-wide BUSTED-E signal collapsed within a single ortholog cluster, suggesting that part of the apparent diversifying signal at the gene-family level reflects inter-subfamily heterogeneity; chrR exhibited the strongest regime structure but its largest orthologous cluster was dominated by Control sequences and 93% of High-regime haplotypes were affiliated with a single bacterial order (Hyphomicrobiales), indicating that the regime contrast for this gene reflects compositional turnover rather than within-lineage evolution; arsC remained largely consistent with neutral or purifying evolution across regimes. Because these inferences derive from metagenomic gene pools sampled across only three hydrological regimes and aggregate variants across taxa, we interpret them as exploratory, hypothesis-generating patterns rather than as demonstrations of population-level adaptation. Our findings highlight environmental resistance genes as candidate indicators of changing biogeochemical conditions in rapidly warming polar ecosystems, while underscoring the importance of orthology and community-composition controls when inferring selection from metagenomic data.},
}

@article {pmid42577359,
year = {2026},
author = {Wu, H and Song, DC and Yao, Z and Wang, Q and Yan, ZZ and He, FL and Guo, SJ and Wang, LD},
title = {Microbial carbon fixation pathways shifts during artificial Haloxylon ammodendron restoration with clay sand barriers in arid deserts: a metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1884493},
pmid = {42577359},
issn = {1664-302X},
abstract = {Soil microbial carbon fixation is influenced by the combined effects of microbial community composition, functional gene distribution, and environmental factors, and is closely associated with vegetation restoration processes. However, the soil carbon fixation process and its coupling mechanisms mediated by microorganisms at different vegetation restoration stages in arid regions remain unclear. In this study, we applied metagenomic sequencing to investigate soil from a clay sand barrier Haloxylon ammodendron sand-fixing restoration area at the southeastern edge of the Badain Jaran Desert, spanning a 60-year vegetation restoration time sequence (1, 5, 10, 20, 40, and 60 years) and shifting sand as a control. We explored the impacts of vegetation restoration and its long-term sequence on soil properties, microbial community structure, carbon fixation genes, and carbon fixation pathways. The results showed that vegetation restoration improved regional soil nutrient levels and organic carbon accumulation, with these positive effects progressively amplified over the restoration time sequence. Additionally, vegetation restoration not only reshaped microbial community composition but also induced changes in carbon fixation-related genes and pathways. A 10-year restoration period served as a critical time point, with microbial community diversity and carbon fixation gene abundance exhibiting pronounced fluctuations during the first 10 years, followed by relative stabilization thereafter. This threshold likely reflects a transition from intense plant-microbe competition to a more balanced coexistence as vegetation succession progresses and soil conditions stabilize. Among the six major microbial carbon fixation pathways, the rTCA cycle had the highest relative gene abundance, making it the dominant carbon fixation pathway in the region. Soil properties, particularly soil water content (SWC) and total phosphorus (TP), were identified as critical factors influencing both microbial community composition and carbon fixation-related genes. These findings suggest that clay sand barrier Haloxylon restoration not only fulfills its role in sand stabilization but also alters the soil environment, driving a functional shift in the microbial community from autotrophic to heterotrophic processes. This study deepens our understanding of soil carbon fixation processes in arid desert ecosystems and provides theoretical guidance for carbon management in similar arid regions.},
}

@article {pmid42577398,
year = {2026},
author = {Zhang, J and Chen, J and Hu, M and Wang, J and Ning, S and Zhang, W and Sun, R},
title = {Viral metagenomic analysis of human bocavirus in pediatric pneumonia: detection pattern and genetic characterization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1868618},
pmid = {42577398},
issn = {2235-2988},
mesh = {Humans ; *Human bocavirus/genetics/isolation & purification/classification ; *Metagenomics ; Retrospective Studies ; Female ; Infant ; Bronchoalveolar Lavage Fluid/virology ; Phylogeny ; Male ; Child, Preschool ; *Parvoviridae Infections/virology/epidemiology ; Child ; Genotype ; China/epidemiology ; High-Throughput Nucleotide Sequencing ; *Pneumonia, Viral/virology ; Genome, Viral ; },
abstract = {BACKGROUND: Human bocavirus (HBoV) is frequently detected in pediatric respiratory samples, but its clinical role remains difficult to interpret because of asymptomatic shedding and frequent co-detection with other pathogens. Data from bronchoalveolar lavage fluid (BALF), which more directly reflects the lower respiratory tract, remain limited.

METHODS: This retrospective study analyzed 179 BALF samples collected from pneumonia patients in the Jiangnan region of China between July and December 2025. Metagenomic next-generation sequencing (mNGS) was used for HBoV detection, mNGS-derived abundance estimation, genotype assignment, and genome coverage analysis. VP1 and NS1 gene fragments were used for phylogenetic analysis, and recombination screening was performed using RDP4.

RESULTS: Using the predefined ≥10-read mNGS screening threshold, HBoV signals were detected in 22 of 30 pediatric samples (73.3%; 95% CI, 54.1-87.7%) and in none of the 149 adult samples (0%; 95% CI, 0-2.45%), showing an age-related detection pattern in this cohort (Fisher's exact test, P = 6.91 × 10[-]²²). HBoV1 was assigned as the dominant genotype in all HBoV mNGS signal-positive samples. RPM values varied among these samples, but they should be interpreted as mNGS-derived relative abundance rather than absolute viral load. Genome coverage analysis and partial VP1/NS1 phylogenetic placement provided additional support for HBoV1 read-based detection and genotype assignment. RDP4 analysis did not detect recombination events involving the study-derived VP1 or NS1 fragments.

CONCLUSIONS: HBoV1 was frequently detected in pediatric BALF samples in this retrospective cohort, suggesting that HBoV1 signals may be relevant to the interpretation of some pediatric lower respiratory tract samples. However, because qPCR validation, healthy controls, and a comprehensive multi-pathogen co-infection assessment were not included, these data do not establish HBoV1 as the direct causative agent of pneumonia. Larger studies with quantitative validation and more complete clinical data are needed.},
}

Humans
*Human bocavirus/genetics/isolation & purification/classification
*Metagenomics
Retrospective Studies
Female
Infant
Bronchoalveolar Lavage Fluid/virology
Phylogeny
Male
Child, Preschool
*Parvoviridae Infections/virology/epidemiology
Child
Genotype
China/epidemiology
High-Throughput Nucleotide Sequencing
*Pneumonia, Viral/virology
Genome, Viral

@article {pmid42577453,
year = {2026},
author = {Rakhmankulova, A and Kozhakhmetov, S and Kovenskiy, A and Mukhanbetzhanov, N and Katkenov, N and Jarmukhanov, Z and Terzic, M and Bapayeva, G and Ukybassova, T and Aimagambetova, G and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Smagulova, B and Vinogradova, E and Kamzayeva, N and Kushugulova, A},
title = {Multi-kingdom cervical microbiome structure in health and dysbiosis: a cross-sectional study from Kazakhstan.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1836889},
pmid = {42577453},
issn = {1664-302X},
abstract = {INTRODUCTION: The cervicovaginal microbiome is a key determinant of reproductive health. Its multi-kingdom structure and ecological interactions remain insufficiently characterized across diverse populations. This study aimed to define the composition and cross-kingdom dynamics of the cervical microbiome in women without HPV infection and with normal cytology in a Kazakhstani population.

METHODS: In this cross-sectional study, cervical samples from 92 reproductive-age women were analyzed using whole-genome metagenomic sequencing to characterize bacterial, viral, fungal, and archaeal communities, together with predicted functional pathways. Microbial communities were stratified into community state types based on dominant bacterial species.

RESULTS: Bacterial composition differed markedly across community states, with Lactobacillus-dominated profiles associated with low diversity and anaerobe-rich communities associated with higher diversity. In contrast, viral, fungal, and archaeal diversity remained relatively stable, although descriptive compositional shifts indicated variation in bacteriophages, methanogenic archaea, and opportunistic fungi in non-Lactobacillus communities. Functional analyses indicated CST-associated pathway differences, suggesting greater metabolic flexibility in dysbiotic states, and exploratory network analysis revealed CST-associated restructuring of bacterial and cross-kingdom co-variation patterns. Notably, more than half of participants exhibited non-Lactobacillus-dominated communities despite the absence of infection or cytological abnormalities, indicating population-specific microbiome configurations.

DISCUSSION: Study demonstrates that the cervical microbiome is accompanied by exploratory cross-kingdom compositional variation and ecological states traditionally considered dysbiotic may represent stable, population-specific configurations, highlighting the need for context-dependent definitions of microbial health.},
}

@article {pmid42577546,
year = {2026},
author = {Zhan, M and Chen, H and Li, Z and Liu, S and Lu, B and Wang, Z and Wang, H},
title = {Lower Respiratory Microbiome Dysbiosis Is Associated With Poor Prognosis in Acute Severe Lower Respiratory Tract Infection.},
journal = {MedComm},
volume = {7},
number = {8},
pages = {e70907},
pmid = {42577546},
issn = {2688-2663},
abstract = {Acute severe lower respiratory tract infections (asLRTIs) pose a significant clinical challenge, especially in critically ill patients, but the role of the lower respiratory tract microbiome (LRTM) remains unclear. This study aimed to characterize LRTM composition and host immune factors to identify prognostic features of clinical outcomes. The study included 53 asLRTI patients and 35 controls. Metagenomics, metabolomics, proteomics, and RNA sequencing were conducted, while analysis of similarities (ANOSIM) and Cox regression were performed for statistics. Clinical data, including pneumonia severity scores, were collected on BALF sampling, with a 100-day follow-up. LRTM samples were grouped into five clusters (C1-C5). Cluster C5 resembled controls, while others showed significantly lower diversity. LRTM composition correlated with prognosis, with higher pathogenic bacteria abundance linked to poorer outcomes. Cluster C3 was associated with poor prognosis and reduced survival. Metabolite analysis revealed elevated α-ketoisocaproic acid in asLRTIs and higher 10-nitrolinoleate in poor-prognosis patients. Immune responses varied across clusters, with distinct gene and cytokine expression patterns. Cluster C1, associated with Acinetobacter baumannii, exhibited heightened IL17 pathway activation. LRTM composition in asLRTIs is linked to clinical outcomes, with no single gradient of difference but distinct community states characterized by varying pathogens, metabolites, and immune responses.},
}

@article {pmid42577578,
year = {2026},
author = {Song, Y and Zhang, X and Wang, H and Wang, Y and Zhang, S and Li, Y and Cui, X and Li, X and Li, Y and Wang, J and Su, J and Zheng, Y and Gai, W and Liu, W},
title = {Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799148},
pmid = {42577578},
issn = {2235-2988},
mesh = {Humans ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Microbiota ; *Endosonography/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; *Neoplasms/complications/drug therapy ; Bacteria/classification/genetics/isolation & purification ; Bronchoscopy ; Aged, 80 and over ; Adult ; Sepsis ; },
abstract = {INTRODUCTION: Patients treated with systemic anti-tumor therapies are more likely to develop pulmonary infections due to weakened immune systems. This study aims to evaluate the clinical application of radial endobronchial ultrasound (R-EBUS) combined with metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infections among patients undergoing systemic anti-tumor therapy.

METHODS: This study is a single-center retrospective analysis that includes 84 patients with pulmonary infections following systemic anti-tumor therapy. Patients were stratified into sepsis (SOFA score ≥2, n=32) and non-sepsis (SOFA score <2, n=52) groups based on Sepsis-3.0 criteria. BALF samples were subjected to both mNGS and conventional microbiological tests (CMT). Pathogen profiles, diagnostic performance, clinical impact on antimicrobial therapy, and microbiome diversity were analyzed.

RESULTS: mNGS demonstrated a significantly higher positive detection rate than CMT (95.24% vs. 30.95%, P < 0.001). mNGS identified a broader spectrum of pathogens, including bacteria, fungi, and viruses, and detected mixed infections more frequently than CMT. The clinical impact of mNGS was positive in 84.52% of cases, primarily by initiating targeted therapy or confirming empirical treatment. Microbiome analysis revealed significantly lower alpha diversity (Shannon, ACE, Chao1 indices) in the severe group compared to the non-severe group.

DISCUSSION: EBUS-guided mNGS of BALF was associated with improved pathogen detection in malignancy patients with pulmonary infections, leading to a high rate of beneficial antimicrobial adjustments. Distinct microbial signatures are associated with infection severity, suggesting potential diagnostic and therapeutic implications.},
}

Humans
Female
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Male
Retrospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Aged
Microbiota
*Endosonography/methods
*Respiratory Tract Infections/diagnosis/microbiology
*Neoplasms/complications/drug therapy
Bacteria/classification/genetics/isolation & purification
Bronchoscopy
Aged, 80 and over
Adult
Sepsis

@article {pmid42577588,
year = {2026},
author = {Brock, R and Schaupp, L and Schütte, A and Zhou-Suckow, Z and Butz, S and Schatterny, J and Mayer, S and Frank, A and Mengel, JP and Weigel, M and Hain, T and Dalpke, A and Boutin, S and Mall, MA},
title = {Preventive intrapulmonary treatment with Ligilactobacillus murinus reduces airway inflammation and mucus plugging in mice with cystic fibrosis-like lung disease.},
journal = {ERJ open research},
volume = {12},
number = {4},
pages = {},
pmid = {42577588},
issn = {2312-0541},
abstract = {BACKGROUND: Chronic airway dysbiosis plays an important role in the pathogenesis of cystic fibrosis (CF) lung disease and may serve as a therapeutic target. However, studies investigating the effects of direct therapeutic targeting of the airway microbiome are lacking. In this study, we therefore used βENaC-overexpressing (βENaC-Tg) mice and determined the evolution of abnormal lung microbiota and effects of re-balancing bacterial communities on chronic airway inflammation and mucus plugging in this model of CF lung disease.

METHODS: The development of the respiratory microbiome was determined by 16S rRNA gene sequencing and the effects of preventive intranasal instillation of endogenous probiotic bacteria on the lung phenotype were determined in βENaC-Tg mice and wild-type littermates.

RESULTS: Neonatal βENaC-Tg mice developed severe respiratory dysbiosis characterised by an increase in the relative abundance of Streptococcus and a decrease in Ligilactobacillus compared to wild-type littermates. Ligilactobacillus murinus SMH17 was identified as the dominant Ligilactobacillus species in the lungs of neonatal wild-type mice. Preventive treatment by intranasal instillation of L. murinus SMH17 was well tolerated and reduced age-specific markers of airway inflammation including inflammatory cell counts and proinflammatory cytokines in neonatal and juvenile βENaC-Tg mice. In addition, preventive treatment with L. murinus SMH17 reduced airway mucus plugging in βENaC-Tg mice by ∼40%.

CONCLUSION: Preventive intrapulmonary application of the endogenous probiotic L. murinus SMH17 reduces airway inflammation and mucus plugging in mice with CF-like lung disease. These data support further elucidation of inhaled probiotics as a strategy to treat chronic airway dysbiosis in patients with CF.},
}

@article {pmid42577598,
year = {2026},
author = {Zhang, Q and Lei, M and Li, H and Yi, G and Li, D},
title = {Case Report: Pediatric Rickettsia felis encephalitis-a rare case and literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1867339},
pmid = {42577598},
issn = {2296-2360},
abstract = {BACKGROUND: Rickettsia felis (R. felis), an obligate intracellular bacterium, has been reported to cause human encephalitis. Clinical reports of R. felis encephalitis remain rare, particularly in children. Herein, we present a pediatric case and review the relevant literature.

CASE REPORT: A previously healthy 9-year-old boy initially presented with fever and headache. Following admission, he developed hyperpyrexia and somnolence. Cranial magnetic resonance imaging revealed a left temporal lobe lesion with ipsilateral temporoparietal meningeal enhancement, and electroencephalography showed background slowing. Metagenomic next-generation sequencing of cerebrospinal fluid detected a high abundance of R. felis sequences, whereas autoantibody testing for central nervous system autoimmune diseases was negative. Based on these findings, a diagnosis of R. felis encephalitis was established. The child fully recovered and was discharged after receiving doxycycline-based antimicrobial therapy combined with glucocorticoids, intravenous immunoglobulin, and intracranial pressure management.

CONCLUSION: This rare case highlights that R. felis infection should be included in the differential diagnosis of encephalitis. Metagenomic next-generation sequencing is recommended for early etiological diagnosis to facilitate timely and effective clinical intervention.},
}

@article {pmid42577830,
year = {2026},
author = {Martínez-Cuesta, R and Hoess, R and Geist, J and Schloter, M and Schulz, S},
title = {The larval gut as a mirror: bacterial community composition and functional potential of mayfly larvae reflect site and seasonality differences.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag192},
pmid = {42577830},
issn = {2730-6151},
abstract = {Land use intensification is a major driver of biodiversity loss across ecosystems, yet its consequences for host-associated microbiomes in freshwater food webs remain poorly understood. In this case study, we used the gut microbiome of mayfly larvae (Ephemera danica) as a sensitive biological interface to assess how site-specific adjacent land use types shape microbial community composition and functions in stream ecosystems. Larvae were sampled in summer and autumn from sites adjacent to forest, extensive grassland, and intensive agriculture along the Otterbach stream (Bavarian Forest, Germany). Combining 16S ribosomal RNA (rRNA) amplicon sequencing with long-read metagenomics, we show that site-specific land use, in interaction with seasonality, significantly restructures larval gut bacterial communities without affecting alpha diversity. Rather than introducing distinct agriculturally derived taxa, agricultural land use acted as a selective environmental filter, enriching bacterial groups with specific functional traits. Taxa enriched in the sites adjacent to agricultural sites harboured genes involved in complex carbon and xenobiotic degradation, short-chain fatty acid production, efflux pumps, and stress response. These functional signatures were further supported by 14 metagenome-assembled genomes linked to these enriched taxa. Together, our results reveal that site in combination with seasonality not only reshaped bacterial community composition without affecting alpha diversity but also triggered shifts in the abundance of genes involved in microbial-host interactions and degradation pathways in E. danica larvae. This study also highlights the larval gut microbiome as a sensitive indicator of environmental change, suggesting that environmental microbial shifts may have cascading consequences for freshwater trophic interactions and ecosystem functioning.},
}

@article {pmid42577885,
year = {2026},
author = {Li, J and Jiang, Z and Li, X and Fang, W and Jiang, Y and Hu, Y and Dong, Y and Xie, X and Shi, L and Kappler, A and Wang, Y},
title = {Dissimilatory iodate-reducing microorganisms inhabit marine oxygen minimum zones.},
journal = {National science review},
volume = {13},
number = {15},
pages = {nwag397},
pmid = {42577885},
issn = {2053-714X},
abstract = {Based on theoretical thermodynamic calculations, microbial IO3 [-] reduction precedes NO3 [-] reduction, and it was previously proposed that dissimilatory iodate-reducing microorganisms (DIRMs) inhabit a unique niche above marine oxygen minimum zones (OMZs). Here we demonstrate that dissimilatory IO3 [-] reduction lags behind NO3 [-] reduction in two representative strains Azonexus hydrophilus NCP973 and Denitromonas iodatirespirans IR-12. Correspondingly, the functional genes idrABP1P2 for DIRMs were found to be exclusively distributed across depth profiles of global OMZs where NO3 [-] reduction is active. Combined with widespread detection and heterologous expression of the idrABP1P2 of metagenome-assembled genomes (MAGs) from the OMZs, these findings suggest that DIRMs inhabit marine OMZs and contribute to I[-] production and accumulation. As OMZs expand under global warming, DIRMs could enhance volatile iodine fluxes to the atmosphere by producing the precursor I[-]. Given the environmental health importance of atmospheric iodine, integrating this pathway into marine iodine biogeochemical models will improve our capability of understanding and predicting the future changes in oceanic iodine emissions.},
}

@article {pmid42577916,
year = {2026},
author = {Demmer, RT and Pope, ZC and Avenido, FRR and Mitchell, NR and Richmond Hubbard, PF and Johnson, S and Sharma, S and McDonough, DJ and Rydell, SA and Johnson, A and Pereira, MA},
title = {The Effect of Physical Activity on the Gut Microbiome in Prediabetes: Results from a Randomized Controlled Trial.},
journal = {Diabetes, obesity, and cardiometabolic CARE},
volume = {1},
number = {2},
pages = {219-229},
pmid = {42577916},
issn = {3067-3534},
abstract = {OBJECTIVE: To test the effect of physical activity on the gut microbiome and circulating short chain fatty acids among sedentary adults with prediabetes and overweight/obesity.

RESEARCH DESIGN AND METHODS: In a pilot and feasibility trial, we randomized 77 adults with prediabetes and a sedentary lifestyle into one of two groups: 1) Intervention: Invited to engage in home-based moderate intensity walking 3x/week for 30 minutes/session in weeks 1-4 and for 45 minutes/session during weeks 5-8 of the 8-week intervention; or 2) Control: Maintained habitual physical activity levels. We performed metagenomic sequencing from stool collected at baseline, week 4, and week 8, with short-chain fatty acids (SCFA) measured from serum collected at baseline and week 8. Taxonomic and functional profiling were performed on the metagenomic reads; alpha diversity metrics were subsequently derived. Linear regression assessed the difference in change between the intervention and control groups for alpha-diversity and SCFA levels.

RESULTS: We screened 1,533 participants for eligibility and consented 132. Of these, 87 entered the run-in phase and 77 were randomized. Participants were 51.4±8.9 years old, 87.7% female, and 74% non-Hispanic White. Mean fasting glucose was 103.3±13.2 while mean BMI was 34.4±5.7. In comparison to control, the intervention group experienced decreased alpha diversity as characterized by Shannon, Richness, and Faith's diversity indices by intervention week 8 (P<0.05). Changes in SCFA levels were not statistically significant different in intervention vs. control.

CONCLUSIONS: Randomization to a walking intervention resulted in modest gut microbiome changes among adults with overweight/obesity and prediabetes.},
}

@article {pmid42577946,
year = {2026},
author = {Du, X and Meng, Q and Wang, L and Zhang, Z},
title = {Exploratory Evaluation of Chlorhexidine Decolonization and Skin Colonization Dynamics of Candida auris in ICU Patients: A Prospective Pilot Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {619168},
pmid = {42577946},
issn = {1178-6973},
abstract = {OBJECTIVE: Candida auris has emerged as a nosocomial pathogen in intensive care units (ICUs), and evidence for chlorhexidine-based decolonization remains limited. We report an exploratory pilot study describing skin colonization dynamics in four ICU patients with C. auris infection or colonization who received chlorhexidine decolonization alongside standard infection control measures.

METHODS: Four consecutive C. auris-positive patients admitted to the ICU of a tertiary teaching hospital in Inner Mongolia, China, between January 31 and March 12, 2026, were enrolled. Two patients (intervention group) received twice-daily 2% chlorhexidine gluconate whole-body skin decolonization; two (non-intervention group) did not, based on family consent. All patients received identical baseline infection control measures. Skin swabs from the nares, axillae, groin, and external ear canals, together with environmental samples, were cultured serially. All isolates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). For one patient, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid was performed as part of routine clinical workup.

RESULTS: Skin colonization burden declined progressively in both intervention patients: Case A fell from 34 colony-forming units (CFU)/swab at baseline to 4 CFU/swab by Day 12, and Case B from 10 CFU/swab (Day 4) to 5 CFU/swab by Day 6 (discharged on Day 10). Colonization burden did not decline in the non-intervention group (Case C: 24-30 CFU/swab in groin across Day 0-12). Clinical outcomes differed between groups, but the non-randomized design, baseline imbalance in infection status, and universal co-infection with multidrug-resistant organisms preclude any causal inference. C. auris was recovered from 1 of 93 environmental surveillance samples (a suction bottle) and was eliminated by targeted disinfection; no healthcare worker hand cultures were positive.

CONCLUSION: In this four-patient pilot study, twice-daily chlorhexidine decolonization was accompanied by a reduction in skin colonization burden, but the findings are hypothesis-generating only. The small sample size, non-randomized design, baseline differences, and lack of molecular typing limit interpretation. Adequately powered, preferably randomized, studies with whole-genome sequencing are needed.},
}

@article {pmid42577950,
year = {2026},
author = {Davis, HE and Torres, J and Adler, MJ and Parker, BJ},
title = {A Wolbachia coinfection in the common bed bug.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag197},
pmid = {42577950},
issn = {2730-6151},
abstract = {The common bed bug (Cimex lectularius) relies on an obligate mutualism with the Wolbachia strain wCle to supplement B vitamins deficient in human blood. Using metatranscriptomic and metagenomic sequencing of hospital-collected bed bugs, we found that some individuals also harbor a second strain of Wolbachia (wChem). Using publicly available data we showed that wChem is distributed in bed bugs worldwide at intermediate frequencies and may have moved recently between C. lectularius and Cimex hemipterus, the tropical bed bug, which also feeds on human hosts. We found that wChem encodes a highly expressed cifA/B operon in males and females, consistent with cytoplasmic incompatibility, a reproductive manipulation strategy used by Wolbachia to increase in frequency in host populations. Together, these results demonstrate that some bed bugs harbor a Wolbachia coinfection of a nutritional mutualist and a potentially manipulative facultative symbiont. This discovery identifies a previously hidden aspect of bed bug biology with significant implications for its evolution, spread, and potential control.},
}

@article {pmid42577959,
year = {2026},
author = {Sun, Z and He, C and Ma, X and Wu, P and Wang, T and Yuan, J and Pu, Y and Zhou, X and Mei, Z and Song, H and Wang, Y and Yue, H and Fu, Y and Zheng, J and Pan, A and Chen, D and Hong, S and Pan, XF and Zheng, Y},
title = {A gut microbiome-lipid axis in early pregnancy is associated with metabolic dysregulation and diabetes risk.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70166},
pmid = {42577959},
issn = {2770-596X},
abstract = {Gestational diabetes mellitus (GDM) reflects metabolic dysregulation that becomes clinically apparent during pregnancy and shares key pathophysiological features with broader forms of diabetes. Gut microbiome-host metabolic interactions may contribute to this process, yet their role in early pregnancy remains incompletely understood. In this prospective nested case-control study within the Tongji-Huaxi-Shuangliu Birth Cohort, 784 pregnant women, including 222 who developed GDM, underwent first-trimester gut metagenomic and plasma lipidomic profiling. Cross-omics analyses were performed to identify microbiome-lipid associations and potential mediation patterns. Women who later developed GDM showed reduced gut microbial diversity and altered microbial profiles in early pregnancy. We identified 26 microbial species associated with GDM risk, with seven species, including Ruminococcus bicirculans (R. bicirculans), showing concordant associations in external type 2 diabetes populations. Microbial pathways related to fatty acid and lipid biosynthesis were enriched in women at higher risk. Plasma lipidomics revealed widespread alterations, particularly among glycosphingolipid-related metabolites. Integrated analyses suggested that lipidomic variation statistically accounted for part of the microbiome-GDM association. A class-level dihexosylceramide feature, DHC 24:1, consistent with lactosylceramide-related metabolites, emerged as a potential mediator and was prioritized for exploratory follow-up. Experimental analyses provided functional support for a microbiome-lipid-host interaction axis. R. bicirculans promoted lactosylceramide 24:1 production in vitro, bacterial colonization and metabolite administration improved insulin tolerance in vivo, and lactosylceramide 24:1 modulated insulin-stimulated AKT signaling dynamics in hepatocytes. These findings identify a gut microbiome-lipid axis associated with metabolic dysregulation in pregnancy and suggest a potential mechanism linking microbial metabolism to host insulin signaling.},
}

@article {pmid42578670,
year = {2026},
author = {Li, Z and Sun, J and Yang, J and Han, P and Min, L and Cheng, Y and Zou, Y and Liu, Z},
title = {Exploring the hypothetical role of Bacteroides species in depression progression: insights from metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0315324},
doi = {10.1128/spectrum.03153-24},
pmid = {42578670},
issn = {2165-0497},
abstract = {Depression, a psychiatric disorder with significant morbidity and mortality, has a complex etiology. Recent advances in microbiome research have highlighted the potential role of fecal microbiota in depression pathogenesis. This study utilized shotgun metagenomic sequencing to compare the fecal microbiota of 28 depression patients and 26 healthy individuals. Significant differences in fecal microbiota composition were observed between the two groups. We generated 350 non-redundant high-quality metagenome-assembled genomes (MAGs) by binning and conducted comparisons between the depression and control groups. Notably, we found that the MAGs enriched in people with depression mostly belonged to Bacteroides, indicating a close link between Bacteroides abundance and the development of depression, suggesting that Bacteroides might be a potential culprit for depression. In the depression group, we found that the module of nitric oxide synthesis was remarkably enriched, and all Bacteroides MAGs contained genes annotated as nitric oxide synthase, suggesting that increased levels of Bacteroides may contribute to elevated nitric oxide synthesis. A distinct microbial signature consisting of Arthrobacter sp._U41, Bacillus cereus, Campylobacter rectus, and Pasteurella dagmatis accurately discriminates between depressed individuals and healthy controls, achieving an average area under the receiver operating characteristic curve of 0.950. This research sheds light on the potential role of fecal microbiota in depression and highlights specific metabolic pathways and microbial markers for further investigation.IMPORTANCEThis research highlighted significant differences in the composition and function of fecal microbiota between individuals with depression and healthy individuals, particularly the enrichment of Bacteroides metagenome-assembled genomes (MAGs) in depression patients. The upregulation of the nitric oxide synthesis pathway associated with these MAGs belonging to Bacteroides in the gut of depression patients had also been observed. The selected bacterial biomarkers reliably differentiate depression cases from healthy controls with high diagnostic accuracy (mean area under the receiver operating characteristic curve = 0.950). Our results suggest the importance of exploring microbial markers as potential diagnostic and therapeutic targets in managing depression.},
}

@article {pmid42578673,
year = {2026},
author = {Mirăuță, B and Riza, A-L and Streata, I and Pirvu, A and Dorobantu, S and Dragos, A and Surleac, M and Netea, MG},
title = {Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0052826},
doi = {10.1128/spectrum.00528-26},
pmid = {42578673},
issn = {2165-0497},
abstract = {The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favorable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. This first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort, a population underrepresented in microbiome studies and characterized by high antibiotic consumption, addresses a gap in current microbiome research. We report an enrichment of Enterobacteriaceae although overall composition is more comparable to other European than non-European cohorts. Community configurations align with established enterotype patterns, and our analysis provides insight into their relationship with within-phylum diversity. The analysis of antimicrobial resistance provides insight into the prevalence of resistance genes within this reservoir. We specifically report the presence of cfr(E), a Clostridioides difficile gene, and tet(X5), a variant from the ubiquitous tet family, genes not previously reported in healthy European populations. Integration with data from the European Centre for Disease Prevention and Control links the overall prevalence of resistance genes in this reservoir to antibiotic classes with higher community consumption in this population, notably beta-lactams and quinolones, highlighting potential targets for antibiotic stewardship programs. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify potential immune-priming roles for Collinsella, Flavonifractor, and Bifidobacterium species.IMPORTANCEThis first comprehensive study of the healthy gut microbiome in a Romanian cohort addresses a gap in current microbiome research, dominated by data sets from a limited number of regions. It sets a baseline for the microbiome and resistome composition of this population, and, while definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such study helps contextualize future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes and the concordance with commonly used antibiotics in the community reinforce the need to address antibiotic use in public health strategies. Although gut microbiome-immunity relationships remain incompletely understood, our findings support a role for microbiome composition in immune-related traits and provide a valuable resource for future studies.},
}

@article {pmid42578999,
year = {2026},
author = {Conway Morris, A and Edgeworth, JD and Povoa, P},
title = {Clinical metagenomics: a call to action.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
pmid = {42578999},
issn = {1432-1238},
support = {MR/V006118/1/MRC_/Medical Research Council/United Kingdom ; },
}

@article {pmid42579079,
year = {2026},
author = {Yu, J and Xiong, Q and Li, X},
title = {Synergistic degradation of sulfamethoxazole by Enterococcus wangshanyuanii F4 and black soldier fly larvae.},
journal = {Biodegradation},
volume = {37},
number = {4},
pages = {},
pmid = {42579079},
issn = {1572-9729},
support = {39829117//Nanjing Tech University/ ; },
mesh = {Animals ; Larva/microbiology/metabolism/growth & development ; *Sulfamethoxazole/metabolism ; *Enterococcus/metabolism ; Biodegradation, Environmental ; *Simuliidae/microbiology/metabolism ; *Diptera/microbiology ; },
abstract = {This study demonstrates that inoculation with the Enterococcus wangshanyuanii strain F4 in a germ-free black soldier fly larval (BSFL) system enhances sulfamethoxazole (SMX) degradation, larval growth, and substrate conversion. Following inoculation with strain F4, the net SMX degradation rate reached 37.08%, and the net substrate consumption rate reached 46.12%, both representing significant improvements compared to the control group. Metagenomic analysis revealed that strain F4 modulated the BSFL gut microbial community structure and enriched functional genes associated with organic pollutant degradation. Accordingly, the activities of key degradation enzymes in the larval gut, including catechol-1,2-dioxygenase (C12O), catechol-2,3-dioxygenase (C23O), and peroxidase (POD), were significantly elevated following inoculation. Taken together, these findings suggest a synergistic effect between Enterococcus wangshanyuanii F4 and the host during the degradation process, which significantly enhances the removal of SMX by black soldier fly larvae. This provides a theoretical basis for the use of symbiotic microbial augmentation strategies in antibiotic bioremediation.},
}

Animals
Larva/microbiology/metabolism/growth & development
*Sulfamethoxazole/metabolism
*Enterococcus/metabolism
Biodegradation, Environmental
*Simuliidae/microbiology/metabolism
*Diptera/microbiology

@article {pmid42579339,
year = {2026},
author = {Douwes, H and Dutkiewicz, Z and Rinke, C},
title = {Predicting the plastic biodegradation potential within microbial lineages and across global ecosystems.},
journal = {Microbial genomics},
volume = {12},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001814},
pmid = {42579339},
issn = {2057-5858},
mesh = {*Plastics/metabolism ; *Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism/enzymology ; Metagenome ; *Archaea/genetics/classification/metabolism/enzymology ; Ecosystem ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Hidden Markov Models ; },
abstract = {Plastic waste pollution is a global issue that threatens biodiversity and human health. Current plastic waste management practices are not sufficient to keep up with increasing plastic production rates. Microorganisms have the capacity to degrade different types of bio-based and synthetic plastics through enzymatic reactions, offering an alternative solution to traditional plastic recycling techniques. A limited number of plastic-degrading enzymes have been identified, sequenced and characterized; however, studies exploring the distribution of homologues of these enzymes across habitats and microbial taxa have remained scarce. Here, we applied analytical techniques to search for genes encoding potential plastic-degrading enzymes in environmental metagenome datasets and genomes of the Genome Taxonomy Database (GTDB) to explore the geographic and taxonomic distribution patterns of plastic-degrading microorganisms. Hidden Markov Models (HMMs) were constructed from amino acid sequences of known, experimentally verified and putative plastic-degrading enzymes. The HMMs were applied to landfill, soil, river, lake and ocean metagenomes and all archaeal and bacterial genomes in the GTDB. An abundance of hits was discovered across aquatic and terrestrial metagenomes with the majority occurring in polluted rivers, polar oceans and deep ocean samples. GTDB hits were mainly consistent with known plastic-degrading microbial lineages, while also revealing potential plastic-degrading archaeal taxa. The results of this study may be able to assist in the discovery of novel plastic-degrading enzymes for application in plastic waste biodegradation solutions.},
}

*Plastics/metabolism
*Biodegradation, Environmental
*Bacteria/genetics/classification/metabolism/enzymology
Metagenome
*Archaea/genetics/classification/metabolism/enzymology
Ecosystem
Phylogeny
Metagenomics
Genome, Bacterial
Hidden Markov Models

@article {pmid42579903,
year = {2026},
author = {Zhang, W and Wei, Z and Liu, Y and Xiao, Y},
title = {Rupture and dissemination of a mycotic aneurysm caused by the Aspergillus fumigatus complex: A diagnostic challenge posed by a non‑sporulating isolate.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {4},
pages = {117595},
doi = {10.1016/j.diagmicrobio.2026.117595},
pmid = {42579903},
issn = {1879-0070},
abstract = {A 45-year-old male with a history of lumbar tuberculosis presented with a ruptured mycotic iliac artery aneurysm as the initial manifestation. Imaging demonstrated aneurysm rupture with pseudoaneurysm formation and concurrent disseminated lesions involving the vertebrae and soft tissues. Intraoperative specimens grew an Aspergillus fumigatus strain that exhibited highly atypical morphology: the colonies were albino‑like, slow‑growing, and non‑sporulating, differing markedly from the classic A. fumigatus phenotype. Peripheral blood metagenomic sequencing detected A. fumigatus, and the serum galactomannan antigen was markedly elevated. Molecular sequencing confirmed the isolate as A. fumigatus sequence type ST26 and identified the multidrug resistance‑associated gene ABCA. The final diagnosis was disseminated aspergillosis presenting as a ruptured mycotic iliac artery aneurysm, complicated by prosthetic graft infection and multiorgan dissemination. The patient received systemic antifungal therapy with voriconazole, along with adequate surgical drainage and debridement. Subsequently, his inflammatory markers declined gradually, and he was discharged on hospital day 58.},
}

@article {pmid42580006,
year = {2026},
author = {Zhang, L and Xu, W and Wang, Y and Liu, Y and Feng, X and Liu, Q},
title = {Metagenomic profiling of tick-borne viromes across four ecologically diverse provinces in China.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {5},
pages = {102693},
doi = {10.1016/j.ttbdis.2026.102693},
pmid = {42580006},
issn = {1877-9603},
abstract = {Ticks are important vectors of emerging viruses, and China's ecological landscapes may influence the transmission dynamics of tick-borne viruses (TBV). In 2021, a total of 2867 ticks collected from Inner Mongolia, Hebei, Hunan, and Hainan provinces were subjected to metagenomic sequencing to characterize TBV diversity. A total of eleven TBVs were identified, comprising three members of the family Phenuiviridae (severe fever with thrombocytopenia syndrome virus, Lihan tick virus, Dabieshan tick virus), three belonging to Nairoviridae (Huangpi tick virus 1, Shanxi tick virus 2, Henan tick virus), one in Chuviridae (Wuhan tick virus 2), one in Rhabdoviridaes (Wuhan tick virus 1), and three unclassified viruses (Hubei tick virus 2, Bole tick virus 4, and Tacheng tick virus 7). Viral composition varied significantly across tick species and geographic regions, with phylogenetic analysis revealing distinct regional clustering patterns. Notably, Lihan tick virus was detected for the first time in Hunan Province, Bole tick virus 4 was identified in argasid ticks from Inner Mongolia for the first time, and a novel lineage of severe fever with thrombocytopenia syndrome virus was discovered in Shijiazhuang, Hubei Province. These findings underscore substantial TBV diversity shaped by tick species and geographic origin, emphasizing the necessity for ongoing surveillance to guide the development of targeted prevention and control strategies.},
}

@article {pmid42580037,
year = {2026},
author = {Kearney, A and Chau, K and Kotay, S and Martin, J and Kirby, A and Mathers, AJ and Stoesser, N},
title = {Hospital sinks and healthcare-associated infection: ecology, transmission, surveillance and mitigation.},
journal = {EBioMedicine},
volume = {131},
number = {},
pages = {106415},
doi = {10.1016/j.ebiom.2026.106415},
pmid = {42580037},
issn = {2352-3964},
abstract = {Hospital sinks are recognised polymicrobial reservoirs for multi-drug resistant organisms and have been implicated in patient transmission and outbreaks. Earlier studies on sink-associated microbes predominantly focused on specific species or resistance mechanisms (e.g. carbapenemases) using targeted microbiological methods. More recently, less selective approaches (e.g. metagenomic sequencing) have enabled broader characterisation of these microbial communities. This review summarises current evidence describing hospital sink-trap microbiomes, examining ecological determinants, surveillance strategies and interventions aiming to mitigate transmission from these reservoirs. We discuss biotic and abiotic factors that shape microbial selection/persistence, assess approaches to managing these reservoirs to reduce patient risk, and highlight priorities for future research to inform evidence-based practice in healthcare settings.},
}

@article {pmid42571590,
year = {2026},
author = {Tinta, T and Fadeev, E and Celussi, M and Balestra, C and Klun, K and Mozetič, P and Herndl, GJ},
title = {Microbial degradation of jellyfish detritus promotes phytoplankton growth in coastal marine ecosystems.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag185},
pmid = {42571590},
issn = {2730-6151},
abstract = {Gelatinous zooplankton (hereinafter cnidarian Medusozoa and ctenophores or "jellyfish") are widespread in marine ecosystems and can form blooms, releasing large amounts of labile, protein-rich organic matter (jelly-OM) upon decay. This material fuels intense bacterial activity, yet its ecological consequences remain poorly understood. We conducted a two-stage microcosm experiment simulating a bloom decay of the invasive ctenophore Mnemiopsis leidyi to examine microbial processing of jelly-OM and its effect on primary production (PP). In the first stage, over the course of 3 days, we observed jelly-OM stimulating rapid growth of opportunistic bacterial community. The community was dominated by Pseudoalteromonadaceae-key degraders of diverse jellyfish, which exhibited enhanced metabolism of amino acids, lipids, and carbohydrates and elevated extracellular enzymatic activities, including leucine aminopeptidase, lipase, chitinase, and alkaline phosphatase. These processes led to marked ammonium accumulation. In the second stage, exposure of a fresh microbial assemblage to residues from jelly-OM degradation resulted in a significant increase of PP and phytoplankton biomass over a period of five days. This was dominated by diatoms and was fueled by accumulated ammonium. Concurrently, the bacterial community shifted toward taxa typically associated with phytoplankton blooms. Together, these results, further supported by in situ observations, reveal a likely coupling between jellyfish decay and phytoplankton growth, suggesting that jellyfish blooms act as transient but powerful nutrient sources capable of triggering ecosystem shifts. As jellyfish are projected to thrive under future ocean conditions, our findings underscore the need to re-evaluate their role in biogeochemical cycles-particularly as overlooked drivers of phytoplankton dynamics.},
}

@article {pmid42571770,
year = {2026},
author = {Qian, D and Xu, Z and Yuan, M and Li, Z and Zhu, Q and Peng, M and Gong, J and Yang, J and Hu, J and Hou, H},
title = {Unlocking the hidden carbon pool: Refractory organic matter drives superior chain elongation in sludge alkaline fermentation liquid.},
journal = {Water research},
volume = {306},
number = {},
pages = {126422},
doi = {10.1016/j.watres.2026.126422},
pmid = {42571770},
issn = {1879-2448},
abstract = {Converting waste activated sludge (WAS) into medium-chain fatty acids (MCFAs) via chain elongation (CE) offers a promising route for sludge valorization. In two-stage sludge CE systems, primary fermentation is typically optimized to maximize the short-chain fatty acid (SCFA) pool for downstream MCFA production; however, whether retained refractory dissolved and undissolved organic matter (rDOM and rUOM) also contributes to CE remains unclear. Here, we evaluated the roles of rDOM and rUOM in ethanol-driven CE using sludge alkaline fermentation liquid (SAFL) and thermal-alkaline pretreatment fermentation liquid (STAPFL) as feedstocks. Although SAFL contained fewer SCFAs after primary fermentation than STAPFL (3.25 vs. 3.60 g COD/L), it yielded 44% more MCFAs during CE (11.56 vs. 8.03 g COD/L). Integrated physicochemical and molecular analyses indicated that this advantage arose from greater retention of refractory organics during primary alkaline fermentation and their continued mobilization during downstream CE. Filtration experiments and COD-based estimation indicated a much greater total apparent COD contribution from retained rUOM and rDOM in SAFL than in STAPFL (2.16 vs. 0.15 g COD/L). FT-ICR-MS and metagenomic analyses further suggested compositional transformation of retained refractory organics and stronger functional potential for coordinated hydrolysis, acidogenesis, and CE in SAFL, which together supported continued precursor supply and higher MCFA production. These results indicate that downstream MCFA production in real sludge fermentation liquids depends not only on the initial soluble SCFA pool, but also on the continued mobilization of retained refractory carbon during CE. This study advances understanding of retained refractory carbon utilization during ethanol-driven CE in two-stage sludge fermentation for MCFA production.},
}

@article {pmid42571814,
year = {2026},
author = {Ge, S and Sun, M and He, J and Pan, Y and Xu, Y and Wang, L and Luo, R and Zhong, Y and Wang, Y and Huang, J and Hu, M and Huang, Z and Wu, G and Wan, Y and Mo, L and Wu, F and Nie, C and Zhou, H and He, Y and Ma, Z and He, X and Gao, J},
title = {Gut microbial DL-endopeptidase protects against alcohol-associated liver disease via hepatocyte NOD2 signaling.},
journal = {Free radical biology & medicine},
volume = {255},
number = {},
pages = {712-729},
doi = {10.1016/j.freeradbiomed.2026.08.020},
pmid = {42571814},
issn = {1873-4596},
abstract = {Chronic alcohol consumption disrupts gut-liver homeostasis not only by inducing direct hepatotoxic injury, but also by perturbing host-microbial defense mechanisms that normally protect the liver from metabolic and inflammatory stress. We show that hepatocyte-specific deletion of Nod2 exacerbates ethanol-induced steatosis, oxidative stress, and mitochondrial dysfunction, establishing NOD2 as a critical protective factor in alcohol-associated liver disease (ALD). Importantly, beyond its direct hepatotoxic effects, ethanol exposure simultaneously diminishes this protective NOD2 pathway by limiting microbiota-derived ligand availability. Guided by this functional deficit, clinical metagenomic analysis (n = 1516) revealed that alcohol consumption is associated with a selective depletion of gut microbial DL-endopeptidase, a rate-limiting enzyme for NOD2 ligand generation, which inversely correlated with liver injury severity. Mice receiving fecal microbiota from donors with low DL-endopeptidase activity showed increased susceptibility to ALD. Importantly, supplementation with a NOD2 ligand or its clinical analogue, mifamurtide, restored mitochondrial homeostasis and alleviated liver injury. Together, these findings identify the gut microbial DL-endopeptidase-NOD2 axis as a key protective mechanism against ethanol-induced liver injury and a promising therapeutic target in alcohol-associated liver disease.},
}

@article {pmid42571819,
year = {2026},
author = {Li, S and Cai, M and Chen, L and Liang, J and Luo, X and Meng, J and Cao, Y and Liu, G and Hu, Y and Cai, S and Zou, M},
title = {Serine synergizes with lipopolysaccharide to induce macrophage pyroptosis through extracellular Hsp90α and early skin immune microenvironment disruption in diabetic foot.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {156732},
doi = {10.1016/j.metabol.2026.156732},
pmid = {42571819},
issn = {1532-8600},
abstract = {BACKGROUND: The pathogenesis of early-stage skin lesions in diabetic foot (DF) remains poorly understood, and cannot be fully explained by conventional theories. Skin microbiota dysbiosis has recently emerged as a critical factor, but the underlying mechanisms remain unclear.

METHODS: In this study, we integrated metabolomics and metagenomics analyses of skin samples to investigate metabolic dysregulation driven by microbial dysbiosis.

RESULTS: We identified elevated serine as a key metabolic alteration strongly correlated with a dysbiotic microbiota structure. Functionally, we demonstrate that abnormal serine accumulation contributes to the dysregulation of the early skin immune microenvironment in the diabetic foot. Mechanistically, our results reveal that excess serine synergizes with lipopolysaccharide (LPS) to stimulate the release of eHsp90α from keratinocytes, which was strictly dependent on the Akt/mTOR/HIF-1α pathway. This released eHsp90α then acts as a damage-associated molecular pattern, promoting both the migration and subsequent pyroptotic cell death of macrophages.

CONCLUSIONS: Collectively, our findings suggest a novel pathogenic axis where a microbiota-host derived metabolite collaborates with a bacterial endotoxin to promote inflammatory cell death, which is closely associated with early skin lesions in DF. This work not only elucidates a new mechanism for DF pathogenesis but also suggests that the serine-eHsp90α-pyroptosis axis may serve as a potential candidate for future therapeutic exploration.},
}

@article {pmid42571835,
year = {2026},
author = {Wang, G and Li, J and Wang, D and Chen, SS and Zheng, G and Zhou, S and Wang, T and Zhou, Y},
title = {Microbial community structure, function and environmental drivers of the urban soil plastisphere in a typical megacity, China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125432},
doi = {10.1016/j.envres.2026.125432},
pmid = {42571835},
issn = {1096-0953},
abstract = {The plastisphere in urban soils remains poorly understood despite its potential ecological significance. Here, 42 samples, including 21 soil samples and 21 plastisphere samples, were collected from seven functional zones in Nanjing, and metagenomic sequencing, bioinformatics, and quantitative modeling with multisource geographic and soil data were employed to investigate the community structure, function and environmental drivers of the soil plastisphere in this typical megacity, China. Fungi, particularly Ascomycota and the genus Fusarium (LDA score=4.73), exhibited stronger selective enrichment in the plastisphere than bacteria did, with this pattern being consistent across all functional zones, suggesting that the intrinsic properties of microplastics (MPs) govern taxonomic assembly. Plastisphere co-occurrence networks were simpler, more modular, and less robust than soil networks were, indicating that the structurally vulnerable microbial community was shaped predominantly by stochastic assembly (R[2]>0.2). Functional analysis further revealed significant alterations in the characteristics of denitrification genes (napA, norB, and narH/narY/nxrB), suggesting modified nitrogen cycling potential. Critically, pollutants, especially MPs themselves, partially overrode geospatial and edaphic factors as direct drivers of plastisphere communities, representing fundamental decoupling from the natural environmental matrix governing bulk soil. Pollutants strongly negatively affected fungal compositions and networks in the plastisphere, amplifying the ecological hazards of coexisting contaminants. These findings revealed that MP pollution modified microbial community assembly in urban soils, creating a decoupled, pollutant-driven microbial system. Integrating these effects into urban environmental risk assessments is therefore urgently needed.},
}

@article {pmid42571869,
year = {2026},
author = {Manzoor, M and Leskelä, J and Könönen, E and Lahti, L and Putaala, J and Pussinen, PJ and Paju, S},
title = {Shotgun Metagenomic Analysis Reveals Taxonomic and Functional Transitions in the Salivary Microbiome During Periodontal Disease Progression.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70184},
pmid = {42571869},
issn = {1600-051X},
support = {296541//Research Council of Finland/ ; 316777//Research Council of Finland/ ; 355532//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 369310//Research Council of Finland/ ; 286246//Research Council of Finland/ ; 318075//Research Council of Finland/ ; 322656//Research Council of Finland/ ; //Finnish Dental Society Apollonia/ ; //Sigrid Juselius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
abstract = {AIM: To characterise multi-kingdom salivary microbiome profiles across clinically defined periodontal states and identify stage-specific taxonomic and functional alterations using shotgun metagenomic sequencing.

MATERIALS AND METHODS: In this cross-sectional study, 204 adults (mean age 40.3 ± 7.6 years) from the SECRETO study (NCT01934725) underwent clinical and radiographic oral examinations and were classified into six periodontal groups: periodontal health, localised gingivitis, generalised gingivitis, gingivitis with pockets, mild periodontitis (Stages I-II) and severe periodontitis (Stages III-IV). Saliva samples were analysed using shotgun metagenomic sequencing to evaluate microbial diversity, taxonomic composition and functional pathways.

RESULTS: Beta diversity differed between periodontal health and the different disease states (Bray-Curtis: p = 0.049; Jaccard: p = 0.043). Gingivitis with pockets and severe periodontitis showed a significant enrichment of disease-associated species Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Porphyromonas endodontalis, Fusobacterium nucleatum and Parvimonas micra. Among non-bacterial taxa, Candida, Moineauvirus, Pyricularia and Roseolovirus were the predominant genera. A composite metagenomic classifier showed high discriminative performance for gingivitis with pockets (AUC = 0.90; 95% CI: 0.770-1.000) and severe periodontitis (AUC = 0.865; 95% CI: 0.762-0.968).

CONCLUSION: Salivary multi-kingdom microbiome transitions closely reflect the progression of periodontal disease and provide promising biomarkers for identifying at-risk individuals.},
}

@article {pmid42572222,
year = {2026},
author = {Kirilina, IV and Roumiantsev, SA and Gaponov, AM and Savchyk, DV and Khusnutdinova, DR and Grigoryeva, TV and Teplyakova, ED and Shestopalov, AV},
title = {[The contribution of the intestinal microbiome to the formation of the general profile of bacterial DNA in the blood of obese children].},
journal = {Voprosy pitaniia},
volume = {95},
number = {3},
pages = {107-116},
doi = {10.33029/0042-8833-2026-95-3-107-116},
pmid = {42572222},
issn = {0042-8833},
support = {//The research was carried out under the contract no. 0373100122119000041 within the project "Creation of a bank of biosamples of blood serum and feces from healthy donors and patients with obesity, metabolic syndrome, type 2 diabetes mellitus, and impaired mucosal barrier of the gastrointestinal tract, in order to identify candidate species nonspecific mediators of the quorum sensing microbiota systems of human, which modulate the endocrine and metabolic function of adipose tissue"/ ; },
mesh = {Humans ; Child ; *DNA, Bacterial/blood ; Cross-Sectional Studies ; Feces/microbiology ; Adolescent ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Pediatric Obesity/microbiology/blood ; Lipid Metabolism ; Carbohydrate Metabolism ; Obesity/microbiology/blood ; *Gastrointestinal Microbiome ; },
abstract = {UNLABELLED: Obesity is a multifactorial disease. The gut microbiome disturbances play a significant role in the development of obesity, but emerging data point to a blood microbiome and its association with obesity and other pathologies. Bacterial DNA in the blood represents a pathogen-associated molecular pattern capable of activating the immune system and thereby triggering a cascade of inflammatory responses. The question remains open as to where the bacterial DNA originates, which biotopes shape it, and what role the gut microbiome plays in forming the pool of bacterial DNA in blood. The aim of the study was to compare the bacterial DNA profiles of feces and blood in obese children, to establish relationships between bacterial DNA in blood and feces, and with carbohydrate and lipid metabolism parameters.

MATERIAL AND METHODS: This single-center, cross-sectional study included children and adolescents aged 10 to 18 years with varying degrees of alimentary-constitutional obesity (n=79) and without obesity (n=84). The taxonomic profile of bacterial DNA in blood and feces was analyzed using metagenomic sequencing. Bacterial DNA was isolated from blood and stool samples, and the v3-v4 variable region of the 16S rRNA gene was sequenced. To identify the relationship between bacterial DNA in blood and feces and lipid and carbohydrate metabolism parameters [glucose, total cholesterol, high-density lipoprotein and low-density lipoprotein (LDL)], Spearman's correlation coefficients were calculated.

RESULTS: When comparing bacterial DNA from blood and feces, obese children more often isolated DNA from the families Lactobacillaceae (p=0.043), Porphyromonadaceae (p=0.022), Ruminococcaceae (p=0.065) and less often from Prevotellaceae (p=0.028) and Coriobacteriaceae (p=0.085) compared to children and adolescents without obesity. In obese children, the contribution of intestinal taxa (Lachnospiraceae, Ruminococcaceae, Bacteroidaceae) to the formation of the bacterial DNA profile of the blood was significantly reduced, but the contribution of extraintestinal biotopes (skin, soil and water) was more diverse. Positive associations were found between bacterial DNA of fecal Ruminococcaceae taxa and the level of total cholesterol (ρ=0.347, p=0.002) and LDL (ρ=0.313, p=0.005) and of fecal Coriobacteriaceae and these lipid metabolism parameters (ρ=0.304, p=0.007 and ρ=0.317, p=0.005) in obese children. No positive associations were found between fecal and blood taxa and glucose level.

CONCLUSION: In obese and non-obese children and adolescents, the general profile of bacterial blood DNA is formed by both intestinal and extra-intestinal biotopes. However, in obese children, taxa from extra-intestinal biotopes predominate in the formation of the blood microbiome, which is confirmed by analyzing the proximity of the taxonomic composition of bacterial DNA in blood and feces based on beta diversity indices. The relationship of taxa with blood cholesterol and LDL levels can be considered as a target for microbiota modification and thus reducing the risks of metabolic complications in obesity.},
}

Humans
Child
*DNA, Bacterial/blood
Cross-Sectional Studies
Feces/microbiology
Adolescent
Female
Male
RNA, Ribosomal, 16S/genetics
*Pediatric Obesity/microbiology/blood
Lipid Metabolism
Carbohydrate Metabolism
Obesity/microbiology/blood
*Gastrointestinal Microbiome

@article {pmid42572739,
year = {2026},
author = {Lin, H and Deng, Y and Chen, Z and Huang, A and Yuan, K},
title = {Clinical Insights into Strongyloides stercoralis Pulmonary Hyperinfection Syndrome.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {628404},
pmid = {42572739},
issn = {1178-6973},
abstract = {BACKGROUND: Strongyloides stercoralis pulmonary hyperinfection syndrome (SPHS) is a rare, frequently fatal complication of strongyloidiasis that is difficult to recognize because of its nonspecific multisystem manifestations. Diagnosis requires a high index of suspicion.

METHODS: This retrospective study identified 29 hospitalized patients with strongyloidiasis at Chaozhou Central Hospital between November 2018 and January 2026. We compared the clinical data of five patients with SPHS (SPHS group) and 21 patients with uncomplicated/chronic strongyloidiasis (non-SPHS group) and described the detailed clinical profiles of the five patients with SPHS.

RESULTS: All five SPHS patients (median age, 67; 4/5 were male) had diabetes mellitus, glucocorticoid exposure, rural soil contact, fever, and nonspecific pulmonary computed tomography (CT) abnormalities; four (4/5, 80%) had gastrointestinal and/or neurological manifestations and intestinal obstruction. All five patients had multisystem laboratory abnormalities without eosinophilia. S. stercoralis was detected in respiratory specimens from all patients, and three (3/5, 60%) were confirmed by bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS) within 2-5 days. All patients had bacterial coinfections. Adequate antimicrobial coverage was achieved in four (4/5, 80%) patients; one patient (1/5, 20%) received both ivermectin and albendazole, and three (3/5, 60%) received albendazole monotherapy. Three patients (3/5, 60%) died of severe complications. Compared with the non-SPHS group, the SPHS group had a significantly lower median eosinophil count (0.01 × 10[9]/L); higher rates of corticosteroid exposure, diabetes mellitus, neurological and gastrointestinal symptoms, intestinal obstruction, severe complications, and mortality; and a longer time to laboratory confirmation (all P < 0.05).

CONCLUSION: In high-risk patients, normal or low eosinophil counts do not exclude SPHS. Early examination of respiratory specimens using microscopy and, when available, mNGS/tNGS may shorten the time to diagnosis. For these patients, early recognition of SPHS, antiparasitic therapy, and the management of bacterial coinfections are essential.},
}

@article {pmid42572760,
year = {2026},
author = {Zhong, L and Yuan, K},
title = {First Case of Concurrent Cytomegalovirus and Aspergillus tamarii Pulmonary Infections in a Mantle Cell Lymphoma Patient: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {623986},
pmid = {42572760},
issn = {1178-6973},
abstract = {Patients with mantle cell lymphoma (MCL) who undergo chemotherapy are at high risk of developing opportunistic pulmonary infections. Concurrent infection with cytomegalovirus (CMV) and the rare pathogen Aspergillus tamarii (A. tamarii) has never previously been reported in MCL patients. In this case report, we present the first documented instance of concurrent CMV and A. tamarii pneumonia in a MCL patient. A 69-year-old man with MCL developed a cough, chills, exertional dyspnoea, and hypoxemia after five cycles of rituximab-bendamustine (R-Benda) chemotherapy. Chest computed tomography (CT) showed bilateral ground-glass opacities. Metagenomic next-generation sequencing (mNGS) of the blood and bronchoalveolar lavage fluid (BALF) simultaneously revealed CMV and A. tamarii infections. The patient initially achieved rapid clinical improvement with ganciclovir and voriconazole. However, the infection relapsed following unauthorised premature discontinuation of ganciclovir and voriconazole without medical advice. Long-term oral voriconazole with regular TDM and close monitoring of ganciclovir-related myelosuppression resulted in sustained remission. This is the first reported case of concurrent CMV and A. tamarii pulmonary coinfection in a MCL patient, and mNGS enables the rapid and accurate diagnosis of mixed rare infections. Voriconazole is effective against A. tamarii; TDM and full-course treatment are essential for preventing relapse. We present a practical workflow for managing immunocompromised patients with rare mixed pulmonary infections to improve outcomes.},
}

@article {pmid42573887,
year = {2026},
author = {Yang, L and Zhao, J and Han, T and Qi, H and Zhao, F and Sun, Z},
title = {Modulating the gut-joint axis: Bifidobacterium longum subsp. infantis B8762 is associated with selective gut microbial and metabolic alterations in knee osteoarthritis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42573887},
issn = {1573-0972},
support = {U25A20733//National Natural Science Foundation of China/ ; 2022YFD2100702//National Key Research and Development Program of China/ ; YLXKZX-NND-006//Inner Mongolia Agricultural University First-Class Discipline Scientific Research Special Program/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {Humans ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Osteoarthritis, Knee/microbiology/metabolism/therapy ; *Probiotics/administration & dosage ; Metabolome ; *Bifidobacterium/physiology ; Metabolomics ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics ; Female ; Knee Joint/microbiology/metabolism ; *Bifidobacterium longum ; },
abstract = {Knee osteoarthritis (KOA) is a debilitating degenerative joint disorder characterized by chronic low-grade inflammation and metabolic dysregulation. The gut microbiota has emerged as an important regulator of systemic inflammatory responses. Building upon our previous clinical findings that Bifidobacterium longum subsp. infantis B8762 (B8762) improved clinical symptoms and inflammatory markers in patients with KOA, the present study investigated the associated alterations in the gut microbiome and fecal metabolome. Fecal samples were collected from probiotic (n = 20) and placebo (n = 20) groups at baseline (0 M) and after a 1-month intervention (1 M). Integrated metagenomic and untargeted metabolomic analyses were performed to characterize changes in gut microbial composition, functional potential, and metabolic profiles. Metagenomic reads mapped to the B8762 reference genome showed a greater increase in B8762-associated mapping rates in the probiotic group than in the placebo group, supporting an association between B8762 supplementation and longitudinal changes in the gut microbiome. Longitudinal analysis further demonstrated greater increases in microbial alpha diversity in the probiotic group. Species-level analyses suggested selective alterations in gut microbial composition, with nominally higher relative abundances of Bifidobacterium pseudocatenulatum and Anaerostipes caccae and lower relative abundances of Holdemania filiformis and Lachnospira SGB5077 (nominal P < 0.05). HUMAnN3-based functional profiling identified enrichment of microbial pathways related to carbon utilization and amino acid biosynthesis, including the bifidobacterial shunt and branched-chain amino acid biosynthesis pathways. Untargeted metabolomics identified nominal between-group differences in metabolites primarily related to lipid metabolism, including lower relative abundances of aldosterone and 7α-hydroxy-4-cholesten-3-one in the probiotic group (nominal P < 0.05). Correlation analysis further revealed associations between differential taxa and selected metabolites, suggesting potential links between gut microbial alterations and steroid-related metabolic pathways. Overall, B8762 supplementation was associated with longitudinal changes in B8762-associated genomic signals, gut microbial diversity and composition, microbial functional potential, and fecal metabolic profiles. These findings provide exploratory multi-omics evidence supporting an association between B8762 supplementation and gut microbial-metabolic remodeling in KOA and generate hypotheses for future mechanistic studies of the gut-joint axis.},
}

Humans
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/drug effects
*Osteoarthritis, Knee/microbiology/metabolism/therapy
*Probiotics/administration & dosage
Metabolome
*Bifidobacterium/physiology
Metabolomics
Male
Bacteria/classification/genetics/isolation & purification/metabolism
Metagenomics
Female
Knee Joint/microbiology/metabolism
*Bifidobacterium longum

@article {pmid42574061,
year = {2026},
author = {Parks, DH and Chaumeil, PA and Chuvochina, M and Hugenholtz, P},
title = {Stop codon reassignment to tryptophan in members of the bacterial phylum Actinomycetota.},
journal = {Microbial genomics},
volume = {12},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001767},
pmid = {42574061},
issn = {2057-5858},
mesh = {*Tryptophan/genetics ; *Codon, Terminator/genetics ; Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Animals ; Metagenome ; *Actinobacteria/genetics/classification ; },
abstract = {Reassignment of stop codons is a significant evolutionary event with recoding of UGA to tryptophan being previously identified in only three bacterial phyla, the Bacillota, Pseudomonadota and Verrucomicrobiota. Here, we present genomic evidence of this reassignment in a fourth bacterial phylum, the Actinomycetota, specifically in the family Eggerthellaceae. We identify the UGA stop-to-tryptophan reassignment in 34 metagenome-assembled genomes recovered from the stool samples of diverse mammalian hosts, including equids and primates. Canonical markers for this reassignment are consistently observed including conserved UGA codons aligning to tryptophan, loss of release factor 2 (prfB) and presence of a tRNA[Trp](UCA) gene. We infer that this reassignment occurred at least twice as the lineages containing reassigned genomes are paraphyletic, forming two distinct groups separated by a third lineage with strains that use UGA as a stop codon. These lineages represent three new Eggerthellaceae genera for which we propose the type species Equivita altericodex, Gorillivita intestinalis and Tapirivita inops reflecting isolation source and genomic properties. Organisms representing these genera have reduced genomes and complete or partial loss of biosynthetic pathways, suggesting increasing host dependency and a transition to obligate symbiosis. This likely facilitated stop codon reassignment in Equivita and Gorillivita and suggests Tapirivita is primed for reassignment. This work expands the known phylogenetic diversity of UGA stop-to-tryptophan reassignment in the bacterial domain and establishes the Eggerthellaceae as a new focal point for understanding the evolutionary drivers of genetic code plasticity.},
}

*Tryptophan/genetics
*Codon, Terminator/genetics
Phylogeny
Genome, Bacterial
Evolution, Molecular
Animals
Metagenome
*Actinobacteria/genetics/classification

@article {pmid42575094,
year = {2026},
author = {Zhai, J and Li, Y and Liu, J and Su, X and Cui, R and Zheng, D and Sun, Y and Yu, J and Dai, C},
title = {Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102974},
doi = {10.1016/j.xcrm.2026.102974},
pmid = {42575094},
issn = {2666-3791},
abstract = {The global rise of inflammatory bowel disease (IBD) reflects environmental shifts, yet how these changes are embedded in the gut microbial ecology remains unclear. We construct a microbiome atlas comprising 245,627 profiles. By classifying countries into three epidemiologic stages, we establish a framework. As the IBD burden increases, the gut microbial alpha diversity declines, and community structures form distinct clusters. This transition is characterized by a gradient of core genera. Integrating six shotgun metagenomic cohorts, we identify the depletion of anabolic pathways in IBD patients. Strain-level analysis reveals that epidemiologic staging shapes genetic architecture within species, identifying an IBD-enriched subclade of Eisenbergiella associated with elevated fecal cholic acid. We develop a microbial inflammatory risk score (MIRS), based on 19 genera, that discriminates IBD from controls (area under the curve [AUC] = 0.92). MIRS correlates with IBD prevalence. Our study provides an atlas linking epidemiology to microbiome ecology and strain evolution, offering a foundation for population-level surveillance and interventions in IBD.},
}

@article {pmid42575174,
year = {2026},
author = {Zhang, J and Zhang, B and Lu, X and Li, S and Wang, X and Kong, F and Diao, M and Shi, J},
title = {Heavy-metal stress shapes habitat-specific microbial survival strategies in estuarine environments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125434},
doi = {10.1016/j.envres.2026.125434},
pmid = {42575174},
issn = {1096-0953},
abstract = {Estuarine ecosystems face increasing heavy metal pollution from rapid urbanization and industrialization, yet the microbial adaptive strategies to multiple metal stressors across different habitats remain poorly understood. This study investigated the diversity and composition of bacterial and fungal communities across free-living (FL), particle-attached (PA), and sediment (SE) fractions from three estuaries with varying heavy metal contamination, and further investigated functional adaptations of bacterial communities. High-throughput amplicon sequencing revealed habitat-specific communities, with SE hosting the highest alpha diversity and enrichment of metal-resistant genera such as Woeseia and Sva1033. Environmental filtering, particularly by Zn, was the dominant driver shaping bacterial assemblages across all habitats, whereas fungal communities displayed greater stochastic assembly patterns. Analysis of 44 high-quality bacterial metagenome-assembled genomes (MAGs) revealed diverse metal resistance genes (cusA, znuB, and zntA), along with enriched metabolic pathways for carbon, nitrogen, and sulfur cycling. Notably, both active efflux/oxidative stress defense and indirect immobilization mechanisms were observed across all habitats, but their relative importance differed: FL and PA communities exhibited a greater reliance on active metal efflux (czcAB) and oxidative stress defense (trxAB) to maintain intracellular homeostasis, whereas SE communities displayed a stronger genomic potential for sulfate reduction (dsrAB) that may contribute to metal immobilization through sulfide precipitation. This metabolic partitioning highlights the complementary roles of different habitats in mediating metal toxicity and biogeochemical cycling, providing new insights into microbial resilience in polluted estuaries and underscoring the urgency of addressing heavy-metal contamination in these critical ecosystems.},
}

@article {pmid42570316,
year = {2026},
author = {Tilves, C and Holingue, C and Wanigatunga, SK and Chia, CW and Zhao, N and Wu, MN and Schrack, JA and Simonsick, EM and Ferrucci, L and Tanaka, T and Spira, AP and Mueller, NT},
title = {Associations of self-reported and actigraphic sleep with gut microbiome composition and diversity among older adults.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsag217},
pmid = {42570316},
issn = {1550-9109},
abstract = {STUDY OBJECTIVES: Poor sleep is linked to adverse health outcomes. Animal studies suggest the gut microbiome may influence sleep, but human findings remain inconsistent. We examined associations of self-reported insomnia symptoms, daytime sleepiness, and actigraphy-measured sleep with gut microbiome diversity and composition in older adults.

METHODS: We studied 869 Baltimore Longitudinal Study of Aging participants with self-reported sleep and shotgun metagenomic sequencing; 332 also had actigraphy. We tested associations of sleep with alpha diversity, beta diversity, and species composition using regression, PERMANOVA, and ANCOM-BC2, adjusting for age, sex, BMI, physical activity, education, and depressive symptoms.

RESULTS: Participants had mean age 70.7 years; 54.8% were female and 66.9% White. Trouble falling asleep ≥5 times/week was associated with higher Shannon diversity (β=0.41 SD; 95% CI: 0.09, 0.73) and Pielou's evenness, but not richness metrics. No actigraphy-measured sleep variables were associated with alpha or beta diversity. Beta diversity analyses suggested excessive sleepiness (1-2 o 3-4 times/week) was associated with different microbial composition, though variance explained was small. In species-level analyses, frequent insomnia symptoms or excessive sleepiness were associated with depleted or undetected Eubacterium sp. CAG:251. In exploratory actigraphy models, each doubling of sleep efficiency was associated with higher Eubacterium sp. CAG:251 prevalence (PR=2.15; 95% CI: 1.47, 3.14), while each 30-minute increase in wake after sleep onset was associated with lower prevalence (PR=0.49; 95% CI: 0.29, 0.81).

CONCLUSIONS: Global diversity findings were limited and inconsistent, whereas subjective and objective sleep disturbances converged on Eubacterium sp. CAG:251. Findings are exploratory and require longitudinal replication.},
}

@article {pmid42570388,
year = {2026},
author = {Malik, K and Iqbal, A and Du, M and Chen, T and Li, C},
title = {Impact of Epichloë endophyte on rhizosphere resistome dynamics in wild barley and bluegrass.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143115},
doi = {10.1016/j.jhazmat.2026.143115},
pmid = {42570388},
issn = {1873-3336},
abstract = {Fungal endophytes are universally present in plant tissues to enhance stress resilience and growth of plants. They can change the microbial communities and functional characteristics of the rhizosphere without harming the host. However, the effect of their colonization on the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in rhizosphere soil remains largely unexplored. In the present study, the impact of the Epichloë bromicola fungal endophyte on the rhizosphere resistome structure and environmental factors in wild barley (Hordeum brevisubulatum) and bluegrass (Poa pratensis) plants was investigated. The rhizosphere ARGs and MGEs communities were characterized through metagenome analysis. Simultaneously, their relationship with key rhizosphere environmental variables was evaluated using redundancy analysis (RDA) and Mantel tests. The results revealed that infection altered the taxonomic distribution of ARGs and MGEs-carrying bacteria. Besides, it reduced the prevalence of the predominant genera Sphingomonas and Nocardioides, while increasing the contribution of the less prevalent genera Bradyrhizobium and Rubrivivax to multidrug efflux and macrolide resistance mechanisms. Co-occurrence network analysis showed decreased modularity, indicating a less compartmentalized resistome-mobilome under infection. The findings revealed that endophyte infection fundamentally restructured the rhizosphere resistome by changing environmental pressures and favoring stress-response mechanisms. The study provides novel insights into how fungal endophytes influence microbial resistome assembly and HGT processes, their role in environmental antibiotic resistance dissemination, and One Health resistome dynamics in the rhizosphere.},
}

@article {pmid42570600,
year = {2026},
author = {Gao, Q and Lu, J and Hou, J and Ding, W and Xu, D and Zhou, C and You, G},
title = {Multi-omics reveals niche partitioning of nitrogen and phosphorus cycling between free-living and particle-attached fractions across an N:P gradient in eutrophic Lake Taihu.},
journal = {Water research},
volume = {306},
number = {},
pages = {126615},
doi = {10.1016/j.watres.2026.126615},
pmid = {42570600},
issn = {1879-2448},
abstract = {Cyanobacterial blooms in hyper-eutrophic lakes are managed through nitrogen-to-phosphorus (N:P) control, yet single-axis nutrient reduction has often been insufficient to achieve sustained bloom suppression in shallow systems such as Lake Taihu, China. We hypothesised that the missing management dimension is spatial: free-living (FL, 0.22-3 µm) and particle-attached (PA, >3 µm) fractions may deploy distinct nutrient-acquisition machineries under the same bulk N:P. Native Lake Taihu assemblages were cultured at four N:P molar ratios (5, 16, 23, 40; TN fixed at 2.0 mg N L[-1]; TP adjusted to 0.886, 0.277, 0.192, and 0.111 mg P L[-1], respectively) for 28 days, then sequentially filtered and analysed by 16S amplicon sequencing, shotgun metagenomics and 15-T Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) of dissolved organic matter (24 paired-fraction biomass samples + 8 DOM samples). Three key findings emerged. First, FL and PA carry the genetic potential for chemically distinct phosphorus-acquisition strategies (hereafter termed the P-currency split): FL is enriched in the high-affinity inorganic-Pi transporter genes pstSCAB (dominated by Synechococcus), whereas PA carries the genetic potential to mobilise organic P via phoD and ugpQ (dominated by Bacteroidota); the PstS + Ppk1 dual-wheel hypothesis was not supported under fraction-resolved testing. Second, PA harbours the genetic potential for a consistent nitrogen-cycle hotspot across all N:P levels, with nifH enriched 1.8-5.0-fold in PA and 87% attributable to the heterotroph Porphyrobacter. Third, Synechococcus shows an apparent stoichiometric niche-shift from FL dominance at N:P = 23 (43.8%) to PA dominance at N:P = 40 (54.1%). Together, the joint N:P × fraction model explained 95.8% of community variance (Mantel r = 0.963 within PA). These findings identify the phoD-anchored Bacteroidota guild and PA-aggregate disruption as candidate fraction-resolved management levers that complement conventional nutrient reduction in shallow eutrophic lakes.},
}

@article {pmid42570687,
year = {2026},
author = {Xu, X and Fan, K and Ling, N and Li, J and Yang, T and Gao, GF and Ma, Y and Nie, L and Zhang, J and Chu, H},
title = {Soil pH regulates organic carbon pool by changing microbial life-history strategy.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.08.028},
pmid = {42570687},
issn = {2090-1224},
abstract = {INTRODUCTION: The stability of the vast soil carbon pool, crucial for climate regulation, depends on microbial processes that govern carbon loss as CO2 or its stabilization in soil. Microbial life-history strategies, representing tradeoffs between resource acquisition (A-strategy) and growth yield (Y-strategy), are central to soil organic carbon (SOC) dynamics. However, how abiotic factors modulate these strategies and, in turn SOC fate remains unclear.

OBJECTIVES: Using the black soil region of Northeast China, which harbors substantial yet vulnerable SOC reserves, this study aimed to identify the dominant abiotic driver shaping microbial life-history strategies and to elucidate how this driver influences SOC stabilization pathways.

METHODS: We conducted a field survey combining metagenomic profiling of microbial attributes (diversity, functional potential, and inferred life-history strategy) with measurements of soil properties including extracellular enzyme activities and SOC fractions. This integrative approach traced the pathway from abiotic drivers to microbial traits and ultimately to carbon allocation.

RESULTS: Soil pH emerged as the key environmental gradient, with a threshold at pH 6.43 marking a systemic shift in microbial ecology and carbon processing. Acidic soils (pH 4.60-6.43) favored A-strategists, characterized by large genomes, enriched carbohydrate-active enzymes, and high extracellular enzyme activity, enabling polymer degradation and humification but limiting mineral-associated organic carbon (MAOC) formation. In contrast, neutral soils (pH 6.43-8.87) supported Y-strategists with streamlined genomes and biosynthetic metabolism, promoting microbial necromass accumulation and MAOC stabilization. Distinct functional guilds underpinned the A- and Y-strategies and frequent horizontal gene transfer in acidic soils further reinforced the A-strategy dominance under low pH.

CONCLUSION: Our findings reveal a mechanistic link between microbial life-history strategies and SOC stabilization, demonstrating that pH may shape the balance between A- and Y-strategists and their contrasting carbon pathways. This insight enhances predictive models of SOC dynamics and highlights pH management as a key lever for agroecosystems carbon retention.},
}

@article {pmid42570745,
year = {2026},
author = {Xia, H and Xie, J and Wang, XY and Wang, Y},
title = {Detection, occurrence, development, diagnosis and treatment of vaginal microbiome in gynecological cancers.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105531},
doi = {10.1016/j.critrevonc.2026.105531},
pmid = {42570745},
issn = {1879-0461},
abstract = {Gynecological cancers, including cervical, endometrial, and ovarian cancers, represent a growing global health burden with increasing incidence and mortality. The vaginal microbiome has emerged as a promising target for early cancer diagnosis and therapeutic intervention. Therefore, this review summarizes the composition and dynamics of the vaginal microbiome, emphasizing its association with the pathogenesis of gynecological cancers through chronic inflammation, immune modulation, and hormonal interactions. Advances in technologies such as 16S rRNA sequencing, metagenomics, and multi-omics have enabled the identification of potential microbial biomarkers. Probiotics, antibiotics, and vaginal microbiota transplantation are treatment technologies of gynecological cancers demonstrating considerable potential in restoring microbial balance and improving clinical outcomes. Furthermore, significant challenges persist in standardizing microbial biomarkers and translating research findings into precision therapies. Future studies should prioritize large-scale clinical validation and develop integrative strategies to harness the potential of the vaginal microbiome for cancer prevention and personalized treatment.},
}

@article {pmid42570953,
year = {2026},
author = {Ladyhina, V and Sternberg-Lewerin, S and Sannö, A and Bongcam-Rudloff, E and Dicksved, J and Rajala, E},
title = {Longitudinal investigation of the resistomes in Swedish pig farms.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {},
pmid = {42570953},
issn = {2731-8745},
abstract = {We conducted a longitudinal profiling of environmental resistomes and microbiomes from ten Swedish pig farms in a low-antimicrobial usage context. Samples were collected from pig pen environments and analysed using shotgun metagenomic sequencing. Resistome and microbiome profiles showed stronger temporal than farm-specific variation, with several age-associated trends. Age-related trajectories diverged between microbiome and resistome, indicating that resistance dynamics are shaped by factors beyond microbial succession. The highest relative abundance of resistance determinants was observed for tetracyclines, followed by aminoglycosides, macrolide-lincosamide-streptogramin antibiotics, beta-lactams, and folic acid synthesis inhibitors-drug classes commonly used in Swedish pig production. Resistome patterns were partially associated with phenotypic resistance profiles from previous studies, while analysis of antimicrobial usage alone could not fully explain the observed resistome. Overall, these findings suggest that additional factors beyond antimicrobial usage contribute to the persistence and dissemination of antibiotic resistance genes in pig farm environments.},
}

@article {pmid42571392,
year = {2026},
author = {Sirimongkol, D and Wongluechai, P and Chamsai, T and Weluwanarak, T and Chaipromkhieo, N and Sangkachai, N and Tonchiangsai, K and Pabutta, C and Kerdsiri, P and Sariya, L},
title = {Metagenomic analysis of commensal small mammal samples from an international cargo shipping area, Bangkok Port, reveals potential zoonotic pathogens and implications for One Health surveillance.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101534},
pmid = {42571392},
issn = {2352-7714},
abstract = {Commensal small mammals, such as rats and shrews, are recognized reservoirs for numerous zoonotic pathogens; however, their role in pathogen circulation at transport hubs remains underexplored. This study employs shotgun metagenomic sequencing to characterize microbial communities and assess zoonotic potential in tissue samples from commensal small mammals captured at Bangkok Port, an international cargo shipping hub in Thailand between June and August 2025. Following host read depletion, taxonomic profiling was performed to identify bacterial taxa of public health relevance, including sequences assigned to Bordetella spp., Yersinia pestis, Bartonella elizabethae, and Acinetobacter baumannii. The virulence factor and antibiotic resistance gene profiles revealed that some of these pathogens have pathogenic potential and are related to drug-resistant bacteria. In addition, Y. pestis was identified as a shared taxon among rats, shrews, and their associated fleas. The findings support the ecological roles of mammalian hosts and their ectoparasites as reservoirs for pathogens of public health concern. These results emphasize the need to strengthen surveillance programs for commensal small mammals to monitor and mitigate the spread of transboundary pathogens at international maritime gateways.},
}

@article {pmid42566961,
year = {2026},
author = {Seeholzer, A and Pfaff, F and Wunderlich, A and Meier, D and Zyla, A and Lueders, T and Einsiedl, F},
title = {In situ treatment of nitrate polluted groundwater by methane-dependent denitrification: meso‑scale flume proof-of-concept.},
journal = {Water research},
volume = {306},
number = {},
pages = {126593},
doi = {10.1016/j.watres.2026.126593},
pmid = {42566961},
issn = {1879-2448},
abstract = {Nitrate concentrations in groundwater frequently exceed the EU drinking water limit of 50 mgL[-1], threatening drinking water quality. This study evaluates a novel in situ nitrate removal strategy based on methane injection to stimulate autochthonous denitrifiers. Methane was injected into a meso‑scale artificial aquifer equipped with horizontal injection wells and a comprehensive monitoring system. We hypothesized that methane injection promotes methanotrophic denitrification and enhances microbial nitrate removal in groundwater. Following methane injection over four months, nitrate concentrations declined from ∼55 mg L[-1] (0.89 mM) to 36 mg L[-1] (0.58 mM). Concurrent isotopic shifts of up to 11‰ in both δ[15]N of dissolved nitrate and δ[13]C of dissolved methane provided strong evidence for enhanced microbial nitrate reduction coupled to methane oxidation. Spatio-temporal analyses of sediment microbiomes revealed successive enrichment of canonical aerobic methano- and methylotrophs (Methylomonandaceae and Methylophilaceae). While only the first hosted metagenomic methane oxidation capacities, the second was associated with complete denitrification. Likely, they thus interacted synergistically under oxygen-limited conditions, suggesting an indirect coupling between oxygen limited methane oxidation and denitrification. Only towards the distal, anoxic end of the flume, true anaerobic methanotrophs affiliated with the Methylomirabilaceae also were enriched. Spatial analyses indicated that sediment heterogeneity influenced methane distribution and, therefore, microbial nitrate removal in the flume. Overall, methane injection effectively stimulated microbial nitrate degradation, providing meso‑scale proof of concept for future pilot-scale remediation of nitrate-contaminated groundwater.},
}

@article {pmid42567235,
year = {2026},
author = {Ma, HC and Wang, DJ and Yuan, ZJ and Shi, B and Chen, ZH and Zhuo, M and Zeng, JY and Aqib, AI},
title = {Systematic approach for revealing biomarkers of diarrheal microbiome of yaks through Metagenomics sequencings.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108700},
doi = {10.1016/j.micpath.2026.108700},
pmid = {42567235},
issn = {1096-1208},
abstract = {Yaks are important food ruminants on the Plateau, but the presence of a diarrhea disease is seriously threatening the yak sector. To detect bacterial biomarkers of diarrhea in this animal, metagenomics sequencing of fecal samples from diarrhea (group D) and normal (group H) yaks was performed. The results showed 61963 936 432 and 63 972 070 354 clean samples in the diarrheal and normal yaks, respectively. Genotyping in group D (20 000) was statistically lower than that in group H (80 000) (p<0.05). Firmicutes and bacteroides levels in diarrheal yaks (1.03) were lower than in normal animals. There were 23 phyla and 696 species significantly different between the two yak groups including species of pathogenic Bacteroides fragilis, Alloprevotella tannerae, Parabacteroides merdae, Anaerococcus marasmi, and beneficial Methanobrevibacter millerae, Elusimicrobium minutum, Adlercreutzia equolifaciens. Our results may contribute to the prevention and treatment of diarrheal in yaks in the cold plains areas.},
}

@article {pmid42567289,
year = {2026},
author = {Ma, J and Xia, Q and Xiong, J and Zhou, J and Zhang, Q},
title = {Impact mechanism of cigarette butt leachate in runoff on the nutrient removal capacity of bioretention cells: metagenomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135553},
doi = {10.1016/j.biortech.2026.135553},
pmid = {42567289},
issn = {1873-2976},
abstract = {Discarded cigarette butts become soaked in surface runoff during rainfall, causing various pollutants within them to leach. The extent to which discarded cigarette butts impair bioretention cell nutrient removal efficiency remains understudied. In this study, three bioretention cells were constructed, exposed to simulated runoff containing non-cigarette-tip, low-concentration cigarette-tip, and high-concentration cigarette butt leachate. The effectiveness of nitrogen, phosphorus, and carbon purification was then determined; metagenomic sequencing was also performed to examine the microorganisms within the filler to propose a mechanism of how cigarette butt leachate input influences bioretention cell nutrient purification. The input of cigarette butt leachate limited filler adsorption capacity, but had little effect on the effluent NH4[+]-N concentration (1.08-1.14 mg/L). Cigarette butt leachate inhibited the nitrification potential in the upper layer of the cells as well as the denitrification potential in the lower layer; effluent NO3[-]-N increased from 0.51 to 1.93 to 0.57-5.47 mg/L. The inflow of cigarette butt leachate had little effect on phosphorus removal, with efficiencies consistently ranging from 50.60% to 73.69%. Cigarette butt leachate enhanced the carbon release potential of slow-release carbon sources within the filler and impeded potential electron donor production. This study demonstrated that cigarette butt disposal significantly impaired the nitrogen removal capacity of bioretention cells.},
}

@article {pmid42567290,
year = {2026},
author = {Wang, K and Wang, D and Li, D and Yu, P and Li, Y and Zeng, H and Ding, F and Zhang, J},
title = {Hydrodynamic control of oxygen intrusion and shear stabilizes functional zonation for nitrogen removal in an integrated UASB.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135585},
doi = {10.1016/j.biortech.2026.135585},
pmid = {42567290},
issn = {1873-2976},
abstract = {Aeration-reflux coupling can establish functional zonation in integrated upflow anaerobic sludge blanket (UASB) reactors, but the hydrodynamic basis remains insufficiently quantified. This study integrated computational fluid dynamics (CFD) with metagenome-derived KO-genus profiling based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) from vertically resolved samples to link hydrodynamic characteristics with microbial functions. CFD analysis showed that aeration established an oxygen-exposed zone in the upper reactor, whereas internal reflux regulated downward bubble entrainment and generated shear hotspots. These hydrodynamic features shaped mixing patterns, maintained stable functional zoning, and preserved a micro-oxic niche for simultaneous anammox and denitrification (SAD) granules. Metagenomic and gene-network analyses revealed distinct vertical stratification of ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing bacteria (AnAOB) along the reactor height. They also identified a coupled NO2[-] supply-sink loop involving Nitrosomonas, Ca. Kuenenia, and denitrifying bacterium, supporting functional partitioning within the UASB. Operationally, a reflux ratio of 15 achieved the highest and most stable total nitrogen removal efficiency 90% within the optimal aeration, corresponding to a dissolved oxygen concentration of approximately 2 mg/L. In addition to nitrogen-transformation pathways, the vertically resolved metagenomes revealed cofactor-related functional potential, including molybdenum-cofactor and folate-associated metabolism, within the spatially structured microbial community. Together, these results demonstrate that aeration-reflux design can mechanistically sustain functional partitioning, granulation, and efficient nitrogen removal in integrated UASB systems by jointly regulating the oxygen and shear threshold. This strategy provides practical guidance for treating low-carbon, ammonia-rich side streams.},
}

@article {pmid42567813,
year = {2026},
author = {Gosai, HB and Panseriya, HZ and Patel, PG and Patel, AC and Shankar, A and Varjani, S and Dave, BP},
title = {Retraction notice to "Exploring bacterial communities through metagenomics during bioremediation of polycyclic aromatic hydrocarbons from contaminated sediments" [Sci. Total Environ. 842 (2022) 156794].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {182131},
doi = {10.1016/j.scitotenv.2026.182131},
pmid = {42567813},
issn = {1879-1026},
}

@article {pmid42568080,
year = {2026},
author = {Ma, S and Zhang, C and Yao, Y and Zhou, M and Chen, A and Chen, Y and Chen, Y and Wang, J and Abudushalamu, G and Cai, S and Zhao, F and Chen, D and Li, X and Zheng, Y and Fan, J and Gao, X and Liu, Y and Fan, W and Zhu, F and Yang, J and Miao, M and Fan, X and Wu, G},
title = {A three-metabolite microbiota-associated signature for early risk stratification of gestational diabetes mellitus.},
journal = {Cardiovascular diabetology},
volume = {25},
number = {1},
pages = {},
pmid = {42568080},
issn = {1475-2840},
support = {82302609//National Natural Science Foundation of China/ ; 82373781//National Natural Science Foundation of China/ ; BK20230840//Natural Science Foundation of Jiangsu Province/ ; JSKLCCM202202015//Jiangsu Provincial Key Laboratory of Critical Care Medicine/ ; },
mesh = {Humans ; Female ; *Diabetes, Gestational/diagnosis/microbiology/blood ; Pregnancy ; *Metabolomics ; Risk Assessment ; Prospective Studies ; Risk Factors ; Biomarkers/blood ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Metagenomics ; Predictive Value of Tests ; Gestational Age ; *Propionates/blood ; Prognosis ; *Bacteria/metabolism/classification ; Multiomics ; },
abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes and long-term metabolic and cardiovascular risk. However, oral glucose tolerance testing at 24-28 gestational weeks limits early risk stratification. Gut microbiota-associated metabolites may reflect early metabolic abnormalities, including those relevant to cardiometabolic health, but robust early-pregnancy biomarkers remain limited.

METHODS: We conducted a multicenter nested case-control and prospective study involving 2,693 pregnant women. Untargeted metabolomics and metagenomics were integrated to identify GDM-associated metabolites and gut microbial alterations. Three consistently dysregulated metabolites, 3-hydroxydecanoic acid, γ-Glu-Leu, and propionic acid, were quantified by targeted LC-MS/MS. Candidate algorithms were compared using repeated 10-fold cross-validation, and a final generalized linear model was externally and prospectively validated.

RESULTS: Women who later developed GDM showed an adverse early-pregnancy metabolic profile, including higher BMI, triglycerides, and platelet count. Untargeted metabolomics identified 14 persistently altered metabolites enriched in energy, oxidative stress, and amino acid metabolism pathways. Metagenomics revealed taxonomic restructuring and coordinated microbiota-metabolite associations. The three-metabolite model achieved AUCs of 0.838 (95% CI, 0.791-0.885) in training, 0.840 (95% CI, 0.769-0.911) in internal validation, 0.955 (95% CI, 0.925-0.985) and 0.917 (95% CI, 0.875-0.958) in two external cohorts, and 0.969 (95% CI, 0.937-1.000) in the prospective cohort.

CONCLUSION: Early microbiota-associated metabolic dysregulation is detectable before routine GDM diagnosis. This compact three-metabolite panel may support early GDM risk stratification and provides metabolic evidence relevant to broader cardiometabolic risk assessment in pregnancy.},
}

Humans
Female
*Diabetes, Gestational/diagnosis/microbiology/blood
Pregnancy
*Metabolomics
Risk Assessment
Prospective Studies
Risk Factors
Biomarkers/blood
Case-Control Studies
*Gastrointestinal Microbiome
Adult
Metagenomics
Predictive Value of Tests
Gestational Age
*Propionates/blood
Prognosis
*Bacteria/metabolism/classification
Multiomics

@article {pmid42568342,
year = {2026},
author = {Tedersoo, L and Prous, M and Chen, M and Anslan, S and Saar, I and Dubois, B and Mikryukov, V},
title = {Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70189},
doi = {10.1111/1755-0998.70189},
pmid = {42568342},
issn = {1755-0998},
support = {101200758//HORIZON EUROPE European Research Council/ ; TK200//Estonian Ministry of Education and Research/ ; 362828//Research Council of Finland/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; *Soil Microbiology ; *Metagenomics/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Benchmarking ; Biodiversity ; },
abstract = {Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (> 500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2 × 500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar-a bioinformatics pipeline presented here-had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.},
}

*DNA Barcoding, Taxonomic/methods/standards
*Soil Microbiology
*Metagenomics/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
DNA, Ribosomal Spacer/genetics/chemistry
Benchmarking
Biodiversity

@article {pmid42568732,
year = {2026},
author = {Saikia, D and Basumatary, P and Nath, A and Kalita, JJ and Neog, K and Purkait, MK and Bora, U},
title = {Metagenomic and Metatranscriptomic Insights into the Structure and Function of the Gut Microbial Community of Antheraea assamensis Helfer.},
journal = {Indian journal of microbiology},
volume = {66},
number = {4},
pages = {982-1001},
pmid = {42568732},
issn = {0046-8991},
abstract = {UNLABELLED: Antheraea assamensis Helfer is an economically important, endemic, lepidopteran insect native to Northeast India that produces a lustrous golden-coloured silk of distinct quality and durability. To date, the gut microbiota of A. assamensis has remained largely unexplored. The present work aimed to comprehensively identify and characterize the gut microbial community of A. assamensis through culture-independent approach. The gene expression analysis of the gut microbial community was studied through metatranscriptomic analysis. The influence of the host leaf-associated microbiota on larval gut microbial composition and its variation to changes in host plant was also investigated. The results have identified over 30 bacterial and archaeal phyla indicating a highly diverse gut microbial community of A. assamensis dominated by Proteobacteria (25.78%), Patescibacteria (12.77%), Planctomycetota (12.66%), Chloroflexi (8.63%), Acidobacteria (6.85%) and Actinobacteria (3.39%). Functional analysis of A. assamensis gut microbiota through shotgun metagenomic and metatranscriptomic investigation revealed key associations between the insect and its gut microbial community including host leaf digestion, metabolite detoxification, chitinase production and fat body metabolism. The host leaf-associated microbiota was found to occupy a major portion of the total larval gut microbiota. However, the diversity of the larval gut microbiota was greater than the host leaf-associated microbiota. The findings of this study will illustrate the structure of the gut microbial community of A. assamensis, their key interactions with the host organism and the role of host leaf-associated microbiota on the holobiont.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01525-5.},
}

@article {pmid42568769,
year = {2026},
author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S},
title = {Correction: Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1927101},
doi = {10.3389/fmicb.2026.1927101},
pmid = {42568769},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1798330.].},
}

@article {pmid42568840,
year = {2026},
author = {Liang, W and Tingting, L and Ying, L and Sa, W and Yuanyuan, Z and Hongxin, Z},
title = {Comprehensive Pathogen Spectrum Analysis Using mNGS in AIDS Patients With Pulmonary Infections: Diagnostic Value and Clinical Implications.},
journal = {Open forum infectious diseases},
volume = {13},
number = {8},
pages = {ofag395},
pmid = {42568840},
issn = {2328-8957},
abstract = {BACKGROUND: This study evaluated the diagnostic value of metagenomic next-generation sequencing (mNGS) in identifying pathogens causing pulmonary infections in 64 acquired immunodeficiency syndrome (AIDS) patients at Beijing Ditan Hospital.

METHODS: Bronchoalveolar lavage fluid (BALF) samples were analyzed using mNGS and conventional microbiological tests (CMT). Diagnostic performance was compared, and random forest analysis was used to assess pathogenicity.

RESULTS: mNGS detected 45 pathogens, including 14 viruses, 3 fungi, and 28 bacteria. Compared with CMT, mNGS showed higher sensitivity for detecting bacteria (75.0% vs 29.17%), fungi (45.0% vs 16.67%), and viruses (80.0% vs 20.83%). Mixed infections were identified in 55.2% of cases, predominantly Pneumocystis pneumonia (PCP) with bacterial coinfections. However, mNGS had lower concordance with CMT for viruses (24.1% for cytomegalovirus) and Mycobacterium tuberculosis (75.0%). Random forest analysis highlighted Candida albicans and Stenotrophomonas maltophilia as highly pathogenic.

CONCLUSIONS: While mNGS demonstrated superior broad-spectrum detection, its limitations in viral and TB diagnosis underscore the need for optimized protocols. The study supports mNGS as a complementary tool for diagnosing complex pulmonary infections in AIDS patients, enhancing precision medicine but requiring further refinement for widespread clinical adoption.},
}

@article {pmid42568886,
year = {2026},
author = {Muigano, MN},
title = {Functional genetic signatures of the gut microbiome in cardiometabolic diseases: mechanisms and translational opportunities.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1847345},
pmid = {42568886},
issn = {2813-4338},
abstract = {The human gut microbiome plays a very important role in the regulation of host metabolism and overall physiological homeostasis. Disruptions in microbial community function have been increasingly implicated in cardiometabolic diseases, including obesity, type 2 diabetes, cardiovascular disease, and metabolic dysfunction-associated liver disease. Advances in metagenomic sequencing have identified functional genetic signatures within the gut microbiome for short-chain fatty acid biosynthesis, bile acid metabolism, lipopolysaccharide (LPS) production, amino acid metabolism, trimethylamine N-oxide (TMAO) generation, and carbohydrate-active enzymes (CAZymes). Across cardiometabolic conditions, a consistent pattern emerges of depletion of beneficial metabolic functions and enrichment of pro-inflammatory and metabolically disruptive pathways. These findings point to the importance of microbial functional capacity, rather than taxonomic composition alone, in shaping disease risk and progression. This review explores the functional genetic signatures for cardiometabolic diseases and translational potential of these signatures including their potential roles as diagnostic biomarkers, therapeutic targets, and tools for precision therapy. This understanding of microbiome-derived functional pathways may inform the development of targeted strategies aimed at restoring metabolic balance and improving cardiometabolic health.},
}

@article {pmid42569238,
year = {2026},
author = {Dolkar, P and Themchuirin, L and Sonia, N and Atri, A and Yadav, P and Siwach, S and Modeel, S and Negi, RK},
title = {Fish gut-water interface as a hotspot for the dissemination of antibiotic resistance genes across natural and aquaculture systems.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100646},
doi = {10.1016/j.crmicr.2026.100646},
pmid = {42569238},
issn = {2666-5174},
abstract = {Freshwater ecosystems are important reservoirs and transmission pathways for antibiotic resistance genes (ARGs), yet host-mediated microbial selection and anthropogenic pressure on fish gut resistome remain poorly characterised, especially in major South Asian river systems. We performed shotgun metagenomics and genome-resolved binning from 194 fish representing four species, along with host-associated water samples, collected from six geographically distinct sites spanning two major river systems (the Yamuna and the Indus) and two aquaculture farms. The fish gut nurtures distinct microbial communities from the surrounding water, revealing strong host-mediated filtering of environmental microbiota. Across all samples, 1108 ARG subtypes conferring resistance to 14 antibiotic classes were detected, including extended-spectrum β-lactamases (blaTEM and blaCTX-M) and WHO critical-priority carbapenemases (blaIMP and blaOXA). Fish from the Indus River maintained diverse but comparatively stable resistomes dominated by intrinsic chromosomal efflux mechanisms, whereas fish from the urbanized Yamuna River, particularly Labeo boggut, exhibited noticeable enrichment of clinically important ARGs. The prevalence of mobile genetic elements (MGEs) and virulence factors (VFs) were consistently more abundant in the fish gut microbiome than in the host's surrounding water, indicating an increased potential for horizontal gene transfer and microbial persistence. A total of 19 metagenome-assembled genomes (MAGs) carrying multiple ARGs, VFs, and plasmid-associated markers were detected, identifying bacterial populations capable of maintaining and disseminating antimicrobial resistance. These outcomes confirm that fish inhabiting anthropogenically influenced river systems can serve as important reservoirs of clinically relevant resistance determinants, highlighting potential risks for environmental dissemination, aquaculture and human exposure through aquatic ecosystems.},
}

@article {pmid42569267,
year = {2026},
author = {Shi, Q and Song, Q and Liu, X and Mei, G and Gao, C and Du, H and Xia, Z and Liu, M and Song, J and Zhang, L and Zhu, R and Cheng, Z and Cao, J and Rao, D and Zhang, Y and Wang, Z and Han, J},
title = {Macrogenomic analysis showcases the diversity of tick RNA viruses in Mentougou, Beijing, China.},
journal = {New microbes and new infections},
volume = {73},
number = {},
pages = {101819},
doi = {10.1016/j.nmni.2026.101819},
pmid = {42569267},
issn = {2052-2975},
abstract = {BACKGROUND: Ticks are the second most significant vector of human pathogens worldwide, with 911 documented species globally and a broad distributed across China. Currently, over 160 tick-borne viruses (TBVs) have been identified, several of which pose substantial threats to human health, such as Dabie bandavirus, Jingmen tick virus, Alongshan virus, Songling virus, Beiji nairovirus, and Langya henipavirus, raising increasing global attention. Despite their significance, the diversity of TBVs in Beijing remains poorly characterized.

METHODS: In this study, we conducted metagenomic sequencing on tick samples collected from Mentougou District, Beijing. The obtained reads were subjected to quality control, de novo assembly, and viral sequence identification, followed by phylogenetic and evolutionary analyses.

RESULTS: Our results identified 19 distinct viral species spanning 12 families, including Hepelivirales, Solemoviridae,Mymonaviridae, Nodaviridae,Permutotetraviridae, Phenuiviridae,Rhabdoviridae, Tombusviridae,Totiviridae, Peribunyaviridae,Flaviviridae, Nodaviridae,Tymoviridae, Tombusviridae. Among these, six novel viruses from five virus families were discovered. A potential pathogen, Tick jingmen-like virus, was also detected in the selected pathogens. These findings underscore the remarkable diversity of RNA viruses harbored by ticks in Mentougou District.

CONCLUSIONS: Our research findings reveal a previously unrecognized diversity of tick-borne viruses in the Mentougou District, Beijing, and provide essential baseline data for informing future surveillance strategies and guiding prevention and control of tick-borne diseases in the Beijing metropolitan area.},
}