@article {pmid41782011,
year = {2026},
author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J},
title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02368-y},
pmid = {41782011},
issn = {2049-2618},
support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.

RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.

CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.},
}

@article {pmid41781966,
year = {2026},
author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X},
title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04231-6},
pmid = {41781966},
issn = {1477-3155},
support = {32272514//National Natural Science Foundation of China/ ; },
abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.},
}

@article {pmid41781897,
year = {2026},
author = {Liu, D and Yu, S and Tian, X and Wang, Z and Lu, Y and Dai, Y and Hu, C and Ma, X and Mao, M and Xue, L and Yi, Z and Zhang, G and Li, S and Wang, Q and Zhang, Z and Tian, Z},
title = {Epidemiological investigation of an acute gastroenteritis outbreak associated with norovirus GΙΙ.17[P17] in a cross-border travel group - Shanghai Port, China, 2024.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12978-4},
pmid = {41781897},
issn = {1471-2334},
support = {2024HK149//General Administration of Customs Project/ ; 2022YFC2302800//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Norovirus is a leading cause of acute gastroenteritis and spreads efficiently in closed, mobile cohorts such as organized travel groups. This case is notable for the real-time detection and genomic confirmation of a cross-border outbreak at a port of entry, including near-identical Norovirus GΙΙ.17[P17] genomes and documented asymptomatic carriage, illustrating the practical value of integrated metagenomic surveillance in border health operations.

CASE PRESENTATION: On July 21, 2024, 26 travelers arrived at Shanghai Port after a 12-day group tour in Europe. Clinical interviews identified 15 individuals (57.7%) with diarrhea, nausea, dizziness, and abdominal pain; no hospitalizations occurred. On-site anal swab testing was negative for SARS-CoV-2, influenza A and B, Vibrio cholerae, and Escherichia coli. RT-qPCR detected Norovirus GII in 10 samples (38.5%), including two asymptomatic individuals. Metagenomic sequencing generated near-complete genomes for all RT-qPCR-positive samples, which were 99.9-100% identical and classified as Norovirus GΙΙ.17[P17], confirming a cross-border outbreak within the travel cohort. Prompt public health response measures were initiated by Shanghai Customs and CDC authorities.

CONCLUSIONS: This case demonstrates the feasibility and impact of rapid, genomically informed surveillance at the border for detecting and characterizing travel-associated enteric virus outbreaks. The findings underscore the need for robust port-of-entry monitoring, rapid diagnostics, and integrated genomic analysis to mitigate transmission in group travel settings.},
}

@article {pmid41781872,
year = {2026},
author = {Tian, N and Liu, M and Zhao, Y and Lian, Y and Jin, M and Yang, F},
title = {Gut microbiota dysbiosis and metabolic reprogramming in pediatric migraine: a multi-omics analysis revealing diagnostic biomarkers.},
journal = {The journal of headache and pain},
volume = {},
number = {},
pages = {},
doi = {10.1186/s10194-026-02315-0},
pmid = {41781872},
issn = {1129-2377},
support = {2022 Budget Approval No. 180 of Hebei Provincial Department of Finance//Provincial Medical Outstanding Talents Project funded by the Provincial Government in 2022/ ; Grant No. 20260868//Hebei Provincial Medical Science Research Project funded by the Health Commission of Hebei Province/ ; 2026 Hebei Provincial Introduction of Foreign Intelligence Project//Hebei Provincial Department of Science and Technology/ ; },
}

@article {pmid41780551,
year = {2027},
author = {Wolf, J and Goggin, KP and Inaba, Y and Allison, KJ and Ahmed, AA and Maron, G and Ferrolino, J and Lazure, L and Kohler, C and Brenner, A and Sun, Y and Tang, L and Gonzalez-Pena, V and Rubnitz, JE and Gawad, C and Margolis, EB and Thomas, P},
title = {Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101312},
doi = {10.1016/j.lanmic.2025.101312},
pmid = {41780551},
issn = {2666-5247},
abstract = {BACKGROUND: Patients receiving myelosuppressive chemotherapy or haematopoietic cell transplantation are at high risk for life-threatening bloodstream infections. A novel pre-emptive treatment paradigm guided by pathogen detection before symptoms appear might reduce this risk, but no validated screening test is available. This study evaluated the sensitivity and specificity of plasma microbial cell-free DNA metagenomic sequencing (mcfDNA-Seq) for predicting bloodstream infections in children and adolescents receiving therapy for high-risk leukaemia.

METHODS: In this prospective cohort study, between Aug 9, 2017, and Feb 28, 2022, leftover clinical plasma samples were prospectively collected up to once per day from patients who were younger than 25 years, receiving care for leukaemia at St Jude Children's Research Hospital (Memphis, TN, USA), and at high risk for life-threatening bloodstream infections. mcfDNA-Seq was used to identify pathogen DNA in blood samples obtained during the 7 days before to 1 day after bloodstream infection onset, and in control samples from the same population in the absence of fever or infection. The testing laboratory was masked to sample status. Primary outcomes were predictive sensitivity of mcfDNA-Seq for detecting the expected bloodstream infection pathogen during the 3 days preceding the day of bloodstream infection onset, with a prespecified favourable sensitivity of 50%, and predictive specificity of mcfDNA-Seq in control samples. Exploratory analyses comprised assessing sensitivity and specificity restricted to bacteria or common bloodstream infection pathogens, and after applying a data-derived DNA fragment concentration cutoff; estimating the predictive sensitivity on each of the 7 days before bloodstream infection onset; identifying clinical characteristics that affected predictive sensitivity or specificity; and examining the clinical relevance of additional organisms identified by mcfDNA-Seq during bloodstream infection episodes. Diagnostic sensitivity was also assessed on samples collected on the day of, or day after, diagnosis of bloodstream infection. This study is registered with ClinicalTrials.gov, NCT03226158.

FINDINGS: 94 evaluable bloodstream infections occurred in 60 (38%) of 158 enrolled participants; 19 episodes were previously described in the pilot phase of this study. The predictive sensitivity of mcfDNA-Seq was 51·9% (95% CI 40·5-63·1) for all bloodstream infection episodes, 53·8% (42·2-65·2) for bacterial infection only, and 51·9% (40·5-63·1) when applying a DNA fragment concentration cutoff of 140 molecules per μL. Sensitivity was lowest at day -7 and increased daily until the day of diagnosis. Diagnostic sensitivity was 81·3% (95% CI 71·0-89·1) for all bloodstream infection episodes and 83·1% (72·9-90·7) for bacterial infections only. Predictive specificity was 82·7% (95% CI 76·0-88·2), but improved to 88·9% (83·0-93·3) for common bloodstream infection pathogens, and to 93·8% (88·9-97·0) when also applying the DNA fragment concentration cutoff. Predictive sensitivity was higher in participants with acute lymphoblastic leukaemia (adjusted odds ratio [aOR] 11·1 [1·7-74·2] vs those with acute myeloid leukaemia), and it was lower in polymicrobial infections (aOR 0·0 [0·0-0·2] vs monomicrobial Gram-positive infections). Clinical false-positive results were positively associated with gastrointestinal disturbance alone (p=0·037) or combined with recent administration of high-dose cytarabine (p=0·012). Additional organisms identified by mcfDNA-Seq that were not identified by blood culture were less likely than expected organisms to have an increasing DNA concentration during the days preceding bloodstream infection diagnosis.

INTERPRETATION: mcfDNA-Seq can detect causative pathogens before the onset of some bloodstream infection episodes in profoundly immunocompromised patients. Predictive specificity might be improved by restricting results to a subgroup of relevant organisms, excluding patients with high risk of false-positive results, or applying a higher concentration cutoff. Clinical trials are needed to evaluate mcfDNA-Seq-guided pre-emptive therapy for preventing life-threatening bloodstream infections in patients with high risk.

FUNDING: The National Cancer Institute, American Lebanese Syrian Associated Charities, St Jude Children's Research Hospital, and Karius.},
}

@article {pmid41780408,
year = {2026},
author = {Wu, H and Qi, F and Huo, Y and Li, R and Ye, M and Topp, E and Qiao, M and Zhu, Y},
title = {Feed additives increase soil risk from antibiotic resistance genes via distinct horizontal gene transfer pathways.},
journal = {Environment international},
volume = {209},
number = {},
pages = {110174},
doi = {10.1016/j.envint.2026.110174},
pmid = {41780408},
issn = {1873-6750},
abstract = {Non-antibiotic components of feed additives can enter farmland soils via livestock manure and accumulate persistently in agroecosystems, presenting potential environmental risks. We established soil microcosms, integrated metagenomes with viromes, and applied a contig-based horizontal gene transfer (HGT)-resolution pipeline to partition vector-level contributions, to assess how saccharin, copper, and their co-contamination affect soil gene flow and health risk. Results indicate divergent vector responses under additive stress: phage-host associations increased under saccharin (82 pairs vs. control 29 pairs), whereas copper strengthened plasmid-host associations. With saccharin, phage nucleotide diversity rose while synonymous nucleotide diversity declined, consistent with stronger purifying selection atop enhanced mutation supply, whereas copper increased lysogeny. Saccharin significantly elevated HGT frequency (∼50% increase), expanded donor-recipient phylogenetic span (class-level P < 0.05), and raised the phage-mediated share (∼100% increase). Copper primarily modestly increased the plasmid-mediated contribution (Cu 2.7%, HS 1.9%). Two-factor analyses revealed a significant antagonistic interaction between saccharin and copper, reducing overall HGT across taxonomic ranks under co-exposure. Although total ARG abundance did not change significantly, the health-risk index increased under saccharin, driven by enhanced ARG-MGE co-occurrence. Under co-contamination, auxiliary metabolic genes were enriched, suggesting phage-conferred metabolic empowerment that mitigates stress, partly explaining the antagonism. Altogether, our findings reveal that feed additives reshape vector-specific gene mobility and ARG risk, and they underpin a three-tiered risk-assessment framework that progresses from mere abundance to network-structured mobility and finally to mobility drivers incorporating phylogenetic transfer distance, offering a more mechanistic basis for soil-health management.},
}

@article {pmid41780396,
year = {2026},
author = {Xia, R and Shi, T and Liu, W and Li, G and Zhi, S and Luo, W and Xu, Z},
title = {Genome-resolved metagenomic insights into cornstalks-mediated reduction of pathogens and antibiotic resistomes during passively aerated static composting of swine manure.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129185},
doi = {10.1016/j.jenvman.2026.129185},
pmid = {41780396},
issn = {1095-8630},
abstract = {Passively aerated static composting is widely adopted for livestock manure treatment; however, its efficacy in eliminating antibiotic resistance genes (ARGs) and pathogens is often inadequate due to ineffective oxygen diffusion to restrict organic biodegradation and thus the formation of thermophilic condition. Despite extensive research on aerobic composting, the optimal amendment strategy and mechanistic role of crop stalks in shaping ARG dynamics during passively aerated static composting of swine manure remain unclear. Here, cornstalks and swine manure were representatively selected to elucidate how their passively aerated static composting was successfully initiated to improve ARG elimination using genome-resolved metagenomics and multivariate statistical analysis. Results show that adding 10% cornstalks significantly enhanced antibiotic resistome removal by improving composting properties (e.g. moisture content and oxygen permeability) and increasing temperature (above 65 °C). This improvement effectively inactivated bacterial hosts of ARGs and restrict horizontal gene transfer (HGT). Under these conditions, cornstalk addition promoted thermal inactivation of ARG hosts (e.g. Actinomycetota), particularly pathogenic antibiotic-resistant bacteria (e.g. Corynebacterium), thereby suppressing HGT. More importantly, chromosomally encoded mobile genetic elements (rather than plasmids and viruses) dominated HGT during composting. The transfer of multidrug, bacitracin, and macrolide-lincosamide-streptogramin resistance genes was primarily facilitated by intra-phylum HGT events, particularly within Bacillota. Cornstalk addition significantly accelerated inactivation of pathogens and ARG hosts (e.g. macrolide-lincosamide-streptogramin resistant bacteria), resulting in an increased removal of over 49.0% for both. These findings provide mechanistic insights into the optimization of passively aerated static composting for safe agricultural reuse of livestock manure.},
}

@article {pmid41780389,
year = {2026},
author = {Du, Y and Zhao, S and Gao, Y and Yan, Y and Kong, Y and Meng, W and Lu, X and Zheng, S and Mu, H and Chen, X and Kong, Q},
title = {The synergistic effect of algal-bacterial granular sludge in a sequencing batch reactor with tetracycline-containing synthetic livestock and poultry breeding wastewater.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129178},
doi = {10.1016/j.jenvman.2026.129178},
pmid = {41780389},
issn = {1095-8630},
abstract = {The concentration of environmental antibiotics, along with their ecological risk, has increased due to the continuous accumulation of livestock and poultry breeding wastewater (LPBW). In this study, two sequencing batch reactors (SBRs) were established-one equipped with algal-bacterial granular sludge (ABGS) and the other with aerobic granular sludge (AGS)-to investigate the treatment performance of tetracycline containing synthetic LPBW. Pollutant removal efficiency and underlying mechanisms were determined by analyzing the physiological and biochemical properties, dynamic changes in the microbial community, and the fate of antibiotic resistance genes (ARGs). Compared to AGS, ABGS resulted in faster granulation and greater lipid production. Exposure to tetracycline significantly altered the contents of extracellular polymeric substances (EPS) and chlorophyll. During the cultivation stage, the removal efficiencies of TN and TP by ABGS were 7.01% and 1.52% higher, respectively, than those by AGS. However, after tetracycline was added, the TN and TP removal efficiencies of ABGS decreased by 0.77% and 6.91%, respectively, compared to those of AGS. The tetracycline removal efficiency of ABGS reached 86.32%, which was 4.49% greater than that of AGS. Metagenomic analysis revealed that the relative abundances of Pseudomonas and Stenotrophomonas (key tetracycline-degrading bacteria) in ABGS were 36.61% and 66.82% greater, respectively, than those in AGS. After tetracycline was added, the relative abundances of tetracycline-related ARGs (tetX and MuxB) increased by 36.01% and 61.68%, respectively, in AGS but decreased by 53.98% and 5.71%, respectively, in ABGS. In this study, ABGS exhibited outstanding performance in enhancing the removal of pollutants from tetracycline-containing synthetic LPBW in SBR systems.},
}

@article {pmid41780383,
year = {2026},
author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X},
title = {Enhancing methane production in anaerobic digestion of food waste by Fe-MOF and Fe-MOF-derived carbon composites: Insights into properties, multi-omics analyses, and mechanisms.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129181},
doi = {10.1016/j.jenvman.2026.129181},
pmid = {41780383},
issn = {1095-8630},
abstract = {In this work, Fe-MOF and Fe-MOF-derived carbon composites (Fe-MDCs) derived at 300, 500, and 700 °C were first applied in anaerobic digestion to achieve efficient renewable energy production from food waste. The enhancement mechanism of methane yield was further explored using metagenomic and metaproteomic analysis. The results showed that compared with the control group, methane yield was enhanced by 9.66%-13.99%, 16.21%-23.56%, and 7.99%-19.84% in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups, respectively. Among them, Fe-MDC-500 possessed superior electronic conductivity and a higher specific surface area, which was beneficial for improving methane production by facilitating interspecies electron transfer and providing abundant surface sites for microbial attachment. Metagenomic analysis demonstrated that the functional microorganisms, key genes related to methane metabolism, and the activity of corresponding coenzymes were increased in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups. The poor syntrophic interaction resulted in the lowest methane yield under Fe-MOF-300 addition. Metaproteomic analysis indicated that the expressions of proteins related to quorum sensing system, transcription, and translation were also up-regulated, indicating that Fe-MDC-500 potentially promoted microbial communication among methanogenic and symbiotic microorganisms, ultimately boosting the metabolic activity of anaerobic digestion system. Meanwhile, the expressions of vital proteins involved in enzyme synthesis and catalytic bioconversion, including RNA polymerase, Ribosome, and Aminoacyl-tRNA biosynthesis, were significantly upregulated. This research clarified the mechanism of exogenous materials enhanced methane production by elucidating the key metabolic pathways and functional genes, which provided valuable insights for optimizing energy recovery system.},
}

@article {pmid41780243,
year = {2026},
author = {Sun, Y and Chen, R and van den Broek, S and Wen, J and Li, Y and Zeng, X and Su, S and Garland, G},
title = {Transmission and migration of antibiotic resistance genes following agricultural fertilization in sloping croplands.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141666},
doi = {10.1016/j.jhazmat.2026.141666},
pmid = {41780243},
issn = {1873-3336},
abstract = {Livestock manure, a major anthropogenic source of antibiotic resistance genes (ARGs) in agricultural soils due to residual veterinary antibiotics, is commonly used as a nutrient-rich fertilizer on sloping cropland. However, the role of landscape features, particularly topographic heterogeneity in shaping ARG transmission and migration remains poorly understood. In this study, we analyzed 76 metagenomes from five environmental habitats collected along three sloping cropland routes in the Dongting Lake region of China. Soil shared 276 ARG subtypes with other habitats, indicating manure fertilization on slopes facilitates ARGs diffusion across ecosystem. ARG abundance exhibited strong spatial patterns in soil samples, associated with distance from fertilized zones and buffer strips. In fertilized highland soils, mobile genetic elements (MGEs), such as transposases and Insertion Sequence Common Region (ISCRs), were significantly correlated with ARG abundance, indicating active horizontal gene transfer. In unfertilized-lowland soils, ARG composition was primarily influenced by heavy metals, particularly arsenic and cadmium. Source-tracking analysis showed that up to 70.3% of microbes migrated downslope via gravitational runoff, facilitating long-distance ARG dispersal. Risk assessment revealed higher ecological than human health risks, with high-risk ARGs linked to crop pathogens. Our findings highlight the need for landscape-based ARG management strategies within the One Health framework.},
}

@article {pmid41782139,
year = {2026},
author = {Mao, K and Zang, Y and Wang, C and Yang, W and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Liang, H and Xu, L and Qu, M and Li, Y},
title = {Rumen microbiota-associated stress alleviation by creatine pyruvate in newly received cattle: a multi-omics study.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02365-1},
pmid = {41782139},
issn = {2049-2618},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; No. 3230810//the National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
abstract = {BACKGROUND: Stress experienced by newly received cattle is a significant challenge in the beef industry, frequently resulting in weakened immune responses and impaired growth. The rumen microbiota is essential to host health, and its imbalance can exacerbate stress. This study investigates the mechanisms by which creatine pyruvate (CrPyr) mitigates stress in newly received cattle through multi-omics approaches, including metagenomics, metabolomics, in vitro and in vivo experiments, and rumen microbiota transplantation (RMT) in mice.

RESULTS: Our results revealed that CrPyr significantly reduces stress-related hormones (cortisol and adrenocorticotropic hormone) and inflammatory markers (IL-6, IL-1β, and TNF-α), and enhanced antioxidant capacity (SOD: 57.38 versus 46.93 U/mL, P < 0.05; GSH-Px: 305.87 versus 217.07 U/mL, P < 0.05; T-AOC: 9.62 versus 7.66 U/mL, P < 0.05). Metagenomic analysis demonstrated that CrPyr increased Prevotella abundance, a key rumen bacterium involved in volatile fatty acid (VFA) production, and enriches metabolic pathways associated with energy metabolism (ATP synthesis, and pyruvate metabolism) and antioxidant defense (glutathione metabolism, FC = 1.08, P < 0.05). In vitro and in vivo experiments, as well as RMT studies in mice, further validate these findings, demonstrating that CrPyr promote VFA synthesis and increased ATP production through the electron transport phosphorylation pathway.

CONCLUSIONS: CrPyr modulates the abundance of ruminal Prevotella in transport-stressed cattle to enhance glutathione and VFA metabolism and to accelerate ATP and nucleotide synthesis, thereby alleviating stress in newly received cattle. This multimodal approach established CrPyr as an effective nutritional intervention that improves rumen function and increases livestock productivity. Video Abstract.},
}

@article {pmid41781883,
year = {2026},
author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J},
title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04902-2},
pmid = {41781883},
issn = {1471-2180},
support = {32171607//National Natural Science Foundation of China/ ; },
}

@article {pmid41781852,
year = {2026},
author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC},
title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04878-z},
pmid = {41781852},
issn = {1471-2180},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
}

@article {pmid41780450,
year = {2026},
author = {Li, Z and Li, X and Jiao, B and Yang, Y and Wang, H and Gu, L and Ai, H and Cheng, H and Cheng, S},
title = {Redox oscillations in riparian zone stimulate carbon loss by enhancing microbial respiration.},
journal = {Water research},
volume = {296},
number = {},
pages = {125672},
doi = {10.1016/j.watres.2026.125672},
pmid = {41780450},
issn = {1879-2448},
abstract = {Redox oscillations within riparian ecosystems emerge as a critical threat to carbon sequestration, yet the mechanistic coupling between abiotic drivers and microbial metabolism remains elusive. Through controlled incubation experiments, we demonstrate that redox-oscillating conditions significantly reduce microbial carbon use efficiency (CUE), thus accelerating carbon loss compared to static oxic or anoxic conditions. Mechanistically, redox oscillations drove the cycling of iron (Fe) species, thereby reducing the amorphous Fe pool and liberating mineral-associated organic carbon (MAOC) composed of substantial biodegradable organic substrates (e.g., lipids and proteins). Concurrently, hydroxyl radicals (•OH) generated during Fe(II) oxidation depolymerize complex aromatic organic matter into labile forms. Integrated metagenomic and metabolomic analyses further demonstrated that redox oscillations significantly reshaped soil metabolite profiles and microbial community. In particular, microbial catabolic pathways such as pentose phosphate pathway and the tricarboxylic acid (TCA) cycle were activated to efficiently mineralize newly available substrate. Together, these results identify a coupled abiotic-biotic "prime and burn" mechanism in which Fe-driven substrate reorganization primes microbial differentiation toward enhanced respiration. This study highlights redox-oscillating zones as potential carbon leakage hotpots in the terrestrial carbon sink.},
}

@article {pmid41780235,
year = {2026},
author = {Xin, Y and Liu, LH and Liu, L and Chen, SH and Zheng, YM and Zhao, QB},
title = {Seasonal variation regulates the efficacy of phytoremediation strategies on the rhizosphere resistome in urban river ecosystems.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141647},
doi = {10.1016/j.jhazmat.2026.141647},
pmid = {41780235},
issn = {1873-3336},
abstract = {Phytoremediation, as a representative nature-based solution, holds significant potential for mitigating the dissemination of antibiotic resistome in urban rivers, which is vital for safeguarding public health and aquatic ecosystems. However, the performance and mechanisms of different phytoremediation strategies (hydroponic or substrate-based strategies) in influencing the rhizosphere resistome across seasonal variation remain poorly understood. This study combined in-situ plant cultivation with metagenomic sequencing and statistical modelling to elucidate rhizosphere resistome dynamics in different phytoremediation strategies. The results showed that the phytoremediation strategies exerted limited influence on the composition and diversity of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). Instead, the above parameters were predominantly regulated by seasonal variation and generally exhibited higher abundances during winter (4.07 ×10[-4]-2.92 ×10[-2]) than summer (3.35 ×10[-4]-2.26 ×10[-2], ANOSIM: R>0.12, P < 0.05). Nonetheless, phytoremediation strategies still led to distinct patterns for the specific resistome (P < 0.05). The relative abundance of specific VFGs was also significantly higher in the substrate-based strategy (7.21 ×10[-4]-8.82 ×10[-4]) than the hydroponic strategy (5.87 ×10[-4]-7.98 ×10[-4]), particularly during summer. The key ARB, such as those belonging to Bacteroidota, showed higher relative abundance in the hydroponic strategy (2.28 ×10[-2]-6.23 ×10[-2]) than substrate-based strategy (1.12 ×10[-2]-3.65 ×10[-2]) across seasonal variation. Mechanistically, rhizosphere exudate-derived dissolved organic matter mediated ARG dynamics by regulating bacterial communities, MGEs, and VFGs (P < 0.05). This study delineates strategy-specific controls of hydroponic and substrate-based phytoremediation on ARG dissemination across seasonal variations, delivering actionable protocols for nature-based solutions optimization in urban rivers.},
}

@article {pmid41780079,
year = {2026},
author = {Zhao, B and Xu, Y and Li, F and Song, S and Liu, Z and Liu, J and Liu, Z and Chen, X and Zhou, M and Zhao, L and Wang, X},
title = {Cyclosporine A ameliorates ulcerative colitis by inhibiting cellular senescence, modulating the JAK2-STAT3/NF-κB signaling pathway, and regulating the gut microbiota-metabolite axis.},
journal = {International immunopharmacology},
volume = {175},
number = {},
pages = {116452},
doi = {10.1016/j.intimp.2026.116452},
pmid = {41780079},
issn = {1878-1705},
abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease characterized by immune dysregulation, compromised intestinal barrier integrity, and disruptions in the microbiota-metabolite axis. Current clinical management of UC remains limited, underscoring the need for novel therapeutic approaches. Cellular senescence is increasingly recognized as a significant contributor to the pathogenesis of this disease. Senescent cells promote inflammatory responses via the sustained release of pro-inflammatory mediators such as IL-6, IL-1β, and TNF-α. Conversely, persistent inflammation drives further cellular senescence, establishing a self-amplifying cycle that exacerbates disease progression. Additionally, gut microbiota dysbiosis (reduced Akkermansia abundance) and metabolic abnormalities (disrupted bile acid metabolism) may further compromise intestinal barrier integrity. Cyclosporine A (CsA), a classical immunosuppressant, has unclear mechanisms in UC, particularly regarding its potential effects on senescence and the microbiota-metabolite axis. In this investigation, using a dextran sulfate sodium (DSS)-induced UC model, we demonstrated that CsA significantly alleviated DSS-induced acute colitis in mice and senescence-associated pathological changes. Multi-omics analyses integrating network pharmacology, transcriptomics, metabolomics, and metagenomics demonstrated that CsA likely exerts its therapeutic effects through inhibition of the JAK2-STAT3/NF-κB signaling pathway. This leads to reduced release of pro-inflammatory cytokines, modulation of intestinal microbiota composition and metabolite profiles, and enhanced intestinal barrier function.These findings elucidate new mechanisms by which CsA improves DSS-induced colitis in mice through anti-senescence effects and microbiota-metabolic regulation, providing potential therapeutic targets for UC.},
}

@article {pmid41779028,
year = {2026},
author = {Ladd-Wilson, SG and Fawcett, RW and Park, SY and Venkatasubrahmanyam, S and Lindner, MS and Davis, S and Spry, A and Singleton, J and Karpathy, SE and Paddock, CD},
title = {Rickettsia lanei Rickettsiosis, Oregon, USA, 2025.},
journal = {Emerging infectious diseases},
volume = {32},
number = {4},
pages = {},
doi = {10.3201/eid3204.251962},
pmid = {41779028},
issn = {1080-6059},
abstract = {Using metagenomic sequencing, we identified a patient infected with Rickettsia lanei who was initially diagnosed with Rocky Mountain spotted fever (RMSF), a clinically similar disease caused by infection with R. rickettsii. Our investigation highlights the importance of clinical, epidemiologic, and laboratory partnerships to leverage the discovery of novel pathogens.},
}

@article {pmid41778823,
year = {2026},
author = {Shean, RC and Tardif, KD and Rangel, A and Dutrschi, J and Bogumil, D and Cruse, A and Hernandez, S and Iremadze, N and Pollock, S and Lipson, D and Bradley, BT},
title = {Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0187425},
doi = {10.1128/spectrum.01874-25},
pmid = {41778823},
issn = {2165-0497},
abstract = {Clinical metagenomic next-generation sequencing (mNGS) is a diagnostic tool allowing near-universal pathogen detection directly from clinical specimens. Despite promising clinical data, broad adoption of mNGS has been hindered by high cost and reduced sensitivity relative to targeted nucleic acid amplification tests (NAATs). Recently, Ultima Genomics introduced the UG 100 NGS platform which advertises 10 billion reads per $2,400 sequencing wafer. By lowering costs and improving sequencing depth, the historical value proposition of mNGS may be improved. This study evaluates the UG 100 sequencer's ability to generate reads for metagenomic pathogen detection from cerebrospinal fluid specimens. Ultima reads demonstrated 93% (26/28) positive agreement with orthogonal test results and 63% (10/16) negative agreement against a syndromic panel for meningitis and encephalitis. Near full-length genomes were recovered for three organisms (human herpesvirus-1 [HSV-1], Streptococcus pneumoniae, and Haemophilus influenzae), with the ability to detect putative antimicrobial resistance genes for H. influenzae. Recovery of Borrelia burgdorferi reads (6.1 reads per million [RPM] and 9.03 RPM) was achieved from clinical samples with late cycle threshold values (39.7 and 43.0, respectively). Limit of detection (LoD) studies demonstrated detection of HSV-1 and S. pneumoniae reads at concentrations of 50 genomes/mL each, which is below the reported LoD for the orthogonal NAATs used in this study. Reducing sequencing costs and improving the analytical sensitivity remove two major hurdles for mNGS adoption by clinical laboratories. While these results are preliminary, they demonstrate a future in which mNGS may be more widely implemented.IMPORTANCEClinical metagenomic next-generation sequencing has struggled to gain wider adoption for nearly a decade, due in part to its high cost and reduced performance versus targeted molecular assays. This study demonstrates the ability of the UG100 sequencing platform to reduce per-base metagenomic sequencing costs while producing reads that maintain high positive agreement with existing molecular assays. Further improvements to cost and analytical performance may shift clinical metagenomics from an expensive test of last resort to a front-line diagnostic for identifying infections.},
}

@article {pmid41778788,
year = {2026},
author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N},
title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0097125},
doi = {10.1128/spectrum.00971-25},
pmid = {41778788},
issn = {2165-0497},
abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.},
}

@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
doi = {10.1080/19490976.2026.2638004},
pmid = {41778780},
issn = {1949-0984},
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}

@article {pmid41778495,
year = {2026},
author = {Lu, J and Bi, H and Zhang, R and Liu, X and Wang, B and Wu, J and Lee, JK and Kalia, VC and Gong, C},
title = {Pesticide Biodegradation Catalyzed by a Cold-Adapted Acetylxylan Esterase Identified from a Metagenome-Assembled Genome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13419},
pmid = {41778495},
issn = {1520-5118},
abstract = {This study identified a putative cold-adapted acetylxylan esterase in Glutamicibacter soli Em07 via a metagenome-assembled genome. The gene encoding this enzyme was cloned and heterologously expressed in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the protein has a molecular weight of 33.24 kDa. Using 1-naphthyl acetate as a substrate, the enzyme activity was optimal at 20 °C and pH 9. Furthermore, the enzyme exhibited excellent cold adaptation, alkali resistance, and salt tolerance. It demonstrated OCP pesticide-degrading activity: 66.48% degradation of carbaryl, 92.14% of cypermethrin, and 97.78% of malathion, underscoring its strong potential in environmental remediation. Notably, this esterase emerged as the first to simultaneously possess cold adaptation, alkali resistance, and salt tolerance. These results positioned the enzyme as a promising candidate for bioremediation strategies in multiextreme environments. Further research will investigate its activity on other persistent organic pollutants.},
}

@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}

@article {pmid41777547,
year = {2026},
author = {Maisto, L and Telegrafo, C and Rubino, F and Santamaria, M and Traka, MH and Tullo, A and Bouwman, J and Sbisà, E and Balech, B},
title = {Multifaceted human gut microbiome data associated with health and nutrition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1722500},
pmid = {41777547},
issn = {1664-302X},
abstract = {The microbiome, also considered the hidden organ, is a fundamental ecosystem directly associated with the disease and health status of the human body. With the availability of high-throughput DNA sequencing technologies, a growing number of studies from clinical and experimental (observation and intervention) samples are constantly revealing new findings on the relationship between human organs and their microbiomes. In such a context, diet and nutrition are among the key factors influencing microbiome composition, richness, and functional behavior. In this review, we illustrate how microbiome-related data and associated metadata are in recent times scattered across primary and specialized databases with different levels of curation, annotation, and standardization, limiting, to some extent, the possibility of deep data discovery, reuse, alignment, and harmonization. Therefore, we describe the way Findable, Accessible, Interoperable, and Reusable (FAIR) data principles would enhance the onset of novel scientific hypotheses and potential microbiome-targeted therapies by improving the standardization policies in data sources. Accordingly, using advanced semantic classification and data mining technologies based on suitable and comprehensive ontologies, annotations of studies present in source databases or in scientific literature would further improve the data and metadata enrichment, integration and alignment relevant to microbiome data associated with health, disease and nutrition.},
}

@article {pmid41777539,
year = {2026},
author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B},
title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771459},
pmid = {41777539},
issn = {1664-302X},
abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).

METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.

RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2] = 0.032, p = 0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.

DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.},
}

@article {pmid41777393,
year = {2026},
author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D},
title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1685007},
pmid = {41777393},
issn = {1664-462X},
abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.},
}

@article {pmid41777069,
year = {2026},
author = {Zamperin, G and Palumbo, E and Castellan, M and Marciano, S and Fusaro, A and Monne, I},
title = {Metagenomic sequencing of zoonotic viruses: evaluation of a CRISPR-Cas-based rRNA depletion system.},
journal = {Veterinaria italiana},
volume = {62},
number = {2},
pages = {},
doi = {10.12834/VetIt.3908.38985.2},
pmid = {41777069},
issn = {1828-1427},
abstract = {Pathogen-agnostic diagnostics are crucial for the early detection of emerging viruses. Shotgun metagenomic sequencing enables unbiased detection of viral genomes but is frequently constrained by the abundance of host and microbial ribosomal RNA (rRNA), which reduces sensitivity and increases sequencing costs. CRISPR-Cas9-based rRNA depletion has emerged as an alternative to enzymatic methods; however, its performance for the characterization of zoonotic viruses across diverse animal hosts and tissues remains underexplored. We compared CRISPR-Cas9 (Jumpcode CRISPRclean™ Plus) and RNase H-based enzymatic depletion (Ribo-Zero Plus, Illumina) using 12 samples positive for rabies lyssavirus, influenza A virus, West Nile virus or norovirus, from multiple host species and tissues, including both high-quality and degraded RNA. CRISPR-Cas9 efficiently reduced rRNA content (14.5%) but recovered fewer viral reads than Ribo-Zero, which achieved up to 60.7× enrichment. Both methods produced complete viral consensus genomes when RNA quality and viral load were sufficient. However, based on the data generated here, enzymatic depletion currently remains more efficient and cost-effective for viral metagenomics. Further optimization of CRISPR-Cas9 workflows could enhance its utility for viral surveillance and diagnostics.},
}

@article {pmid41634542,
year = {2026},
author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y},
title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41634542},
issn = {1471-2180},
support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; },
abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear.

METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10⁸ CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process.

RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties.

CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04776-4.},
}

@article {pmid41776697,
year = {2026},
author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X},
title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00533-0},
pmid = {41776697},
issn = {2524-4671},
}

@article {pmid41776502,
year = {2026},
author = {Tümmler, B and Schulz, A and Minso, R and Alfeis, N and Tamm, S and Rademacher, J and Ringshausen, FC},
title = {CFTR activity in nasal potential difference of adults with idiopathic bronchiectasis.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03599-1},
pmid = {41776502},
issn = {1465-993X},
}

@article {pmid41776310,
year = {2026},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {41776310},
issn = {2662-8465},
support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

@article {pmid41776033,
year = {2026},
author = {Yu, Q and Liu, H and Shi, H and Abdrakhmanov, Y and Shen, J and Zhang, C and Dong, Z and Zong, L and Si, L and Dai, L and Li, Y},
title = {Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {41776033},
issn = {2157-846X},
abstract = {Identifying evolutionarily remote antimicrobial peptides (AMPs) is crucial for discovering underexplored clinical candidates to combat antibiotic resistance. Existing experimental and computational methods are limited by their reliance on sequence identity to known AMPs, missing distant homologues. Here we introduce HMD-AMP, a protein language model-based approach for AMP discovery. HMD-AMP outperforms previous methods in identifying evolutionarily distant AMPs and enables the discovery of unknown and highly potent AMPs from metagenomic data. Applied to host and gut microorganism genomes of nine mammals, HMD-AMP revealed over 37 million predicted AMPs. Of 91 high-confidence sequences experimentally validated, 74 showed strong antibacterial activity and 48 were evolutionarily remote from known AMPs. Four of these AMPs exhibited broad-spectrum antibacterial activity at low effective concentrations and showed low toxicity, with the most potent peptide demonstrating therapeutic efficacy in a mouse model of peritoneal Escherichia coli infection. This study introduces an effective strategy to uncover AMPs.},
}

@article {pmid41775849,
year = {2026},
author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM},
title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41937-x},
pmid = {41775849},
issn = {2045-2322},
}

@article {pmid41775798,
year = {2026},
author = {Nearman, A and Lamas, ZS and Niño, EL and Fine, J and Mayack, C and Seshadri, A and Boncristiani, D and Huang, WF and Evans, JD and Chen, YP},
title = {Metagenomic and gene expression patterns in declining commercial honey bee colonies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42605-w},
pmid = {41775798},
issn = {2045-2322},
support = {FSA25IRA0012292//Farm Service Agency/ ; 8130-0960//Animal and Plant Health Inspection Service/ ; },
}

@article {pmid41775707,
year = {2026},
author = {Wang, J and Wang, S and Li, T and Hou, W and Deng, Y},
title = {A watershed-scale potential pathogenic bacteria dataset from the Yangtze River Basin.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06983-0},
pmid = {41775707},
issn = {2052-4463},
support = {42277104//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial safety is fundamental to ensuring water quality, particularly in the Yangtze River Basin, China's most critical drinking water source. Despite its ecological and economic importance, the basin faces significant anthropogenic pressures, including wastewater discharge, which may elevate the risk of pathogenic contamination. However, fragmented sampling efforts and limited coverage have hindered a systematic understanding of pathogenic microbial diversity and distribution across this vast ecosystem. A novel bioinformatic pipeline leveraging Genome-Specific Markers to accurately identify and quantify potential pathogenic taxa in metagenomic data was applied to 625 publicly available metagenomes, spanning water, sediments, and riparian soils along the 6,300 km Yangtze River continuum. We reconstructed a potential pathogen catalog comprising 403 taxa, largely expanding the pathogen diversity in the large river ecosystem. We also generate the Richness distribution maps of potential pathogens for water, sediments and soils along Yangtze River. The basin-scale pathogen inventory not only establishes a baseline for potential pathogenic bacteria communities in the Yangtze Basin but also serves as a reference library for quick biosurveillance and risk management from genomic resolution.},
}

@article {pmid41775307,
year = {2026},
author = {Li, Y and Pan, J and Li, Y and Zhao, Z and Zhang, Y},
title = {Direct interspecies electron transfer-based methanogenic aggregate: A survival strategy to overcome defensive attack from type VI secretion system during syntrophic cooperation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134329},
doi = {10.1016/j.biortech.2026.134329},
pmid = {41775307},
issn = {1873-2976},
abstract = {Physically tight structure of methanogenic aggregates formed by syntrophic microbes that exchange electrons via interspecies hydrogen/formate transfer (IHT/IFT) can activate defensive attack from type VI secretion system (T6SS), which has been recognized as the primary cause for poor stability. Direct interspecies electron transfer (DIET) may alleviate the technical bottleneck of proximity-triggered defensive attack from T6SS, since syntrophic microbes function long-distance electron transfer via electrically conductive pili (e-pili) or its displayed c-type cytochromes. Here, three up-flow anaerobic sludge blanket reactors, respectively with ethanol, propionate, and butyrate as a sole substrate, were used to culture DIET- and IHT/IFT-based aggregates. DIET-based aggregates were generally larger and exhibited a looser, porous structure compared to IHT/IFT-based aggregates. However, rheological behavior showed that they possessed higher rigidity and toughness, attributed to the structural support of the conductive pili network. 3D reconstruction and imaging of a single DIET-based aggregate by nano-industrial computed tomography showed that syntrophic microbes did not display a pronounced localized aggregation pattern. Conductivity-temperature/pH response showed that the DIET-based aggregates exhibited a metallic-like conductance similar to that found in e-pili. Meanwhile, the surface-enhanced Raman spectra showed that the intensities of characteristic peaks associated with c-type cytochromes in DIET-based aggregates were higher than those in IHT/IFT-based aggregates. Analysis of metagenomic and metaproteomic data showed that in DIET-based aggregates expression of key proteins of T6SS was suppressed. These results demonstrated that in DIET-based aggregates syntrophic microbes did not aggregate to form a physically tight structure, eluding defensive attack from T6SS and strengthening their stabilities.},
}

@article {pmid41775298,
year = {2026},
author = {Luo, J and Yang, S and Feng, Q and Zou, X and Wu, Y and Wang, F},
title = {Triazine-induced extracellular polymeric substance disruption drives metabolic reprogramming and enhanced volatile fatty acid production in anaerobic sludge fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134322},
doi = {10.1016/j.biortech.2026.134322},
pmid = {41775298},
issn = {1873-2976},
abstract = {The accumulation of antimicrobial contaminants in waste-activated sludge (WAS) posed challenges to anaerobic fermentation processes, with mechanistic impacts on volatile fatty acids (VFAs) production remaining poorly understood. 1,3,5-triazine (triazine), a widely detected triazine-based antimicrobial agent, paradoxically enhanced VFAs production in a concentration-dependent manner, achieving maximum yields of 1771 mg COD/L (18.4-fold increase compared with control). Enhanced production was accompanied by a distinct metabolic shift from propionate to acetate dominance (from 38.7 to 54.3%), driven by systematic disruption of extracellular polymeric substances (EPS), especially proteins. Molecular docking revealed that triazine induced conformational instability and structural damage in proteins through hydrogen bonding and hydrophobic interactions. Meanwhile, the increase in ammonium nitrogen concentration under triazine stress provided further confirmation of the hydrolysis of proteins, providing readily fermentable substrates for VFAs production (particularly acetate). High-throughput 16S rRNA sequencing uncovered concentration-dependent microbial community restructuring, characterized by enrichment of proteolytic bacteria (Petrimonas) and acetate producers (Anaerovorax), concurrent with the suppression of methanogens. Functional metagenomic analysis using PICRUSt2 revealed upregulation of proteolytic enzymes (e.g., EC:3.4.16.4) and acetyl-CoA synthesis genes (e.g., PDHA), facilitating enhanced protein hydrolysis and acetate biosynthesis. Critically, triazine stress activated quorum sensing and two-component regulatory systems, with luxS expression increasing 5.7-fold, promoting metabolic coordination and stress resilience rather than community collapse. Partial least squares path modeling confirmed that substrate availability (λ = 0.459) served as the primary driver of VFAs accumulation, mediated by microbial community adaptation (λ = 0.560). These findings unveil how antimicrobial stress enhanced resource recovery via EPS-mediated metabolic reprogramming.},
}

@article {pmid41775266,
year = {2026},
author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J},
title = {Competition and compromise between exogenous probiotics and native microbiota.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101516},
doi = {10.1016/j.cels.2025.101516},
pmid = {41775266},
issn = {2405-4720},
abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.},
}

@article {pmid41775198,
year = {2026},
author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z},
title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141645},
doi = {10.1016/j.jhazmat.2026.141645},
pmid = {41775198},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.},
}

@article {pmid41775197,
year = {2026},
author = {Lin, L and Su, Z and Yang, X and Yang, F and Zhang, L and Adyari, B and Yang, X and Liu, S and Hu, A},
title = {Impacts of tributaries and sewage effluents on antibiotic resistance genes and pathogens in an urban river.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141641},
doi = {10.1016/j.jhazmat.2026.141641},
pmid = {41775197},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) within urban rivers presents an increasingly public health threat. This study utilized shotgun metagenomics to assess the distribution, drivers, and risks associated with ARGs and ARG-carrying pathogens (APs) in the Xiaoqing River, focusing on impacts from sewage treatment plant (STP) effluents and tributaries. Results demonstrated significantly elevated ARG and AP abundance and diversity in urban segments and STP effluents relative to upstream and downstream areas. Macrolide-lincosamide-streptogramin resistance genes dominated the urban river resistome. Tributaries were characterized by elevated concentrations of ARGs and identified as important reservoirs. STP effluents introduced APs, including Acinetobacter johnsonii, Enterobacter asburiae and Escherichia coli. Although overall ARG pollution decreased downstream, 44.8% of ARG subtypes and clinically relevant APs persisted, with downstream E. coli strains notably carrying an 8-fold higher ARG load. Mobile genetic elements showed a strong correlation with ARG propagation (R[2] > 0.60, P < 0.001), which may be facilitated by erythromycin and clarithromycin. Semi-quantitative source tracking analysis indicated that tributaries and STP effluents likely represent nonnegligible contributors to ARGs and APs in the urban river. This study demonstrates that sustained urban and tributary discharges drive resistome dissemination, posing persistent risks that require integrated riverine antimicrobial resistance management.},
}

@article {pmid41775186,
year = {2026},
author = {Geromino, P and LeMoine, CM and Drahun, I and Cassone, BJ},
title = {Co-supplementation of a polyethylene diet for improved fitness of Galleria mellonella larvae.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141617},
doi = {10.1016/j.jhazmat.2026.141617},
pmid = {41775186},
issn = {1873-3336},
abstract = {A growing number of plastivore insects have been discovered that readily consume and biodegrade various petro plastics, including LDPE. The caterpillar larvae of Galleria mellonella are capable of breaking down the polymers at expedited rates; however, feeding on LDPE as a sole nutrient source is inefficient and detrimentally impacts larval survival, growth, and development. The objective of our study was to improve fitness parameters and feeding activities of LDPE-fed larvae through the addition of various macro- and micronutrients. Each co-supplementation recovered fitness and consumption to some extent in comparison to pure LDPE; however, artificial sources produced outcomes that were well below those of the caterpillar's natural diet, regardless of the combination. Co-supplementation of LDPE, honeycomb, and corn syrup was the most successful, with larval fitness and consumption approximating their natural diet. To provide mechanistic insights into this recovery, qPCR and metagenomics analyses indicated the co-supplementation promoted greater gut bacterial abundance and species richness and evenness. In addition, GC-MS analyses identified notable differences in their fat body metabolic profiles that may contribute to slower developmental rates. We also assessed the capability of the larvae to eliminate food wastes, which showed promise and could represent a potential co-supplement source for LDPE biodegradation.},
}

@article {pmid41775040,
year = {2026},
author = {Liu, T and Sun, X and Huang, D and Kong, T and Huang, W and Lin, Z and Wang, Z and Li, B and Sun, W},
title = {Differential patterns of antibiotic resistance, virulence, and dissemination risks in floating and sedimented plastispheres.},
journal = {Water research},
volume = {296},
number = {},
pages = {125644},
doi = {10.1016/j.watres.2026.125644},
pmid = {41775040},
issn = {1879-2448},
abstract = {The plastisphere, a unique ecological niche on plastic surfaces, enriches microbial antibiotic resistance genes (ARGs) and virulence factors (VFs), posing environmental and health risks. Although aquatic sediment is a major sink for plastic contaminants, the resistance, virulence and dissemination potentials of sedimented plastispheres remain poorly characterized compared to floating plastics. Through investigation of metagenomes from two sites in the Pearl River in China, one of the world's plastic pollution hotspots, we report that water plastisphere showed 2.4 and 3.6 times more ARG and VF genes than those in sediment plastisphere and surrounding environments, together with higher mobile genetic element (MGE) abundances and a denser ARG-VF co-occurrence network (5,879 vs. 2,874 edges; density 0.043 vs. 0.025), indicating enhanced horizontal gene transfer potential. These differences coincide with contrasting ARG/VF assembly mechanisms, with deterministic and stochastic assembly processes dominating ARG/VF profiles in water and sediment plastispheres, respectively. Genome-resolved analyses further revealed that dominant plastisphere populations harbored multiple ARGs and VFs, with 41 MAGs predicted with pathogenicity capacities, most of which belonged to the families Mycobacteriaceae, Aeromonadaceae, Moraxellaceae, and Pseudomonadaceae. Notably, these taxa have been repeatedly reported as common plastisphere members across diverse ecosystems, suggesting that elevated resistance and virulence in floating plastispheres may be a widespread phenomenon across aquatic ecosystems. Together, our findings demonstrate that floating plastics act as dynamic vectors of antimicrobial resistance and pathogenicity, as well as their dissemination potentials, highlighting water-sediment transition may reduce these ecological risks within the plastisphere.},
}

@article {pmid41775000,
year = {2026},
author = {Mammeri, M and Obregon, D and Chevillot, A and Abuin-Denis, L and Skičková, Š and Kratou, M and Wu-Chuang, A and Maitre, A and Christine, J and Polack, B and Cabezas-Cruz, A and Adjou, KT},
title = {Yeast probiotic protects gut microbiota diversity and metabolic potential against Cryptosporidiosis-induced disruption in goat kids.},
journal = {Veterinary parasitology},
volume = {343},
number = {},
pages = {110729},
doi = {10.1016/j.vetpar.2026.110729},
pmid = {41775000},
issn = {1873-2550},
abstract = {Cryptosporidiosis, caused by Cryptosporidium parvum, is a major cause of enteric disease and gut microbiota disruption in neonatal ruminants. It can lead to impaired growth, increased susceptibility to pathogens, and long-term gut dysfunction. In this study, we investigated whether supplementation with a live yeast probiotic (Saccharomyces cerevisiae Sc47) could help preserve gut microbiota resilience and functional homeostasis during an experimental C. parvum oral infection in goat kids. Thirty male French Alpine goat kids were assigned to three groups: uninfected control (healthy), infected, and infected with yeast supplementation. Longitudinal 16S rRNA gene sequencing, network analysis, and functional metagenomic predictions were used to assess microbial diversity, community composition, co-occurrence patterns, and metabolic potential, with a focus on short-chain fatty acid (SCFA) biosynthesis. Infection induced marked dysbiosis, characterised by a substantial reduction in microbial richness and a widespread loss of SCFA-producing commensals and metabolic functions. In contrast, yeast supplementation significantly reduced oocyst excretion by more than 84% throughout the experiment, attenuated pathogen-induced community shifts, and maintained beneficial genera such as Butyricicoccus and members of the Oscillospiraceae family. Furthermore, network analysis revealed that probiotic treatment preserved microbial association structures and reduced community fragmentation. Consistent with these findings, functional profiling showed the retention of pathways involved in carbohydrate metabolism, amino acid biosynthesis, and SCFA production, suggesting enhanced microbiota resilience. These findings demonstrate that S. cerevisiae supplementation can mitigate infection-associated dysbiosis by controlling pathogenic overgrowth while sustaining commensal bacterial stability and functional capacity. This highlights its potential as a microbiota-targeted strategy to support gut health in neonatal ruminants.},
}

@article {pmid41774281,
year = {2026},
author = {Kapoor, V and Sanchez-Vicente, S and Donovan, W and Park, J and Nagapurkar, A and Gokden, A and Shrivastava, P and Horn, E and Briese, T and Lipkin, WI and Tokarz, R},
title = {Adaptation of custom capture sequencing panels to the Oxford Nanopore MinION platform.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41774281},
issn = {1573-4978},
support = {75A50122C00012//Biomedical Advanced Research and Development Authority/ ; },
abstract = {BACKGROUND: Next generation sequencing (NGS) remains underutilized in clinical microbiology applications despite providing broad pathogen spectrum detection superior to other molecular methods. This is primarily because of lower sensitivity of metagenomic NGS (mNGS) compared to PCR, lengthy turn-around times, cost, and complexity of data analysis. Capture sequencing is a technique that can mitigate some of the limitations of mNGS. Using probes that are engineered to selectively bind and pull down desired nucleic acids, capture sequencing enriches for targets of interest and can result in up to a 10,000-fold increase in sensitivity compared to mNGS. In this study, we describe the application of capture sequencing on Oxford Nanopore Technology's portable sequencer, the MinION MK1C.

METHODS: We examined the performance of VirCapSeq-VERT and TBDCapSeq, two distinct capture sequencing assays that target vertebrate viruses and tick-borne pathogens, respectively. Both assays were originally established on the Illumina platform. To enable sequencing on the MinION instrument, we developed a modified hybrid workflow using our established library preparation and capture protocol for Illumina, followed by the addition of the ONT sequencing adaptor. In tests using contrived and clinical samples, we compared sensitivity thresholds and sequencing output, including pathogen genome coverage and relevant read counts.

RESULTS: The addition of capture enrichment to MinION NGS provided significant improvement in pathogen detection when compared to mNGS. Assessment of assay performance on pathogen-positive samples revealed equivalent sensitivity on the MinION MK1C and Illumina NextSeq. We found that the elevated read counts and sequencing depth generated by Illumina NGS were offset by the greater read length obtained on the MinION MK1C and resulted in comparable pathogen genome coverage between the two platforms.

CONCLUSION: This study demonstrates the utility for employment of VirCapSeq and TBDCapSeq on different sequencing platforms and suggest the potential of the MinION platform for broad-spectrum clinical diagnostics.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41773858,
year = {2026},
author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M},
title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/spectrum.02220-25},
pmid = {41773858},
issn = {2165-0497},
abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.

IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.},
}

@article {pmid41773588,
year = {2026},
author = {Sun, S and Subramaniyan, S and Ranjani, G and Cid Gomes, L and Bernin, D and Bayer, T and Bornscheuer, UT and Hakkarainen, M and Syrén, PO},
title = {Polyurethane Cascade Depolymerization by a Combination of Thermal Pretreatment and Enzymatic Hydrolysis.},
journal = {ChemSusChem},
volume = {19},
number = {5},
pages = {e202502633},
doi = {10.1002/cssc.202502633},
pmid = {41773588},
issn = {1864-564X},
support = {CTS 23:2626//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 2021-02509//Svenska Forskningsrådet Formas/ ; NNF23OC0086236//Novo Nordisk Fonden/ ; NNF25OC0100562//Novo Nordisk Fonden/ ; },
abstract = {Enzymatic depolymerization of postconsumer polyurethanes (PURs) offers a promising route for sustainable plastic waste management. However, the complex chemistry of PURs containing carbamate, ether, and ester bonds poses a challenge for such a biotechnological process. Here, we explored the deconstruction of a commercial polyether-polyester-PUR through a cascade depolymerization approach, in which a low-temperature thermal pretreatment (180°C, 4 h) was combined with tandem enzymatic hydrolysis. Heat treatment modified the polymer's physicochemical properties, enabling the cutinase HiC from Humicola insolens to cause more than 8% weight loss of the treated PUR films, versus less than 2% of the untreated control after 48 h incubation. Furthermore, the addition of the metagenomic urethanase SP2 completed the one-pot enzymatic cascade, achieving not only depolymerization to the constituent monomer, 4,4'-methylenedianiline (MDA), but also a nearly 3-fold increase in MDA yield compared to using SP2 alone. Docking studies highlighted HiC's specificity toward ester bonds in the PUR polymeric units, and two HiC variants further enhanced degradation within 24 h. Altogether, this work lays the foundation for future investigation and process design for the depolymerization of polyether-polyester-PURs and related materials by cascade enzymatic reactions.},
}

@article {pmid41773475,
year = {2026},
author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M},
title = {Correction to "Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation".},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01914},
pmid = {41773475},
issn = {1520-5118},
}

@article {pmid41773424,
year = {2026},
author = {Valdés-Varela, L and Goyache, I and Virto, R and Sáinz, N and López-Yoldi, M and Sánchez-Vicente, A and López-Giral, N and Gil, AG and Milagro, FI and Aranaz, P},
title = {Companilactobacillus alimentarius CNTA 209 alleviates diet-induced obesity in mice through adipose tissue browning and gut barrier modulation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04242a},
pmid = {41773424},
issn = {2042-650X},
abstract = {The use of probiotics with health-promoting effects has emerged as a promising therapeutic strategy for managing obesity and metabolic syndrome. In this study, we characterized the probiotic properties of a novel strain, Companilactobacillus alimentarius CNTA 209, and investigated its potential anti-obesity effects and safety in rodent models. C. alimentarius exhibited sensitivity to all tested antibiotics, resistance to simulated gastric and intestinal conditions in vitro, and functional activities including β-galactosidase activity and short-chain fatty acid (SCFA) production. C. alimentarius supplementation mitigated liver damage induced by a high-fat, high-fructose diet and significantly reduced adiposity in obese C57BL/6 mice by enhancing brown adipose tissue metabolic activity. Metagenomic analysis revealed a beneficial modulation of gut microbiota composition, associated with improved intestinal barrier function. A comprehensive toxicological assessment conducted in Wistar rats confirmed the safety of the strain at a dose of 1 × 10[9] CFU per animal per day for oral administration. This study provides the first documented evidence of anti-obesity and metabolic benefits conferred by a strain of C. alimentarius, positioning CNTA 209 as a novel and safe candidate for the development of probiotic-based interventions targeting obesity and related metabolic disorders.},
}

@article {pmid41773230,
year = {2026},
author = {Li, X and Feng, Q and Yu, H},
title = {A Rare Case of Concurrent Tropheryma Whipplei and Pneumocystis Jirovecii Pneumonia in a Patient During Endocrine Therapy for Breast Cancer.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {580235},
pmid = {41773230},
issn = {1178-6973},
abstract = {Tropheryma whipplei (TW), a rare Gram-positive bacterium, is an uncommon cause of pulmonary infection, typically being reported in the context of gastrointestinal or neurological Whipple's disease. We present a case of a patient receiving endocrine therapy and ovarian suppression for breast cancer who developed a concurrent pulmonary infection with both Pneumocystis jirovecii (PJ) and TW. The diagnosis was secured through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, which successfully identified both pathogens. Following the initiation of targeted antimicrobial therapy, the patient exhibited significant clinical and radiological improvement.},
}

@article {pmid41772733,
year = {2026},
author = {Buscaglia, M and Castillo-Inaipil, W and Schulz, F and Guajardo-Leiva, S and Iriarte, JL and Aparicio-Rizzo, P and Masotti, I and Díez, B},
title = {Unveiling the viral frontier in a warming world: temperature as a key ecological driver of viral diversity in subantarctic Chilean Patagonia fjords.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00869-9},
pmid = {41772733},
issn = {2524-6372},
support = {21190726//ANID/ ; AUB1900003//ANID/ ; DG_06-20//INACH/ ; 151500003//ANID-FONDAP/ ; 1523A0002//ANID-FONDAP/ ; CIMAR25F//CONA-SHOA/ ; ICN2021_044//ANID - Millennium Science Initiative Program/ ; },
abstract = {BACKGROUND: The fjords of Chilean Patagonia (~ 41.5-55.9 °S) lie at the forefront of global warming, where rising temperatures threaten to disrupt microbial processes central to ocean productivity and carbon cycling. Despite their ecological relevance, the diversity and environmental drivers of viral communities, both giant viruses and prokaryotic viruses, remain poorly understood in high-latitude fjords.

RESULTS: Here, we leveraged metagenomics across a 500 km latitudinal gradient in Chilean Patagonia (4-10 °C; salinity 18-33 PSU) to decode the structure and distribution of marine viral communities. We recovered 126 giant viruses (polB sequences dereplicated at 100% average nucleotide identity) and 9213 prokaryotic viruses (viral contigs dereplicated at 95% average nucleotide identity), primarily affiliated with Prasinoviridae (proposed genus g177, order Algavirales) and Caudoviricetes, respectively. Consistent with global-scale studies, temperature emerged as the strongest driver structuring viral communities, outpacing the effects of salinity, depth, dissolved oxygen, chlorophyll-a, and geography. Viral diversity was consistently higher in the northern warmer waters (7.5-10.4 °C), while southern colder sites (4.0-7.4 °C) harbored less diverse and compositionally distinct communities. Giant viruses shift from Pandoravirales and AG_04 (Algavirales) at lower temperatures to increasing dominance of IM_01 (Imitervirales) and Prasinoviridae (AG_01) in warmer habitats. Prokaryotic virus communities also displayed strong temperature structuring, with additional influence from salinity.

CONCLUSIONS: Together, our findings underscore the environmental sensitivity of viral communities in subpolar marine systems and highlight their vulnerability to climate-driven changes. Given the critical role of viruses in microbial turnover, nutrient cycling, and ecosystem resilience, shifts in their diversity and structure may have far-reaching consequences for biogeochemical fluxes and food web dynamics in the fjords of Chilean Patagonia.},
}

@article {pmid41772715,
year = {2026},
author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD},
title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02362-4},
pmid = {41772715},
issn = {2049-2618},
support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.

RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.

CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.},
}

@article {pmid41771902,
year = {2026},
author = {Qian, Y and Xu, S and He, X and Lai, Y and Zhang, Y and Mo, C and Ai, P and Yang, X and Xiao, Q},
title = {Gut ecosystem dysfunction in parkinson's disease: deciphering faecal metabolome-metagenome links for novel diagnostic panels.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01299-7},
pmid = {41771902},
issn = {2373-8057},
support = {81901283//National Natural Science Foundation of China/ ; 81801254//National Natural Science Foundation of China/ ; 82171246//National Natural Science Foundation of China/ ; 22YF1440200//Shanghai Sailing Program/ ; 22QA1405700//the Shanghai Rising-Star Program/ ; 2018B030337001//Key Field Research and Development Program of Guangdong Province/ ; SHDC2020CR3012A//Clinical Research Plan of SHDC/ ; 2022YFE0210100//National Key Research and Development Program of China/ ; },
abstract = {Gut ecosystem dysfunction is implicated in Parkinson's disease (PD), but integrative faecal metabolome-metagenome links are undefined. We explored these interactions in Chinese PD patients to develop diagnostic panels. Targeted faecal metabolomics (LC‒MS/MS) was performed on 132 PD and 113 healthy controls (HCs) and shotgun metagenomics was integrated for 39 PD/HC pairs. We identified 33 significantly altered faecal metabolites in PD (FDR-P < 0.05). A novel 12-metabolite panel could distinguish PD from HCs. Multi-omic integration revealed gut ecosystem dysfunction manifests via co-disruptions in microbial genes (e.g., amino acid metabolism genes) and metabolites. Critically, a combinatorial diagnostic panel integrating faecal metabolites and microbial gene markers achieved exceptional PD detection (AUC = 0.961, 95% CI = 0.923-0.998). This study deciphers metabolome-metagenome links driving gut dysfunction in PD, identifying amino acid metabolism as a core perturbed pathway. The novel diagnostic panels provide mechanistic insights and clinical tools for PD precision diagnosis.},
}

@article {pmid41771597,
year = {2026},
author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R},
title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e100158},
doi = {10.1136/bmjopen-2025-100158},
pmid = {41771597},
issn = {2044-6055},
abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.

METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged ≥40 years; n=50) and Group B (patients aged ≥40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged ≥65 years (or ≥55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150 bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.

ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.},
}

@article {pmid41771407,
year = {2026},
author = {Zhao, Y and Zhang, X and Chen, X and Zhu, Z and Jiao, P and Ma, L and Li, Y},
title = {Evidence for Propioniciclava as a novel polyphosphate-accumulating organism and construction of its metabolic profile.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134320},
doi = {10.1016/j.biortech.2026.134320},
pmid = {41771407},
issn = {1873-2976},
abstract = {Enhanced biological phosphorus removal (EBPR) relies on polyphosphate-accumulating organisms (PAOs). This study identifies Propioniciclava as a novel putative PAO. High phosphorus release and uptake rates were achieved in two lab-scale Propioniciclava-dominated sequencing batch reactors (SBRs), reaching up to 2.37 and 2.10 mmolP/(gVSS·h), respectively. Metabolic pathway reconstruction for Propioniciclava was based on its most abundant metagenome-assembled genome (bin70), which accounted for 28.8% in SBR1 and 45.5% in SBR2. Functional annotation of bin70 revealed genes for phosphorus and glycogen metabolism but not for polyhydroxyalkanoate synthesis, suggesting a distinct storage strategy. Fluorescence in situ hybridization combined with 4',6'-diamidino-2-phenylindole (FISH-DAPI) staining provided evidence for intracellular polyphosphate granules. Metatranscriptomic analysis further highlighted genes related to phosphorus and glycogen synthesis being actively transcribed by Propioniciclava. The enrichment of Propioniciclava was crucially dependent on glucose. These findings expand the known diversity of PAOs and elucidate the metabolic profile of Propioniciclava, enhancing our understanding of EBPR microbiology.},
}

@article {pmid41771404,
year = {2026},
author = {Zhang, C and Zheng, L and Zhang, Q and Zhang, Y and Zheng, X},
title = {Synergistic removal of methanethiol and other odorant gases by a metabolically complementary synthetic consortia isolated from food waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134313},
doi = {10.1016/j.biortech.2026.134313},
pmid = {41771404},
issn = {1873-2976},
abstract = {Methanethiol (MeSH), a typical volatile sulfur compound, contributes significantly to environmental malodor and poses ecological risks. In this study, three bacterial strains capable of MeSH removal efficiencies exceeding 40% were isolated from food waste. These strains were taxonomically identified asAgrobacterium cavarae,Mycolicibacterium neoaurum, andPseudomonas qingdaonensis. Metagenomic annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that all strains possess key enzymes for the methionine and cysteine metabolism pathway, suggesting potential for MeSH degradation. In binary consortia, the combination of A. cavarae R1 and P. qingdaonensis CF (5:1 ratio) exhibited the optimal degradation performance, achieving removal efficiency of 87.2% for MeSH, 98.7% for H2S, and complete NH3 elimination (100%) after a 6-day cultivation. Among ternary consortia, the A. cavarae R1/M. neoaurum CD/ P. qingdaonensis CF combination at 3:2:1 and 3:1:2 ratios demonstrated superior removal efficiency for all three target odorants. Specifically, the 3:2:1 ratio consortium achieved 94.7% MeSH degradation, while the 3:1:2 ratio showd 91.7% NH3 removal efficiency. These results demonstrate the feasibility of using composite microbial agents for odor control in waste management systems.},
}

@article {pmid41770401,
year = {2026},
author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J},
title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {2},
pages = {},
pmid = {41770401},
issn = {1573-5168},
support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; },
abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.},
}

@article {pmid41770210,
year = {2026},
author = {Du, Y and Wang, Y and Sun, F},
title = {Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.},
journal = {Current protocols},
volume = {6},
number = {3},
pages = {e70341},
pmid = {41770210},
issn = {2691-1299},
support = {EF-2125142//NSF/ ; },
abstract = {Metagenomic Hi-C (metaHi-C) links mobile genetic elements to their cellular hosts directly within complex microbial communities. Once shotgun and Hi-C libraries have been generated, however, the main challenges shift to the bioinformatics required for preprocessing, genome binning, taxonomic annotation, and network-level interpretation. Here, we present metaHi-C protocols that span from raw reads to downstream data analyses. Basic Protocol 1 describes quality control of shotgun and Hi-C reads, metagenomic assembly, Hi-C read mapping, and viral contig identification from assembled contigs. Basic Protocol 2 details the use of ViralCC to recover viral metagenome-assembled genomes (vMAGs) and infer virus-host linkages. Support Protocol 1 introduces NormCC and ImputeCC for normalization of raw Hi-C contacts and host genome binning. Support Protocols 2 and 3 describe taxonomic annotation of host MAGs with GTDB-Tk and viral bins with Virgo, respectively. Support Protocol 4 shows how to integrate these outputs in MetaHiCNet to generate cross-taxa and cross-bin Hi-C interaction networks. Together, these protocols provide a reproducible workflow for reconstructing viral and host genomes, assigning consistent taxonomies, and visualizing metaHi-C-derived virus-host interaction structure across diverse microbiomes. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preprocessing raw metagenomic Hi-C data Basic Protocol 2: Viral genome binning and virus-host interaction inference using ViralCC Support Protocol 1: Host genome binning using ImputeCC Support Protocol 2: Host MAG taxonomic annotation with GTDB‑Tk Support Protocol 3: Viral bin taxonomic annotation with Virgo Support Protocol 4: Visualization of virus-host interaction networks with MetaHiCNet.},
}

@article {pmid41770016,
year = {2026},
author = {Martins, I and Silva, JM and Almeida, JR},
title = {HYMET: A Hybrid Metagenomic Pipeline for Accurate and Efficient Taxonomic Classification.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag024},
pmid = {41770016},
issn = {2047-217X},
abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a two-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor (LCA) classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.

RESULTS: Across seven CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93 s runtime and a mean peak memory of 6.24 GB. Performance remained stable under mutation rates up to 30% for most domains (F1 ≥ 0.8), with viral sequences showing the expected decline (F1 ≈ 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson r = 0.998, Bray-Curtis =0.04) across bacteria, fungi, and archaea.

CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.},
}

@article {pmid41769655,
year = {2026},
author = {Ray, S and Shankaran, P},
title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1761992},
pmid = {41769655},
issn = {2296-861X},
abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.},
}

@article {pmid41769651,
year = {2026},
author = {Wang, L and Yu, Y and Shen, X and Li, X and Wang, D and Zhai, Y and Jiang, W and Zhao, W and Yu, Q and Liong, MT and Chen, D and Zhao, A},
title = {Bifidobacterium supplementation maintains gut microbiota stability and enhances well-being during short-term travel.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1724829},
pmid = {41769651},
issn = {2296-861X},
abstract = {BACKGROUND: International travel exposes individuals to abrupt environmental, dietary, and circadian changes that can disturb gut microbiota and overall well-being. While probiotics are known to support gastrointestinal and systemic health, their effects during short-term travel remain incompletely characterized in randomized trials.

METHODS: This randomized, double-blind, placebo-controlled study investigated whether a multi-strain Bifidobacterium probiotic could maintain gut microbiota stability and support health during a five-day trip from China to Japan. Forty healthy adults were randomly assigned to receive either probiotic (n = 22) or placebo (n = 18) daily from Day 1 to Day 4. Stool samples collected before departure (Day 0) and after return (Day 5) were analyzed by metagenomic sequencing, quantitative PCR, and fecal secretory immunoglobulin A (sIgA) assays. Participants completed validated questionnaires on gastrointestinal and respiratory symptoms, sleep quality (PSQI), anxiety (GAD-7), and well-being (WHO-5).

RESULTS: Compared with placebo, participants receiving the probiotic showed maintenance of microbial diversity (Chao1 and Fisher indices, both p = 0.044), prevented enrichment of potentially harmful taxa (Bilophila, Flavonifractor), and increased Bifidobacterium abundance. Clinically, the probiotic group reported fewer respiratory and systemic symptoms, including sore throat (p = 0.034) and fatigue (p = 0.043). Sleep quality also improved, with longer sleep duration (p = 0.023), fewer total occurrence days of PSQI >5 (p = 0.009), lower anxiety scores (p = 0.001) and higher WHO-5 well-being scores (p = 0.041). Functional profiling showed up-regulation of vitamin biosynthesis pathways (folate, biotin, retinol) and decreased antibiotic resistance gene prevalence.

CONCLUSION: Short-term probiotic administration demonstrated gut microbiota resilience and improved physiological and psychological stability during travel. Probiotics may serve as an accessible strategy to support well-being under transient environmental and lifestyle stress.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier NCT07163819.},
}

@article {pmid41769388,
year = {2026},
author = {Chang, ACG and Amaral, MWW and Keepers, K and Ikudaisi, C and Greenwood, M and Li, J and Hamsher, SE and Miller, SR and Kociolek, JP},
title = {An alternative technique for organelle genome recovery in diatoms using culture-independent, minimal-cell whole genome amplification.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20767},
pmid = {41769388},
issn = {2167-8359},
abstract = {BACKGROUND: This study presents an alternative method in diatom genomics using two raphid diatoms-Campylodiscus clypeus and Plagiotropis lepidoptera-whose organellar genome characteristics have remained unexplored due to cultivation constraints. Only a small fraction of the estimated 200,000 diatom species has been cultured in the laboratory. This research showcases the use of minimal-cell genomics as a viable alternative for studying diatoms and other eukaryotic microorganisms that do not respond well to traditional laboratory culture methods.

METHODS: Initial attempts to culture C. clypeus and P. lepidoptera were unsuccessful, hindering the acquisition of genomic data. To overcome these challenges, we employed minimal-cell whole genome amplification (mcWGA) techniques for two uncultured species, followed by metagenomic sequencing and assembly. This enabled direct genomic recovery from minimally isolated and pooled cells, eliminating the need for cultivation.

RESULTS: Using mcWGA approach, we successfully obtained the complete chloroplasts and mitochondrial genomes of C. clypeus and P. lepidoptera using only 8-12 viable cells isolated from fresh environmental samples. The plastome size of C. clypeus was 143,367 bp and mitogenome size was 46,274 bp, while P. lepidoptera has plastome and mitogenome sizes of 116,161 bp and 49,356 bp, respectively. The data generated provides a valuable resource for further research, highlighting the importance of culture-independent techniques in microbial genomics.},
}

@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}

@article {pmid41769339,
year = {2026},
author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Sangtian, M and Panmontha, W and Bunlungsup, S and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sriswasdi, S and Viangteeravat, T},
title = {Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1751074},
pmid = {41769339},
issn = {2235-2988},
abstract = {BACKGROUND: The BIOTIA-DX platform (BDX), a commercially available clinical-grade mNGS-based test in the United States, has not been analytically validated for urinary tract infections (UTIs) in a Southeast Asian cohort, where microbial epidemiology and antimicrobial resistance (AMR) patterns differ significantly.

OBJECTIVE: Our primary objective was to evaluate the analytical performance and concordance with standard urine culture of the BIOTIA-DX platform in a Thai tertiary hospital setting, thereby assessing its transportability to a Southeast Asian population with distinct microbial epidemiology.

METHODS: We analyzed 398 retrospectively collected urine samples from patients with suspected UTI at a private hospital in Bangkok. Each sample was processed in parallel using standard-of-care urine culture and the BDX mNGS workflow. After excluding 30 samples with insufficient sequencing reads (<500 non-human reads), 368 samples (231 culture-positive, 137 culture-negative) were included. Diagnostic accuracy was assessed against culture, and genotypic AMR predictions were compared to phenotypic antimicrobial susceptibility testing (AST) N = 192.

RESULTS: The BIOTIA-DX platform demonstrated high analytical sensitivity at the sample level (98.7% [95% CI: 0.95-0.99]; 228/231 culture-positive samples detected) and organism level (94.6%; 229/242 culture-identified organisms correctly detected). Among 137 culture-negative samples, BIOTIA-DX detected microbial DNA in 98 samples (71.5%), identifying 264 organisms not detected by standard culture. These additional detections predominantly comprised anaerobic organisms (150/264, 56.8%) and fastidious species (54/264, 20.5%); however, the clinical significance of these detections (infection vs. colonization vs. contamination) could not be determined without clinical correlation. For AMR prediction, genotype-phenotype concordance rates were 94.1% for fluoroquinolone resistance in E. coli (96/102 resistant isolates correctly predicted), 91.4% for beta-lactams (106/116), 91.3% for aminoglycosides (21/23), and 81.5% for sulfamethoxazole/trimethoprim (75/92). Specificity and positive predictive value could not be calculated because organisms detected by BIOTIA-DX but not by culture could not be definitively classified as true positives or false positives without independent confirmation.

CONCLUSIONS: The BIOTIA-DX platform demonstrates robust analytical concordance with urine culture in a Thai patient population. Prospective clinical validation studies are needed to assess clinical utility and impact on patient outcomes, particularly in culture-negative and polymicrobial cases. This study represents the first analytical validation of this platform using Oxford Nanopore Technology and the first validation in Southeast Asia.},
}

@article {pmid41768933,
year = {2025},
author = {Ameer, A and Saleem, F and Keating, C and Afzal, F and Irshad, H and Ahmed, K and Sattar, S and Ijaz, UZ and Javed, S},
title = {Avian cecal microbiome response and resilience to Newcastle disease are dictated by breed background.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1659648},
pmid = {41768933},
issn = {2674-0702},
abstract = {A wide range of viral infections threaten the long-term sustainability of poultry production. Newcastle disease (ND), caused by Newcastle disease virus (NDV), is endemic in most Asian countries, including Pakistan, causing 50%-100% mortality in young and mature chickens. Some local chicken breeds show resistance to certain diseases and have greater survival probability. The chicken gut microbiome is linked to immune response against infections and to production performance parameters. The present study aims to comprehend disease resistance patterns in multiple chicken breeds with respect to gut microbial communities. Day-old Naked Neck, Black Australorp, Rhode Island Red, white layer, and broiler chicks were raised on an antibiotic-free diet in a semi-controlled setup. Vaccinated and non-vaccinated birds were challenged with NDV. Disease onset was delayed in breeds other than broilers, in which disease symptoms appeared at day 3 post-challenge with maximum severity and mortality. Other breeds, irrespective of vaccination, survived through the challenge period. Naked Neck showed the least variation in clinical features and growth parameters. A lower diversity in broiler groups with a significant decrease after NDV challenge was revealed by 16S rRNA amplicon sequencing of cecal DNA. Furthermore, broiler cecal core microbiome membership was found to be more variable than other breeds. Moreover, differentially abundant genera were observed across treatment groups and breeds with a similar effect on the predicted metabolic pathways, indicating varied energy metabolism responses. Shotgun metagenomics revealed a higher abundance of functional genes, including antimicrobial resistance (AMR) genes, stress genes, virulence genes, and amino acid degradation genes in the broiler NDV-infected group compared to the control group. The gut microbiota in chickens affects immunity to infections, health, and productivity. Compared to broilers, local chicken breeds, specifically Naked Neck, are found to have high immune competence in resisting ND while maintaining most performance metrics. Broilers show lower alpha diversity with an unstable core microbiome. Therefore, stable core microbiome maintenance may help the birds cope with the viral infection. The results support the farming of resistant chicken breeds over broilers to reduce production losses from NDV outbreaks.},
}

@article {pmid41768492,
year = {2025},
author = {Vignal, L and de Lahondès, R and Gillibert, A and Tavolacci, MP and Prifiti, E and Formstecher, E and Ribet, D and Quillard, M and Coeffier, M and Déchelotte, P},
title = {Metagenomic analysis of salivary microbiota in patients with anorexia nervosa and association with functional digestive disorders (ORMICAN pilot study).},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e001112},
pmid = {41768492},
issn = {2516-5542},
abstract = {BACKGROUND: Patients with anorexia nervosa (AN) have intestinal dysbiosis and are frequently affected by oral and upper gastrointestinal disorders. Until now, no metagenomic sequencing data were available on oral microbiota in AN.

DESIGN: This observational study enrolled 46 patients with restrictive/purging AN and 20 controls. Salivary samples were performed after fasting. DNA of oral microbiota from salivary samples was analysed by whole genome shotgun deep sequencing. The primary objective was to compare the diversity of oral microbiota between patients with AN and healthy individuals. Secondary endpoints were to assess the associations between the diversity of oral microbiota and the severity of functional digestive disorders, between patients with a restrictive type of AN and patients with a mixed/purging type and between the diversity of oral microbiota and the severity of AN.

RESULTS: We observed not only a significant decrease in the alpha diversity of oral microbiota in AN patients (4.47 (4.05; 4.75)) versus controls (4.81 (4.68; 5.04)) (p=0.001) but also in gene richness (p=0.00023). There was no significant correlation (95% CI) between oral microbiota diversity and functional digestive disorders nor between patients with a restrictive type of AN and patients with a mixed/purging type of AN, nor between the diversity of oral microbiota and the severity of AN. In addition, we observed four bacterial taxa that were decreased in AN patients.

CONCLUSION: Our study highlights a decreased diversity of oral microbiota in AN patients. Future larger studies may help identify the prognostic and therapeutic value of oral microbiota in AN.},
}

@article {pmid41768489,
year = {2025},
author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Iwasaki, M and Dinassing, A and Senthilkumar, R and Preethy, S and Abraham, SJK},
title = {Randomised trial of Aureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation.},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e000776},
pmid = {41768489},
issn = {2516-5542},
abstract = {OBJECTIVE: Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Anti-inflammatory, antifibrotic effects and enhancement of muscle regeneration biomarkers after oral consumption of Aureobasidium pullulans strain N-163-produced beta 1,3-1,6-glucan (Neu REFIX) having been demonstrated in clinical and preclinical studies of DMD; in this study, we have investigated the effects on the gut microbiome in patients with DMD.

DESIGN: Twenty-seven patients with DMD were included in the study (control (n=9), N-163 (n=18)). Whole-genome metagenomic sequencing was performed in pre-N-163 and post-N-163 intervention faecal samples of each of these participants.

RESULTS: After N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such as Roseburia and Faecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria and Alistipes.

CONCLUSION: Beneficial reconstitution of the gut microbiome after Neu REFIX beta-glucan administration and its safety have been confirmed. These outcomes correlating with the anti-inflammatory, anti-fibrotic effects along with increase in dystrophin in skeletal muscle and plasma, reported earlier make us recommend further in-depth exploration on its role in epigenetic manipulation which when found encouraging might help other genetic diseases as well.

TRIAL REGISTRATION NUMBER: CTRI/2021/05/033346.},
}

@article {pmid41768378,
year = {2026},
author = {Li, J and Zeng, P and Mu, X and Cai, C},
title = {Clinical Characteristics and Risk Factors Analysis of Nontuberculous Mycobacterial Pulmonary Disease Complicated with Bronchiectasis.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {483326},
pmid = {41768378},
issn = {1178-6973},
abstract = {BACKGROUND: Nontuberculous mycobacteria pulmonary disease (NTM-PD) frequently coexists with bronchiectasis. This study aimed to compare clinical profiles and identify risk factors between NTM-PD patients with/without bronchiectasis and explore differences between rapid- vs slow-growing non-tuberculous mycobacteria (NTM) species.

METHODS: A retrospective analysis was conducted on patients diagnosed with NTM-PD and admitted to Beijing Tsinghua Changgung Hospital between April 2021 and April 2025. Among 496 inpatients with pulmonary diseases who underwent metagenomic next-generation sequencing (mNGS) analysis of bronchoalveolar lavage fluid, NTM were identified in 57 patients. Ultimately, 43 of these cases were confirmed and diagnosed as having NTM-PD. Relevant clinical data were collected, and the association between each variable and adverse outcomes was assessed using univariate and multivariate logistic regression analyses.

RESULTS: Among the 43 confirmed NTM-PD patients, 24 had concurrent bronchiectasis (NTM-PD with bronchiectasis group) and 19 did not (NTM-PD group). In terms of baseline characteristics, the NTM-PD with bronchiectasis had a significantly higher proportion of females (79.17% vs 31.57%, P=0.002) and lower BMI (19.46 vs 22.46, P=0.023). Slow-growing NTM (SGM, mainly Mycobacterium avium complex [MAC]) was more common in the NTM-PD with bronchiectasis group (70.83% vs 31.58%, P=0.010); rapid-growing NTM (RGM, mainly M. abscessus) was more prevalent in the NTM-PD group (57.89% vs 20.83%, P=0.013). The positive rate of T-SPOT.TB in the NTM-PD group was higher than that in the NTM-PD with bronchiectasis group (47.37% vs 8.33%, P=0.010). Multivariate logistic regression identified female sex as an independent risk factor for NTM-PD complicated with bronchiectasis (OR=17.784, 95% CI: 1.103-286.857, P=0.042), while T-SPOT.TB was not (OR=0.047, 95% CI: 0.002-1.341, P=0.074).

CONCLUSION: Female sex is an independent risk factor for NTM-PD complicated with bronchiectasis. NTM-PD patients with bronchiectasis are more likely to be infected with SGM (especially MAC), while those without bronchiectasis tend to have RGM (especially M. abscessus) infection.},
}

@article {pmid41768053,
year = {2026},
author = {Lv, M and Tian, D and Wang, G and Hou, C and Fan, T and Li, W},
title = {Salinity gradients alter root-zone soil microbiome structure and nitrogen-related functional potential in alfalfa (Medicago sativa L.): a pot experiment.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1753229},
pmid = {41768053},
issn = {1664-462X},
abstract = {INTRODUCTION: Soil salinization constrains agricultural sustainability in arid and semi-arid regions. This study examined integrated soil-plant-microbe responses of alfalfa (Medicago sativa L.) to a salinity gradient.

METHODS: A pot experiment was conducted with control, low-, and moderate-salinity treatments. Root-zone soil and plants were sampled to measure soil EC, pH, and inorganic nitrogen forms, and to assess plant growth traits. Shotgun metagenomics was used to characterize microbial community composition and metagenome-inferred functional potential.

RESULTS: Salinity increased soil EC and pH and altered inorganic nitrogen forms, with higher NO3 [-]-N under moderate salinity and lower NH4 [+]-N under salinity compared with the control. Plant height peaked under low salinity, whereas fresh and dry biomass decreased under both salinity treatments. Microbial β-diversity differed among treatments, while α-diversity showed limited responses. Functional annotations indicated treatment-associated trends in nitrogen- and stress-related categories and KEGG level 3 pathways; however, most differences were not significant after FDR correction.

DISCUSSION: This integrative root-zone assessment links salinity-driven soil chemistry changes with alfalfa performance and suggests coordinated shifts in soil chemistry, microbiome structure, and plant growth under salinity stress.},
}

@article {pmid41767950,
year = {2026},
author = {Tang, L and Luo, Z and Gao, S and Lin, Z and Sun, M and Li, R and Gao, SH and Wu, G and Li, Y and Huang, L and Fan, L},
title = {A hot origin of dissimilatory sulfite reduction catalyzed by DsrAB in the Paleoarchean Era.},
journal = {mLife},
volume = {5},
number = {1},
pages = {108-121},
pmid = {41767950},
issn = {2770-100X},
abstract = {Dissimilatory sulfite reduction (DSR) has been essential to microbial energy metabolism in the biogeochemical sulfur cycle since the Paleoarchean Era. However, due to the lack of an integrated assessment of geological record and genomic data, the evolutionary origin of DSR remains elusive in terms of time, habitat, and genetic basis. In this study, we reconstructed the evolutionary pathways and the ancestral sequences of Dsr proteins by mining metagenomes ranging from mesothermal to hyperthermal environments. A phylogenetic analysis of the key catalytic enzyme, DsrAB, and other Dsr proteins indicates that the earliest and most basic functional cascade, DsrABCNM, emerged prior to the latest common ancestor of several basal branching DsrAB clusters encoded by bacteria and archaea. Using a molecular dating strategy that calibrates the protein tree with a species tree, we predicted that the DSR originated 3.508 billion years ago (Ga). This finding strongly confirms the earliest geological evidence of DSR (~ 3.47 Ga). Further predictions from ancestral sequence reconstruction indicate that the optimal catalytic temperature of DsrA at the time of DSR origin was approximately 73°C, which is consistent with the petrographic and geochemical evidence in early Archean hydrothermal deposits. After its hot origin, DsrA diversified into subclades that adapted to various temperature levels following the Great Oxidation Event. This is exemplified by the evolution of the reductive archaeal-type DsrA. Our results synchronize the molecular ages with the geological record, which advances our understanding of the earliest DSR systems and highlights the enzymatic adaptations of microbial life in the Archean biosphere.},
}

@article {pmid41767718,
year = {2026},
author = {Cao, M and Zhang, X and Huang, L},
title = {Advanced renal tuberculosis due to misdiagnosis as recurrent urinary tract infection: A case report.},
journal = {IDCases},
volume = {43},
number = {},
pages = {e02527},
pmid = {41767718},
issn = {2214-2509},
abstract = {Renal tuberculosis (RTB) lesions often initially localize to a specific part of the kidney, presenting with minimal clinical symptoms and a very slow disease progression, which makes the condition highly susceptible to misdiagnosis. We report an instructive case from the Second Affiliated Hospital of Zhejiang University School of Medicine, where a patient was ultimately diagnosed with advanced RTB after a 20-year diagnostic odyssey. The patient exhibited atypical clinical symptoms and was repeatedly diagnosed with recurrent urinary tract infection (UTI). Initial urinalysis revealed microscopic hematuria (52 RBCs/μL), pyuria (615 WBCs/μL), and 1 + proteinuria (0.7 g/L). A urine culture tested positive for Escherichia coli. Ultrasound imaging indicated a right renal calculus, and intravenous pyelography demonstrated significantly diminished right renal function. Suspicion for RTB was raised by CT findings and a positive tuberculosis infection T-cell spot (T-SPOT.TB) test. Acid-fast bacilli were consistently detected in two consecutive urine sediment examinations. The diagnosis was ultimately confirmed through metagenomic next-generation sequencing (mNGS) and postoperative pathological examination. This case underscores that the early diagnosis of RTB is challenging and requires a high index of clinical suspicion, comprehensive analysis of manifestations, and the strategic integration of modern diagnostic tools.},
}

@article {pmid41767535,
year = {2026},
author = {Chen, J and Yang, J and Zhang, Y},
title = {Case Report: Rare pulmonary infection and cytomegalovirus retinitis revealed a case of lymphoma.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1732360},
pmid = {41767535},
issn = {2296-858X},
abstract = {BACKGROUND: Recurrent cytomegalovirus retinitis (CMVR) and rare opportunistic pulmonary infections may be the initial manifestations of underlying immunodeficiency caused by occult hematologic malignancy. Epstein-Barr virus-positive diffuse large B-cell lymphoma, not otherwise specified (EBV[+]DLBCL-NOS) is an aggressive lymphoma associated with immune dysfunction, predisposing patients to severe opportunistic infections, including CMVR. However, pulmonary co-infection with Tropheryma whipplei and Penicillium digitatum has not been previously described as a presenting feature of EBV[+] DLBCL-NOS.

CASE: A 66-year-old male presented with blurred vision and was diagnosed with CMVR, with profoundly low CD4[+] T-cell counts (102 cells/μL) and high cytomegalovirus (CMV) DNA levels in blood and aqueous humor. He initially responded to ganciclovir, but CMVR recurred five months later, accompanied by new pulmonary nodules. Despite negative conventional microbiological tests, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified co-infection with Tropheryma whipplei and P. digitatum. Broad-spectrum antimicrobial therapy led to partial clinical improvement, but pulmonary lesions persisted. PET-CT revealed hypermetabolic lung and lymph node lesions, and subsequent lung biopsy confirmed EBV[+] DLBCL-NOS. The patient's progressive immunodeficiency, recurrent CMVR, and refractory pulmonary infection were ultimately attributed to underlying lymphoma.

CONCLUSION: This case highlights that severe, unexplained immunodeficiency with recurrent CMVR and rare opportunistic pulmonary infections should prompt a high index of suspicion for underlying hematologic malignancy. mNGS and PET-CT are critical tools in the diagnostic workup, but definitive diagnosis relies on histopathological confirmation. Early recognition of such presentations can prevent delays in diagnosing aggressive lymphomas.},
}

@article {pmid41766731,
year = {2026},
author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF},
title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73172},
pmid = {41766731},
issn = {2045-7758},
abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.},
}

@article {pmid41766220,
year = {2026},
author = {Schwedhelm, C and Pinart, M and Forslund-Startceva, SK and Oluwagbemigun, K and Dötsch, A and Schlicht, K and Schwarz, F and Siampani, SM and Avraam, D and De Angelis, M and Bouwman, J and Brigidi, P and Caderni, G and Calabrese, FM and Cuadrat, RRC and De Filippo, C and De Filippis, F and Ercolini, D and Fabbrini, M and Laudes, M and Nöthlings, U and Özsezen, S and Sharon, I and Schulze, MB and Turroni, S and Vitali, F and Pischon, T and Nimptsch, K},
title = {Associations of Adiposity With Gut Microbiota Composition Among Adults-Results From a Federated Analysis of Individual Participant Data From Eight European Observational Studies.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70106},
doi = {10.1111/obr.70106},
pmid = {41766220},
issn = {1467-789X},
support = {FKZ 01EA1906A//Bundesministerium für Bildung und Forschung/ ; 01EA1906B//Bundesministerium für Bildung und Forschung/ ; 01EA1906F//Bundesministerium für Bildung und Forschung/ ; BMBF//Bundesministerium für Bildung und Forschung/ ; //Fund for Scientific Research (FRS-FNRS, Belgium)/ ; //Research Foundation-Flanders (FWO, Belgium)/ ; //Institut National de la Santé et de la Recherche Médicale/ ; //Bundesministerium für Ernährung und Landwirtschaft/ ; //Ministero dell'Istruzione, dell'Università e della Ricerca/ ; //National Institute of Health Carlos III/ ; //the Netherlands Organization for Health Research and Development (ZonMw, the Netherlands)/ ; //Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie/ ; //Ministry of Science and Technology (Israel)/ ; //Formas (Sweden) and HDHL-Intimic Era-Net (EarlyFOOD)/ ; JTC-2017-7//Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"/ ; //European Union/ ; DZD Grant 82DZD00302//Ministerium für Ländliche Entwicklung, Umwelt und Landwirtschaft des Landes Brandenburg/ ; 442326535//National Research Data Infrastructure for Personal Health Data (NFDI4Health) by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; },
abstract = {Gut microbiota may contribute to the adiposity-associated disease risk, but human studies reported inconsistent associations of adiposity with gut microbiota composition. We examined associations of body mass index (BMI) with alpha diversity and relative microbial abundance at the phylum and genus taxonomic levels (based on 16S rRNA amplicon sequencing or metagenomics) among 7415 adults from eight European observational studies in a joint federated analysis of harmonized data using DataSHIELD. Higher BMI (per 5 kg/m[2]) was associated with lower alpha diversity (β: -0.05; 95% CI: -0.07, -0.03) and, on the phylum level, positively associated with Proteobacteria, but neither with Firmicutes nor Bacteroidetes nor their ratio, where high between-study heterogeneity was observed. On the genus level, BMI was inversely associated with the relative abundance of Faecalibacterium of the Firmicutes phylum (β: -0.11; 95% CI: -0.14, -0.07) but positively with the odds of detection of Dorea, Streptococcus, and Clostridium (all three Firmicutes) as well as Collinsella (Actinobacteria). This federated analysis of multiple studies found lower alpha diversity, alongside depleted Faecalibacterium, as well as higher odds of detection of Dorea, Streptococcus, Clostridium, and Collinsella with higher adiposity. By combining data from diverse study populations using harmonized data and statistical methods, our analysis partly overcomes sources of heterogeneity that may explain previously observed inconsistencies.},
}

@article {pmid41629849,
year = {2026},
author = {Li, L and Wang, J and Li, Z and Xing, D},
title = {High fever with rash: a case report of spotted fever group rickettsial infection at a construction site.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {41629849},
issn = {1471-2334},
abstract = {BACKGROUND: Spotted Fever Group Rickettsiae (SFGR) infection is one of the global public health threats. With the improvement of current hygiene conditions, the incidence of rickettsial infections has significantly decreased compared with previous years; however, in clinical practice, rickettsial infections should still be considered in the differential diagnosis of febrile cases of unknown etiology.

CASE PRESENTATION: A construction worker, residing in crowded and poor sanitary conditions, presented with high fever and diffuse cutaneous rash, without reporting other associated discomfort. Empirical treatment with cephalosporin antibiotics failed to alleviate the symptoms. Given the unknown etiology of the patient’s high fever and rash, routine etiological tests yielded negative results, with concurrent abnormalities in the white blood cell differential count of the complete blood count. A strong suspicion of infection by an unusual microorganism prompted the performance of metagenomic next-generation sequencing (mNGS) on venous blood. This test identified infection with Rickettsia rickettsii belonging to the spotted fever group, confirming a rickettsial infection. Following the establishment of the etiology, the antimicrobial treatment regimen was adjusted, and the patient was administered doxycycline for antimicrobial therapy. After treatment, the patient’s body temperature returned to normal, the rash resolved, and the patient was discharged in a state of full recovery.

SUMMARY: For patients working at construction sites with poor living conditions who present with high fever and rash but lack evidence of conventional microbial infection, clinicians should enhance their differential diagnostic capabilities and maintain vigilance for the occurrence of rickettsial infection.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12735-7.},
}

@article {pmid41765668,
year = {2026},
author = {Nian, YP and Ning, SS and Li, SS and Yu, PB and Meng, Y and Zhao, X and Ren, RQ and Yan, J and Han, XY and Zheng, ZX and Zhang, QF and Wang, X and Zhang, Y},
title = {[Investigation and management of the first case of human infection with avian influenza A(H10N3) virus in northern China].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {47},
number = {2},
pages = {275-280},
doi = {10.3760/cma.j.cn112338-20250616-00397},
pmid = {41765668},
issn = {0254-6450},
abstract = {Objective: To summarize and analyze the epidemiological characteristics and field investigation of the first case of human infection with avian influenza A(H10N3) virus in northern China and to provide reference for the investigation and management of human infection with animal-derived influenza in the future. Methods: Case epidemiological investigation, identification and medical observation of co-exposed people and close contacts, and tracing investigation and analysis of infection source were carried out. Samples were collected from the case, co-exposed persons, close contacts, poultry, and the external environment. Real-time fluorescent quantitative RT-PCR was used to detect influenza A virus. The positive samples were subjected to metagenomic sequencing and compared. Results: This is the first case of human infection with the avian influenza A(H10N3) virus in northern China, and a third-party laboratory performed the detection. The patient became ill on April 13, 2025, with no history of contact with similar cases prior to symptom onset but with a history of exposure to poultry. The macrogene test of bronchoalveolar lavage fluid was positive for avian influenza A(H10N3) virus on April 28, 2025. A total of 168 samples were collected from co-exposed individuals, close contacts, poultry, and the external environment, and all were negative for avian influenza A(H10N3) virus. Metagenomic sequencing analysis showed that the sequence had high homology with the human infection case of avian influenza A(H10N3) virus reported in Guangxi Zhuang Autonomous Region in December 2024. After taking emergency measures such as medical observation of close contacts, harmless treatment of poultry in the sick home, and disinfection of suspected exposure places, no secondary cases occurred. The case was cured and discharged on May 14. Conclusions: The source of the first human case of avian influenza A(H10N3) infection in northern China remains unclear, but no human-to-human transmission has been found. It is important to improve the sensitivity of surveillance for new subtypes of animal-derived influenza viruses, such as avian influenza A(H10N3), and to strengthen joint prevention and control between health and animal husbandry departments to support scientific approaches to preventing and controlling human infection with these viruses.},
}

@article {pmid41765557,
year = {2026},
author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W},
title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {573-583},
doi = {10.1016/j.jes.2025.05.044},
pmid = {41765557},
issn = {1001-0742},
abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.},
}

@article {pmid41765316,
year = {2026},
author = {Lyu, Y and Ye, Y and Zhang, C and Zhong, W and Zhu, L},
title = {Bisphenol A bis (diphenyl phosphate) Disrupted Tryptophan Metabolism Through Microbiota Dysbiosis to Promote Intestinal Toxicity.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124140},
doi = {10.1016/j.envres.2026.124140},
pmid = {41765316},
issn = {1096-0953},
abstract = {Organophosphorus flame retardants (OPFRs) are associated with intestinal injury. Bisphenol A bis(diphenyl phosphate) (BDP), an emerging OPFR that is widely present in organisms and humans, may induce intestinal toxicity, yet the effect and underlying mechanism remains unclear. In this study, zebrafish were exposed to BDP at 2, 20 and 200 μg/L for 21 days. Distinct histopathological changes in the intestine of zebrafish were observed, and the relative expressions of mucus secretion and tight junction related genes (MUC-2, Occuludin a and ZO-1) were all downregulated. Through the integrated analysis combining metabolomics and metagenomics, the results demonstrated that BDP exposure downregulated the abundances of microbiota Peptostreptococcus, Clostridium, Bombilactobacillus and Sporolactobacillus in zebrafish intestines, to depress tryptophan metabolism and eventually reduce the abundances of tryptophan metabolites. As a result, the expression of AhR, an important receptor activated by tryptophan metabolites, was inhibited to downregulate IL-22 expression, promoting intestinal toxicity. In vivo experiment with indole-3-propionic acid supplement alleviated the pathological changes, which further confirmed that BDP destroyed microbiota-tryptophan metabolism homeostasis to interfere with the AhR-IL-22 axis, eventually promoted pathological toxicity in the intestines. This study highlights vulnerability of intestines to BDP, and provides first insight into the mechanism through which BDP threats intestinal health.},
}

@article {pmid41765175,
year = {2026},
author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C},
title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.02.016},
pmid = {41765175},
issn = {1878-3554},
abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.

METHODS: Samples from 25 teeth with large (>8mm) and 20 with small periapical lesions (<2mm) were analyzed. Quantitative PCR, 16S next-generation and whole genome sequencing (WGS) were used to assess microbial load, diversity, and composition. Functional predictions were performed using the KEGG and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.

RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (p = 0.011), but comparable alpha diversity and number of species per group in 16S and Whole genome analysis (P > 0.05). Lesion size showed significance by ANOSIM (p = 0.04) but not in PERMANOVA (p = 0.36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, p = 0.012; PERMANOVA R[2] = 0.063, p = 0.046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.

CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.},
}

@article {pmid41764980,
year = {2026},
author = {Xie, J and Hu, T and He, J and Cai, Y and Wu, Q and Li, L and Liu, H},
title = {Genome characterization and evolutionary analysis of a novel Anativirus from a wild Muscovy duck in Guangdong, China.},
journal = {Virology},
volume = {618},
number = {},
pages = {110849},
doi = {10.1016/j.virol.2026.110849},
pmid = {41764980},
issn = {1096-0341},
abstract = {A novel member of the genus Anativirus was identified and characterized from a naturally deceased wild Muscovy duck (Cairina moschata) collected in Maoming, Guangdong Province, China. This strain, provisionally designated Anativirus GD2411, was detected through metagenomic next-generation sequencing (mNGS), which yielded a complete genome of 8,085 nucleotides. The genome comprises a single open reading frame (nt 413-7,873) encoding the canonical picornaviral polyprotein, flanked by a 5' untranslated region (UTR; 412 nt) and a 3' UTR (209 nt) with a poly(A) tail. Whole-genome nucleotide identity analysis revealed that GD2411 clustered with duck-origin strains, sharing 88.0% identity with CH01 and 81.2% with TW90, but only 50.6% with the chicken-derived strain CHK1. High amino acid conservation was observed across functional regions, particularly in 2C (≥91.9%), 3C (≥92.4%), and 3D (≥97.0%), reflecting the preservation of RNA-dependent RNA polymerase function. Phylogenetic analyses based on complete genomes and 3D protein sequences using maximum likelihood methods consistently placed GD2411 within the duck Anativirus clade, indicating a close evolutionary relationship with TW90 and CH01. Although an experimental infection model was not established, PCR screening revealed broad gastrointestinal distribution of the virus, with the highest viral load detected in the cecum, suggesting fecal-oral transmission as a primary route. These findings provide preliminary evidence of Anativirus infection in wild Muscovy ducks in southern China, though the limited sample size precludes definitive conclusions regarding host range expansion. The highly conserved 3D region is highlighted as a potential target for antiviral therapy or vaccine development.},
}

@article {pmid41764931,
year = {2026},
author = {Wang, G and Wei, J and Qiu, G and Guo, Z and Wang, W and Liu, X and Song, Y},
title = {Mechanism of activated carbon enhanced activated sludge (ACEAS) in treating recalcitrant chemical wastewater.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129058},
doi = {10.1016/j.jenvman.2026.129058},
pmid = {41764931},
issn = {1095-8630},
abstract = {Recalcitrant chemical accident wastewater, especially nitrobenzene-containing wastewater, has posed a significant treatment challenge due to complex hazardous compounds as well as elevated toxicity. Activated carbon combined activated sludge processes can effectively remove hazardous organic pollutants from chemical wastewater. However, the interaction mechanism between activated carbon and activated sludge remains unclear. This study proposed the activated carbon enhanced activated sludge (ACEAS) process for treating nitrobenzene-containing wastewater. Combined with material characterization and metagenomic analysis, the removal efficiency of nitrobenzene was evaluated, and the interaction mechanisms between activated carbon and activated sludge was further investigated. The key findings include: The effluent nitrobenzene concentration in conventional activated sludge (AS) process was 6.5 and 9.2 times higher than in the original ACEAS (OS) and regenerated ACEAS (RS) processes, respectively. Without activated carbon replenishment, chemical oxygen demand (COD) removal efficiency in OS and RS processes increased by 10.19%-15.86% and 11.41%-14.60%, respectively, compared to AS process during long-term operation (6-24 h). Due to the formation of biofilms on the surface of activated carbon, and the content of C-O/C=O and C-N/C=N on OS increased by 13.2% and 17.3%, respectively, compared to original activated carbon (OC). Eventually, four enhanced mechanisms of activated carbon were proposed, each contributing to distinct degradation stages in the ACEAS system. In prophase, activated carbon might reduce toxicity and improve microbial degradation capacity by adsorption. During metaphase, biofilms on activated carbon surface further diminished adsorption/desorption effect. In the telophase, microbial carrier's fixation affected strengthens, reshaping microbial community structure, functional gene expression, and metabolic pathway selection, thereby enhancing activated sludge degradation efficiency.},
}

@article {pmid41764882,
year = {2026},
author = {Huang, L and Feng, L and Sun, Y and Li, Z and Deng, L and Zhang, P and Li, X and Gao, D and Wang, Y and Deng, S and Shen, F and Fang, D},
title = {Oxygen stress drives overcompensation of carbon sources for enhanced polymer denitrification.},
journal = {Water research},
volume = {296},
number = {},
pages = {125631},
doi = {10.1016/j.watres.2026.125631},
pmid = {41764882},
issn = {1879-2448},
abstract = {Dissolved oxygen (DO) is traditionally considered as a strong inhibitor of denitrification. However, its impact on polymer-based denitrification, where carbon bioavailability is rate-limiting, remains poorly understood. Here, we investigated the response of a polycaprolactone (PCL)-supported biofilm system to long-term DO stress (2-8 mg/L). Contrary to conventional expectations, elevating DO from 2 to 8 mg/L significantly accelerated nitrate removal (from 8.06 to 10.50 mg N/L) rather than suppressing it. Stoichiometric modeling and metabolomic analysis revealed an oxygen-induced carbon release mechanism, where high DO stimulated the secretion of extracellular esterases and intensified the β-oxidation pathway, increasing polymer carbon release by 17.71 mg/L. This excess carbon overcompensated for aerobic consumption, effectively alleviating electron donor limitations. Metagenomics further confirmed a structural shift towards an oxygen-tolerant consortium, with significant enrichment of dual-function genera (e.g., Pseudoxanthomonas) and enhanced coupling of respiratory chain complexes (I-III). The biofilm achieved spatial decoupling, utilizing the outer aerobic layer for rapid hydrolysis and oxygen consumption to protect the inner anoxic denitrification zone. These findings overturn the strict anoxic requirement for denitrification, providing a robust strategy for advanced nitrate removal in oxygen-fluctuating tailwaters.},
}

@article {pmid41764843,
year = {2026},
author = {Das, N and Pandey, P},
title = {Striking a microbial balance: Rhizoremediation of crude oil-contaminated soils suppresses resistomes and reconstructs hydrocarbon-degrading microbial networks.},
journal = {The Science of the total environment},
volume = {1022},
number = {},
pages = {181586},
doi = {10.1016/j.scitotenv.2026.181586},
pmid = {41764843},
issn = {1879-1026},
abstract = {Integrated plant-microbe systems are crucial for restoring hydrocarbon- and heavy metal-contaminated soils. Here, Azadirachta indica inoculated with a hydrocarbon-degrading bacterial consortium (SynCom) was used in microcosm and field trials to remediate chronically oil-contaminated soils. SynCom treatment enhanced degradation of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) up to 99%, reduced heavy metal concentrations, and neutralized soil pH, while improving organic matter, soil aggregation, and nutrient mobilization (N, P, K). Metagenomic analyses revealed a shift from Proteobacteria to Actinobacteria, with a 10-fold reduction in antibiotic resistance genes, particularly multidrug resistance and efflux pump genes. Key functional taxa (Nocardioides, Bradyrhizobium japonicum, Rhodopseudomonas) were enriched, correlating with enhanced nutrient cycling, soil enzyme activity, and hydrocarbon degradation. Functional gene profiling indicated reduced oxidative stress and ecological recovery. This study demonstrates that targeted rhizoremediation effectively detoxifies soils while mitigating ARGs dissemination, offering a sustainable One Health-aligned strategy for environmental and public health protection.},
}

@article {pmid41764831,
year = {2026},
author = {Peng, X and Zhang, L},
title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {2},
pages = {117321},
doi = {10.1016/j.diagmicrobio.2026.117321},
pmid = {41764831},
issn = {1879-0070},
abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.},
}

@article {pmid41764643,
year = {2026},
author = {Zeller, LM and Schorn, S and Nicolas-Asselineau, L and Zopfi, J and Ahmerkamp, S and Schubert, CJ and Lepori, F and Kuypers, MMM and Graf, JS and Milucka, J},
title = {Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag043},
pmid = {41764643},
issn = {1751-7370},
abstract = {Bacterial endosymbionts of the family Ca. Azoamicaceae obligately associate with anaerobic ciliates belonging to the class Plagiopylea. The symbionts' unique role for their host involves anaerobic respiration of nitrate and generation of ATP, analogous to the role of mitochondria in aerobic eukaryotes. As this symbiosis remains so far uncultured, insights into its functioning have been mainly inferred from environmental metagenomes. Here we investigated the distribution and environmental role of this symbiosis in the anoxic basins of two freshwater lakes Zug and Lugano (Switzerland) over a course of several years. We found that the environmental niche of the ciliate host is defined by the combined effects of sulfide, oxygen and nitrate, the latter of which is essential for the symbiont's respiratory function. Moreover, the distribution and abundances of ciliates with denitrifying endosymbionts in the water column suggests that they may substantially contribute to nitrate consumption in Lake Zug. Our microscopic analyses further demonstrated a coordinated division of the Candidatus Azoamicus ciliaticola symbionts and their ciliate hosts, implying a vertical inheritance of denitrifying symbionts. These observations offer new insights into the evolution of ciliates with denitrifying endosymbionts and their ecological role in oxygen-depleted lakewaters.},
}

@article {pmid41764576,
year = {2026},
author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S},
title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41764576},
issn = {1674-9782},
support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.

RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.},
}

@article {pmid41764388,
year = {2026},
author = {Zhu, K and Amirali, A and Auch, B and Babler, KM and Biswas, P and Bowie, K and Choudhary, S and Currall, BB and Grills, GS and Healy, HG and Liachko, I and Lucaci, AG and Mason, CE and Sharkey, M and Shigeno Risse-Adams, O and Shukla, BS and Sisson, Z and Stevenson, M and Williams, SL and Zulli, A and Peccia, J and Solo-Gabriele, HM},
title = {Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.},
journal = {Journal of water and health},
volume = {24},
number = {2},
pages = {148-159},
pmid = {41764388},
issn = {1477-8920},
support = {//4Catalyzer/ ; U01DA053941/DA/NIDA NIH HHS/United States ; P30AI073961/NH/NIH HHS/United States ; },
abstract = {The proliferation of antimicrobial resistance genes (ARGs) poses public health risks globally, with wastewater treatment plants (WWTPs) serving as dissemination hubs for horizontal gene transfer. In this study, we evaluated the potential of applying Hi-C sequencing coupled with metagenomic bioinformatics for surveillance of ARGs and other microbial fitness traits using samples from WWTPs. Hi-C sequencing has the advantage over other molecular approaches by directly associating genes conveying fitness to their host microbe, plus to their element type (in plasmids, phages, or within the core genome of its host microbe). Results from Hi-C analyses confirm results from more laborious approaches by showing that aminoglycoside resistance is disseminated by plasmids. Mercury resistance was found in Zoogloea bacteria. Resistance genes to quaternary ammonium compounds were found within bacteriophages. Results from this study provide proof-of-concept for the potential value of Hi-C metagenome sequencing in wastewater attribution studies by illustrating the breadth of information that can be obtained about the microbial community, the exchange of genes, and their interconnections. We believe that with further development, Hi-C sequencing can be integrated into routine monitoring of wastewater for the purpose of providing near-real-time information about the dissemination of fitness traits, including ARGs.},
}

@article {pmid41764386,
year = {2026},
author = {Mtetwa, HN and Amoah, ID and Mthethwa-Hlongwa, NP and Pieerneef, R and Kumari, S and Bux, F and Reddy, P},
title = {Decoding mycobacterial ecology in Sub-Saharan African wastewater: metagenomic and metatranscriptomic insights for tuberculosis surveillance.},
journal = {Journal of water and health},
volume = {24},
number = {2},
pages = {109-127},
pmid = {41764386},
issn = {1477-8920},
support = {96086//South African Medical Research Council/ ; },
abstract = {Tuberculosis (TB) remains a major public health challenge in sub-Saharan Africa, driven by high transmission, delayed diagnosis, and limited surveillance. This study presents one of the first integrated applications of shotgun metagenomic and metatranscriptomic sequencing to investigate Mycobacterium communities in wastewater across six TB-endemic countries: Cameroon, Ghana, Kenya, Nigeria, South Africa, and Uganda. Twelve untreated and treated wastewater samples were analysed to characterise taxonomic composition, strain-level diversity, and transcriptional activity. Metagenomic analyses revealed diverse Mycobacterium communities, including M. tuberculosis, M. canettii, M. bovis, and members of the M. avium complex. Metatranscriptomic data detected MTBC-associated transcripts, indicating transcriptional activity and/or persistence of MTBC RNA signals in wastewater, with higher signal predominance in influent samples, consistent with community-level shedding. Metagenome-assembled genomes (MAGs) recovered from South Africa, Cameroon, and Uganda showed >82% completeness and included zoonotic species. MTBC strains clustered into Lineages 1, 2, 4, and 6, with animal-adapted strains linked to livestock and rodents, highlighting One Health relevance. Overall, this dual-omics approach supports wastewater-based epidemiology as a scalable tool for TB surveillance in high-burden settings.},
}

@article {pmid41763967,
year = {2026},
author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC},
title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2026.01.018},
pmid = {41763967},
issn = {1468-2060},
abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).

METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.

RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.

CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.},
}

@article {pmid41763050,
year = {2026},
author = {Cai, F and Wang, C and Liu, H and Shen, J and Wang, J and Yang, Y and Wang, X},
title = {Partitioning dynamics and microbial responses drive the fate of polycyclic aromatic hydrocarbons in a plateau lake.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129097},
doi = {10.1016/j.jenvman.2026.129097},
pmid = {41763050},
issn = {1095-8630},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent organic contaminants of concern in freshwater drinking-water sources, yet their environmental fate in hydrologically dynamic plateau lakes remains poorly constrained. Here, we investigated the multi-compartment distribution, apparent particle-water partitioning, microbial functional potential, and associated ecological and human-health risks of PAHs in Erhai Lake, a large subtropical plateau lake in southwestern China. PAHs were quantified simultaneously in the dissolved, suspended particulate, and surface-sediment phases across three seasons. Dissolved low-molecular-weight PAHs dominated the water column, exhibiting pronounced seasonal variability with summer peaks (12.9-49.8 ng L[-1]) driven by intensified tourism and hydrological inputs. In contrast, high-molecular-weight PAHs preferentially accumulated in sediments, forming depositional hotspots in the southern basin. Apparent organic-carbon-normalized partition coefficients (KOC,app) revealed that suspended particulates act as dynamic regulators of PAH transport and microbial accessibility. Metagenomic analysis revealed that the distribution of PAH-degradation-related functional genes co-varied with chemical partitioning patterns, suggesting potential microbial mediation of PAH fate. Ecological and human health risk assessments, including probabilistic Monte Carlo simulations, indicated that PAH-related risks remained within a low-risk regime across all seasons. Collectively, these findings provide a mechanistic framework for understanding how partitioning and microbial metabolism jointly regulate the fate of PAHs in plateau lakes, offering critical insights for the management of sensitive freshwater resources.},
}

@article {pmid41762837,
year = {2026},
author = {Wang, Y and Zhang, X and Wu, Y and Sun, X and Zhang, X and Lv, J},
title = {Biodegradation pathway of organophosphate esters in sludge composting implications for environmental safety.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141622},
doi = {10.1016/j.jhazmat.2026.141622},
pmid = {41762837},
issn = {1873-3336},
abstract = {Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation during sludge composting. In this study, under the stress of 100 mg/kg ∑7OPEs, three bacterial strains with degradation capabilities-Bacillus subtilis, Bacillus licheniformis, and Ralstonia pickettii-were screened and isolated, and a synthetic bacterial community (SynCom) was constructed. During 55 days sludge composting, the concentration of ∑7OPEs decreased significantly. In CK, TnBP degraded the fastest (> 90%). For the exogenous OPE-added groups strengthened with SynCom (T1B and T2B), the removal rates of TCPP and TPhP were nearly complete (> 93%). However, high concentrations of ∑7OPEs inhibited the degradation of compounds such as TCrP and EHDPP. Hydrolysis was identified as the preferentially initiated pathway for ∑7OPEs degradation during sludge composting. Functional enzyme such as phosphatase, as well as bacterial strains from the Rhodococcus and Paracoccus, synergistically participated in the degradation process. Multiple linear regression analysis confirmed that SynCom promoted ∑7OPEs removal by boosting phosphomonoesterase activity and enriching phosphatase-producing microorganisms. pH and total phosphorus (TP) emerged as critical environmental factors influencing this degradation. Composting significantly lowered OPE-associated ecological risks, ensuring the safe resource recovery of sludge. This study focused on the biological removal of OPEs during sludge composting. It first systematically evaluated the biodegradation efficiency of ∑7OPEs and clarified core metabolic pathways. Furthermore, key microbial communities and functional genes associated with ∑7OPEs degradation were identified, revealing their regulatory roles. It provides scientific support for controlling OPEs pollution and promoting sludge resource utilization.},
}

@article {pmid41762508,
year = {2026},
author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X},
title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129121},
doi = {10.1016/j.jenvman.2026.129121},
pmid = {41762508},
issn = {1095-8630},
abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.},
}

@article {pmid41762498,
year = {2026},
author = {Jiang, PY and Tang, H and Tong, WK and Liu, J and Liu, K and Tang, W and Liu, JB and Gao, MT and Liu, N and Hu, J and Li, J},
title = {Interface modification of membrane substrates: Mitigating microbial interfacial adhesion and augmenting adsorptive capacity for seawater uranium recovery.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129080},
doi = {10.1016/j.jenvman.2026.129080},
pmid = {41762498},
issn = {1095-8630},
abstract = {Seawater is endowed with vast reserves of high-value trace metals (gold, lithium, uranium) for resource recovery. However, their extremely low concentrations entail extensive, long-duration seawater processing in membrane-based systems, leading to pronounced microbial fouling and a substantial deterioration in adsorption efficiency. Given that practical membrane modules possess a multi-component architecture, this study mitigated microbial fouling via indigo modification of membrane supporting substrates, while maintaining the structural and functional integrity of the adsorptive membrane. This approach avoids the impairment of adsorption sites and porous structures induced by direct antimicrobial modification of the membrane. Column breakthrough experiments were employed to assess the fouling characteristics and severity of membrane modules in terms of macroscopic retention and structural evolution. Before modification, the membrane module exhibited interception rates of 79.8% and 77.3% for single strains and in-situ marine microbial communities (multiple strains), respectively, which were reduced to 45.6% and 57.1% after modification. Analysis using the dual-kinetic-site attachment-detachment model demonstrated that indigo-modified substrates reduced Langmuirian attachment and ripening, while the functional complementarity within microbial communities mitigated these effects. Metagenomic analysis confirmed that the modification selectively suppressed the attachment of microorganisms with strong adhesion and biofilm-forming ability. In a 28-day adsorption validation in real seawater, the modification increased the uranium adsorption capacity from 1.05 to 2.38 mg/g, effectively attenuating the performance decline induced by microbial contamination. The spatially decoupled integration of substrate anti-adhesion and membrane adsorption offers a new paradigm for membrane module design and optimization, extending its application potential in marine uranium recovery.},
}

@article {pmid41762491,
year = {2026},
author = {Yan, S and Li, R and Shen, X and Li, Y and Zhang, L and Xu, M and Xie, S},
title = {Redox potential drives divergent microbial carbon fixation in mangrove wetland sediments, with ammonium exerting context-dependent effects.},
journal = {Marine pollution bulletin},
volume = {227},
number = {},
pages = {119457},
doi = {10.1016/j.marpolbul.2026.119457},
pmid = {41762491},
issn = {1879-3363},
abstract = {Mangrove wetlands represent dynamic coastal interfaces where redox conditions and nutrient cycling shape microbial communities and their biogeochemical functions. However, tidal-driven siltation continuously transports sediment from low- to high-tide zones, altering sediment redox potential and nutrient content. The microbial responses to these changes, particularly the response mechanisms of carbon-fixing microorganisms, remain unclear. We integrated metagenomic and metatranscriptomic sequencing with [13]C and [15]N isotope labeling to examine how oxidation-reduction potential (ORP) and ammonium (NH4[+]) availability regulate microbial assembly and metabolism in mangrove sediments. ORP emerged as the primary determinant of microbial composition and diversity, while NH4[+] exerted variable effects on microbial traits. Under high ORP, CBBL-microorganisms predominantly utilized the cmmG CO2-concentrating mechanism, and carbon fixation rates decreased with increasing NH4[+] concentration. Under low ORP, CBBM-harboring genera dominated, primarily utilizing another mechanism cmmE, while NH4[+] had little effect and total organic carbon (TOC) exerted stronger control. ORP thus acts as the dominant environmental filter, with NH4[+] selectively affecting nitrifiers and carbon-fixing taxa. This was the first study to simultaneously measure ammonia oxidation and carbon fixation rate in mangrove sediments, revealing their mechanistic coupling. This work provides new mechanistic insights into the regulation of microbial metabolic potential in mangrove ecosystems and contributes to a broader understanding of their resilience and function in coastal biogeochemical cycles under fluctuating climate and environmental conditions.},
}

@article {pmid41762466,
year = {2026},
author = {Ma, Q and López, MJ and Zhang, S and Jin, L and Wei, D and Yang, J and Liu, J and Ruan, Z},
title = {Carbon source-dependent activation of herbicide-mixture degradation in a synthetic microbial community enriched from black soil.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141615},
doi = {10.1016/j.jhazmat.2026.141615},
pmid = {41762466},
issn = {1873-3336},
abstract = {The extensive use of herbicides in agriculture has resulted in persistent soil contamination. Although microbial degradation of single herbicides has been extensively investigated, the responses and co-metabolism of microbial consortia to complex herbicide mixtures remain unclear. This study aimed to investigate the influence of a simple carbon source (glucose) on herbicide degradation by a natural microbial consortium (NMC) and identify key degraders for constructing an efficient synthetic microbial community (SynCom). An NMC enriched from herbicide-stressed agricultural black soil in Northeast China was inoculated into mineral salt media containing a mixture of herbicides (atrazine, nicosulfuron and mesotrione) as the sole carbon/nitrogen source, without (MSM) or with glucose supplementation (GSM). Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days. Integrated 16S rRNA gene sequencing and metagenomic analysis linked the glucose amendment to a specific shift in the microbial community structure and activation of central carbon metabolism (tricarboxylic acid [TCA] and glycolytic), which enhanced cellular energy supply and environmental acidification for co-metabolic degradation of herbicides. In contrast, metabolism in the MSM system was biased toward biosynthesis. Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa. Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase). A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system. These findings elucidate the role of labile carbon in driving the co-metabolism of complex herbicides and provide direct candidate strains and a construction strategy, facilitating practical bioremediation applications.},
}

@article {pmid41762461,
year = {2026},
author = {Shen, S and Wang, L and An, X and Liu, H and Shi, M and Tu, Y and Ji, W and He, Z and Li, A},
title = {Basin governance coincides with lower MGE loads yet rewired ARG mobility: a hazard‑oriented, platform‑centric assessment.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141608},
doi = {10.1016/j.jhazmat.2026.141608},
pmid = {41762461},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) serve as critical indicators for evaluating the ecological success of river restoration policies. We investigated the restructuring of the riverine resistome in the Yangtze River following the implementation of the "Ten-Year Fishing Ban" and the Yangtze River Protection Law. Using basin-wide surveys in the Jiangsu reach (2021 vs. 2023), we integrated shotgun metagenomics and RT-qPCR functional validation with a noise-filtering sampling design to assess how the removal of anthropogenic pressures reshaped resistance dissemination. Results show that policy-driven ecological recovery significantly altered microbial assembly mechanisms. While total ARG abundance declined, microbial communities shifted toward a more dispersal-dominated regime, with neutral model fits increasing from 0.817 to 0.913. Crucially, RT-qPCR analysis confirmed that the transcriptional activity of key resistance elements remained significantly elevated relative to a pristine baseline, suggesting persistent functional risks despite lower overall abundance. As localized selective pressures relaxed, the resistome transitioned toward integrated genetic platforms, evidenced by a significant rise in the mosaic index (MGI) from 12.81% to 22.50% (p < 0.05). Structural equation modeling (R2 = 0.766) identified a dominant sequential pathway from environmental co-selectors to mobile genetic elements and subsequently to ARGs, with intensified roles for integrons and insertion sequences (intI1, IS26). These findings demonstrate that policy success requires evaluation through both abundance-based and structural indicators. We propose a platform-centric surveillance framework incorporating the mosaic index as an early-warning tool for environmental agencies.},
}

@article {pmid41762333,
year = {2026},
author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S},
title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41762333},
issn = {1573-0972},
}

@article {pmid41762314,
year = {2026},
author = {Dabravolski, SA and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Orekhov, AN},
title = {A metagenomic perspective on microbial hydrocarbon degradation: uncovering novel pathways and community dynamics.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {5},
pages = {},
pmid = {41762314},
issn = {1573-2983},
support = {202760-2-000//RUDN University/ ; },
abstract = {The microbial degradation of petroleum hydrocarbons is a fundamental biogeochemical process and a cornerstone of environmental bioremediation. While traditional culture-based studies have outlined the basic principles, the advent of metagenomics has revolutionised our understanding by revealing the full genetic and functional diversity of hydrocarbon-degrading communities in situ. This review synthesises the current state of knowledge on both aerobic and anaerobic hydrocarbon biodegradation, providing a critical comparative analysis of traditional versus multi-omics methodologies. We provide an in-depth examination of aerobic mechanisms, initiated by oxygenases (e.g., alkB, PAH-RHDα), and contrast them with the diverse array of anaerobic activation pathways, including fumarate addition (bssA) and the recently elucidated direct carboxylation pathway for polycyclic aromatic hydrocarbons (PAHs). Furthermore, we highlight groundbreaking metagenomic insights into anaerobic benzene degradation and the critical role of syntrophic networks driven by interspecies electron transfer. Finally, we present specific case studies demonstrating the translation of genomic data into practical bioremediation strategies, such as the rational design of synthetic consortia. This review charts these recent advances, highlights remaining knowledge gaps, and outlines future directions for harnessing multi-omics to translate genomic potential into effective, field-scale environmental solutions.},
}

@article {pmid41762228,
year = {2026},
author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X},
title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41762228},
issn = {1432-0991},
support = {82270598//National Natural Science Foundation of China/ ; },
abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.},
}

@article {pmid41761979,
year = {2026},
author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X},
title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {48584},
doi = {10.31083/FBL48584},
pmid = {41761979},
issn = {2768-6698},
support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; },
abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.

METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.

RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.

CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.},
}

@article {pmid41761378,
year = {2026},
author = {Biggel, M and Oberhänsli, T and Kümmerlen, D and Walkenhorst, M and Stephan, R and Holinger, M},
title = {Diversity and abundance of antimicrobial resistance genes in manure from pig farms with varying antibiotic use: a long-read metagenomic sequencing approach.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00496-3},
pmid = {41761378},
issn = {2055-5660},
support = {04.1240.PZ//Swiss Expert Committee for Biosafety (SECB)/ ; },
}